example of acknowledgements in research paper

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How to Write Acknowledgement for Research Paper (5 Samples)

July 12, 2023

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By Mohsin Khurshid

Writing acknowledgements is an essential part of crafting a comprehensive research paper. It allows you to express gratitude and recognize the contributions of individuals and institutions who have supported your work. In this article, we will delve into the art of writing acknowledgement for research papers, providing you with valuable insights, practical tips, and five sample acknowledgements to guide you in acknowledging the people and resources that have played a significant role in your research journey.

Table of Contents

• 1 Understanding the Role of Acknowledgements in Research Papers
• 2 Key Elements of an Effective Acknowledgement
• 3 10 Tips for Writing an Acknowledgement for a Research Paper
• 4.1 Sample 1: Acknowledgement for Collaborative Research:
• 4.2 Sample 2: Acknowledgement for Funding Support:
• 4.3 Sample 3: Acknowledgement for Mentorship and Guidance:
• 4.4 Sample 4: Acknowledgement for Institutional Support:
• 4.5 Sample 5: Acknowledgement for Peer Reviewers:
• 6 Conclusion

Understanding the Role of Acknowledgements in Research Papers

Acknowledgements serve as a platform to express appreciation and recognize the collective effort that goes into the completion of a research paper. They provide an opportunity to acknowledge the guidance, support, and assistance received throughout the research process. By including acknowledgements, you can demonstrate your gratitude and give credit to those who have contributed to your success.

Key Elements of an Effective Acknowledgement

Crafting an effective acknowledgement involves considering various elements to ensure its sincerity and clarity. It is crucial to mention specific individuals, institutions, and their contributions, while keeping the acknowledgement concise and relevant. By adhering to ethical considerations and cultural norms, you can create an acknowledgement that reflects your gratitude and professionalism.

10 Tips for Writing an Acknowledgement for a Research Paper

• Be sincere and genuine : Write your acknowledgements with heartfelt gratitude, expressing sincere appreciation for the support and contributions received during your research.
• Identify specific individuals and institutions: Mention the names of people who have played a significant role in your research, such as mentors, advisors, collaborators, and funding agencies. Also, acknowledge the contributions of institutions that provided resources or facilities.
• Be concise and focused: Keep your acknowledgements concise and to the point. Focus on the key individuals and organizations that have made a substantial impact on your research.
• Use a formal tone: Maintain a professional and formal tone throughout your acknowledgements. Remember that this section is a formal acknowledgment of support, not a casual conversation.
• Follow ethical considerations: Ensure that you acknowledge individuals and organizations according to ethical guidelines and norms. Respect the privacy and confidentiality of individuals who may prefer not to be mentioned.
• Include personal touches: If appropriate, you can include personal anecdotes or specific instances where individuals or organizations made a significant impact on your research.
• Tailor acknowledgements to your research context: Consider the nature of your research and tailor your acknowledgements accordingly. For example, if you conducted interdisciplinary research, acknowledge experts from different fields who provided valuable insights.
• Proofread and edit: Like any other section of your research paper, proofread and edit your acknowledgements for grammar, spelling, and clarity. Ensure that the acknowledgements are well-written and free of errors.
• Seek feedback if needed: If you’re uncertain about whom to acknowledge or how to express your gratitude, seek feedback from your mentors, advisors, or colleagues. They can provide valuable guidance and suggestions.
• Show appreciation beyond formal requirements: While it’s important to acknowledge the required individuals and institutions, also consider extending your appreciation to others who may have supported you indirectly, such as family, friends, or colleagues who provided emotional support during your research journey.

Remember, acknowledgements are an opportunity to express your gratitude and recognize the contributions of those who have helped you along the way. Take the time to craft a thoughtful and sincere acknowledgement section that reflects the support and collaborative spirit of your research endeavor.

5 Samples for Acknowledgment in Research Paper

Explore these 5 carefully crafted acknowledgment samples to effectively express gratitude in your research paper.

Sample 1: Acknowledgement for Collaborative Research:

In this sample, we showcase an acknowledgement that acknowledges the collaborative efforts of research collaborators and team members. It highlights the importance of recognizing the joint contributions made towards the research project.

“I would like to express my deepest appreciation to the members of the research team, [Collaborators’ Names], for their invaluable contributions and collaborative spirit throughout this research project. Our collective efforts and synergistic teamwork have significantly enhanced the quality and depth of this study. Each member’s unique expertise and perspectives have brought forth diverse insights, resulting in a more comprehensive and well-rounded analysis.

I am grateful for the dedication, commitment, and professionalism demonstrated by each team member. The constructive discussions, intellectual debates, and shared enthusiasm have fostered an enriching research environment that has truly pushed the boundaries of our collective knowledge. This research project stands as a testament to the power of collaboration and the collective pursuit of knowledge.”

Sample 2: Acknowledgement for Funding Support:

This sample acknowledgement focuses on acknowledging the financial support received for the research. It emphasizes the significance of recognizing funding agencies or organizations that have provided the necessary resources for the research to take place.

“I would like to extend my sincere gratitude to the funding agencies and organizations that have provided financial support for this research. Their generous contributions have made it possible to conduct this study and have significantly contributed to its successful completion. The financial support has allowed for the procurement of necessary research materials, access to specialized equipment, and the opportunity to engage in valuable research experiences.

I would like to express my appreciation to [Name of Funding Agency/Organization 1] for their generous grant, which has played a crucial role in supporting this research project. Their belief in the significance of this study and their commitment to advancing knowledge in this field have been instrumental in its realization.

Furthermore, I would like to acknowledge the support received from [Name of Funding Agency/Organization 2]. Their funding has been vital in facilitating data collection, analysis, and the dissemination of research findings. Their investment in this project has not only provided financial resources but has also validated the importance and potential impact of this research.”

Sample 3: Acknowledgement for Mentorship and Guidance:

Here, we present a sample acknowledgement that expresses gratitude towards mentors and advisors who have provided guidance and support throughout the research journey. It underscores the critical role of mentorship in academic and research endeavors.

“I am deeply grateful to my mentor, [Mentor’s Name], for their exceptional guidance and unwavering support throughout this research endeavor. Their expertise, insightful feedback, and continuous encouragement have been invaluable in shaping the direction and outcomes of this study. Their unwavering commitment to my academic growth and professional development has been truly inspiring.

I am indebted to [Mentor’s Name] for their generous allocation of time and resources, their willingness to share their wealth of knowledge, and their unwavering dedication to pushing me to new heights. Their mentorship has not only enriched the quality of this research but has also had a profound impact on my personal and intellectual growth. I am truly fortunate to have had the privilege of working under their guidance.”

Sample 4: Acknowledgement for Institutional Support:

In this sample, we illustrate an acknowledgement that acknowledges the support and resources provided by institutions. It emphasizes the institutional backing that has facilitated the research process and contributed to its success.

“I would like to express my heartfelt gratitude to the faculty members and academic advisors who have provided guidance, feedback, and support throughout my academic journey. Their expertise, wisdom, and dedication to teaching and mentoring have been instrumental in shaping my research skills and scholarly pursuits.

I am grateful to [Name of Faculty Member/Advisor 1] for their unwavering support and invaluable insights. Their expertise and guidance have been critical in refining the research design, analyzing data, and interpreting findings. Their constructive feedback and intellectual discussions have truly enriched this study.

I would also like to acknowledge the contributions of [Name of Faculty Member/Advisor 2]. Their mentorship and encouragement have played a pivotal role in the development of my research abilities and have inspired me to reach for new heights. Their belief in my potential has been a constant source of motivation throughout this research journey.”

Sample 5: Acknowledgement for Peer Reviewers:

“I would like to express my deepest gratitude to the anonymous peer reviewers who have dedicated their time and expertise to provide valuable feedback and constructive criticism on this research paper. Their rigorous evaluation, insightful comments, and suggestions for improvement have immensely contributed to the quality and credibility of this work.

The meticulous review process conducted by the peer reviewers has helped shape and refine the content, methodology, and interpretation of this study. Their expertise in the field and their commitment to upholding scholarly standards have been crucial in ensuring the accuracy, validity, and relevance of the research findings.

I am sincerely grateful for the time and effort invested by each reviewer in thoroughly assessing this paper. Their detailed comments and recommendations have not only helped enhance the clarity and coherence of the manuscript but have also encouraged further reflection and refinement of the research.

The contributions of the peer reviewers are invaluable in the advancement of scientific knowledge and the improvement of academic publications. Their commitment to maintaining the rigor and integrity of the research process plays a pivotal role in fostering academic excellence and promoting the dissemination of high-quality research outcomes.”

When writing an acknowledgement in a research paper, begin by expressing gratitude to individuals, institutions, or organizations who have contributed to the research. Provide a sincere and concise acknowledgement, mentioning their specific contributions and the impact they made on the study.

While specific examples may vary depending on the research context, an acknowledgement section in a journal article typically acknowledges the contributions of individuals, funding sources, or institutions involved in the research process. It expresses gratitude for their support, guidance, or resources.

The purpose of the acknowledgement section in a research paper is to recognize and express gratitude to individuals or entities who have supported the research. It acknowledges their contributions, whether through funding, mentorship, technical assistance, data provision, or other forms of support.

When writing acknowledgements for a publication , start by identifying the key individuals or entities that have contributed to the research. Express gratitude for their support, mentioning specific contributions and the value they added to the study. Keep the acknowledgements concise and focused on the research context.

The acknowledgement section of a research paper should include acknowledgements for individuals or entities that have contributed to the research process. This may include mentors, advisors, funding agencies, research collaborators, or others who have provided valuable support, guidance, or resources.

While including an acknowledgement section in a research paper is not mandatory, it is a common practice in academic publishing. It provides an opportunity to acknowledge and appreciate the contributions of individuals or entities who have supported the research.

When writing an acknowledgements section for a literature review, acknowledge individuals or sources that have influenced and contributed to your understanding of the topic. Express gratitude for their insights, guidance, or resources that have shaped your literature review.

The terms “acknowledgement” and “acknowledgment” are both correct and interchangeable. The choice of spelling (with or without the “e”) may depend on regional or personal preferences.

To acknowledge a source in a research paper, use proper citation and referencing techniques according to the specific citation style guidelines. Include in-text citations and a corresponding entry in the reference list or bibliography to give credit to the original source.

Yes, you can acknowledge individuals who provided personal support in the acknowledgement section, such as family, friends, or loved ones. Recognize their emotional support, encouragement, or understanding during the research process.

Writing acknowledgements for a research paper allows you to express gratitude and acknowledge the invaluable contributions of individuals and institutions who have supported your work. By following the tips and utilizing the sample acknowledgements provided in this article, you can effectively and sincerely express your appreciation. Remember, acknowledgements are an opportunity to show your gratitude and give credit where it is due.

Acknowledgement for Paper Publication (10 Samples)

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• Thesis & Dissertation Acknowledgements | Tips & Examples

Thesis & Dissertation Acknowledgements | Tips & Examples

Published on May 3, 2022 by Tegan George . Revised on July 18, 2023.

The acknowledgements section is your opportunity to thank those who have helped and supported you personally and professionally during your thesis or dissertation process.

Thesis or dissertation acknowledgements appear between your title page and abstract  and should be no longer than one page.

In your acknowledgements, it’s okay to use a more informal style than is usually permitted in academic writing , as well as first-person pronouns . Acknowledgements are not considered part of the academic work itself, but rather your chance to write something more personal.

To get started, download our step-by-step template in the format of your choice below. We’ve also included sample sentence starters to help you construct your acknowledgments section from scratch.

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Table of contents

Who to thank in your acknowledgements, how to write acknowledgements, acknowledgements section example, acknowledgements dos and don’ts, other interesting articles, frequently asked questions about the acknowledgements section.

Generally, there are two main categories of acknowledgements: professional and personal .

A good first step is to check your university’s guidelines, as they may have rules or preferences about the order, phrasing, or layout of acknowledgements. Some institutions prefer that you keep your acknowledgements strictly professional.

Regardless, it’s usually a good idea to place professional acknowledgements first, followed by any personal ones. You can then proceed by ranking who you’d like to thank from most formal to least.

• Chairs, supervisors, or defense committees
• Funding bodies
• Other academics (e.g., colleagues or cohort members)
• Editors or proofreaders
• Librarians, research/laboratory assistants, or study participants
• Family, friends, or pets

Typically, it’s only necessary to mention people who directly supported you during your thesis or dissertation. However, if you feel that someone like a high school physics teacher was a great inspiration on the path to your current research, feel free to include them as well.

Professional acknowledgements

It is crucial to avoid overlooking anyone who helped you professionally as you completed your thesis or dissertation. As a rule of thumb, anyone who directly contributed to your research process, from figuring out your dissertation topic to your final proofread, should be mentioned.

A few things to keep in mind include:

• Even if you feel your chair didn’t help you very much, you should still thank them first to avoid looking like you’re snubbing them.
• Be sure to follow academic conventions, using full names with titles where appropriate.
• If several members of a group or organization assisted you, mention the collective name only.
• Remember the ethical considerations around anonymized data. If you wish to protect someone’s privacy, use only their first name or a generic identifier (such as “the interviewees”)/

Personal acknowledgements

There is no need to mention every member of your family or friend group. However, if someone was particularly inspiring or supportive, you may wish to mention them specifically. Many people choose to thank parents, partners, children, friends, and even pets, but you can mention anyone who offered moral support or encouragement, or helped you in a tangible or intangible way.

Some students may wish to dedicate their dissertation to a deceased influential person in their personal life. In this case, it’s okay to mention them first, before any professional acknowledgements.

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After you’ve compiled a list of who you’d like to thank, you can then sort your list into rank order. Separate everyone you listed into “major thanks,” “big thanks,” and “minor thanks” categories.

• “Major thanks” are given to people who your project would be impossible without. These are often predominantly professional acknowledgements, such as your advisor, chair, and committee, as well as any funders.
• “Big thanks” are an in-between, for those who helped you along the way or helped you grow intellectually, such as classmates, peers, or librarians.
• “Minor thanks” can be a catch-all for everyone else, especially those who offered moral support or encouragement. This can include personal acknowledgements, such as parents, partners, children, friends, or even pets.

How to phrase your acknowledgements

To avoid acknowledgements that sound repetitive or dull, consider changing up your phrasing. Here are some examples of common sentence starters you can use for each category.

Note that you do not need to write any sort of conclusion or summary at the end. You can simply end the acknowledgements with your last thank you.

Here’s an example of how you can combine the different sentences to write your acknowledgements.

A simple construction consists of a sentence starter (in purple highlight ), followed by the person or entity mentioned (in green highlight ), followed by what you’re thanking them for (in yellow highlight .)

Acknowledgements

Words cannot express my gratitude to my professor and chair of my committee for her invaluable patience and feedback. I also could not have undertaken this journey without my defense committee, who generously provided knowledge and expertise. Additionally, this endeavor would not have been possible without the generous support from the MacArthur Foundation, who financed my research .

I am also grateful to my classmates and cohort members, especially my office mates, for their editing help, late-night feedback sessions, and moral support. Thanks should also go to the librarians, research assistants, and study participants from the university, who impacted and inspired me.

Lastly, I would be remiss in not mentioning my family, especially my parents, spouse, and children. Their belief in me has kept my spirits and motivation high during this process. I would also like to thank my cat for all the entertainment and emotional support.

• Write in first-person, professional language
• Thank your professional contacts first
• Include full names, titles, and roles of professional acknowledgements
• Include personal or intangible supporters, like friends, family, or even pets
• Mention funding bodies and what they funded
• Appropriately anonymize or group research participants or non-individual acknowledgments

Don’t:

• Use informal language or slang
• Go over one page in length
• Mention people who had only a peripheral or minor impact on your work

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In the acknowledgements of your thesis or dissertation, you should first thank those who helped you academically or professionally, such as your supervisor, funders, and other academics.

Then you can include personal thanks to friends, family members, or anyone else who supported you during the process.

Yes, it’s important to thank your supervisor(s) in the acknowledgements section of your thesis or dissertation .

Even if you feel your supervisor did not contribute greatly to the final product, you must acknowledge them, if only for a very brief thank you. If you do not include your supervisor, it may be seen as a snub.

The acknowledgements are generally included at the very beginning of your thesis , directly after the title page and before the abstract .

In a thesis or dissertation, the acknowledgements should usually be no longer than one page. There is no minimum length.

You may acknowledge God in your dissertation acknowledgements , but be sure to follow academic convention by also thanking the members of academia, as well as family, colleagues, and friends who helped you.

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Acknowledgement in Research Paper – A Quick Guide [5 Examples]

The acknowledgement section in your research paper is where you thank those who have helped or supported you throughout your research and writing. It is a short section of 3-5 paragraphs or no more than 300 words you put on a page after the title page.

In this post, we are going to provide you with five examples of acknowlegdement section and a handful of best practices you can make your work look professional.

Saying thank you with style

How to write an acknowledgement: the complete guide for students, why should i include an acknowledgement in my research paper.

Acknowledging assistance and contributions from others can establish your integrity as a researcher. This will eventually make your work more credible.

What should be acknowledged about (aka thankful for)?

In your acknowledgement, you can show gratitude for those who provide you with resources in the following area:

• Technical help may include people who helped you by providing materials and supplies.
• Intellectual help includes academic advice and assistance.
• Mental help can be any kind of verbal support and encouragement.
• Financial support that is obviously related to monetary support

Who should be included in the acknowledgement of a research paper?

You can include everyone who helped you technically, intellectually, or financially (assistance with grants or monetary help) in the process of researching and writing your research paper. Except for your family and friends, you should always include the full names with the title of these individuals:

• Your profession, supervisor, or teacher
• Academic staff (e.g. lab assistant) of your school/college
• Your department, faculty, college, or school
• Classmates, teammates, co-workers, or colleague
• Friends and family members

You can start with your professor or the individuals who supported you the most throughout the research. And then you can continue by thanking your institution and then the reviewer who reviewed your paper. Then you can thank your friends and families and any other individual who helped.

What is the tone of the acknowledgement in a research paper?

You should write your acknowledgement in formal language with complete sentences. It is appropriate to write in the first person (‘I’ for a single author or ‘we’ for two or more).

Note that  personal pronouns  such as ‘I, my, me …’ are nearly always used in the acknowledgements only. For the rest of the research paper, such  personal pronouns  are generally avoided.

Writing an acknowledgement for research paper is one of the important parts of your project report. You need to thank everyone for  helping you with your paper . Here are some examples of acknowledgement for your research paper.

Acknowledgement in Research Paper: Example 1

Acknowledgement in research paper: example 2, acknowledgement in research paper: example 3, acknowledgement in research paper: example 4, acknowledgement in research paper: example 5.

You can use these or try to create your own version for your project report. Also, you can use our auto  acknowledgement generator tool  to automatically generate acknowledgement for your project.

Where should I put the acknowledgement section?

The acknowledgements section should appear between your title page and your introduction in your research paper.

How long is an acknowledgement in a research paper?

The acknowledgement section (usualy inserted as a page) of your research paper should consist of 3-5 paragraphs or no more than 300 words you put on a page after the title page.

Should I use the full names of family members in an acknowledgement?

You do not necessarily need to use the full name for your family and friends (it would sound pretty awkward to use the full name of your parent or spouse right?), you should always include the full names with the title for all other individuals in your acknowledgement.

Can I use “first person” in an acknowledgement?

Yes. It is appropriate to write in the first person (‘I’ for a single author or ‘we’ for two or more).

What is an acknowledgement in academic writing?

An acknowledgement is a page is where you show appreciation to people who helped or supported you intellectually, mentally, or financially in your academic writing.

It should be no longer than one page.

More Definitions on Acknowledgement

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“Acknowledgement” vs “Acknowledgment”… …what the hack?

Both “acknowledgement” and “acknowledgment” are used in the English-speaking world. However, acknowledgement with the “e” in the middle is more commonly used. It is up to 24.5 times more popular in the top 5 English-speaking countries in the world.

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Acknowledgement Examples for School/College Projects

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How-to Guides on Academic Writing and Others

Most popular How to Write an Acknowledgement: The Complete Guide for Students How to Write an Acknowledgement for College Project? How to Write a Dedication Page for a Thesis or Dissertation? More on acknowledgements How to Write Acknowledgment for a Dissertation or a Thesis? Is Acknowledgement and Dedication the Same? Thesis or Dissertation How to Write a Master’s Thesis: The Ultimate Guide How to Write a Thesis Proposal? How to Write an Abstract for a Thesis? How to Write a Preface for a Thesis? Others How to Write an Introduction for a Research Paper? 7 Real Research Paper Examples to Get You Started How to Write Cover Letter for an Internship Program? How to Write an Internship Acceptance Letter? How to Write a Leave Application? For Schools and the Workplace How to Write a Resignation Letter?

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The Acknowledgements Section

How to write the acknowledgements for your thesis or dissertation

By: Derek Jansen (MBA) | Reviewers: Dr Eunice Rautenbach | January 2024

Writing the acknowledgements section of your thesis might seem straightforward, but it’s more than just a list of names . In this post, we’ll unpack everything you need to know to write up a rock-solid acknowledgements section for your dissertation or thesis.

Overview: The Acknowledgements

• What (exactly) is the acknowledgements section?

Who should you acknowledge?

• How to write the section
• Practical example
• Free acknowledgements template
• Key takeaways

What is the acknowledgements section?

The acknowledgements section of your thesis or dissertation is where you give thanks to the people who contributed to your project’s success. Generally speaking, this is a relatively brief, less formal section.  

With the acknowledgements section, you have the opportunity to show appreciation for the guidance, support, and resources provided by others during your research journey. We’ll unpack the exact contents, order and structure of this section in this post.

Need a helping hand?

Although this is a less “academic” section, acknowledging the right people in the correct order is still important. Typically, you’ll start with the most formal (academic) support received, before moving on to other types of support.

Here’s a suggested order that you can follow when writing up your acknowledgements:

Level 1: Supervisors and academic staff

Start with those who have provided you with academic guidance, including your supervisor, advisors, and other faculty members.

Level 2: Funding bodies or sponsors

If your research was funded, acknowledging these organisations is essential. You don’t need to get into the specifics of the funding, but you should recognise the important role that this made in bringing your project to life.

Level 3: Colleagues and peers

Next you’ll want to mention those who contributed intellectually to your work, including your fellow cohort members and researchers.

Level 4: Family, friends and pets

Last but certainly not least, you should acknowledge your personal (non-academic) support system – those who have provided emotional and moral support. If Fido kept you company during those long nights hunched over the keyboard, you can also thank him here 🙂

As you can see, the order of the acknowledgements goes from the most academic to the least . Importantly, your thesis or dissertation supervisor (sometimes also called an advisor) generally comes first . This is because they are typically the person most involved in shaping your project (or at least, they should be). Plus, they’re oftentimes involved in marking your final work and so a kind word never hurts…

All that said, remember that your acknowledgements section is personal . So, feel free to adjust this order, but do pay close attention to any guidelines or rules provided by your university. If they specify a certain order or set of contents, follow their instructions to the letter.

How to write the acknowledgements section

In terms of style, try to strike a balance between conveying a formal tone and a personal touch . In practical terms, this means that you should use plain, straightforward language (this isn’t the time for heavy academic jargon), but avoid using any slang, nicknames, etc.

As a guide, you’ll typically use some of the following phrases in the acknowledgements section:

I would like to express my appreciation to… for their help with… I’m particularly grateful to… as they provided… I could not have completed this project without… as this allowed me to… Special thanks to… who did… I had the pleasure of working with… who helped me… I’d also like to recognise… who assisted me with…

In terms of positioning, the acknowledgements section is typically in the preliminary matter , most commonly after the abstract and before the table of contents. In terms of length, this section usually spans one to three paragraphs , but there’s no strict word limit (unless your university’s brief states otherwise, of course).

If you’re unsure where to place your acknowledgements or what length to make this section, it’s a good idea to have a look at past dissertations and theses from your university and/or department to get a clearer view of what the norms are.

Practical Example

Alright, let’s look at an example to give you a better idea of what this section looks like in practice.

I would like to express my deepest gratitude to Professor Smith, whose expertise and knowledge were invaluable during this research. My sincere thanks also go to the University Research Fund for their financial support.   I am deeply thankful to my colleagues, John and Jane, for their insightful discussions and moral support. Lastly, I must acknowledge my family for their unwavering love and encouragement. Without your support, this project would not have been possible.

As you can see in this example, the section is short and to the point , working from formal support through to personal support.

To simplify the process, we’ve created a free template for the acknowledgements section. If you’re interested, you can download a copy here .

FAQs: Acknowledgements

Can i include some humour in my acknowledgements.

A touch of light humour is okay, but keep it appropriate and professional. Remember that this is still part of an academic document.

Can I acknowledge someone who provided informal or emotional support?

Yes, you can thank anyone who offered emotional support, motivation, or even informal advice that helped you during your studies. This can include friends, family members, or a mentor/coach who provided guidance outside of an academic setting.

Should I mention any challenges or difficulties I faced during my research?

While the acknowledgements section is primarily for expressing gratitude, briefly mentioning significant challenges you overcame can highlight the importance of the support you received. That said, you’ll want to keep the focus on the gratitude aspect and avoid delving too deeply into the challenges themselves.

Can I acknowledge the contribution of participants in my research?

Absolutely. If your research involved participants, especially in fields like social sciences or human studies, acknowledging their contribution is not only courteous but also an ethical practice. It shows respect for their participation and contribution to your research.

How do I acknowledge posthumous gratitude, for someone who passed away during my study period?

Acknowledging a deceased individual who played a significant role in your academic journey can be done respectfully. Mention them in the same way you would a living contributor, perhaps adding a note of remembrance.

For example, “I would like to posthumously acknowledge John McAnders for their invaluable advice and support in the early stages of this research.”.

Is there a limit to the number of people I can acknowledge?

How do i acknowledge a group or organisation.

When thanking a group or organization, mention the entity by name and, if applicable, include specific individuals within the organization who were particularly helpful.

For example, “I extend my thanks to The Speakers Foundation for their support, particularly Mr Joe Wilkins, for their guidance.”

Recap: Key Takeaways

Writing the acknowledgements section of your thesis or dissertation is an opportunity to express gratitude to everyone who helped you along the way.

Remember to:

• Acknowledge those people who significantly contributed to your research journey
• Order your thanks from formal support to personal support
• Maintain a balance between formal and personal tones
• Keep it concise

In a nutshell, use this section to reflect your appreciation in a genuinely and professionally way.

Psst… there’s more (for free)

This post is part of our dissertation mini-course, which covers everything you need to get started with your dissertation, thesis or research project. 

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• Acknowledgements for PhD Thesis and Dissertations – Explained
• Doing a PhD

The Purpose of Acknowledgements

The acknowledgement section of a thesis or dissertation is where you recognise and thank those who supported you during your PhD. This can be but is not limited to individuals, institutions or organisations.

Although your acknowledgements will not be used to evaluate your work, it is still an important section of your thesis. This is because it can have a positive (or negative for that matter) influence the perception of your reader before they even reach the main body of your work.

Who Should I Acknowledge?

Acknowledgements for a PhD thesis will typically fall into one of two categories – professional or personal.

Within these categories, who you thank will ultimately be your decision. However, it’s imperative that you pay special attention to the ‘professional’ group. This is because not thanking someone who has played an important role in your studies, whether it be intentional or accidental, will more often than not be seen as a dismissal of their efforts. Not only would this be unfair if they genuinely helped you, but from a certain political aspect, it could also jeopardise any opportunities for future collaborations .

Professional Acknowledgements

This may include, but is not limited to:

• Funding bodies/sponsorship providers
• Supervisors
• Research group and lab assistants
• Research participants
• Proofreaders

Personal Acknowledgements

• Key family members and friends
• Individuals who inspired you or directly influenced your academic journey
• Anyone else who has provided personal support that you would like to mention

It should be noted that certain universities have policies which state only those who have directly supported your work, such as supervisors and professors, should be included in your acknowledgements. Therefore, we strongly recommend that you read your university guidelines before writing this section of your thesis.

How to Write Acknowledgements for PhD Thesis

When producing this section, your writing style can be more informal compared to the rest of your thesis. This includes writing in first person and using more emotive language. Although in most cases you will have complete freedom in how you write this section of your thesis, it is still highly advisable to keep it professional. As mentioned earlier, this is largely because it will be one of the first things your assessors will read, and so it will help set the tone for the rest of your work.

In terms of its structure, acknowledgements are expected to be ordered in a manner that first recognises the most formal support before moving onto the less formal support. In most cases, this follows the same order that we have outlined in the ‘Who Should I Thank’ section.

When thanking professionals, always write out their full name and provide their title. This is because although you may be on a first-name basis with them, those who read your thesis will not. By providing full names and titles, not only do you help ensure clarity, but it could also indirectly contribute to the credibility of your thesis should the individual you’re thanking be well known within your field.

If you intend to include a list of people from one institution or organisation, it is best to list their names in alphabetical order. The exception to this is when a particular individual has been of significant assistance; here, it would be advisable to list them.

How Long Should My Acknowledgements Be?

Acknowledgements vary considerably in length. Some are a single paragraph whilst some continue for up to three pages. The length of your acknowledgement page will mostly depend on the number of individuals you want to recognise.

As a general rule, try to keep your acknowledgements section to a single page. Although there are no word limits, creating a lengthy acknowledgements section dilutes the gratitude you’re trying to express, especially to those who have supported you the most.

Where Should My Acknowledgements Go?

In the vast majority of cases, your acknowledgements should appear directly after your abstract and before your table of contents.

However, we highly advise you to check your university guidelines as a few universities set out their own specific order which they will expect you to follow.

Phrases to Help You Get Started

We appreciate how difficult it can be to truly show how grateful you are to those who have supported you over the years, especially in words.

To help you get started, we’ve provided you with a few examples of sentences that you can complete or draw ideas from.

• I am deeply grateful to XXX…
• I would like to express my sincere gratitude to XXX…
• I would like to offer my special thanks to XXX…
• I would like to extend my sincere thanks to XXX…
• …for their assistance at every stage of the research project.
• …for their insightful comments and suggestions.
• …for their contribution to XXX.
• …for their unwavering support and belief in me.

Thesis Acknowledgement Examples

Below are three PhD thesis acknowledgment samples from which you can draw inspiration. It should be noted that the following have been extracted from theses which are freely available in the public domain. Irrespective of this, references to any individual, department or university have been removed for the sake of privacy.

First and foremost I am extremely grateful to my supervisors, Prof. XXX and Dr. XXX for their invaluable advice, continuous support, and patience during my PhD study. Their immense knowledge and plentiful experience have encouraged me in all the time of my academic research and daily life. I would also like to thank Dr. XXX and Dr. XXX for their technical support on my study. I would like to thank all the members in the XXX. It is their kind help and support that have made my study and life in the UK a wonderful time. Finally, I would like to express my gratitude to my parents, my wife and my children. Without their tremendous understanding and encouragement in the past few years, it would be impossible for me to complete my study.

I would like to thank my supervisors Dr. XXX and Dr. XXX for all their help and advice with this PhD. I would also like to thank my sisters, whom without this would have not been possible. I also appreciate all the support I received from the rest of my family. Lastly, I would like to thank the XXX for the studentship that allowed me to conduct this thesis.

I would like to thank my esteemed supervisor – Dr. XXX for his invaluable supervision, support and tutelage during the course of my PhD degree. My gratitude extends to the Faculty of XXX for the funding opportunity to undertake my studies at the Department of XXX, University of XXX. Additionally, I would like to express gratitude to Dr. XXX for her treasured support which was really influential in shaping my experiment methods and critiquing my results. I also thank Dr. XXX, Dr. XXX, Dr. XXX for their mentorship. I would like to thank my friends, lab mates, colleagues and research team – XXX, XXX, XXX, XXX for a cherished time spent together in the lab, and in social settings. My appreciation also goes out to my family and friends for their encouragement and support all through my studies.

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How to Write Acknowledgement in Research Paper

Table of Contents

Writing an acknowledgement in a research paper is an integral part of the process. It is a formal way of expressing gratitude to the individuals and institutions that contributed to the completion of your research.

This section, though not mandatory, holds significant value as it acknowledges the efforts of those who assisted you in the successful completion of your project. In this comprehensive guide, we will delve into the intricacies of writing an effective acknowledgement for your research paper.

Introduction

Acknowledgements serve a crucial role in research papers. They not only express gratitude but also provide a sense of credibility to your work. Acknowledging the contributions of others shows that your research is a collective effort, which can enhance the perceived validity of your findings.

Moreover, acknowledgements can also serve as a platform for you to demonstrate your professional courtesy and respect for the individuals and institutions that have supported your research. This can help in fostering positive relationships, which can be beneficial for your future research endeavors.

Who to Acknowledge in Your Research Paper

Deciding who to acknowledge in your research paper can be a challenging task. It is important to ensure that you do not overlook anyone who has contributed to your research. Here are some categories of individuals and institutions that you might consider acknowledging:

Academic Advisors and Supervisors

Your academic advisors and supervisors are likely to be your first point of contact for guidance and support during your research. They provide valuable insights, feedback, and direction, which can significantly influence the outcome of your research.

Therefore, acknowledging them in your research paper is a way of expressing your gratitude for their assistance and guidance. It also shows your respect for their expertise and dedication to your research.

Research Participants and Collaborators

Research participants and collaborators play a crucial role in the success of your research. They provide the data or information necessary for your research, making their contribution invaluable.

Acknowledging them in your research paper is a way of showing your appreciation for their time and effort. It also symbolizes your respect for their contribution to your research.

Funding Bodies and Institutions

Funding bodies and institutions provide the financial support necessary for conducting your research. Without their support, it might be challenging to carry out your research effectively.

Therefore, acknowledging them in your research paper is a way of expressing your gratitude for their financial support. It also shows your appreciation for their trust in your research capabilities.

How to Write Acknowledgements for Your Research Paper

Writing acknowledgements for your research paper involves more than simply listing names. It requires a thoughtful and sincere expression of gratitude. Here are some steps to guide you in writing effective acknowledgements:

Start with the Most Significant Contributions

Begin your acknowledgements by expressing gratitude to those who have made the most significant contributions to your research. This could be your academic advisors, supervisors, or funding bodies. Starting with the most significant contributions helps to set the tone for the rest of your acknowledgements.

Ensure that you express your gratitude sincerely and professionally. Avoid using overly emotional or informal language as this can undermine the professionalism of your acknowledgements.

Acknowledge Other Contributors

After acknowledging the most significant contributors, proceed to acknowledge other individuals and institutions that have supported your research. This could include research participants, collaborators, and other supportive individuals or institutions.

When acknowledging these contributors, be sure to express your gratitude sincerely and professionally. Also, ensure that you acknowledge each contributor individually to show your appreciation for their unique contribution.

Use Appropriate Language and Tone

The language and tone you use in your acknowledgements can significantly influence how they are perceived. Therefore, it is important to use appropriate language and maintain a professional tone throughout your acknowledgements.

Use formal language and avoid using jargon or colloquial expressions. Also, maintain a consistent tone throughout your acknowledgements to ensure that they are coherent and easy to read.

Examples of Acknowledgements in Research Papers

Here are a few examples that demonstrate how to acknowledge different contributors effectively:

"I would like to express my deepest gratitude to my advisor, Professor ABC , for his invaluable guidance and support throughout this research. His expertise and dedication have been a source of inspiration and motivation."

"I am deeply grateful to all the participants who generously shared their time and experiences for this research. Their contributions have been instrumental in the success of this study."

"This research was made possible by the generous funding from ABC Foundation . I am profoundly grateful for their support and trust in my research capabilities."

Writing acknowledgements in a research paper is a thoughtful process that requires careful consideration of who to acknowledge and how to express gratitude. By following the guidelines and examples provided in this article, you can write effective acknowledgements that reflect your appreciation and respect for the contributions of others to your research.

Remember, acknowledgements are more than just a formality. They are an opportunity to express your gratitude and respect for the individuals and institutions that have supported your research journey. So, take the time to write acknowledgements that are sincere, professional, and reflective of your gratitude.

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Dissertation acknowledgments [with examples]

What are dissertation acknowledgements?

What to consider when writing your dissertation acknowledgments, who to thank in your dissertation acknowledgments, what (and what not) to write in your dissertation acknowledgments, good examples of dissertation acknowledgments, a final word on writing dissertation acknowledgments: have fun, frequently asked questions about dissertation acknowledgments, related articles.

While you may be the sole author of your dissertation, there are lots of people who help you through the process—from your formal dissertation advisors to the friends who may have cooked meals so that you could finish your last chapter . Dissertation acknowledgments are a chance to thank everyone who had a hand in the completion of your project.

Dissertation acknowledgments are a brief statement of your gratitude to advisors, professors, peers, family, and friends for their help and expertise.

In this guide, we’ll cover:

• the most important things to consider when you’re writing your dissertation acknowledgments
• who to thank in your dissertation acknowledgments
• what (and what not) to write in your dissertation acknowledgments
• short examples of dissertation acknowledgments

Once you’re at the stage where you’re writing your dissertation acknowledgments, you may be tempted to kick back and relax. After all, the hard part of writing the dissertation itself is over and a list of thanks should be simple to churn out.

However, the acknowledgments are an important part of your overall work and are something that most people who read your dissertation, including prospective employers, will look at.

Tip: The best dissertation acknowledgements are concise, sincere, and memorable.

Approach this part of the process, brief as it may be compared to the long haul of writing the dissertation, with the same high level of care and attention to detail. It’s an explicit and permanent statement of who made a real impact on your work and contributed to your academic success.

Plus, the people you thank are often deeply moved by being included—some even go so far as to frame the acknowledgments. Aim to make yours sincere, memorable and something that people will be touched by.

First things first: who should you include in your dissertation acknowledgments? If you’re not sure who to thank, try the brainstorming technique to generate some ideas. Consider these two approaches:

• Make a list of everyone, both professional and personal, who was involved at any point during your work on your dissertation, and then thin down the list from there.
• Make a list of the pivotal aspects of your process and think about who was involved and how they helped.

As you select the people and groups to include in your dissertation acknowledgments, keep in mind that it’s essential to acknowledge your supervisor and anyone else with a visible connection to your work.

It’s an unfortunate reality that not every supervisor goes above and beyond to provide feedback and guidance to the students they are supposed to supervise. However, leaving them out, even if you personally felt disappointed by their involvement or lack thereof, could be seen as a snub.

You should end up with a fairly short list of people to thank. While being mindful of professional etiquette and personal feelings, be choosy about who makes the final cut since your acknowledgments should be limited to no more than a page.

Now that you have your list of people and groups to thank, it’s time to start writing. Before your first pen or keystroke, however, check your university’s guidelines as your institution may have specific rules around what can and cannot be included.

The standard practice is to begin with the formal and then progress to the informal, so the first people to mention would be:

• supervisors
• committee members
• other professional contacts

Use their full names and titles and go into brief detail about how they contributed to your work.

Once those are done, you can move on to the personal thanks, which can include friends, family, even pets. If you are so inclined, it is also considered appropriate to thank God or make mention of spiritual support.

You may also choose to inject a little humor at this point, but don’t get carried away and definitely don’t include sarcasm or critical comments of any kind, including self-critical ones. Remember that the acknowledgments precede your dissertation, so you want to be taken seriously.

A couple more basics that are essential when creating your acknowledgments:

• Position: Acknowledgments should be placed after the title page and before the abstract.
• Perspective: Write from the first-person perspective and speak in your own voice.

A really good way to get a sense of how to write your own dissertation acknowledgments is to read ones written by others. Notice which ones you respond particularly well to and use them as a model upon which to base your own.

Here are some good examples to help you get started:

I couldn’t have reached this goal without the help of many people in my life. I’d like to take this opportunity to thank them for their support.

First, my sincere thanks to my dissertation committee. The value of their guidance cannot be overstated. Dr. Elaine Gooding and Dr. Matthew Hunter provided much wisdom that helped me chart my course. I couldn’t have asked for a better supervisor than Dr. Fiona Moore, whose knowledge and experience guided me every step of the way.

Next, I’d like to thank my partner, Elliott. Your votes of confidence kept me going when my spirits dipped. I couldn’t have done this without you.

Last but not least, I’d like to acknowledge the emotional support provided by my family and friends. We made it to the top of the mountain! I look forward to celebrating with all of you.

This example is shorter, but still contains the key components:

Several people played a decisive role in my success and I would like to take this opportunity to thank them.

My chair, Dr. Ronald Saulk, provided invaluable support and infinite patience and I am truly grateful for all of his wisdom and guidance. I also owe the entire staff of the Wilhelm Library a debt of gratitude. From tracking down books and arranging for interlibrary loans to keeping the coffee maker in the lobby well-stocked and in good working order, they offered the practical help and kind gestures that made all the difference.

I’d also like to thank my family and God, for always being there for me.

One final piece of advice: enjoy this process. Writing a dissertation doesn’t happen every day, and the opportunity to acknowledge the important people in your life in a published format is as rare as it is wonderful.

What’s more, this part of your dissertation is unlike any other. It’s unbounded by the conventions that apply to the formal work. It’s a chance to really flex some creative muscle and let your personality shine through. So make the most of it and have fun!

In your dissertation acknowledgments, you thank everyone who has contributed to your work or supported you along the way. Who you want to thank is a very personal choice, but you should include your supervisors and anyone else with a visible connection to your work. You may also thank friends, family, and partners.

First, you need to come up with a list of people you want to thank in your dissertation acknowledgments. As a next step, begin with the formal and then progress to the informal, so the first people to mention would be supervisors, mentors, committees, and other professional contacts. Then, you can move on to the personal thanks, which can include friends, family, even pets.

Who you acknowledge in your dissertation is ultimately up to you. You should, however, thank your supervisor and anyone else with a visible connection to your work. Leaving them out, even if you personally felt disappointed by their involvement or lack thereof, could be seen as a snub. In addition, you can thank friends, partners or family.

There are many ways so you can acknowledge your dissertation supervisor. Some examples can be found in this article above. If you need more examples, you can find them here .

While acknowledgments are usually more present in academic theses, they can also be a part of research papers. In academic theses, acknowledgments are usually found at the beginning, somewhere between abstract and introduction. In research papers, acknowledgments are usually found at the end of the paper.

Recognizing Contributions: Acknowledge In Research Paper

Learn how to acknowledge in research paper with our simple guide, and ensure that your work gains recognition.

When we work on any project, it’s not just about our individual effort, it’s about teamwork as well. It’s important to acknowledge the contributions of others who have helped you along the way. This is where the acknowledgment section comes in. In this part of your paper, you can express your gratitude to those who have supported you throughout the research process, such as funders, advisors, assistants, collaborators, participants, and editors.

However, it’s important to be mindful of ethical considerations and avoid any promotion or advertising of specific individuals or organizations. In this guide, we’ll cover everything you need to know about acknowledgments, including how to acknowledge in research paper ,  tips for writing them, common mistakes to avoid, and ethical considerations. So, let’s get started!

What Is Acknowledgement In A Research Paper?

The acknowledgment section in a research paper credits individuals, institutions, or organizations that aided in the research or manuscript preparation. It’s usually found after the conclusion.

While optional, acknowledgments are commonly added to recognize and thank contributors for their efforts. This section typically starts with a statement thanking those who funded or supported the project, along with colleagues, research assistants, or other contributors who provided valuable feedback or assistance.

Being specific and detailing the contributions of each individual or organization is crucial to show their importance in the research process. However, it’s unnecessary to acknowledge everyone who helped, and acknowledgments should be kept brief and relevant to the project.

Why Is Acknowledgment Important?

Acknowledgment holds significant importance in research as it acknowledges and provides credit to individuals or organizations who have contributed to the research project. It expresses gratitude for their guidance, support, and assistance during the research process.

Acknowledgments are commonly included in research papers to build relationships and encourage future collaborations with those who have supported the research. By acknowledging their contributions, researchers demonstrate their appreciation for the input of others and the importance of collaboration in the research process.

Moreover, the acknowledgment section ensures academic integrity by recognizing and crediting all contributors to the research project. It also prevents any potential issues related to plagiarism or lack of attribution. 

Who Should Be Acknowledged?

Acknowledgments in a research paper should recognize and give credit to individuals, organizations, or institutions that contributed to the research project in some way. This can include: 

• Funding sources: Acknowledge those who provided financial support for the research project.
• Academic advisors or mentors: Acknowledge those who provided guidance or supervision throughout the research process.
• Research assistants: Acknowledge those who provided technical or administrative support during the research.
• Participants : Acknowledge those who took part in the research study, such as survey respondents.
• Collaborators : Acknowledge colleagues or other researchers who contributed to the research project in some way.
• Editors or proofreaders: Acknowledge those who helped with editing or proofreading the manuscript .
• Institutions or organizations: Acknowledge the institution or organization that provided resources or support for the research project. 

Types Of Acknowledgement

Acknowledgment in a research paper can take various forms, depending on the purpose and context of the project. Here are some common types of acknowledgments: 

1. Formal Acknowledgments

These are typically written in a formal tone and are used to recognize and give credit to people, organizations, or institutions that provide financial or technical support to the research project. These acknowledgments often appear at the beginning or end of the research paper and may include formal language and formatting.

2. Informal Acknowledgments

These acknowledgments are often more personal and informal in tone. They may include acknowledging friends, family members, or colleagues who provided emotional support or helped in some way during the research process.

3. Professional Acknowledgments

These acknowledgments are typically used in academic or professional settings and are aimed at giving credit to individuals or organizations that contributed to the research project. These acknowledgments may include thanking mentors, colleagues, research assistants, or funding agencies.

4. Collaborative Acknowledgments

These acknowledgments are used to recognize the collaborative nature of research projects. They may include acknowledging co-authors, collaborators, or other researchers who contributed to the project in some way.

Tips For Writing An Acknowledgement

When writing acknowledgment in a research paper, it’s important to keep the following tips in mind: 

• Be specific: Clearly mention the contributions made by individuals or organizations, and how they helped in the research process.
• Use appropriate tone: Write in a professional tone and avoid using overly emotional language.
• Keep it concise: Avoid lengthy paragraphs and keep the acknowledgment section brief and relevant.
• Follow the required format: Check the guidelines provided by the journal or institution and ensure that you follow the required format.
• Proofread: Carefully proofread the acknowledgment section for any errors or typos.
• Be grateful: Show appreciation and gratitude to the individuals or organizations who contributed to the research project.
• Avoid self-promotion: The acknowledgment section should not be used to promote oneself or one’s organization.

 Examples Of Acknowledgement

Examples of acknowledgments in a research paper include thanking the funding sources, academic advisors or mentors, research assistants, participants, collaborators, editors or proofreaders, and institutions or organizations that provided support. Here are some sample acknowledgments that are concise and relevant to the research project:

Acknowledge In Research Paper: Example 1

“I would like to thank Dr. Ram for his invaluable guidance and support throughout this project. I am also grateful to my research assistant, Priya, for her technical expertise and administrative assistance. This project would not have been possible without the generous financial support of the XYZ Foundation. Lastly, I would like to acknowledge the study participants who generously shared their time and insights.”

Acknowledge In Research Paper: Example 2

“I am indebted to Dr. Mary for her continuous support and feedback throughout the research process. I also want to thank my colleagues, Shahin and Sarah, for their valuable input and suggestions. The editorial assistance provided by XYZ Editing Services was also greatly appreciated. I am also grateful to the ABC Institution for providing the necessary resources for this research project.”

Common Mistakes To Avoid When Writing An Acknowledgement

When writing acknowledgment, it’s important to avoid certain mistakes, such as:

• Forgetting to acknowledge someone who contributed to the research project.
• Using vague language instead of specific details about how someone contributed.
• Focusing too much on personal anecdotes or stories, rather than keeping the acknowledgment concise and relevant to the research project.
• Using the acknowledgment section to promote or advertise specific individuals or organizations.
• Forgetting to proofread the acknowledgment section for errors in grammar or spelling.
• Including acknowledgments that are not relevant to the research project.
• Making it too formal or too casual, rather than matching the tone of the rest of the research paper.

To avoid these mistakes, it’s important to carefully consider who should be acknowledged, what specific contributions they made, and to keep the language concise and relevant to the research project. It’s also helpful to have someone else review the acknowledgment section to ensure that it’s free of errors and strikes the right tone.

How To Acknowledge In Research Paper? 

• When citing an acknowledgment in a research paper, it should be listed as a separate section at the end of the paper, following the references section. It should be titled “Acknowledgement” and be placed after the conclusion but before the reference list.
• Acknowledgment section should not be included within the text citation or reference list. However, if a person or organization mentioned in the acknowledgment section was cited within the text, it should be included in the in-text citation and reference list.
• It’s important to make sure that acknowledgments are cited correctly in order to give credit to those who contributed to the research project. This will help to ensure academic integrity and avoid plagiarism. Learn more about Plagiarism here .

Ethical Considerations For Acknowledging Others In Your Research Paper

It is essential to consider ethical principles when acknowledging others in your research paper. First and foremost, ensure that you acknowledge all individuals and organizations that made significant contributions to your research. This acknowledgment must be honest and accurate and should not falsely claim credit for the work of others.

Additionally, it is crucial to obtain consent from individuals before acknowledging them in your research paper, particularly when using their personal information. Ensure that you have informed them about how their contribution will be acknowledged and seek their permission to do so.

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About Sowjanya Pedada

Sowjanya is a passionate writer and an avid reader. She holds MBA in Agribusiness Management and now is working as a content writer. She loves to play with words and hopes to make a difference in the world through her writings. Apart from writing, she is interested in reading fiction novels and doing craftwork. She also loves to travel and explore different cuisines and spend time with her family and friends.

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Writing Acknowledgments for Your Research Paper

• Research Process
• Peer Review

In this article, we describe what types of contributions warrant mention in the acknowledgments section of a paper .

Updated on July 8, 2014

In another article , we discuss four criteria that must be met for an individual to qualify for manuscript authorship. In this article, we describe what types of contributions warrant mention in the acknowledgments section of a paper instead. The International Committee of Medical Journal Editors (ICMJE) describes several roles that merit acknowledgment, rather than authorship :

“acquisition of funding; general supervision of a research group or general administrative support; and writing assistance, technical editing, language editing, and proofreading.”

You should also acknowledge direct technical assistance, including help with animals, cells, equipment, patients, procedures, or techniques or provision of data, equipment, reagents, or samples, as well as more indirect assistance via intellectual discussions. Note that all of these contributions are typically more mechanical, indirect, and/or one-dimensional than those of authors. Additionally, some argue that individuals who provided help and could be chosen as a peer reviewer, leading to a potential conflict of interest, should be cited.

In any case, the ICMJE states that contributors may be cited individually or collectively and that their precise contributions should be specified.

e.g., “We thank Dr. X and Dr. Y for performing the surgeries” or “We thank the physicians who performed the surgeries"

Institutional affiliations may or may not be mentioned, depending on the journal's guidelines. Finally, the ICMJE encourages written permission from acknowledged individuals “because acknowledgment may imply endorsement.”

Funding sources should also be mentioned in the acknowledgments section, unless your target journal requires a separate section for this information. Whether the funding was partial or full, relevant grant numbers, and the author(s) who received the funding, if applicable, should be detailed as well. Note that acknowledging grants and fellowships is in fact required by many funding agencies and research institutions.

In contrast, contributions that are not specifically related to your research, including personal encouragement (e.g., by your friends or parents) and very general help (e.g., from a laboratory manager who purchases all supplies for your research group), should not be cited. Additionally, anonymous editors and peer reviewers are usually not thanked in the acknowledgments section; many journals (such as American Physical Society journals ) explicitly discourage this practice because it is difficult to comprehensively acknowledge all anonymous support and because this practice could potentially bias reviewers.

The writing style of acknowledgments sections may vary according to the journal, but generally, these sections are written in the first person and are as succinct as possible. A statement about conflicts of interest, citation of previous publication in poster or abstract form, and other information may also be included in this section, again depending on the journal. As you proceed through revisions for one journal or if you change your target journal, remember to reformat as necessary and to update your acknowledgments if additional help was obtained during the revision, such as with editing or new experiments.

Although an acknowledgments section may be appended to the end of your manuscript or relegated to a footnote, it is not a trivial component. By acknowledging all help received with your research, you are demonstrating your integrity as a researcher, which in turn encourages continued collaboration. You may also be bolstering your colleagues' careers, as being credited in an acknowledgments section is emerging as one of many gauges of a researcher's professional impact beyond citations (see ImpactStory , based on altmetrics ). Furthermore, information about who provided certain data, equipment, protocols, reagents, or samples may be of help to other researchers in your field.

This editing tip has hopefully elucidated what to include in the acknowledgments section of your manuscript and why this section is significant. If you have any comments or questions, please contact us . Best wishes in your research and writing!

Michaela Panter, PhD

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Acknowledgements Example for an Academic Research Paper

Posted by Rene Tetzner | Sep 1, 2021 | How To Get Published | 0 |

Acknowledgements Example for an Academic or Scientific Research Paper This example of acknowledgements for a research paper is designed to demonstrate how intellectual, financial and other research contributions should be formally acknowledged in academic and scientific writing. As brief acknowledgements for a research paper, the example gathers contributions of different kinds – intellectual assistance, financial support, image credits etc. – into a single Acknowledgements section. Do note, however, that the formats preferred by some scholarly journals require the separation of certain contributions such as financial support of research into their own sections.

Although authors often write acknowledgements hastily, the Acknowledgements section is an important part of a research paper. Acknowledging assistance and contributions establishes your integrity as a researcher as well as your connections and collaborations. It can also help your readers with their own research, affect the influence and impact of the researchers and other professionals you thank, and demonstrate the value and purpose of the agencies that fund your work. The contents of the example I have prepared here are appropriate for a research paper intended for publication in a peer-reviewed journal, but the author, the research project, the manuscript studied, the journal publishing the paper and all those to whom gratitude is extended are entirely fictional. They were created for the purpose of demonstrating the following key concerns when writing the acknowledgements for a formal research paper:

•   Writing in the first person (‘I’ for a single author or ‘we’ for two or more) to offer concise but sincere acknowledgements of specific contributions to your research. •   Maintaining formal language, complete sentences and a professional tone to give specific and thorough information about contributions and convey collegial gratitude. •   Expressing respect and appreciation in an appropriate fashion for each and every contribution and avoiding artificial or excessive flattery. •   Using the complete names and preferred name formats for individuals, funding agencies, libraries, businesses and other organisations. Here, for example, I posit that the library holding the relevant manuscript has indicated that the name of the collection (lengthy though it is) should not be abbreviated. •   Acknowledging contributions to your research and paper in the order that best represents the nature and importance of those contributions. The assistance of the author’s mentor comes first here, for instance, whereas the language editor is acknowledged much further down the list. •   Meeting the requirements for acknowledgements set by the journal or other publisher of the research paper. For the example below, the goal is to record all relevant contributions to the research and paper in a single brief Acknowledgements section of 500 words or less – a set of parameters that would suit the acknowledgement requirements or expectations of many academic and scientific journals and even fit into a footnote or endnote if necessary.

Example Acknowledgements for an Academic Research Paper This paper and the research behind it would not have been possible without the exceptional support of my supervisor, Lawrence Magister. His enthusiasm, knowledge and exacting attention to detail have been an inspiration and kept my work on track from my first encounter with the log books of British Naval Ships MS VII.2.77 to the final draft of this paper. Margaret Kempis and Matthew Brown, my colleagues at Western University, have also looked over my transcriptions and answered with unfailing patience numerous questions about the language and hands of British Naval Ships MS VII.2.77. Samantha McKenzie, head librarian of the Southern Region Central Collegiate Library Special Collections and Microfilms Department where British Naval Ships MS VII.2.77 currently resides, not only provided colour images of the manuscript overnight, but unexpectedly shared the invaluable information on the book that she has been gathering for almost twenty years. I am also grateful for the insightful comments offered by the anonymous peer reviewers at Books & Texts. The generosity and expertise of one and all have improved this study in innumerable ways and saved me from many errors; those that inevitably remain are entirely my own responsibility.

Studying British Naval Ships MS VII.2.77 has proved extremely costly and I am most thankful for the Western University Doctoral Fellowship that has provided financial support for the larger project from which this paper grew. A travel grant from the Literary Society of the Southern Region turned the hope of working in person with British Naval Ships MS VII.2.77 into a reality, and the generous offer of free accommodation from Ms McKay (Samantha McKenzie’s aunt) allowed me to continue my research with the book much longer than I could have hoped. The final design of the complicated transcription tables in Appendices I–III is the creative and technical work of Sam Stone at A+AcaSciTables.com, and the language and format of the paper have benefited enormously from the academic editing services of Veronica Perfect. Finally, it is with true pleasure that I acknowledge the contributions of my amazing partner, Kendric James, who has given up many a Friday evening and Sunday afternoon to read every version of this paper and the responses it has generated with a combination of compassion and criticism that only he could muster for what he fondly calls ‘my odd obsession with books about the sea.’

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Acknowledgments and References

Acknowledgments.

This usually follows the Discussion and Conclusions sections. Its purpose is to thank all of the people who helped with the research but did not qualify for authorship (check the target journal’s Instructions for Authors for authorship guidelines). Acknowledge anyone who provided intellectual assistance, technical help (including with writing and editing), or special equipment or materials.

TIP: The International Committee of Medical Journal Editors has detailed guidelines on who to list as an author and who to include in the Acknowledgments that are useful for scientists in all fields.

Some journals request that you use this section to provide information about funding by including specific grant numbers and titles. Check your target journal’s instruction for authors for specific instructions. If you need to include funding information, list the name(s) of the funding organization(s) in full, and identify which authors received funding for what.

As references have an important role in many parts of a manuscript, failure to sufficiently cite other work can reduce your chances of being published. Every statement of fact or description of previous findings requires a supporting reference.

TIP: Be sure to cite publications whose results disagree with yours. Not citing conflicting work will make readers wonder whether you are really familiar with the research literature. Citing conflicting work is also a chance to explain why you think your results are different.

It is also important to be concise. You need to meet all the above needs without overwhelming the reader with too many references—only the most relevant and recent articles need to be cited. There is no correct number of references for a manuscript, but be sure to check the journal’s guidelines to see whether it has limits on numbers of references.

TIP: Never cite a publication based on what you have read in a different publication (such as a review), or based only on the publication’s abstract. These may mislead you and readers. Read the publication itself before you cite it, and then check the accuracy of the citation again before submitting your manuscript.

You should reference other work to:

• Establish the origin of ideas

When you refer to an idea or theory, it is important to let your readers know which researcher(s) came up with the idea. By citing publications that have influenced your own work, you give credit to the authors and help others evaluate the importance of particular publications. Acknowledging others’ contributions is also an important ethical principle.

• Justify claims

In a scientific manuscript, all statements must be supported with evidence. This evidence can come from the results of the current research, common knowledge, or from previous publications. A citation after a claim makes it clear which previous study supports the claim.

• Provide a context for your work

By highlighting related works, citations help show how a manuscript fits into the bigger picture of scientific research. When readers understand what previous studies found and what puzzles or controversies your study relates to, they will better understand the meaning of your work.

• Show there is interest your field of research

Citations show that other researchers are performing work similar to your own. Having current citations will help journal editors see that there is a potential audience for your manuscript.

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How to Write Acknowledgement in Research Paper

December 27, 2023

In research papers, acknowledgements play a crucial role in recognizing the contributions and support of individuals or organizations who have helped in the completion of the study. They provide an opportunity to express gratitude towards people who provided guidance, resources, or encouragement during the research process.

Acknowledgements serve several important purposes. Firstly, they acknowledge the intellectual and technical support received, ensuring that credit is given where it is due. Secondly, they foster a sense of collaboration and community by recognizing the efforts of others within the research field. Furthermore, acknowledgements help to establish credibility by showcasing the individuals, institutions, or funding bodies that have contributed to the research.

The importance of acknowledgements goes beyond mere courtesy; they are a record of the network of support that exists within the research community. By recognizing the contributions of others, researchers can foster goodwill and build lasting relationships in their field. As such, it is crucial to understand the significance of acknowledgements and to include them thoughtfully and sincerely in research papers.

What to Include in the Acknowledgements

When writing acknowledgements in a research paper, it is important to consider the key elements that should be included. Here are some points to consider when deciding what to include in your acknowledgements:

• Mentors and Advisors: Acknowledge the individuals who provided guidance, advice, or supervision throughout the research process. This could include your research advisor, committee members, or other mentors who played a significant role in shaping your work.
• Funding Sources: Acknowledge any funding bodies or organizations that provided financial support for your research. This could include grants, scholarships, or fellowships.
• Research Participants: If your study involved human participants or subjects, it is important to thank them for their participation and contribution to the research. Ensure that their privacy and confidentiality are maintained by using initials or codes instead of full names.
• Collaborators and Colleagues: If you worked closely with other researchers or colleagues on the project, acknowledge their contributions and highlight their specific roles or expertise.
• Technical and Administrative Support: Recognize individuals or institutions that provided technical assistance, equipment, or administrative support during the research process.
• Family and Friends: It is common to express gratitude to loved ones for their support and understanding throughout the research journey. Although personal acknowledgements should be kept brief, acknowledging their support can be a significant gesture.

Remember to be sincere and genuine in your acknowledgements, recognizing the specific contributions and support each individual or entity provided.

Structure and Formatting of the Acknowledgements

The structure and formatting of acknowledgements in a research paper play a vital role in conveying gratitude in a clear and organized manner. Here are some guidelines to follow when structuring and formatting your acknowledgements:

• Placement: The acknowledgements section is typically placed towards the end of the paper, after the conclusion but before the references.
• Title: Use a clear and concise title such as “Acknowledgements” or “Acknowledgments” at the top of the section to indicate its purpose.
• Formatting: In general, acknowledgements are written in paragraph form. However, if you have a long list of individuals or organizations to acknowledge, you can also use a bullet-point or numbered list.
• Tone: The tone of acknowledgements should be professional and appreciative. Use a sincere and heartfelt tone to express your gratitude.
• Length: Acknowledgements should be kept concise and to the point. A few paragraphs or a short list of names and institutions are typically sufficient.
• Order: It is customary to acknowledge individuals and organizations in order of their significance and contribution to the research. Start with your most important mentors, advisors, or sponsors, and then proceed to acknowledge collaborators, research participants, and others who provided support.
• Style: Follow the formatting guidelines specified by the journal or academic institution. This may include font type, size, and spacing.

Remember, while acknowledgements provide an opportunity to express gratitude, it is important to maintain professionalism and adhere to the guidelines set by the journal or your academic institution.

Examples of Well-Written Acknowledgements

Example 1: “I would like to express my deepest gratitude to Professor [Name] for their unwavering guidance, invaluable insights, and constant support throughout this research journey. Their expertise and dedication have been instrumental in shaping this study. I would also like to thank my research committee members, [Names], for their thoughtful feedback and constructive criticism. I am grateful to [Funding Body/Institution] for providing financial support that made this research possible. Special thanks to all the participants who generously volunteered their time and contributed to this study. I would also like to acknowledge [Support Staff/Technicians] for their technical assistance. Lastly, I am indebted to my family and friends for their unwavering support, love, and encouragement throughout this endeavor.”

Example 2: “We extend our sincere appreciation to Professor [Name] for their mentorship and guidance, which have been invaluable in the completion of this research. We would like to thank [Funding Body/Institution] for their financial support, without which this study would not have been possible. We are grateful to the participants who willingly shared their experiences and expertise, providing the foundation for our research. Our gratitude also extends to our collaborators and fellow researchers who provided valuable insights and feedback throughout the project. We would like to acknowledge the technical support provided by [Support Staff/Technicians]. Lastly, we express our heartfelt thanks to our families and friends for their unwavering support and understanding.”

Remember, these examples are just a guide. It is important to personalize your acknowledgements based on the individuals and organizations that have contributed to your specific research project.

Tips for Writing Acknowledgements

• Be specific: Clearly mention the names of individuals, institutions, or organizations that have made significant contributions to your research.
• Focus on contributions: Acknowledge the specific ways in which each person or entity has contributed to your research, whether it’s through mentorship, funding, technical support, or intellectual guidance.
• Maintain professionalism: While expressing gratitude, maintain a professional tone and avoid overly personal or informal language.
• Be concise: Keep your acknowledgements brief and to the point, focusing on the most essential contributors.
• Follow guidelines: Adhere to any specific formatting guidelines provided by the journal or academic institution.
• Review and proofread: Ensure that your acknowledgements are free of spelling or grammatical errors by reviewing and proofreading them carefully.
• Express sincerity: Convey genuine appreciation and gratitude in your acknowledgements to show the true extent of your appreciation.

Remember, acknowledgements are an opportunity to show gratitude to those who have supported your research, so be sure to express your thanks sincerely and respectfully.

Common Mistakes to Avoid in Acknowledgements

• Excessive length: Avoid making your acknowledgements overly lengthy. Keep them concise and focus only on those who have made substantial contributions to your research.
• Forgetting important contributors: Take the time to think through all the individuals and organizations that have played a role in your research and ensure that you acknowledge them appropriately. Leaving out key contributors can be unintentionally dismissive.
• Being vague: Be specific when acknowledging the contributions of individuals or institutions. Avoid using generic statements that don’t adequately highlight the specific ways in which they have supported your research.
• Inclusion of personal anecdotes: While it’s important to express gratitude, acknowledgements should remain professional. Avoid including personal anecdotes or unrelated stories that distract from the purpose of the section.
• Neglecting proofreading: Treat acknowledgements with the same level of attention and care as the rest of your research paper. Proofread for spelling and grammatical errors before submitting your final document.
• Inconsistent formatting: Ensure that your acknowledgements follow the same formatting as the rest of your research paper, adhering to any journal or institution guidelines.

By avoiding these common mistakes, you can ensure that your acknowledgements accurately reflect the contributions of those involved in your research while maintaining a professional and concise tone.

Struggling with your research paper’s acknowledgement section? Our auto essay writer can make it easy, guiding you to express your gratitude flawlessly.

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Acknowledgement Examples

Examples of Acknowledgement for Project, Thesis and Assignments

Acknowledgement For Research Paper

Acknowledgement is the process of formally recognizing someone’s effort and thanking them for it. When it comes to research papers, acknowledgements are a way of giving credit where credit is due. They can be a great way to show your appreciation for all the help and support you’ve received while writing your paper.

If you’re wondering how to write acknowledgement for research paper, you’re in luck. In this article, I’ll be providing examples of acknowledgements for research paper.

Acknowledgement Writing Tips For Research Paper

It is always nice to be able to look back on a research project and see all of the people who made it possible. Acknowledgements are one way to do that.

Here are some tips for writing acknowledgements for research papers:

First, make sure to include all of the people who directly helped with your research. This includes your supervisor, research assistants, and anyone else who played a role in your project.

Second, don’t forget to acknowledgements the financial support that made your research possible. This could include funding from your university, government grants, or private donors.

Third, you can also use your acknowledgement to thank anyone who provided moral support during your project. This could include family, friends, or fellow researchers.

Fourth, if you want to, you can also use your acknowledgement to thank the people who inspired your research. This could be other researchers, writers, or public figures.

Finally, make sure to proofread your acknowledgement carefully before you publish it. You don’t want to accidentally leave anyone out!

Other Acknowledgement Article: 

• Acknowledgement For Social Science Project
• Acknowledgement For It Project
• Acknowledgement For Account Project

Acknowledgement Examples For Research Paper

There are many different ways to write an acknowledgement for a research paper, and the best way to do it will vary depending on the project and the circumstances. However, some elements are common to most acknowledgements, such as thankfulness to supervisors, colleagues, and co-authors. Acknowledgements can also be a good way to signal the end of a research project.

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How to Draft the Acknowledgment Section of a Manuscript

What is the Purpose of the Acknowledgements Section in a Research Paper?

The acknowledgment section is an integral part of all academic research papers. It provides appropriate recognition to all contributors for their hard work. We discuss here,  the relevant guidelines for acknowledging contributors.

Defining Who Is Acknowledged

The acknowledgment section helps identify the contributors responsible for specific parts of the project. It can include:

• Non-authors (colleagues, friends, supervisor, etc.)
• Funding sources
• Editing services ,
• Administrative staff

In academic writing, the information presented in the acknowledgment section should be kept brief. It should only mention people directly involved with the project. In other words, one should not consider thanking ones’ parents for moral and financial support.

Acknowledging contributors is necessary. However, you must know the difference between an author and a contributor . The International Committee of Medical Journal Editors ( ICMJE ) defines four criteria to assign authorship.

He or she has to have

• Made substantial conceptual or design contributions or gathered and analyzed important data, and
• Either helped draft or critically revise the paper in keeping with important intellectual content, and
• Provided final approval before publishing, and
• Agreed to be accountable for the accuracy of the work

These authors and their affiliations will be listed at the beginning of the paper. The “corresponding author” will also be listed a second time and will directly correspond with the journal to ensure documentation requirements are met.

Many journals now ask that you provide the role of each author in your acknowledgment section. For example, a typical statement of authors’ contributions might be as follows (note that only last names are used unless ambiguous):

Smith conducted the data analysis and created the tables and figures. Jones provided his technological expertise for GIS tracking. Johnson provided a factual review and helped edit the manuscript.

This type of acknowledgment provides your reader with a good sense of who was responsible for each part of your research and manuscript.

Non-Author Contributors

There are many people involved in a research project who are not authors but have provided valuable contributions. For example, one person’s responsibility might be to seek project funding; another’s might be to supervise laboratory staff. A few others might have provided valuable services such as technical editing and writing or offering help in reviewing and revising the manuscript for grammar and syntax. These people should also be mentioned in the acknowledgment section of your manuscript.

Acknowledgment should also be provided  for  writing assistance, technical editing, language editing, and proofreading . Therefore, editing companies need to be duly acknowledged in professionally edited manuscripts as per the  ICMJE guidelines.

It is necessary to acknowledge editing companies in professionally edited manuscripts, even though these companies are paid for their work.

Acknowledgment Format

Unlike the main body of your paper, the format for your acknowledgment section can be more personal. It is permissible to use personal pronouns in this section. For example,

I thank the following individuals for their expertise and assistance throughout all aspects of our study and for their help in writing the manuscript.

Keep in mind that many guidelines indicate that funding sources be listed separately from the acknowledgment section. In addition, the sources (funding agencies) might have specific guidelines that you must follow. Please be sure to comply with these sources and your author guidelines.

For more information on authors and contributors , read articles on the Enago Academy website.

What types and formats of acknowledgments have you incorporated into your manuscripts? Please share your thoughts in the comments section below. Do you need help with manuscript editing ? Make sure you visit enago.com today!

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Acknowledgement in Research Paper | How to Write | Perfect Example

What is acknowledgement in research paper.

Acknowledgement in a research paper is the section where the author expresses gratitude to individuals and organizations who have contributed to the completion of the study. This section is usually placed at the beginning or end of the paper and is an important part of the research process. It allows the author to recognize the support, assistance, and guidance they have received from others in the course of their research.

What is the purpose of acknowledgement in research paper?

The acknowledgement section is an opportunity for the author to show appreciation for anyone who has helped them in the research process, including mentors, advisors, colleagues, and funding agencies. It is also a way to acknowledge the contributions of participants, interviewees, or anyone else who has played a role in the study.

Acknowledgements can also include thanks to individuals who have provided critical feedback, technical assistance, or resources that have been essential to the research project. Overall, this section is a way for the author to show their appreciation for the collaborative and supportive nature of the research community.

How to write acknowledgement in research paper?

• Identify Key Contributors : Make a list of individuals and organizations that have contributed significantly to your research. This includes advisors, mentors, collaborators, funders, participants, and institutions.
• Understand the Purpose : Acknowledgments are meant to recognize and thank those who have supported or contributed to your research in various ways. Understand the purpose of this section is to express gratitude and recognize their contributions.
• Be Genuine and Specific : Your acknowledgments should be sincere and specific. Avoid generic expressions of thanks and instead, mention the specific contributions each person or organization made to your research.
• Start with Formality : Begin your acknowledgment section with a formal tone and expression of gratitude. Address individuals with their appropriate titles, such as Dr., Prof., Mr., or Ms., and mention any institutional affiliations if relevant.
• Personalize Your Thanks : Tailor your acknowledgments to acknowledge each individual’s specific contributions. Mention how their support, guidance, or expertise influenced your research or contributed to its success.
• Maintain Professionalism : While acknowledgments can be personal, maintain a professional tone and avoid overly informal language or colloquialisms. Remember that this section is part of your scholarly work.
• Consider Cultural Sensitivities : Be mindful of cultural norms and sensitivities when expressing gratitude, especially if your research involves international collaborations. Tailor your acknowledgments to reflect cultural expectations or customs, as appropriate.
• Proofread Carefully : Ensure your acknowledgments are free of grammatical errors and typos. Take the time to review and edit this section to ensure clarity and coherence.
• Respect Space Limitations : While it’s important to acknowledge all key contributors, be mindful of space limitations in your research paper. Prioritize mentioning those who made significant contributions while being respectful of length constraints.
• End on a Positive Note : Conclude your acknowledgment section with a positive and appreciative tone. Express your gratitude to everyone who supported your research journey, including family, friends, colleagues, and institutions.

Example of Acknowledgement in Research

I am immensely grateful to the individuals and organizations whose support and guidance have been instrumental in the completion of this research paper. Their assistance and expertise have significantly contributed to the development and refinement of my study.

Firstly, I extend my heartfelt appreciation to Dr. Aurora Rivera, my mentor and advisor throughout this research journey. Her insightful feedback, encouragement, and scholarly guidance have been invaluable in shaping the direction and methodology of my study.

I am also deeply thankful to Mr. Santiago Cruz, Director of Research at the Philippine Social Sciences Institute, for his generous support and assistance in accessing research resources. His expertise and encouragement have greatly facilitated the progress of my research.

Special gratitude is extended to my research collaborators, including Dr. Sofia Ramirez and Mr. Miguel Hernandez, for their collaborative efforts and insightful perspectives that have enriched the depth and analysis of my research findings.

I would like to acknowledge the valuable contributions of the staff and researchers at the Philippine Research Center for Social Sciences, whose support and expertise have been indispensable in navigating complex research methodologies and data analysis.

Furthermore, I extend my sincere appreciation to the participants of my study for their cooperation and willingness to share their experiences, which have provided essential insights and perspectives.

I wish to express my profound gratitude to my family and friends for their unwavering support, encouragement, and understanding throughout this research endeavor. Their belief in my abilities has been a constant source of motivation and inspiration.

Acknowledgement in Research Paper Example

We extend our heartfelt gratitude to the individuals and institutions whose unwavering support has been indispensable in the completion of this research paper. Their guidance, encouragement, and expertise have greatly contributed to the success of our study.

Firstly, we express our sincere appreciation to Dr. Juanita Cruz, Professor of Economics at the University of the Philippines, for her invaluable mentorship and insightful feedback throughout the research process. Her expertise in the field has been instrumental in shaping the direction of our study.

We are also indebted to Dr. Manuel Reyes, Director of the Philippine Economic Development Institute, for his generous assistance and provision of research resources. His support has been pivotal in enhancing the quality and depth of our analysis.

Special thanks are extended to our research collaborators, including Dr. Sofia Garcia from the Department of Political Science at Ateneo de Manila University, and Dr. Miguel Hernandez from the Department of Sociology at Mapua University. Their collaboration and expertise have enriched our research with diverse perspectives and profound insights.

We would like to acknowledge the invaluable assistance provided by the staff and researchers at the Philippine Institute for Development Studies, who generously shared their knowledge and resources throughout the duration of our study.

Furthermore, we extend our gratitude to the participants of our study, whose cooperation and willingness to share their experiences have been instrumental in shaping our findings.

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Most academic papers have many people who have helped in some way in the preparation of the written version or the research itself. This could be someone from a sponsoring institution, a funding body, other researchers, or even family, friends or colleagues who have helped in the preparation. These people need to be mentioned in the Acknowledgments section of the paper.

Acknowledgments section in different academic documents

The Acknowledgments section is present in both a paper and an academic thesis . For papers, the Acknowledgments section is usually presented at the back, whereas in a thesis, this section is located towards the front of the manuscript and is commonly placed somewhere between the abstract and Introduction . However, the exact location varies between each university , as each establishment possesses its own style guide for theses and student submissions. So, it is always worthwhile consulting your university’s academic style guide before writing a manuscript for undergraduate/postgraduate submission.

Acknowledgments section in theses

For academic theses, there is no right or wrong way to acknowledge people, and who you want to acknowledge is down to personal preference. However, the common types of people authors acknowledge in their academic theses include:

• Supervisor’s contributions
• Research group (especially if the thesis in question is a master’s and the work is helped along by a PhD student)
• Support staff (laboratory technicians, etc.)
• Any students who undertook side projects with them (e.g. final year undergraduates, summer students, master’s students)
• Administrative staff (there can be a lot of bureaucracy for thesis submissions)
• Referees that got them onto the course (postgraduate only)
• Funding bodies
• Any collaboration with industry and the people they worked with at said establishment(s)

Acknowledgments section in journal papers

Now, whilst university manuscripts can include any combination of the above (including all and none in some cases), academic publications in journals more commonly acknowledge the same kind of people/organizations, but again it is up to the author(s) what they feel should be acknowledged; not every piece of help needs to be acknowledged, just the most useful/prevalent help. Also, acknowledgments should be written in the first person .

Examples of whom and what should be acknowledged in a journal publication are listed below:

• Direct technical help (e.g. supply of animal subjects, cells, equipment setup, methods , statistics/data manipulation, samples, chemicals/reagents, analytical/spectroscopy techniques)
• Indirect assistance (topical and intellectual discussions about the research which can lead to generation of new ideas)
• Affiliated institutions
• Grant numbers
• Who received the funding (if not the author, e.g. a supervisor)
• Any associated fellowships

Whom to acknowledge - and whom not to acknowledge

• Other authors/contributors : It is not common practice for the lead paper writer (i.e. the person writing and publishing the manuscript) to acknowledge the other authors/direct contributors to the paper. Only those who are not recognized as authors may be thanked and acknowledged.
• Reviewers : Authors are also not allowed to thank reviewers personally, or those who inspire them but cannot directly receive their appreciation – although reviewers can be thanked if they are kept anonymous .
• Friends and family : Unlike university manuscripts, journal manuscripts should not include help and guidance from family and friends.

Other acknowledgments

• Titles and institutions : Titles such as Mr, Mrs, Miss, etc. are not commonly included, but honorary titles such as Dr, Professor, etc. are. The institutions of the acknowledged people are usually mentioned.

For example, the following would not be acceptable:

We dedicate this work to the deceased Prof. Bloggs.

However, the following would be acceptable:

We acknowledge Prof. Bloggs for discovering the secret of anonymity.

Additional pointers for writing the Acknowledgments section

• The  tone  of the section should be in an active voice.
• Do not use pronouns indicating possession (i.e. his, her, their, etc.).
• Terms associated with specific companies should be written out in full, e.g. Limited, Corporation, etc.
• If the results have been published elsewhere, then this should also be acknowledged.
• Any abbreviations should be expanded unless the abbreviation appears in the main body of the text.

Below are examples of the Acknowledgments sections taken from a couple of papers from Nature Communications :

Duan L., Hope J., Ong Q., Lou H-Y., Kim N., McCarthy C., Acero V., Lin M., Cui B., Understanding CRY2 interactions for optical control of intracellular signalling, Nature Communications, 2017,  8:547

Xu Q., Jensen K., Boltyanskiy R., Safarti R., Style R., Dufresne E., Direct measurement of strain-dependent solid surface stress, Nature Communications, 2017,  8:555

Many people think that the Acknowledgments section of a manuscript is a trivial and unimportant component. However, it constitutes a vital means to ensure that all affiliated support for the paper can be duly and transparently mentioned. By acknowledging people for their efforts and contributions, you demonstrate your integrity as an academic researcher. In addition, crediting other people for their help can also increase their presence in the academic world and possibly help to boost their career as well as your own.

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• Thesis & Dissertation Acknowledgements | Tips & Examples

Thesis & Dissertation Acknowledgements | Tips & Examples

Published on 4 May 2022 by Tegan George . Revised on 4 November 2022.

The acknowledgements section is your opportunity to thank those who have helped and supported you personally and professionally during your thesis or dissertation process.

Thesis or dissertation acknowledgements appear between your title page and abstract  and should be no longer than one page.

In your acknowledgements, it’s okay to use a more informal style than is usually permitted in academic writing , as well as first-person pronouns . Acknowledgements are not considered part of the academic work itself, but rather your chance to write something more personal.

To get started, download our step-by-step template in the format of your choice below. We’ve also included sample sentence starters to help you construct your acknowledgments section from scratch.

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Table of contents

Who to thank in your acknowledgements, how to write acknowledgements, acknowledgements section example, acknowledgements dos and don’ts, frequently asked questions.

Generally, there are two main categories of acknowledgements: professional and personal .

A good first step is to check your university’s guidelines, as they may have rules or preferences about the order, phrasing, or layout of acknowledgements. Some institutions prefer that you keep your acknowledgements strictly professional.

Regardless, it’s usually a good idea to place professional acknowledgements first, followed by any personal ones. You can then proceed by ranking who you’d like to thank from most formal to least.

• Chairs, supervisors, or defence committees
• Funding bodies
• Other academics (e.g., colleagues or cohort members)
• Editors or proofreaders
• Librarians, research/laboratory assistants, or study participants
• Family, friends, or pets

Typically, it’s only necessary to mention people who directly supported you during your thesis or dissertation. However, if you feel that someone like a secondary school physics teacher was a great inspiration on the path to your current research, feel free to include them as well.

Professional acknowledgements

It is crucial to avoid overlooking anyone who helped you professionally as you completed your thesis or dissertation. As a rule of thumb, anyone who directly contributed to your research should be mentioned.

A few things to keep in mind include:

• Even if you feel your chair didn’t help you very much, you should still thank them first to avoid looking like you’re snubbing them.
• Be sure to follow academic conventions, using full names with titles where appropriate.
• If several members of a group or organisation assisted you, mention the collective name only.
• Remember the ethical considerations around anonymised data. If you wish to protect someone’s privacy, use only their first name or a generic identifier (such as ‘the interviewees’).

Personal acknowledgements

There is no need to mention every member of your family or friend group. However, if someone was particularly inspiring or supportive, you may wish to mention them specifically. Many people choose to thank parents, partners, children, friends, and even pets, but you can mention anyone who offered moral support or encouragement, or helped you in a tangible or intangible way.

Some students may wish to dedicate their dissertation to a deceased influential person in their personal life. In this case, it’s okay to mention them first, before any professional acknowledgements.

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After you’ve compiled a list of who you’d like to thank, you can then sort your list into rank order. Separate everyone you listed into ‘major thanks’, ‘big thanks’, and ‘minor thanks’ categories.

• ‘Major thanks’ are given to people who your project would be impossible without. These are often predominantly professional acknowledgements, such as your advisor , chair, and committee, as well as any funders.
• ‘Big thanks’ are an in-between, for those who helped you along the way or helped you grow intellectually, such as classmates, peers, or librarians.
• ‘Minor thanks’ can be a catch-all for everyone else, especially those who offered moral support or encouragement. This can include personal acknowledgements, such as parents, partners, children, friends, or even pets.

How to phrase your acknowledgements

To avoid acknowledgements that sound repetitive or dull, consider changing up your phrasing. Here are some examples of common sentence starters you can use for each category.

Note that you do not need to write any sort of conclusion or summary at the end. You can simply end the acknowledgements with your last thank-you.

Here’s an example of how you can combine the different sentences to write your acknowledgements.

A simple construction consists of a sentence starter (in purple highlight ), followed by the person or entity mentioned (in green highlight ), followed by what you’re thanking them for (in yellow highlight .)

Acknowledgements

Words cannot express my gratitude to my professor and chair of my committee for her invaluable patience and feedback. I also could not have undertaken this journey without my defense committee, who generously provided knowledge and expertise. Additionally, this endeavor would not have been possible without the generous support from the MacArthur Foundation, who financed my research .

I am also grateful to my classmates and cohort members, especially my office mates, for their editing help, late-night feedback sessions, and moral support. Thanks should also go to the librarians, research assistants, and study participants from the university, who impacted and inspired me.

Lastly, I would be remiss in not mentioning my family, especially my parents, spouse, and children. Their belief in me has kept my spirits and motivation high during this process. I would also like to thank my cat for all the entertainment and emotional support.

• Write in first-person, professional language
• Thank your professional contacts first
• Include full names, titles, and roles of professional acknowledgements
• Include personal or intangible supporters, like friends, family, or even pets
• Mention funding bodies and what they funded
• Appropriately anonymise or group research participants or non-individual acknowledgments

Don’t:

• Use informal language or slang
• Go over one page in length
• Mention people who had only a peripheral or minor impact on your work

You may acknowledge God in your thesis or dissertation acknowledgements , but be sure to follow academic convention by also thanking the relevant members of academia, as well as family, colleagues, and friends who helped you.

Yes, it’s important to thank your supervisor(s) in the acknowledgements section of your thesis or dissertation .

Even if you feel your supervisor did not contribute greatly to the final product, you still should acknowledge them, if only for a very brief thank you. If you do not include your supervisor, it may be seen as a snub.

In the acknowledgements of your thesis or dissertation, you should first thank those who helped you academically or professionally, such as your supervisor, funders, and other academics.

Then you can include personal thanks to friends, family members, or anyone else who supported you during the process.

The acknowledgements are generally included at the very beginning of your thesis or dissertation, directly after the title page and before the abstract .

In a thesis or dissertation, the acknowledgements should usually be no longer than one page. There is no minimum length.

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Acknowledgement Letter

Get All Types Of Acknowledgement Samples.

Acknowledgement For Paper Publication

Post by Ruben Patel Leave a Comment

Writing a paper and getting it published is no easy feat. It requires a lot of hard work, dedication, and effort from the authors. Therefore, it is important to recognize and acknowledge the contributions of all those who have helped in the process of publishing a paper.

An acknowledgement for paper publication is a section at the end of a research paper that gives credit to all the individuals and organizations that have contributed to the publication of the paper. This can include researchers, professors, mentors, funding agencies, and other institutions that have provided support and assistance.

In this blog post, we will provide a few sample acknowledgements for paper publication to give you an idea of how to recognize and thank those who have contributed to your research. Also , these samples will cover different types of contributors, including researchers, mentors, funding agencies, and collaborators, and will illustrate different writing styles and formats.

Table of Contents

Why are acknowledgements important in a paper publication?

Acknowledgements serve several important purposes in a paper publication. Firstly , they give credit to all the individuals and organizations that have contributed to the paper’s publication. This includes researchers, professors, mentors, funding agencies, and other institutions that have provided support and assistance. Acknowledgments allow the authors to recognize and thank these individuals and organizations for their support and help.

Secondly , acknowledgements serve as a way of establishing the credibility and legitimacy of the research paper. By acknowledging the contributions of others, the authors demonstrate that their research is based on the work of others and that it has been reviewed and supported by experts in the field. This helps to build trust and credibility among the readers of the paper.

Finally , acknowledgements provide a way for the authors to express their gratitude and appreciation for the support and assistance they have received. This can be particularly important for young researchers who may have received support and guidance from more experienced colleagues. Acknowledgements can also be a way for the authors to express their appreciation for the funding agencies and institutions that have provided financial support for their research.

Acknowledgement For Paper Publication Sample

We would like to express our sincere gratitude to our supervisor, Professor John Doe, for his valuable guidance and support throughout the research process. His expertise and insights were invaluable in shaping our research and helping us to overcome challenges.

We also want to thank our colleagues at XYZ University for their helpful feedback and support. In particular, we would like to thank Dr. Jane Smith and Dr. Tom Johnson for their invaluable contributions to our research.

We are also grateful to the XYZ Foundation for providing financial support for our research. Their generous funding allowed us to conduct our study and complete our work.

Finally, we would like to thank our family and friends for their encouragement and support throughout the research process. Without their love and support, we would not have been able to complete this research.

Paper Publication Acknowledgement Sample

We would like to express our sincere gratitude to all the individuals and organizations that have contributed to the publication of this research paper.

First and foremost, we would like to thank our supervisor, Professor [Name], for his invaluable guidance and support throughout the research process. His expertise and insights were instrumental in shaping the direction and focus of our research. We are also grateful to the [Department] at [University] for providing us with the resources and support we needed to complete this project.

We would also like to thank our colleagues at [Institution] for their feedback and support throughout the research process. In particular, we would like to thank [Name] and [Name] for their valuable insights and suggestions.

We are also grateful to the [Funding Agency] for providing financial support for this research. Without their support, it would not have been possible for us to complete this project.

Finally, we would like to thank all the participants in this study for their time and willingness to share their experiences. Their contributions have been invaluable in helping us to understand the topic and draw meaningful conclusions.

We would also like to express our appreciation to the [Journal] for considering our work and providing the opportunity to publish our findings.

Acknowledgement Sample For Paper Publication

We would like to express our heartfelt gratitude to our supervisor, Dr. Mary Smith, for her unwavering support and guidance throughout the research process. Her expertise, insights, and encouragement were invaluable in helping us to complete this work.

We also want to thank our colleagues at ABC University for their helpful feedback and support. In particular, we would like to thank Professor Jane Doe and Professor Tom Johnson for their valuable contributions to our research.

We are also grateful to the National Science Foundation for providing financial support for our research. Their generous funding allowed us to conduct our study and complete our work.

Finally, we would like to thank our family and friends for their love and support throughout the research process. Without their encouragement and support, we would not have been able to complete this research.

Read Also:-

• Acknowledgement For Internship Report
• How To Write Acknowledgement For Research Paper

FAQs On Acknowledgement For Paper Publication

What is an acknowledgement for a paper publication?

Ans: An acknowledgement for a paper publication is a section at the end of a research paper that gives credit to all the individuals and organizations that have contributed to the publication of the paper. This can include researchers, professors, mentors, funding agencies, and other institutions that have provided support and assistance.

Where do you put acknowledgements in a research paper?

Ans: In a research paper, the acknowledgement section is typically placed at the end of the paper, after the conclusion and before the reference list. This allows the authors to give credit to all the individuals and organizations that have contributed to the publication of the paper and to express their gratitude for the support and assistance they have received.

Who should be included in the acknowledgements?

Ans: There are several types of individuals and organizations that should be included in the acknowledgements of a paper publication. These can include researchers and professors, mentors, funding agencies and institutions, collaborators, and institutions that have provided support or assistance.

Is it necessary to include an acknowledgement section in every paper publication?

Ans: It is not necessary to include an acknowledgement section in every paper publication. However, it is generally a good idea to include an acknowledgement section if you have received significant support or assistance from others during the research process. This can include funding from a grant or research agency, guidance and mentorship from professors or colleagues, or assistance from institutions or organizations. Including an acknowledgement section is a way to recognize and thank these individuals and organizations for their support and to establish the credibility and legitimacy of your research.

Can I include a list of funding sources in the acknowledgement section?

Ans: Yes, it is common to include a list of funding sources in the acknowledgement section of a paper publication. This can include grants, research funding, or other sources of financial support that have helped to fund your research. It is important to be specific about the funding sources and to include the names and details of the funding agencies or institutions.

Is it appropriate to include personal acknowledgements, such as thanking family and friends, in a research paper for a professional publication?

Ans: It is generally appropriate to include personal acknowledgements, such as thanking family and friends, in a research paper for a professional publication. However, it is important to keep these acknowledgements brief and to the point, and to focus mainly on thanking individuals and organizations that have contributed directly to the publication of the paper. Personal acknowledgements should not take up a significant portion of the acknowledgement section, and should not distract from the main focus of the paper.

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• Published: 02 April 2024

Efficient DNA-based data storage using shortmer combinatorial encoding

• Inbal Preuss 1 , 3 ,
• Michael Rosenberg 2 ,
• Zohar Yakhini 1 , 3 &
• Leon Anavy 1 , 3  

Scientific Reports volume  14 , Article number:  7731 ( 2024 ) Cite this article

Metrics details

• Computational biology and bioinformatics
• Computational methods
• Computational science
• Computer science
• DNA and RNA
• DNA computing
• Information technology

Data storage in DNA has recently emerged as a promising archival solution, offering space-efficient and long-lasting digital storage solutions. Recent studies suggest leveraging the inherent redundancy of synthesis and sequencing technologies by using composite DNA alphabets. A major challenge of this approach involves the noisy inference process, obstructing large composite alphabets. This paper introduces a novel approach for DNA-based data storage, offering, in some implementations, a 6.5-fold increase in logical density over standard DNA-based storage systems, with near-zero reconstruction error. Combinatorial DNA encoding uses a set of clearly distinguishable DNA shortmers to construct large combinatorial alphabets, where each letter consists of a subset of shortmers. We formally define various combinatorial encoding schemes and investigate their theoretical properties. These include information density and reconstruction probabilities, as well as required synthesis and sequencing multiplicities. We then propose an end-to-end design for a combinatorial DNA-based data storage system, including encoding schemes, two-dimensional (2D) error correction codes, and reconstruction algorithms, under different error regimes. We performed simulations and show, for example, that the use of 2D Reed-Solomon error correction has significantly improved reconstruction rates. We validated our approach by constructing two combinatorial sequences using Gibson assembly, imitating a 4-cycle combinatorial synthesis process. We confirmed the successful reconstruction, and established the robustness of our approach for different error types. Subsampling experiments supported the important role of sampling rate and its effect on the overall performance. Our work demonstrates the potential of combinatorial shortmer encoding for DNA-based data storage and describes some theoretical research questions and technical challenges. Combining combinatorial principles with error-correcting strategies, and investing in the development of DNA synthesis technologies that efficiently support combinatorial synthesis, can pave the way to efficient, error-resilient DNA-based storage solutions.

Introduction

DNA is a promising media storage candidate for long-term data archiving, due to its high information density, long-term stability, and robustness. In recent years, several studies have demonstrated the use of synthetic DNA for storing digital information on a megabyte scale, exceeding the physical density of current magnetic tape-based systems by roughly six orders of magnitude 1 , 2 . Physical density is one of several quantitative metrics for evaluating the efficiency of DNA-based storage systems, measured by the data unit per gram of DNA. Another performance metric, which was introduced in 3 , is called logical density, refering to the amount of data encoded in each synthesis cycle. Since DNA synthesis is the main cost component in DNA-based storage systems, increasing the logical density is the main focus of this work.

Research efforts in the field of DNA-based storage systems have mainly focused on the application of various encoding schemes, while relying on standard DNA synthesis and sequencing technologies. These include the development of error-correcting codes for the unique information channel of DNA-based data storage 4 , 5 , 6 , 7 , 8 . Random access capabilities for reading specific information stored in DNA also require advanced coding schemes 9 , 10 , 11 . Yet, despite the enormous benefits potentially associated with capacity, robustness, and size, existing DNA-based storage technologies are characterized by inherent information redundancy. This is due to the nature of DNA synthesis and sequencing methodologies, which process multiple molecules that represent the same information bits in parallel. Recent studies suggest exploiting this redundancy to increase the logical density of the system, by extending the standard DNA alphabet using composite letters (also referred to as degenerate bases), and thereby encoding more than 2 bits per letter 12 , 13 . In this approach, a composite DNA letter uses all four DNA bases (A, C, G, and T), combined or mixed in a specified predetermined ratio \(\sigma =({\sigma }_{A},{\sigma }_{C},{\sigma }_{G},{\sigma }_{T})\) . A resolution parameter \(k={\sigma }_{A}+{\sigma }_{C}+{\sigma }_{G}+{\sigma }_{T}\) is defined, for controlling the alphabet size. The full composite alphabet of resolution \(k\) , denoted \({\Phi }_{k}\) , is the set of all composite letters, so that \({\Sigma }_{i\in (A,C,G,T\}}{\sigma }_{i}=k\) . Writing a composite letter is done by using a mixture of the DNA bases, determined by the letter’s ratio in the DNA synthesis cycle. Current synthesis technologies produce multiple copies, and by using the predetermined base mixture each copy will contain a different base, thus preserving the ratio of the bases at the sequence-population level.

While the use of numerical ratios supports higher logical density in composite synthesis, it also introduces challenges related to the synthesis and inference of exact ratios. Combinatorial approaches, which also consist of mixtures, address these challenges in a different way. Studies by Roquet et al. (2021) and Yan et al. (2023) contribute significantly to advancing DNA-based data storage technology. To encode and store data, Roquet et al. focus on a novel combinatorial assembly method for DNA. Yan et al. extend the frontiers of this technology by enhancing the logical density of DNA storage, using enzymatically-ligated composite motifs 13 , 14 .

In this paper, we present a novel approach for encoding information in DNA, using combinatorial encoding and shortmer DNA synthesis, leading to an efficient sequence design and improved DNA synthesis and readout interpretation. The method described herein leverages the advantages of combinatorial encoding schemes while relying on existing DNA chemical synthesis methods with some modifications. Using shortmer DNA synthesis also minimizes the effect of synthesis and sequencing errors. We formally define shortmer-based combinatorial encoding schemes, explore different designs, and analyze their performance. We use computer-based simulations of an end-to-end DNA-based data storage system built on combinatorial shortmer encodings, and study its performance. To demonstrate the potential of our suggested approach and experimentally test its validity, we performed an assembly-based molecular implementation of the proposed combinatorial encoding scheme and analyzed the resulting data. Finally, we discuss the potential of combinatorial encoding schemes and the future work required to enable these schemes in large-scale DNA-based data storage systems and other DNA data applications.

Design of shortmer combinatorial encoding for DNA storage

We suggest a novel method to extend the DNA alphabet while ensuring near-zero error rates.

Let \(\Omega\) be a set of DNA k-mers that will serve as building blocks for our encoding scheme. Denote the elements in \(\Omega\) as \({X}_{1},\dots ,{X}_{N}\) . Elements in \(\Omega\) are designed to be sufficiently different from each other, to minimize mix-up error probability. Formally, the set is designed to satisfy \(d\left({X}_{i},{X}_{j}\right)\ge d;\forall i\ne j\) , with the minimal Hamming distance \(d\) serving as a tunable parameter.

Other design criteria can be applied to the shortmers in \(\Omega\) , taking into consideration the properties of DNA synthesis, manipulation, and sequencing. These may include minimal Levenshtein distance, GC context, and avoiding long homopolymers. Clearly, any such filtering process will result in reduced alphabet size and reduced logical density.

Note that \(N=\left|\Omega \right|\le {4}^{k}\) . The elements in \(\Omega\) will be used as building blocks for combinatorial DNA synthesis in a method similar to the one used for composite DNA synthesis 3 . Examples of k-mer sets \(\Omega\) are presented in Supplementary Sect.  8.3 .

We define a combinatorial alphabet \(\Sigma\) over \(\Omega\) as follows. Each letter in the alphabet represents a non-empty subset of the elements in \(\Omega\) . Formally, a letter \(\sigma \in \Sigma\) , representing a subset \(S\subseteq \Omega /\varnothing\) , can be written as an N-dimensional binary vector where the indices for which \({\sigma }_{i}=1\) represents the k-mers from \(\Omega\) included in the subset S. We denote the k-mers in \(S\) as member k-mers of the letter \(\sigma\) . For example, \(\sigma =(\mathrm{0,1},\mathrm{0,1},\mathrm{1,0})\) represents \(S=\{{X}_{2},{X}_{4},{X}_{5}\}\) and \(\left|\Omega \right|=N=6\) . Figure  1 a,b illustrate an example of a combinatorial alphabet using \(N=16\) , in which every letter represents a subset of size 5 of \(\Omega\) . In Sect. “ Binary and binomial combinatorial alphabets ” includes a description of the construction of different combinatorial alphabets.

Our combinatorial encoding and synthesis approach. ( a ) Schematic view of a combinatorial alphabet (Encode legend). A set of 16 trimers, \({{\varvec{X}}}_{1},\dots ,{{\varvec{X}}}_{16}\) , is used to construct 4096 combinatorial letters, each representing a subset of 5 trimers as indicated on the right and depicted in the grayed-out cells of the table. ( b ) A suggested approach for combinatorial shortmer synthesis. A modified synthesizer would include designated containers for the 16-trimer building blocks and a mixing chamber. Standard DNA synthesis is used for the barcode sequence (1), while the combinatorial synthesis proceeds as follows: The trimers included in the synthesized combinatorial letter are injected into the mixing chamber and introduced into the elongating molecules (2). The process repeats for the next combinatorial letter (3), and finally, the resulting molecules are cleaved and collected (4).

To write a combinatorial letter \(\sigma\) in a specific position, a mixture of the member k-mers of \(\sigma\) is synthesized. To infer a combinatorial letter \(\sigma\) , a set of reads needs to be analyzed to determine which k-mers are observed in the analyzed position (See Sects. “ Binary and binomial combinatorial alphabets ” and “ Reconstruction probabilities for binomial encoding ” for more details). This set of k-mers observed in the sequencing readout and used for inferring \(\sigma\) is referred to as inferred member k-mers. While the synthesis output and the sequencing readout will include different counts for the member k-mers, the determination of the set of inferred k-mers will force binary assignment for each k-mer to fit into the design scheme of combinatorial encoding.

From a hardware/chemistry perspective, the combinatorial shortmer encoding scheme can potentially be based on using the standard phosphoramidite chemistry synthesis technology, with some alterations (See Fig.  1 b and Supplementary Sect.  8.1 ) 15 , 16 . First, DNA k-mers should be used as building blocks for the synthesis 17 . Such reagents are commercially available for DNA trimers and were used, for example, for the synthesis of codon optimization DNA libraries 18 , 19 . In addition, a mixing step should be added to each cycle of the DNA synthesis to allow mixing of the member k-mers prior to their introduction to the elongating molecules. Such systems are yet to be developed and current attempts for combinatorial DNA synthesis are based on enzymatic assembly of longer DNA fragments 13 , 14 .

Similar to composite DNA encoding, combinatorial encoding requires the barcoding of the sequences using unique barcodes composed of standard DNA barcodes. This design enables direct grouping of reads pertaining to the same combinatorial sequence. These groups of reads are the input for the process of reconstructing the combinatorial letters.

The extended combinatorial alphabets allow for a higher logical density of the DNA-based storage system, while the binary nature of the alphabet minimizes error rates.

Binary and binomial combinatorial alphabets

The main parameter that defines a combinatorial encoding scheme is the alphabet \(\Sigma\) . More specifically, it is the set of valid subsets of \(\Omega\) that can be used as letters. We define two general approaches for the construction of \(\Sigma\) . Namely, the binomial encoding and the full binary encoding .

In the binomial encoding scheme, only subsets of \(\Omega\) of size exactly \(K\) represent valid letters in \(\Sigma\) , so that every letter \(\sigma \in \Sigma\) consists of exactly \(K\) member k-mers. Therefore, all the letters in the alphabet have the same Hamming weight \(K\) . \(w\left(\sigma \right)=K, \forall \sigma \in \Sigma\) . This yields an effective alphabet of size \(\left|\Sigma \right|=\left(\begin{array}{c}N\\ K\end{array}\right)\) letters, where each combinatorial letter encodes \({{\text{log}}}_{2}\left(\left|\Sigma \right|\right)={{\text{log}}}_{2}\left(\begin{array}{c}N\\ K\end{array}\right)\) bits. An r-bit binary message requires \(\frac{r}{{{\text{log}}}_{2}\left(\begin{array}{c}N\\ K\end{array}\right)}\) synthesis cycles (and a DNA molecular segment with length \(\frac{kr}{{{\text{log}}}_{2}\left(\begin{array}{c}N\\ K\end{array}\right)}\) ). In practice, we would prefer working with alphabet sizes that are powers of two, where each letter will encode for \(\left\lfloor {\log_{2} \left( {\begin{array}{*{20}c} N \\ K \\ \end{array} } \right)} \right\rfloor\) bits. Note that this calculation ignores error correction redundancy, random access primers, and barcodes, which are all required for message reconstruction. See Supplementary Sect.  8.2 and Fig.  1 a, which illustrate a trimer-based binomial alphabet with \(N=16\) and \(K=5\) , resulting in an alphabet of size \(\left|\Sigma \right|=\left(\begin{array}{c}16 \\ 5 \end{array}\right)=\mathrm{4,368}\) that allows to encode \(\lfloor {log}_{2}(4368)\rfloor =12\) bits per letter or synthesis position.

In the full binary encoding scheme, all possible nonempty subsets of \(\Omega\) represent valid letters in the alphabet. This yields an effective alphabet of size \(\left|\Sigma \right|={2}^{N}-1\) letters, each encoding for \(\left\lfloor {\log_{2} \left( {\left| \Sigma \right|} \right)} \right\rfloor = N - 1\) bits.

From this point on, we focus on the binomial encoding.

Reconstruction probabilities for binomial encoding

In this section, the performance characteristics of binomial encoding are investigated. Specifically, we present a mathematical analysis of the probability of successfully reconstructing the intended message. In Sects. “ An end-to-end combinatorial shortmer storage system ” and " Experimental proof of concept ", results are presented from our simulations and a small-scale molecular implementation of the binomial encoding, respectively.

Reconstruction of a single combinatorial letter

Since every letter \(\sigma \in \Sigma\) consists exactly of the \(K\) member k-mers, the required number of reads for observing at least one read of each member k-mer in a single letter follows the coupon collector distribution 20 . The number of reads required to achieve this goal can be described as a random variable \(R={\sum }_{i=1}^{K}{R}_{i}\) , where \({R}_{1}=1\) and \({R}_{i}\sim Geom\left(\frac{K-i+1}{K}\right), i=2,\dots ,K\) . Hence, the expected number of required reads, is:

where \(Har(\cdot )\) is the harmonic number.

The expected number of reads required for reconstructing a single combinatorial letter thus remains reasonable for the relevant values of \(K\) . For example, when using a binomial encoding with \(K=5\) the expected number of reads required for reconstructing a single combinatorial letter is roughly \(11.5\) , which is very close to the experimental results presented in Sect. " Experimental proof of concept ".

By Chebyshev’s inequality (See Sect. " Reconstruction probability of a binomial encoding letter "), we can derive a (loose) upper bound on the probability of requiring more than \(E\left[R\right]+cK\) reads to observe at least one read of each member k-mer, where \(c>1\) is a parameter:

For example, when using a binomial encoding with \(K=5\) , the probability of requiring more than \(26.5\) reads (corresponding to \(c=3\) ) is bounded by \(0.18\) , which is consistent with the experimental result shown in Fig. 5 d.

Reconstruction of a combinatorial sequence

When we examine an entire \(K\) -subset binomial encoded combinatorial sequence of length \(l\) , we denote by \(R(l)\) the required number of reads to observe \(K\) distinct k-mers in every position. Assuming independence between different positions and not taking errors into account, we get the following relationship between \(c\) and any desired confidence level \(1-\delta\) (See Sect. " Reconstruction probability of a binomial encoding letter " for details):

And therefore:

The number of reads required to guarantee reconstruction of a binomial encoded message, at a \(1-\delta\) probability, with \(K=5,\) and \(l\) synthesized positions, is thus \(KHar\left(K\right)+cK\) when

Supplementary Table S2 shows several examples of this upper bound. As demonstrated in the simulations and the experimental results, this bound is not tight (See Sects. “ An end-to-end combinatorial shortmer storage system ” and " Experimental proof of concept ").

Note that with an online sequencing technology (such as nanopore sequencing) the sequencing reaction can be stopped after \(K\) distinct k-mers are confidently observed.

To take into account the probability of observing a k-mer that is not included in \(\Omega\) (e.g., due to synthesis or sequencing error), we can require that at least \(t>1\) reads of each of the \(K\) distinct k-mers will be observed. This is experimentally examined in Sect. " Experimental proof of concept ", while the formal derivation of the number of required reads is not as trivial, and will be addressed in future work.

The above analysis is based only on oligo recovery, which depends solely on the sampling rate, ignoring possible mix-up errors (i.e., incorrect k-mer readings). This assumption is based on the near-zero mix-up probability attained by the construction of \(\Omega\) , which maximizes the minimal Hamming distance between elements in \(\Omega\) . In Sect. " Experimental proof of concept ", this analysis is compared to experimental results obtained from using synthetic combinatorial DNA.

An end-to-end combinatorial shortmer storage system

We suggest a complete end-to-end workflow for DNA-based data storage with the combinatorial shortmer encoding presented in Fig.  2 . The workflow begins with encoding, followed by DNA synthesis, storage, and sequencing, and culminates in a final decoding step. A 2D Reed-Solomon (RS) error correction scheme, which corrects errors in the letter reconstruction (for example, due to synthesis, sequencing, and sampling errors) and any missing sequences (such as dropout errors), ensures the integrity of the system. Table 1 shows the encoding capacities of the proposed system, calculated on a 1 GB input file with standard encoding and three different binomial alphabets (See Supplementary Sect.  8.5 ). All calculations are based on error correction parameters similar to those previously described (See Sect. " Information capacities for selected encodings ") 3 , 4 , 21 , 22 . With these different alphabets, up to a 6.5-fold increase in information capacity is achieved per synthesis cycle, compared to standard DNA-based data storage. While different error correction codes can be used in this system, for our work we chose to implement a 2D RS.

End-to-end workflow of a combinatorial DNA storage system. A binary message is broken into chunks, barcoded, and encoded into a combinatorial alphabet (i). RS encoding is added to each chunk and each column (ii). The combinatorial message is synthesized using combinatorial shormer synthesis (iii), and the DNA is sequenced (iv). Next, the combinatorial letters are reconstructed (v). Finally the message goes through 2D RS decoding (vi), followed by its translation back into the binary message (vii).

An example of the proposed approach, using a binomial alphabet with \(N=16\) and \(K=5\) and 2D RS, is detailed below. A binary message is encoded into a combinatorial message using the 4096-letter alphabet. Next, the message is broken into 120-letter chunks, and each chunk is barcoded. The 12nt barcodes are encoded using RS(6,8) over \(GF({2}^{4})\) , resulting in 16nt barcodes. Each chunk of 120 combinatorial letters is encoded using RS(120,134) over \(GF({2}^{12})\) . Every block of 42 sequences is then encoded using RS(42,48) over \(GF\left({2}^{12}\right)\) (See Sect. " An end-to-end combinatorial storage system " for details).

To better characterize the potential of this proposed system, we implemented an end-to-end simulation using the parameters mentioned above. We simulated the encoding and decoding of 10 KB messages with different binomial alphabets and error probabilities, and then measured the resulting reconstruction and decoding rates throughout the process. Figure  3 a depicts a schematic representation of our simulation workflow and indicates how the error rates are calculated (See Sect. " Reconstruction ").

Simulation of an end-to-end combinatorial shortmer encoding. ( a ) A schematic view of the simulation workflow. A text message is translated into a combinatorial message (1), and encoded using RS error correction on the barcode and payload (2). Each block is encoded using outer RS error correction (3). DNA synthesis and sequencing are simulated under various error schemes, and the combinatorial letters are reconstructed (4–5). RS decoding is performed on each block (6) and on each sequence (7) before translation back to text (8). The Roman numerals (i-iv) represent the different error calculations. ( b ) Error rates in different stages of the decoding process. Boxplot of the normalized Levenshtein distance (See Sect. " Reconstruction ") for the different stages in a simulation (30 runs) of sampling 100 reads, with an insertion error rate of 0.01. The X-axis represents the stages of error correction (before 2D RS decoding (iv), after RS payload decoding (iii), and after 2D RS decoding (ii)). ( c , d ) Sampling rate effect on overall performance. Normalized Levenshtein distance as a function of sampling rate before RS decoding ( c ) and after 2d RS decoding (ii). Different lines represent different error types (substitution, deletion, and insertion) introduced at a rate of 0.01.

The results of the simulation runs are summarized in Fig.  3 b–d. Each run included 30 repeats with random input texts of 10 KB encoded using 98 combinatorial sequences, each composed of 134 combinatorial letters and 16nt barcode, as described above. Each run simulated the synthesis of 1000 molecules on average per combinatorial sequence and sampling of a subset of these molecules to be sequenced. The subset size was drawn randomly from \(N\left(\mu ,\sigma =100\right),\) where \(\mu\) is a parameter. Errors in predetermined rates were introduced during the simulation of both DNA synthesis and sequencing, as expected in actual usage 23 (See Sect. " Synthesis and sequencing simulation with errors " for details on the simulation runs). Reconstruction rates and Levenshtein distances are calculated throughout the simulation process, as described in Fig.  3 a.

Notably, the sampling rate is the dominant factor where even with zero synthesis and sequencing errors, low sampling rates yield such poor results (Fig.  3 c) that the RS error correction is unable to overcome (Fig.  3 d). The effect of substitution errors on the overall performance is smaller and they are also easier to detect and correct. This is because substitution errors occur at the nucleotide level rather than at the trimer level. The minimal Hamming distance \(d=2\) of the trimer set \(\Omega\) allows for the correction of single-base substitutions. The use of 2D RS error correction significantly improved reconstruction rates, as can be observed in Fig.  3 b.

To assess the effect of using the suggested approach on the cost of DNA-based data storage systems, we performed an analysis of the different cost components. In brief, we analyzed the effect on the number of synthesis cycles and the number of bases to sequence, taking into account the required sequencing depth to achieve a desired reconstruction probability (See Sect. " Cost analysis "). Figure  4 depicts the costs of storing 1 GB of information using different combinatorial alphabets. Clearly, combinatorial DNA encoding can potentially reduce DNA-based data storage costs as the alphabet size grows and each letter encodes more bits. This is especially relevant in comparison with the composite encoding scheme presented in 3 . While both methods increase the logical density by extending the alphabet using mixtures of DNA letters/k-mers and thus reducing the synthesis cost (See Fig.  4 a), a crucial difference lies in the effect on sequencing costs. Composite DNA uses mixed letters with varying proportions of the different letters, which makes reconstruction very challenging in larger alphabets and results in very high sequencing costs that undermine the reduced synthesis costs. On the other hand, combinatorial DNA encoding uses binary mixtures, which are much simpler to reconstruct, therefore maintaining the sequencing costs relatively constant as the alphabet grows (See Fig.  4 b). For assessing the sequencing costs, we used a coupon collector model presented in 24 to calculate the required sequencing depth that ensures a decoding probability with an error rate of less than \({10}^{-4}\) (See Supplementary Sect.  8.5 ). In comparison with the composite encoding scheme, our analysis demonstrates a required sequencing depth that grows moderately. Figure  4 c analyzes the normalized overall cost, based on different assumptions regarding the ratio between synthesis costs and sequencing costs, \({C}_{syn}:{C}_{seq}\) . With a cost ratio of 500:1, 1000:1, 2000:1, it is evident that synthesis costs outweigh the fluctuations in sequencing costs, indicating a monotonic reduction in overall costs. This is an improvement compared to the composite DNA approach presented in 3 , where costs are reduced only up to a certain alphabet size, and then increase again due to the increased sequencing cost. In combinatorial DNA encoding, costs continue to drop, while alphabet size increases.

Cost analysis for a combinatorial DNA-based data storage system using different alphabets. ( a ) synthesis cost as a function of the alphabet size (presented as bit per letter, for simplicity). The cost is calculated as the number of synthesis cycles required for storing 1 GB of information. ( b ) Sequencing cost as a function of the alphabet size. Similarly to ( a ). ( c ) Normalized total cost as a function of the alphabet size for different synthesis-to-sequencing cost ratios. Costs are normalized by the total cost of a standard DNA-based system.

Experimental proof of concept

To assess and establish the potential of large combinatorial alphabets, we performed a small-scale experimental proof of concept study demonstrating the encoding and decoding of a 96-bit input message, which is equivalent to the text “DNA Storage!”. Since combinatorial DNA synthesis technology is not yet available, we demonstrated the combinatorial approach using Gibson assembly as an ad-hoc imitation for combinatorial synthesis. We constructed two combinatorial sequences, each containing a barcode and four payload cycles over a binomial alphabet with \(N=16\) and \(K=5\) . The assembly was performed using DNA fragments composed of a 20-mer information sequence and an overlap of 20 bp between adjacent fragments, as shown in Fig.  5 a. The assembled DNA was then stored and sequenced for analysis using Illumina Miseq (See Table 3 and Sect. " Cost analysis " for details about the sequencing procedures).

Experiment analysis. ( a ) A schematic view of the Gibson assembly. Each combinatorial sequence consists of a barcode segment and four payload segments (denoted as cycles 1–4). ( b ) Reconstruction results of the two combinatorial sequences. The color indicates read frequency, and the member k-mers are marked with orange boxes. ( c ) The distribution of reads over the 16 k-mers in an example combinatorial letter. Overlaid histograms represent the percentage of reads for each of the 16 k-mers for the same position in our two combinatorial sequences. This, in fact, is an enlarged view of the two c4 columns of panel b. ( d ) Required number of reads for reconstructing a single combinatorial letter. A histogram of the number of reads required to observe at least \(t=\mathrm{1,2}\) reads from \(K=5\) inferred k-mers. The results are based on resampling the reads 500 times, the data represents cycle 4. ( e ) Required number of reads for reconstructing a four-letter combinatorial sequence. Similar to d. ( f ), Reconstruction failure rate as a function of the required multiplicity \(t\) . Erroenous reconstruction rate shown for different values of required copies to observe each inferred k-mer ( \(t=\mathrm{1,2},\mathrm{3,4}\) ). The mean required number of reads for reconstruction is displayed using a secondary Y-axis in the dashed lines.

The sequencing output was then analyzed using the procedure described in Sect. “ Decoding and analysis ”. Both combinatorial sequences were successfully reconstructed from the sequencing reads, as presented in Fig.  5 b, and Supplementary Figs. S1, S2, and S3. The experiment also demonstrated the robustness of the binomial DNA encoding for synthesis and sequencing errors, as described in Fig.  5 c. We observed a minor leakage between the two synthesized sequences, which was overcome by the reconstruction pipeline (See Fig.  5 c, and Supplementary Figs. S1 , S2 , and S3 ). Note that there is a partial overlap between the member k-mers of the two sequences.

For comparison, a recent study by 14 encoded the 84-bit phrase “HelloWord” using a different encoding and synthesis approach. A comparison between the two experiments is shown in Table 2 . For example, while we used Gibson assembly as our synthesis method, they introduced a new method called Bridge Oligonucleotide Assembly. We encoded 12 bits per synthesis cycle and assembled four combinatorial fragments in each sequence, while 14 encoded 84 bits in a single combinatorial cycle. Our 96-bit were split and encoded using two combinatorial sequences, while they encoded the same 84-bits message, in its full format, on eight different sequences repeatedly. Our \({\text{N}}=16\) and 5 combinatorial factor, while their \(N=96\) and a higher 32 combinatorial factor.

To test the effect of random sampling on the reconstruction of combinatorial sequences, we performed a subsampling experiment with \(N=500\) repeats, presented in Fig.  5 d–f. We subsampled varying numbers of reads from the overall read pool and ran the reconstruction pipeline. Note that, as explained, the reconstruction of a single binomial position requires finding \(K=5\) inferred k-mers. That is, observing five unique k-mers at least \(t\) times. We tested the reconstruction performance using \(t=\mathrm{1,2},\mathrm{3,4}\) and recorded the effect on the successful reconstruction rate and required number of reads.

For \(t=1\) , reconstruction required analyzing 12.26 reads on average. These included 0.45 reads that contained an erroneous sequence that could not be mapped to a valid k-mer, and thus ignored. Note that the design of the set \(\Omega\) of valid k-mers allows us to ignore only the reads for which the Hamming distance for a valid k-mer exceeded a predefined threshold ( \(d=3\) ). If we ignored all the reads containing a sequence with non-zero Hamming distance to all k-mers, we would have skipped 2.26 extra reads, on average.

As expected, requiring \(t=2\) copies of each inferred k-mer resulted in an increase in the overall number of analyzed reads. Reconstruction of a single combinatorial letter required analyzing an average of 21.6 reads with 0.83 skipped and 3.99 non-zero Hamming distance reads. The complete distribution of the number of reads required for the reconstruction of a single position using \(t=\mathrm{1,2}\) is presented as a histogram in Fig.  5 d.

To reconstruct a complete combinatorial sequence of 4 positions, we required the condition to hold for all positions. For \(t=1\) , this entailed the analysis of 55.60 reads on average, out of which 1.04 reads were identified as erroneous and thus ignored, and with 7.36 non-zero Hamming distance reads. For \(t=2\) , an average of 102.66 reads were analyzed with 1.97 skipped and 13.24 non-zero Hamming distance reads. The complete distribution of the number of reads required for reconstructing a complete combinatorial sequence using \(t=\mathrm{1,2}\) is presented as a histogram in Fig.  5 e.

Note that these results correspond to the analysis presented in Sect. “ Reconstruction probabilities for binomial encoding ”, for the reconstruction of a single binomial position and a complete binomial sequence. Calculating the bound presented in Supplementary Table S2 , with \(K=5\) and \(l=4\) , yields a requirement of approximately 140 reads to obtain \(1-\delta =0.99\) probability of reconstruction. Clearly, this is well above the observed number of 55.60 reads. Note, as explained, the calculated bound is a loose bound.

The reconstruction procedure ends with a set of inferred k-mers that represent the inferred combinatorial letter. This set is not guaranteed to be correct, especially when using \(t=1\) , which means that noisy reads may result in an incorrect k-mer included in the inferred letter. Figure  5 f depicts the rate of incorrect reconstructions as a function of the number of required copies for each inferred k-mer ( \(t=\mathrm{1,2},\mathrm{3,4}\) ). Note that with \(t\ge 3\) results in 100% successful reconstruction. This, however, comes with a price, where more reads must be analyzed.

In this study, we introduced combinatorial shortmer encoding for DNA-based data storage, which extends the approach of composite DNA by resolving some of its sensitivity related issues. Combinatorial shortmer encoding allows for increased logical density while maintaining low error rates and high reconstruction rates. We explored two encoding schemes, binary and binomial, and evaluated some of their theoretical and practical characteristics. The inherent consistency of the binomial encoding scheme, where every letter in the sequence consists of exactly \(K\) distinct member k-mers, ensures uniformity in the encoded DNA sequences. This approach not only simplifies the reading process, but also allows for a more streamlined decoding. For instance, technologies like nanopore sequencing enable continuous sequencing until all k-mers at a given position are confidently observed.

Our suggested approach is designed to inherently overcome base substitution errors, which are the most common errors expected in every DNA-based data storage system that includes DNA sequencing. This is achieved by the selection of a set of \(N\) k-mer building blocks to be resilient to single-base substitutions. Other considerations may also be incorporated in the selection of the set of valid k-mers, taking into account any biological, chemical, or technological constraints. This represents an inherent tradeoff in DNA-based data storage between sequence constraints and information density. Insertion and deletion errors, which usually originate in the synthesis process, are more challenging to overcome. We introduced a 2D RS error correction scheme on the shortmer level, allowing for a successful message reconstruction even with error levels exceeding those expected in reality.

Our study highlights the significant effect of sampling rates on the overall performance of the system. The accuracy and completeness of sequence reconstruction require each of the sequences to be observed with a sufficiently high coverage. Our subsampling experiments underpin this observation, demonstrating the need for calibration of sampling rates to ensure the desired fidelity in DNA-based data storage. The crucial role of the sampling rate was also highlighted in 3 . However, while composite DNA uses mixed letter with varying proportions of the different letters, the combinatorial encoding, studied in this current work, uses binary mixtures and does not rely on proportions. This potentially allows scaling up the combinatorial encoding without a significant effects on the required sampling rates.

Combinatorial DNA coding can potentially reduce the overall costs of DNA-based data storage. Considering both sequencing costs, which fluctuate, and synthesis costs, which consistently drop, the increase in the alphabet size is accompanied by a decrease in overall cost. However, combinatorial DNA synthesis or assembly is still unavailable for large-scale commercial use. Thus, further development of combinatorial DNA synthesis technologies will continue to impose limitations and constraints on combinatorial encoding, and determine the overall costs.

While our proof-of-concept experiment showed success on a small scale, there are complexities to be addressed in considering large-scale applications. These include synthesis efficiency, error correction, and decoding efficiency. Nonetheless, the resilience of our binomial DNA encoding for both synthesis and sequencing errors highlights its practical potential and scalability. One specific aspect is the effect of combinatorial encoding on possible sequence-related constraints. While sequences with unwanted compositions (e.g., containing homopolymers) will unavoidably be part of the synthesized mixtures, the uniform sampling of the combinatorial shortmers in each position, together with the independence of the different positions, guarantees that only very few such sequences will be aythesized. In particular—these will not interfere with successful reconstruction. Another challenging aspect of scaling up combinatorial DNA systems is the need to use longer DNA k-mers to construct larger sets with the desired constraints. This may make the combinatorial synthesis impractical and will require balancing the increase in logical density with the technological complexity.

Several future research directions emerge from our study. First, it is important to develop error correction methods for better handling insertion and deletion errors. One approach for achieving this goal, is to adjust sampling rates: optimizing the sampling rate, especially in large-scale experiments, can lead to data retrieval at high accuracy. While our study highlighted the role of sampling rates in achieving desired outcomes, delving deeper into the underlying theory will lead to more improvements. For example, based on theoretical bounds of sampling rates, more concrete recommendations can be provided for real-world applications. The development of error correction codes, designed specifically to overcome the error types that characterize combinatorial encoding, is another important direction for future research. Most notably, transitioning from small-scale proof-of-concept experiments to larger-scale implementations is an important next step. Evaluating the scalability of our method across various scales and complexities will be enlightening, especially when considering synthesis efficiency and error rates. Finally, the consideration of advanced sequencing technologies could redefine the potential and efficacy of our proposed method, including its future practical implementation.

To sum up, combinatorial DNA synthesis and sequence design are important beyond the scope of DNA-based data storage. Generating combinatorial DNA libraries is an efficient tool in synthetic biology, better supporting large-scale experiments. DNA synthesis technologies that can incorporate a combinatorial synthesis of longer DNA fragments will enable the design and generation of more DNA libraries with applications in data storage and beyond.

Reconstruction probability of a binomial encoding letter

Let the number of reads required for reconstruction be a random variable \(R={\sum }_{i=1}^{K}{R}_{i}\) where \({R}_{1}=1\) and \({R}_{i}\sim Geom\left(\frac{K-i+1}{K}\right), i=2,\dots ,K\) . Hence, the expected number of required reads, is:

Using the independence of \({R}_{i}\) , the variance of \(R\) can be bound by (See 25 ):

By Chebyshev’s inequality, we get an upper bound (a loose bound) on the probability of requiring more than \(E\left[R\right]+cK\) reads to observe at least one read of each member k-mer:

Let \(c=b\frac{\pi }{\sqrt{6}}\) , or \(b=\frac{c\sqrt{6}}{\pi }\) , and we obtain:

Or specifically:

We now turn to address the reconstruction of an entire oligo of length \(l\) . Let \(R(l)\) be the random variable representing the number of reads required to have observed all the \(K\) member k-mers in every position. Setting any \(\delta >0\) , if we show that \(P\left(R\left(l\right)>m\right)\ge 1-\delta\) , then we know that by accumulating \(m\) reads the probability of correct full reconstruction is more than \(1-\delta\) . From Eq. ( 11 ), and assuming independence of the positions (in terms of observing all \(K\) member k-mers), we get Eq. ( 12 ):

From which we can extract \(c\) , so that:

Which yields:

This process allows us to evaluate the sequencing depth complexity. For example, consider \(l=100\) and \(\delta =0.01\) . We want to find \(c\) , so that using \(KHar\left(K\right)+cK\) reads will reconstruct the entire sequence with 0.99 probability. We therefore set:

And therefore, using 128 reads guarantees reconstruction with 0.99 probability.

An end-to-end combinatorial storage system

In Sect. “ An end-to-end combinatorial shortmer storage system ” we propose an end-to-end combinatorial storage system, as follows.

Combinatorial encoding and padding

A binary message is encoded using a large k-mer combinatorial alphabet (e.g., trimer-based alphabet of size \(\left|\Sigma \right|=4096\) letters, with \(N=\left|\Omega \right|=16\) ), resulting in \(r=12\) bits per combinatorial letter. The binary message is zero-padded to ensure its length is divisible by \(r\) prior to the combinatorial encoding. The complete message is broken into sequences of set length \(l=120\) , each sequence is then marked with a standard DNA barcode and translated using the table presented in the Encode legend (See Supplementary Sect.  8.2 ).

The length of the complete combinatorial sequence must be divisible by the payload size \(l\) and by the block size \(B\) . As described in Fig.  6 , this is ensured using another padding step, and the padding information is included in the final combinatorial sequence.

Example of message coding, including padding and RS error correction. Encoding of a ~ 0.1 KB message into a 512 letter binomial alphabet ( \(N=16, K=3)\) . First, bit padding is added, included here in the letter \(_{{\sigma_{257} }}^{1}\) . Next, block padding is added, included here in \(_{{\sigma_{1} }}^{2}\) and \(_{{\sigma_{1} }}^{3}\) . Padding information is included in the last sequence of all blocks. The last sequence holds the number of padding binary bits. In this example, \(_{{\sigma_{149} }}^{4}\) represents 148 bits of padding, composed of \(4+\left(4*9\right)+\left(12*9\right) bits\) , 4 bits from \(_{{\sigma_{257} }}^{1}\) , 4 letters from \(_{{\sigma_{1} }}^{2}\) and 12 letters from \(_{{\sigma_{1} }}^{3}\) .

Error correction codes

The 2D error correction scheme includes the use of three RS 26 encodings: on each barcode, on the payload part of each sequence, and an outer error correction code on each block of sequences.

Each barcode is encoded using a systematic RS(6,8) code over \(GF({2}^{4})\) , transforming the unique 12nt barcode into a 16nt sequence.

Each 120 combinatorial letter payload sequence is encoded using an RS(120,134) code over \(GF({2}^{12})\) , resulting in a sequence of length 134 combinatorial letters.

To protect against sequence dropouts, an outer error correction code is used on the columns of the matrix (See Fig.  6 ). Each block of \(B=42\) sequences, is encoded using a RS(42,48) RS code \(GF\left({2}^{12}\right)\) . This is applied in each column separately.

For simplicity, Fig.  6 demonstrates the encoding of ~ 0.1 KB using shorter messages with simpler error correction codes. The following parameters are used:

A barcode length of 6nt encoded using RS(3,5) code over \(GF\left({2}^{4}\right)\) to get 10nt.

A payload length of \(l=12\) encoded using RS(12,18) over \(GF\left({2}^{9}\right)\) for the \(\left(\begin{array}{c}16\\ 3\end{array}\right)\) binomial alphabet.

A 10-sequence block encoded, column-wise, using a (10,15) RS code over \(GF({2}^{9})\) .

The 824 bits are first padded to be \(828=92*9\) . The 92 combinatorial letter message is split into \(7\) sequences of 12 letters and an additional sequence of 8 letters. Finally, a complete block of 12 sequences (total of \(10*12=120\) letters) is created by padding with one additional sequence of 12 letters and including the padding information as the last sequence.

Synthesis and sequencing simulation with errors

Simulating the synthesis process. DNA molecules pertaining to the designed sequences are synthesized using combinatorial k-mer DNA synthesis (See Fig.  1 b). For each combinatorial sequence, we first determine the number of synthesized copies by sampling from \(X\sim N(\mu =1000, {\sigma }^{2}=100)\) . Let \(x\) be the number of copies for a specific sequence. Next, for every position in the sequence, we uniformly sample \(x\) independent k-mers from the set of member k-mers of the combinatorial letter in the specific position. We concatenate the sampled k-mers to the already existing \(x\) synthesized molecules.

Error simulation. Synthesis and sequencing errors are simulated as follows. Error probabilities for deletion, insertion, and substitution are given as parameters denoted as \({P}_{d}, {P}_{I},\) and \({P}_{s}\) respectively. Deletion and insertion errors are assumed to occur during k-mer synthesis and thus implemented on the k-mer level (i.e., an entire k-mer is deleted or inserted in a specific position during the synthesis simulation). Substitution errors are assumed to be sequencing errors and hence implemented on a single base level (i.e., a single letter is substituted, disregarding the position within the k-mer).

Mixing. Post synthesis, molecules undergo mixing to mirror genuine molecular combinations. This is achieved through a randomized data line shuffle using an SQLite database, enabling shuffle processes even for sizable input files 27 .

Reading and sampling. From the simulated synthesized molecule set, a subsample of predefined size \(S*number of synthesized seqeunces\) is drawn, simulating the sampling effect of the sequencing process.

Reconstruction

Barcode decoding The barcode sequence of each read is decoded using the RS(6,8) code.

Grouping by barcode The reads are then grouped by their barcode sequence to allow the reconstruction of the combinatorial sequences.

Filtering of read groups Barcodes (set of reads) with less than 10% of the sampling rate \(S\) reads are discarded.

Combinatorial reconstruction For each set of reads, every position is analyzed separately. The \(K\) most common k-mers are identified and used to determine the combinatorial letter \(\sigma\) in this position. Let \(\Delta\) be the difference between the length of the analyzed reads and the length of the designed sequence. \(\Delta =l-len(read)\) . Reads with \(\left|\Delta \right|>k-1\) are discarded from the analysis. Invalid k-mers (not in \(\Omega )\) are replaced by a dummy k-mer \({X}_{dummy}\) .

Missing barcodes Missing barcodes are replaced with dummy sequences to enable correct outer RS decoding.

Normalized Levenshtein distance Levenshtein distance between the observed sequence \(O\) and the expected sequence \(E\) is calculated 28 , 29 . Normalized Levenshtein distance is calculated by dividing the distance by the length of the expected sequence:

Cost analysis

Synthesis cost estimation was performed using the logical density calculation presented in Supplementary Sect.  8.5 and Supplementary Table S1 . To calculate the sequencing costs, we used the coupon collector model presented in 24 to assess the required sequencing depth given the combinatorial alphabet. Figure  4 b indicates the total number of reads required for reconstructing the sequences, calculated as the required sequencing depth multiplied by the number of sequences from Supplementary Sect.  8.5 and Supplementary Table S1 . The analysis was performed on the following set of combinatorial alphabets: Standard DNA, \(\left(\begin{array}{c}8\\ 4\end{array}\right), \left(\begin{array}{c}16\\ 3\end{array}\right), \left(\begin{array}{c}16\\ 5\end{array}\right), \left(\begin{array}{c}16\\ 7\end{array}\right), \left(\begin{array}{c}32\\ 10\end{array}\right), \left(\begin{array}{c}32\\ 16\end{array}\right), \left(\begin{array}{c}64\\ 32\end{array}\right), \left(\begin{array}{c}96\\ 32\end{array}\right)\) .

Proof of concept experiment

The proof-of-concept experiment was performed by imitating combinatorial synthesis using Gibson assembly of larger DNA fragments. Each DNA fragment was composed of a 20-mer information sequence and an overlap of 20 bp between adjacent fragments, as depicted in Fig.  5 a. Two combinatorial sequences were designed, each composed of a barcode fragment, 4 payload fragments, and Illumina Miseq P5 and P7 anchors at the ends. The information fragments included in each combinatorial position were chosen from a set of 16 sequences with sufficient pair-wise distance. The full list of DNA sequences and the design of combinatorial sequences is listed in Supplementary Sect.  8.6 .

DNA assembly and sequencing

Payload, barcode, and P7 anchor fragments with 20 bp overlaps for the purpose of Gibson assembly were produced by annealing complementary oligonucleotides manufactured by Integrated DNA Technologies (IDT). Oligos were dissolved in Duplex Buffer (100 mM Potassium Acetate; 30 mM HEPES, pH 7.5; available from IDT) to the final concentration of 100 micromolar. For annealing, 25 µl of each oligo in a pair were combined to the final concentration of 50 micromolars. The oligo mixes were incubated for 2 min at 94 0 C, and gradually cooled down to room temperature. The annealed payload oligos that belonged to the same cycle (5 oligos total) were mixed to the final concentration of 1 micromolar per oligo—a total of 5 micromolar, by adding 2 µl of each annealed oligo into the 90 µl of nuclease-free water—a final volume of 100 µl. Annealed barcode and P7 anchor oligos were also diluted to the final concentration of 5 micromolar in nuclease-free water, after thorough mixing by vortexing. The diluted oligos were stored at −20 °C.

Immediately prior to the Gibson assembly, payload oligo mixes, barcode, and P7 anchor oligos were further diluted 100-fold to the final working dilution of 0.05 pmol/microliter in nuclease-free water. Gibson reaction was assembled by adding 1 µl (0.05 pmol) of barcode, 4 × cycle mixes, and P7 anchor to the 4 µl of nuclease-free water and supplemented with 10 µl of NEBuilder HiFi DNA assembly master mix (New England Biolabs (NEB)) to the final volume of 20 µl, according to the manufacturer instructions. The reactions were incubated for 1 h at 50 °C, and purified with AmpPure Beads (Thermo Scientific) at 0.8X ratio (16 µl of beads per 20 µl Gibson reaction) to remove free oligos / incomplete assembly products. After adding beads and thorough mixing, the reactions were incubated for 10 min at room temperature and then placed on a magnet for 5 min at room temperature. After removing the sup, the beads were washed twice with 100 µl of 80% ethanol. The remaining washing solution was further removed by a 20 µl tip, and the beads dried for 3 min on the magnet with an open lid. After removing from the magnet, the beads were resuspended in 22 µl of IDTE buffer (IDT), incubated for 5 min at room temperature, and then placed back on the magnet.

20 µl of eluate were transferred into the separate 1.7 ml tube. 5 µl of the eluted DNA were used as a template for PCR amplification combined with 23 µl of nuclease-free water, 1 µl of 20 micromolar indexing primer 5, 1 µl of 20 micromolar indexing primer 7, and 10 µl of rhAMPseq master mix v8.1—a total of 40 µl. After initial denaturation of 3 min at 95 °C, the PCR reaction proceeded with 50 cycles of 15 s at 95 °C, 30 s at 60 °C, and 30 s at 72 °C, followed by final elongation of 1 min at 72 °C and hold at 4 °C. The PCR reactions were purified with Ampure beads at 0.8X ratio (32 µl beads per 40 µl of PCR reaction) as outlined above, and eluted in 22 µl IDTE buffer. The concentration and the average size of the eluted product were determined by Qubit High Sensitivity DNA kit and Agilent 2200 TapeStation system with D1000 high-sensitivity screen tape respectively. The eluted product was diluted to 4 nM concentration, and used as an input for denatured sequencing library preparation, per manufacturer instructions. The sequencing was performed on Illumina Miseq apparatus (V2 chemistry, 2 × 150 bp reads) using 6 picomolar denatured library supplemented with 40% PhiX sequencing control.

Decoding and analysis

This section outlines the key steps involved in our sequencing analysis pipeline, aimed at effectively processing and interpreting sequenced reads. The analysis pipeline gets the sequencing output file containing raw reads in “.fastq” format and a design file containing the combinatorial sequences.

Analysis steps:

Length filtering. We saved reads that were 220 bp in length, retaining only those corresponding to our designed read length.

Read retrieval. We carefully checked each read for the presence of BCs, universals, and payloads. To keep our data accurate, we discarded reads where the BCs, universals, or payloads had a Hamming distance of more than 3 errors.

Identifying inferred k-mers. For every BC and each cycle, we counted the \(K\) most common k-mers. We then compared these with the design file to quantify those matching (Fig.  5 b) (See Table 3 ).

Information capacities for selected encodings

Table 1 illustrates the logical densities derived from encoding a 1 GB binary message using oligonucleotides with a 12nt barcode and an additional 4nt for standard DNA RS error correction, and a 120 letters payload with 14 extra RS for the payload in combinatorial encoding schemes with parameters \(N\) and \(K\) .

The densities were calculated as follows:

Ethics declaration

No animal or human subjects were involved in the study.

Data availability

The raw data is available in ENA (European Nucleotide Archive). The datasets generated and/or analyzed during the current study are available in the ENA (European Nucleotide Archive) repository, Accession Number—ERR12364864.

Code Availability

Implementation of the algorithms and instructions on how to use them can be found in the GitHub repository in the following links: https://github.com/InbalPreuss/dna_storage_shortmer_simulation ,  https://github.com/InbalPreuss/dna_storage_experiment .

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Acknowledgements

This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement No. 101115134 (DiDAX project). The authors of this paper thank the Yakhini research group for the fruitful discussions. The authors also thank Eland Nagar for his support and problem-solving approach regarding the experimental proof of concept.

European Union's Horizon Europe Research and Innovation Programme, 101115134.

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Inbal Preuss, Zohar Yakhini & Leon Anavy

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Contributions

I.P., Z.Y. and L.A conceived the idea, designed the experiments, interpreted and analyzed the data. I.P performed all computational work, including the simulations and the data analysis. M.R. was solely responsible for conducting the experimental work. All authors wrote the manuscript.

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Zohar Yakhini, Leon Anavy have competing interests as defined by Nature Research. Z. Yakhini and L. Anavy are named as inventors on a patent related to the content of this paper: L. Anavy, Z. Yakhini, and R. Amit, "Molecular data storage systems and methods". United States of America Patent US20210141568A1, 2021.

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Preuss, I., Rosenberg, M., Yakhini, Z. et al. Efficient DNA-based data storage using shortmer combinatorial encoding. Sci Rep 14 , 7731 (2024). https://doi.org/10.1038/s41598-024-58386-z

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Received : 11 December 2023

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DOI : https://doi.org/10.1038/s41598-024-58386-z

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