How to prepare a manuscript for publication

Effective scientific communication is not only about delivering sound results but making sure your results are presented in an accessible, reproducible, and valuable way for the scientific community.

But preparing a manuscript for publication can be a challenging process – there are rules, conventions, and best practices you need to know to make your paper stand out. This article will walk you through every aspect of manuscript preparation, from structuring your ideas to formatting your final document for submission.

Note: Publishers accept a wide range of article types. This page focuses on original research articles. Learn more about article types.

A strong manuscript is not just about what you find but how you present it. Journals typically require a standardized format, such as introduction, methods, results, discussion, and conclusion (often simplified to IMRaD. Following the IMRaD format ensures that readers can efficiently locate the information they need, from your hypothesis and methods to your key findings.

Before these sections, manuscripts also include a title, an abstract, and keywords. After these main sections come the acknowledgments and references. Some journals may vary slightly in this structure, but IMRaD remains the backbone of most scientific papers.

Benefits of IMRaD:

• It provides a logical flow of information.

• It keeps manuscripts consistent and straightforward to read.

• It creates a map that enables readers to locate relevant content quickly.

Examples

Mixed discussion with results (poor practice)

Under 'Results' section: “We observed a significant decrease in enzyme activity (p < 0.05). This suggests that our new inhibitor is highly effective and could potentially replace current treatments in clinical settings.”

Why it’s poor: The sentence jumps to implications (“highly effective” and “replace current treatments”) that belong in the discussion, not the results.

Example of a clear results vs. discussion separation

In the ‘Results’ section: “We observed a significant decrease in enzyme activity (p < 0.05) in the presence of the new inhibitor.”

In ‘Discussion’ section: “These results indicate strong inhibitory effects of our compound, which, if proven safe, might compete with existing clinical treatments in the future.”

Why it’s better: The results are presented objectively in one section, and interpretation and broader implications are saved for the discussion.

Although the final publication often shows the sequence: title, abstract, introduction, methods, results, discussion, and conclusion, there is a recommended writing order that can make the process more coherent and less time-consuming. Here’s an example of a common approach.

1. Materials and methods: while running your experiments or soon after.

2. Results: as soon as you have data, you can describe it, create figures/tables, and interpret descriptive results.

3. Introduction: once you clearly understand the context and have preliminarily analyzed your results.

4. Discussion: interpreting your results in the context of existing literature.

5. Conclusions: summarizing the research outcomes and their implications.

6. Title and abstract: write them last so they accurately reflect the full content of your study.

This order helps you avoid rewriting sections as you gain a better understanding of your data. Focusing on methods and results early ensures you have a strong factual base for the rest of your manuscript.

Crafting an effective title

The title is often the first (and sometimes only) aspect of your paper that readers see. A strong title should:

• convey the main topic of the study

• highlight the importance of the research

• be concise and attention-grabbing

• appeal to broad audiences where relevant or a more specialized community if it is a new or niche topic

Note: some article types (such as case reports and editorials) require specific title formats. An example of this might be 'Case report: spuriously low sodium and calcium in a 36-year-old male.'

We also recommend that your title avoids:

• posing a question without giving the answer

• unambitious titles, for example, starting with 'Towards,' 'A description of,' 'A characterization of,' or 'Preliminary study on.'

• vague titles, for example, starting with 'Role of,' 'Link between,' or 'Effect of' that do not specify the role, link, or effect

• include terms that are out of place, such as the taxonomic affiliation sepafrom the species name.

Examples

Overly long title

“An extensive exploration into whether administering high-concentration dietary calcium supplements to healthy adult cats in rural regions of Southeastern Europe over a six-month period improves bone density and overall health outcomes as measured by multiple clinical parameters and owner surveys.”

Why it’s poor: The title includes excessive details about location, duration, dosage, and methodology, making it hard to read.

Vague title

“Dietary calcium supplements in cats.”

Why it’s poor: The title does not reference the study design, outcomes, or population specifics.

Effective revised title

“High-calcium supplementation improves bone density in adult cats: a six-month controlled trial.”

Why it’s better: the title states the intervention (high-calcium supplementation), outcome (improved bone density), duration (six months), and design (controlled trial) succinctly.

TIP: Brainstorm multiple titles and seek feedback from colleagues. Spending time on the title can increase your paper’s visibility and reader engagement.

The abstract summarizes your study, often limited to around 250–300 words, depending on the journal. It’s also worth checking whether the journal requires a structured abstract (with headings similar to those in the full manuscript) or an unstructured abstract (as shown in the example below).

Many readers (and even potential reviewers) base their decision to read the full paper on the abstract alone. Your abstract should answer these main questions:

1. What was done? (Explain the main objective or hypothesis).

2. Why did you do it? (Highlight the research gap or significance).

3. What did you find? (Summarize the key results).

4. Why are these findings important? (Indicate potential applications, implications, or future directions).

Given that your abstract is indexed in databases like PubMed or Web of Science, it might be the most accessed section of your work. A concise, informative abstract also helps referees decide whether they have the right expertise to review your paper.

Examples

Incomplete abstract

“We tested a new drug on 100 patients. Some improvements were noted. Conclusions are discussed.”

Why it’s poor: the abstract doesn’t clarify what was tested, how it was tested, or the significance of the findings.

Detailed, balanced abstract

“We conducted a double-blind, randomized trial on 100 patients diagnosed with moderate hypertension to evaluate the efficacy of Drug X. Participants received either 10 mg/day of Drug X or a placebo for eight weeks. Patients in the Drug X group exhibited a 15% greater reduction in systolic blood pressure (p < 0.01) compared to the placebo group. No severe adverse events were reported. These preliminary findings suggest that Drug X could be an effective, well-tolerated therapy for moderate hypertension and warrant further investigation in larger, long-term studies.”

Why it’s better: Defines the population, intervention, duration, key results, and conclusion concisely.

Tip: Don't include references or overly specialized abbreviations in your abstract. Adhere to your target journal's word limit and formatting guidelines.

Selecting keywords

Keywords help search engines and indexing services find your paper. Relevant keywords can significantly improve the reach and impact of your study. The best keywords:

• reflect on the core concepts of your manuscript

• are used commonly by researchers in your field to find similar work

• are specific and avoid vague terms.

Examples

Manuscript title: “Direct observation of nonlinear optics in an isolated carbon nanotube.”

Poor keywords: molecule, optics, lasers, energy lifetime

Better keywords: single-molecule interaction, Kerr effect, carbon nanotubes, energy level structure

Consider how someone searching for your research might phrase their query - this should guide your choice of keywords.

Length and language

Manuscript length

Follow the word count guidance provided on your journal’s ‘article types’ page. This helps ensure your manuscript meets the journal’s expectations for scope and structure.

Word count policies can differ between journals. For most Frontiers journals:

• Included: main text, footnotes, and in-text citations

• Excluded: abstract, headings, figure/table captions, funding statement, acknowledgments, and reference list

Always check your specific journal’s submission guidelines to confirm which sections are counted toward the word limit.

Tip: Indicate the total word count and the number of figures and tables on the first page of your manuscript.

Language quality

High-quality English is essential for publication. To enhance clarity and highlight your research, consider professional language editing services.

See our author services page for suggested services

Introduction, methods, and results

Introduction

The introduction section sets the stage for your entire study. This is where you:

1. present background information on your topic

2. explain why the question you address is important

3. describe the purpose or aim of your research.

While writing the background, ensure your citations:

• include studies with conflicting results to show the debate in the field

• if possible, cite relevant work published within the last 10 years, but do not omit key older studies that first introduced crucial concepts

• only reference work closely related to your question or methodology.

Tip: You don’t need to include an exhaustive literature review in the introduction of a research article, unless the journal guidelines specifically request it. Focus instead on providing just enough background to establish the context and significance of your research question.

After summarizing existing knowledge, clearly highlight the gap your study addresses. End the introduction with a concise statement of your research objectives or hypothesis. This clarity helps readers and reviewers quickly understand the purpose of your study.

Note: If you are submitting a review article, a comprehensive literature overview is expected. Check your journal’s author guidelines for specific requirements.

Materials and methods

The materials and methods section should provide all the details needed for another researcher to replicate your study. To achieve this:

• Use subheadings to group different experiments or procedures.

• Write in the past tense since you are describing what was done.

• Detail new methods thoroughly and cite references for established methods.

• Include statistical tests and parameters.

• Specify any special equipment or reagents, including brand names, if relevant to reproducibility.

Clarity here is critical because reproducibility is the cornerstone of scientific integrity.

TIP: Some journals have very strict formats for the methods section. Review the instructions for authors for your target journal and follow the examples in recently published papers from that journal.

Results

In this section, present your experimental findings clearly, without interpretation (that belongs in the discussion). Follow these best practices:

• Use subheadings to group results by study section or experiment

• Report findings in a logical order of importance or chronology

• Avoid repeating data across formats. If it’s shown in a table or figure, don’t restate every number in the text

• Include results of all statistical analyses, with p-values or confidence intervals where appropriate

• Use the past tense for findings, but refer to figures/tables in the present tense (e.g. “Figure 2 shows…”)

For systematic reviews or meta-analyses, consider having a statistician review your results before submission.

Use relevant reporting checklists (such as CONSORT, PRISMA, or STROBE) to ensure completeness. These can help structure your results and avoid missing essential information.

A clear and well-structured results section helps readers grasp your key findings and prepares them for interpretation in the subsequent section.

Discussion and conclusions

Your discussion section should interpret and contextualize your findings.

1. Discuss your conclusions in order of importance.

2. Compare and contrast existing literature. If your results differ from previous findings, suggest why.

3. Address any inconclusive results, acknowledging potential limitations or alternative explanations.

4. Mention the limitations of your study explicitly. This honesty can strengthen your credibility.

5. Explain the implications of your findings, both within your field and potentially in broader contexts.

The conclusions section (sometimes combined with discussion in a single “discussion and conclusion” section) is where you:

• summarize your main findings and their significance

• indicate how your research advances the current state of knowledge

• possibly recommend directions for future research.

Ending with a concise, forward-looking statement leaves the reader with a clear sense of why your study matters and what comes next.

Figures and tables

Figures, tables, maps, and schematics are often the most effective means of communicating complex data and relationships. Many readers will look at display items before deciding whether to read your full text, so each one should be easy to understand on its own.

A well-designed figure or table can significantly enhance the impact of your work. Be sure to:

• allocate time to design them carefully

• use high-resolution images

• label them clearly and provide concise, informative captions or legends

• avoid repeating the same results across multiple formats

• If using AI-generated images or illustrations, check that:

• the content is scientifically accurate and appropriate

• captions clearly explain the image

• all elements are legible and meaningful

• any AI use is acknowledged, following Frontiers’ authorship and AI policies

Always follow the submission guidelines for your journal. Some journals request display items be placed within the text, others at the end, or uploaded separately.

Tables

Tables are ideal for large amounts of data and can be more readable than text for reporting numbers or small sets of results. A good table:

• has a clear, concise caption or legend describing what is shown

• divides data into logical categories or columns

• includes units wherever necessary

• uses a legible font with adequate spacing

Minimal lines and uncluttered formatting help readers quickly grasp the findings.

Note: Many journals ask that large tables be placed in the supplementary information rather than in the main manuscript. Be sure to check your journal’s guidelines before submission.

Figures

Images

Images (photographs, micrographs, or other visuals) are crucial when words alone are insufficient. An image is often invaluable when representing microscopic or nanoscopic features. Key best practices include:

• using scale bars

• clearly label important areas or features

• indicate the meaning of colors or symbols used.

Data plots

Data plots (graphs, charts) can convey statistical or functional relationships clearly. For example, a scatter plot may illustrate the correlation between two variables, while a bar chart may display comparisons across multiple conditions. Always:

• label axes with quantity and units

• use legible font sizes

• include legends explaining different data sets or conditions.

Maps

If your work involves geography or field sites, maps help contextualize your results. A good map:

• has a scale bar and includes latitude/longitude references

• labels key locations important to your study

• may include a map legend (if multiple symbols, shading, or color gradients are used).

Schematics

Schematics are useful to illustrate conceptual processes or system diagrams where an actual photograph would be confusing or impossible. Include only essential components and label them clearly to avoid clutter.

Technical tips and ethical considerations

• For print, aim for at least 100 ppi; 72 ppi is typically acceptable for online, but requirements vary. Check your journal’s guidelines.

• Be aware of the RGB (red, green, blue) color model for digital applications and the CMYK (cyan, magenta, yellow, black) color model for print. Ensure that the final figures are presented in the format requested by the journal.

• You should never manipulate images to alter or enhance results. Only minimal adjustments to brightness or contrast (applied uniformly) are acceptable. Do not crop images in a way that omits critical information. Always keep the original files and metadata in case the journal requests them.

Acknowledgments and references

Acknowledgments

After the discussion and conclusions, you typically include an acknowledgments section to credit individuals or organizations who contributed to the study but do not meet the authorship criteria. This may include:

• technical staff or lab assistants

• collaborators who provided data or equipment but did not participate in the analysis or writing

• colleagues or mentors who offered critical discussion or editorial assistance

• funding agencies or institutions (including specific grant numbers, if applicable).

Tip: Follow guidelines from the International Committee of Medical Journal Editors (ICMJE) or your specific journal regarding criteria for authorship versus acknowledgments.

References

Your references should support every statement of fact in the manuscript. Citing previous work in your field is essential for:

1. Give credit to theories or concepts you have built upon.

2. Show the evidence that supports your statements.

3. Help readers understand how your study fits into the broader literature.

4. Demonstrate that your field is active and that others are working on related questions.

Best practices for citing

• Always read the original publication before citing it. Do not rely on another paper’s summary.

• Balance your references – include studies that have contradictory findings to yours, if relevant.

• Check the instructions for authors for the required citation style (eg APA, Harvard, Vancouver).

• Avoid ‘citation dumping’ by including only the most relevant and recent references.

• Ensure you don’t cite an article that has been retracted

TIP: Many journals have a maximum allowed number of references. Plan accordingly so you do not have to remove crucial citations at the last minute. There are also many online reference tools available for use. Some useful resources include RefMe, Zotero, and Mendeley.

Formatting your manuscript

Once you have drafted all sections of your manuscript, it is critical to ensure it meets the submission guidelines of your target journal. Formatting may seem minor compared to your experimental work, but proper formatting can be beneficial.

• A well-formatted paper suggests a careful, detail-oriented researcher.

• Proper headings, consistent style, and clear references help reviewers and readers focus on the content.

Ensuring compliance with journal guidelines

One strategy that can save considerable time is to select an initial target journal before beginning to write. Each journal has unique rules for:

• word limits for abstracts, introductions, or the entire paper.

• file formats for figures (e.g. .jpg, .png, .pdf, .ppt).

• reference formatting (e.g. numeric vs. author-year systems).

• submission portals that may require separate uploads of figures or structured abstracts.

You can avoid extensive rewrites later by tailoring your manuscript to a journal’s requirements from the outset.

Before submitting, create a checklist based on the journal’s 'instructions for authors.'

• Word and character limits for title, running title (if required), abstract, and main text.

• Section requirements – some journals require a structured abstract with specific subheadings or a stand-alone conclusions section.

• US or UK English, or a specific style guide.

• Ensure correct email and affiliations for the corresponding author.

• Figure placement should be inserted in text, appended at the end, or uploaded separately.

• Reference style – numeric, alphabetical, or chronological.

• File formats – figures may need to be in TIFF, EPS, or PDF at a specified resolution.

• Conflict of interest statement – many journals require explicit declarations.

• Ethics statements – for clinical or animal research, confirm you have the necessary approvals and mention them clearly.

• Author consents – make sure you have the agreement of all co-authors on the final version.

TIP: Some journals offer templates for Microsoft Word or LaTeX. Using these from the start can reduce the risk of formatting issues later.

Use of generative AI technologies

Authors must not list generative AI tools as authors or co-authors. These tools cannot be held accountable for the content and therefore do not meet authorship criteria.

If you use written or visual content created or edited using generative AI (e.g. ChatGPT, DALL·E), you must:

• ensure all content is factually accurate and free from plagiarism

• check that AI-generated figures match the data in your manuscript

• acknowledge AI use in the manuscript (in the acknowledgements, and methods section if relevant)

• include the AI tool’s name, version, and source

• consider uploading prompts and outputs as supplementary files

Authors are fully responsible for the accuracy and integrity of any AI-assisted content.

Pulling it all together: final checks and submission

Don't rush to submit your manuscript once you have written, revised, and formatted it. A few final checks can greatly improve your chances of acceptance:

1. Proofread for grammar, spelling, and clarity. Consider asking a colleague or professional editor to conduct a final language check.

2. Check your references carefully: are they cited in the proper order? Do the in-text citations match the reference list?

3. Ensure each figure and table is labeled correctly and clearly referred to in the text. Confirm captions are accurate and add value beyond simple labels.

4. Are your title and abstract still accurate after any rewrites? Do they capture the essence and significance of your findings?

5. Ensure your paper aligns well with the journal's interest, scope, and audience. If you have any doubts, read a few recently published articles in that journal and see how your paper compares in style and content.

If you confirm all these points, you can confidently log into the journal’s submission system and upload your manuscript. Congratulations, you’ve reached a major milestone in sharing your scientific contribution.

What’s next?

As a quick recap, preparing a manuscript for publication is a multi-step process. Every step requires attention to detail and commitment to scientific integrity. Although it can be time-consuming, the result – a well-prepared manuscript that advances knowledge in your field – makes your effort worthwhile.

Next steps

See Frontiers’ guidelines for authors

Find out how to submit to Frontiers

Get help choosing a journal