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Tips for Paper Writing

Example Manuscripts

Publication Tips (Cover Letter, Status Enquiry Letter, etc)

I. Format

Files for Submission

  1. Cover Letter.docx (1 page)
  2. Suggested Reviewers.docx (6 reviewers)
  3. Manuscript - Main text.docx (see sections below)
  4. Figures.pdf (save as from PPT file)
  5. Supplementary Info.pdf (save as from docx file)
  6. Supplementary file 1.xlsx, Supplementary file 2.xlsx, ...

Sections in Main text

  1. Title, Authors and Affiliations
  2. Abstract and Keywords
  3. Introduction
  4. Results
  5. Conclusion and Discussion
  6. (Online) Methods

Font and Line Space

  1. Check Font: Times New Roman, 11pt or 10.5pt
  2. Check Line: double space (except for References)
  3. No indent for the first sentence of a new paragraph.

Abstract

  • (1) Background - (2) Results - (3) Conclusions

Keywords

  • Replace with the key words we want to be searched. If number of key words is limited, we may not repeat with title only if this keyword is very important.

II. Writing Rules

Grammar and English Writing Tools

Grammarly (app.grammarly.com) is very helpful. It has web version, desktop (MAC/Windows) version and chrome/firefox/safari plugin. You can also install it into your office word from this add-in.

AI tools like ChatGPT and ChatGLM (智谱清言）are even more powerful tools to modify and improve your English writing.

  1. Check plural or single.
  2. Check if Past tense is used when we describe results (e.g., "We sequenced 50 samples ...").
  3. Check if Present tense is used when we make a claim or conclusion (e.g., usually in the last sentence of a paragraph, "This result suggests that …" ).
  4. Check number list (First, Second, Third, ...) see Firstly, Secondly, Thirdly - Grammarly Blog
  5. Check When do you use 'the' in English? - Learning English Grammar

Terms

  1. Check the writing of specific terms in right format in the whole paper:
    • noncoding, cross-validation
    • P-value (italicize and capitalize the P here)
    • vs. (lower case with one dot after)
    • i.e., something ( "," is needed)
    • e.g., something ( "," is needed)
  2. Check if the Abbreviations are consistent in the whole paper. Check if full name is used when it is mentioned first time. Occasionally, we may use full time several times in the beginning of Introduction, Methods and Suppl. Info., because they are separated documents when published.)

Figure and Figure Legend

Figure and Figure legend sometimes are more IMPORTANT than main text, because many senior readers read figures first.

  1. Check if Figure Legends contain sufficiently detailed descriptions. (We got this suggestion from a previous reviewer who rejected our paper.)
  2. Check if the colors are easy to see. (We got this suggestion from a previous reviewer who rejected our paper.)
  3. Font, key's and axis label's fonts in particular, in Figure need to be as large as possible.

Main Text

  1. Check first and last sentence in the whole paper. To make it easy to read, in every paragraph, first and last sentences are important. Usually, first sentence introduces and summarizes the whole paragraph; last sentence concludes the whole paragraph (e.g. "This result suggests that ...").
  2. Check voice:
  3. n Results, we prefer active voice, such as "We analyzed the data …", not "The data were analyzed …".
  4. In Methods, we may use passive voice sometimes , such as " The difference was tested by a paired t test.".
  5. Recommended words:
  6. We performed RT-qPCR (RNA-seq …) for … → XX was validated (sequenced ...) by RT-qPCR.
  7. We built a Random Forest model … → We used/developed a Random Forest model to …
  8. We assayed/analyzed … datasets.
  9. We assessed, calculated, detected, estimated, evaluated, examined, ...
  10. We curated/collected … datasets from … OR 100 datasets were curated/collected from ...
  11. XX was significantly enriched in the noncoding sequences (t test P-value: 0.002).
  12. The enrichment is/was calculated with RNApromo (ref.). The P-value cutoff is/was 0.001; the xx is/was 0.5; the xx is/was 0.8. (depends on if you are talking to the audience about a plot or describe a result you have done.)

Statistics

  1. Check every result to see if it needs statistical test: Was a test used? Which one? What is the P-value?
  2. Check every enrichment to see if it was statistically determined to be enriched: What test was used? Which one? What is the P-value?

Using the right tense

In your scientific paper, use verb tenses (past, present, and future) exactly as you would in ordinary writing. Use the past tense to report what happened in the past: what you did, what someone reported, what happened in an experiment, and so on. Use the present tense to express general truths, such as conclusions (drawn by you or by others) and atemporal facts (including information about what the paper does or covers). Reserve the future tense for perspectives: what you will do in the coming months or years. Typically, most of your sentences will be in the past tense, some will be in the present tense, and very few, if any, will be in the future tense.

  • Past tense

Work done

We collected blood samples from . . .

Groves et al. determined the growth rate of . . .

Consequently, astronomers decided to rename . . .

Work reported

Jankowsky reported a similar growth rate . . .

In 2009, Chu published an alternative method to . . .

Irarrázaval observed the opposite behavior in . . .

Observations

The mice in Group A developed, on average, twice as much . . .

The number of defects increased sharply . . .

The conversion rate was close to 95% . . .

  • Present tense

General truths

Microbes in the human gut have a profound influence on . . .

The Reynolds number provides a measure of . . .

Smoking increases the risk of coronary heart disease . . .

Atemporal facts

This paper presents the results of . . .

Section 3.1 explains the difference between . . .

Behbood's 1969 paper provides a framework for . . .

  • Future tense

Perspectives

In a follow-up experiment, we will study the role of . . .

The influence of temperature will be the object of future research . . .

Note the difference in scope between a statement in the past tense and the same statement in the present tense: "The temperature increased linearly over time" refers to a specific experiment, whereas "The temperature increases linearly over time" generalizes the experimental observation, suggesting that the temperature always increases linearly over time in such circumstances.

In complex sentences, you may have to combine two different tenses — for example, "In 1905, Albert Einstein postulated that the speed of light is constant . . . . " In this sentence, postulated refers to something that happened in the past (in 1905) and is therefore in the past tense, whereas is expresses a general truth and is in the present tense.

III. 网友的写作建议

Effective Writing by Nature

写出第一稿

  • 两步走：1、写出尽可能多的内容，不要担心语法、拼写、组织；2、修改文稿变得更好。（参考海明威的写作方式）
  • 当你写作时，不要编辑！写作和编辑使用不同的半脑，交叉这两件事不容易。
  • 每个结果和相应的讨论一起写，以免之后忘记结果的解释和意义。再写方法，最后写介绍（基于结果和讨论）。
  • 用照片做类比：
    • Introduction：Why was the picture taken?
    • Results：What do you see?
    • Conclusion and Discussion：What does it mean?
    • Methods：How was it taken？

编辑最终稿

  • 阅读投稿期刊的『Instructions for authors』，了解期刊期望的行文风格。
  • 介绍部分说明本研究的理由，不是文献综述。讨论部分不用『可能』，如果不确定结论，做更多的实验。
  • 结果部分不使用『could』、『can』（受中文影响），减少不确定性。
  • 不使用『etc』、『and so on』，这些词说明作者懒。
  • 『observed』很弱很被动，改用：assess, calculate, detect, estimate, evaluate, examine...
  • 不用『obviously』，读者不一定容易理解。
  • 结果部分避免『significantly』，改为报 P-value 。讨论部分可用。