Structure the Paper

Must have a bottom line

  • bottom line is the important information you want to convey in your paper:

  • What was the question that you wanted to answer?

  • What is the significance of the conclusion?

  • What is the new advance of your discovery?

  • Repeat the bottom line over and over again:

    • at the end of abstract
    • in the introduction
    • in the results
    • in the discussion
    • 总之,一定要让文章的概括句重复多次出现在不同部分,让读者知道你在干嘛


  • The title should reflect the factual content of the paper.

  • A good title is straightforward and uses keywords that researchers in a particular field will recognize.

  • Make the title as strong as the data can withstand. (标题要高度凝练的概括出你的发现)

  • Specificity is very important! (体现出该研究的不同之处,也就体现出了价值)

  • Make title concise by omitting unnecessary words.

    study of, nature of (unnecessary words)

    non-pulmonary tissues instead of liver, brain, and stomach, but not lung

  • If possible, put the most important word first.

    LAZY1 controls rice shoot gravitropism (this word is specific) through regulating polar auxin transport.

    Increased expression of MAPKK7 causes deficiency in polar auxin transport and leads to plant architectural abnormality in Arabidopsis.

Running title

  • A running title is a short phrase that appear at the top or bottom of every page of a journal article.

  • Should be recognizable as a short version of the title.

    Title: Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis.

    Running title: ROS-induced gene expression

    Title: Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells.

    Running title: Dlk1-Dio3 region regulates cell pluripotency


An abstract should contain:

  • background
  • a question
  • what was done
  • what was found
  • the conclusion / answer
  • implications (optional)

What first got you excited about this research?

– make sure you convey the reason and that excitement.


  • Three basic elements of introduction:

    • The big picture of significance of the field/topic.
    • Summary of previous discoveries.
    • How your work adds to or contradicts to the existing picture.
  • Only present relative information. Introduction is not a review of literatures!!!

  • logic follow:

    Known –> unknown –> your specific question

  • Briefly summarize what the reader is going to learn and why it is important at the end of introduction.


  • Arrange paragraphs either chronologically or put the most important results first.

  • It often works well to let the story unfold in the way it actually happened.

  • Data are facts, results are statements that interpret those data.

  • Explain your data to help readers to understand.

    the expression was higher in mutant

    the enzyme activity increased

  • In each paragraph, put the most important result (e.g. central finding) first and less important results (e.g. control) later.

  • When citing the work of others, try to state their findings (“Sec9 is up-regulated in rho-cells”) rather than or in addition to their conclusion (“secretion is controlled by mitochondria”).

  • Summarize the trend and conclusion of your figures, but do not repeat data from figures.

Figures and Tables

  • Each figure should have a clear point/purpose.
  • Avoid complicated figures if you can.
  • Figure legends are important.
  • If possible, use simple labels so that people can get a quick idea of the figure’s logic without reading the legend.
  • Decide what you are trying to compare, and make it easy for the readers.

Materials and Methods

  • List what methods were used to generate the results, then write down what you did to carry out the experiments.
  • Order your materials and methods part logically as the flow of your experiments.
  • Keep the section brief by describing your unique techniques and condensing those that are common practice.
  • Define or expand all non-standard abbreviations.


  • Discussion is the place where you can put your findings in perspective, propose a model, outline a direction of investigation, and make the readers think.

  • But, do not stretch too much.

  • Clearly distinguish what you have shown and what you imagine.

  • Provide extra evidence to support your findings and the bottom line of your paper.

  • Start by a quick run-through of the main results.

    • state the answer to your main question
    • briefly summarize the supporting evidence
  • Organize subsequent topics from most to least important.

  • End by restarting the answer and/or discussing implications and future directions.

What to discuss

  • How your results affect the field, not the details of your results.

  • To what extent your findings are new vs. confirmatory.

  • Reveal any shortcomings. conflicts, or limitations of your data.

  • Outline explanations for unexpected data.

  • State advantages or shortcomings of your methods, if there is any.

  • Reveal any large areas that remain as a complete mystery.

  • Include some speculations, if possible.

  • Include different levels at which your results are significant .

Commonly used expressions

  • Several lines of evidence have shown …
  • Our results suggested
  • The findings reported here indicated
  • Results reported here will shed light on
  • We speculate …
  • Be cautious when using important, significant, great, excited


  • Do not rush in sending out your manuscript!
  • Rewrite the title and abstract after completing the draft.
  • Put the finished manuscript aside for a few days, then read it again.
  • Pay specific attention to logic flow.
  • Read at least 5 times before submission!
  • Double check references.
  • Ask someone else to read your manuscript.

Write cover letter

  • Be short (usually no longer than one page)
  • Emphasize on what is known and why your finding is important
  • Follow the journal’s requirement
  • Address to the right journal

Write response letter

  • Be polite

    We agree with the referee that…,but
    The referee is right to point out…,yet
    In accordance with the referees' wishes,we have now changed this sentence to…
    Whilst we agree with the referee that…
    It is true that…,but
    We acknowledge that our paper might have been…., but
    We too were disappointed by the low response rate…
    We agree that this is an important area that requires furthr research…
    We support the referee's assertion that…,although
    With all due respect to the reviewer,we felt that this point is  not correct…
  • Answer the reviewer’s questions point-by-point

  • Be political ???啥意思???


Pursuing the dream and the best future

CHENYUAN Blog Homepage

因为不想遗忘! 在这个信息大爆炸的年代,最重要的是对知识的消化-吸收-重铸。每天学了很多东西,但是理解的多少,以及能够运用多少是日后成功的关键。作为一个PhD,大脑中充斥了太多的东西,同时随着年龄的增长,难免会忘掉很多事情。所以只是为了在众多教程中写一个自己用到的,与自己...… Continue reading