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How To Write a Scientific Paper: 6 Key Steps For Beginners

You’ve put in the [hopefully metaphorical] sweat, blood, and tears. After countless hours in the lab, probably a few incorrect hypotheses, and undoubtedly some unexpected, exciting results, you finally have a scientific story that is ready for publication. Congratulations! Now comes the writing part; where to begin?

Don’t become paralyzed by thoughts of those perfectly polished Cell papers you’ve read, complete with figure panels a-z. Here’s a guide to get you started with some pointers from those who have struggled before you.

Common misconceptions of first-time scientific authors

Myth #1:
 A paper should be written intro-to-conclusion.

Start with the figures/results! Often you don’t realize how to best frame a paper until you’ve seen the results altogether.

Myth #2:
 Results should be written in the order that they were obtained.

Honesty is paramount in scientific studies, but it’s ok to arrange the results in an order that tells a coherent story. The goal is to clearly communicate your results and demonstrate why these findings are important. Rarely does science happen in the most clear and concise order.

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Assemble your FIGURES


Ideally, you’ve already made many of your figures for lab meetings or your notebook. Finish them up, put them in a tentative order in PowerPoint (or whatever you use), and write your legend descriptions.

  • Don’t spend too much time formatting size/color/etc. Better to do final touches at the end, especially since specific journals have their own requirements.
  • Stick all your “figures” files in one folder so it’s easy to go back and edit later. Many journals now require the exact sample size and statistical test listed for each graph. Save yourself a headache later by listing these values in the legend as you go.
  • Be honest. Don’t exclude outliers that look “wrong”, re-run one sample ten times to boost your “n” or alter images in ways that obscure or exaggerate a result. Scientific misconduct will come back to bite you!


Use your figures to write a concise RESULTS section


For each section, briefly orient the reader by stating your question and experimental approach, then dive into the specific results. Be concise and focus on the data.

  • This should be an objective description of your experimental findings. Save your interpretation for the discussion, and an in-depth, procedural explanation for the methods.
  • Don’t cherry-pick the results that support your conclusions. It’s ok to have a couple of “weird” results but ignoring them may raise a red flag for reviewers. Remember, these could provide rationale for your next paper.


Start compiling your MATERIALS/METHODS with enough detail that someone could replicate your study


  • Don’t procrastinate on this section, or you may find yourself waiting on a protocol or catalog number from a collaborator.
  • No need to be creative here – feel free to look at previous papers from your lab. This doesn’t need to be hard.
  • Check with the journal for specific requirements, such as catalog numbers, city of manufacturer, or resource repository requirements.


Interpret (but don’t repeat!) your results in the DISCUSSION


By addressing:

a. How does my study support what others in the field have shown?

Ex: “Our finding that XYZ–knockout mice develop cancer is consistent with previous findings that people with XYZ mutations have increased cancer risk.”

b. How does my study challenge previous findings?

Ex: “In contrast to epidemiological data showing increased heart disease in people who consume a cheese-only diet, we observed improved cardiac function in cheese-fed rats.”

c. What are the study’s main conclusions and how do they advance the field?

Ex: “Together, our pharmacologic and genetic experiments demonstrate that Protein ABC is a novel stress factor that could be targeted for treatment of VBAD Disease.”

d. What are the most important future directions?

Ex: “Here we show the in vitro kinetics of Inhibitor RBG. Future studies should examine the pharmacological properties of RBG in vivo.”

Now that you’ve crafted your story and identified the major findings, set the stage for the reader in the INTRODUCTION


Start with the big picture and then get more and more focused on your specific topic. By the time you finish, your study should seem like the most obvious and important one in the field!

  • The scope of the intro will depend upon the scope of the journal. No need to explain the structure of DNA if publishing in a nucleic acids journal.
  • Be sure to reference the relevant and important papers in the scope of your study to help set the scene of what has already been done.


Finally, craft an ABSTRACT that briefly summarizes the paper’s highlights


It should contain a concise intro, problem statement, general methods, big picture results, and the broad impact of your findings.

  • This may be the shortest section, but perhaps the most important! Assume many people will only read this section. What do they need to know?
  • Focus on the big picture; don’t list the result of every experiment or get into detailed methods.
  • Consult the specific journal for style and length.


Final tips


Be sure to REFERENCE work done by others!

  • Cite as much as you reasonably can, but as a general rule, you don’t need to cite information you’d find in an introductory textbook (ex: the nucleus contains DNA).
  • Do your best to cite the original sources, rather than a review (or a source that cites the original source). Wouldn’t you be annoyed if someone else was cited for YOUR discovery?
  • Use a reference management program like Mendeley or EndNote, which makes adding citations a breeze. Once papers are imported, simply insert citations within the text, then the program will format them in your chosen reference style.


Proofread and follow the journal guideline

  • Maximize your chances of favorable reviews! You want your reviewers to focus on the science, rather than get distracted by spelling and grammar typos, awkward sentence structure, or incorrect formatting.
  • It’s especially important to have a colleague proofread if you’re a non-native English speaker – and not something to feel bad about.
  • Don’t forget to define abbreviations the first time they are used. Some obvious abbreviations (like DNA) won’t need to be defined, but check the journal for this.
  • Be sure to use correct italicization and capitalization. This is key when you are referring to a gene symbol versus protein name, and can also vary between species.


If you’re feeling paralyzed by the writing process, give yourself permission to write a sloppy first draft and just START! Getting something down on paper is always better than a blank page.

Good luck!

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