Writing tips & finishing a paper

When writing a paper, my target audience is always a first year PhD student. Keeping this target audience in mind with every decision means that the reader is smart but doesn’t know the field (terminology, debates, important papers, history) as well as other colleagues, eager and full of energy and optimism to learn and possibly to try to re-derive all of your formulas and proofs, and may keep this paper in their mind as they read more papers. They will give you the benefit of the doubt. Make sure every word of your paper earns that trust.

However, first year PhD students are also learning to read research critically, and can scrutinize a paper and its methods, results, and conclusions better than most reviewers. If your paper doesn’t include an honest discussion of assumptions and limitations of the study, and they think of others, you may lose this reader for all of your future work.

All of this is based on myself as a first year PhD student. I think I always write for that person: how eagerly I read papers to learn more and find references to other papers, and how soul-crushing it was to realize a paper had a major mistake in a derivation or some fatal flaw in the assumptions that wasn’t spelled out properly. That said, I also still remember those papers from 2001 that I read that changed my life with their clarity and ability to teach a subject, not just overwhelm the reader with artificial novelty and complexity. Write for me, circa 2001.

Basic writing

Early on in graduate school, my collaborator advised me to read the full Strunk and White book on Grammar. I am not a perfectionist, but this experience has stuck with me, and I believe that it is important first to learn the rules of grammar and then to learn when they can be broken. This is a summary of the rules for scientific writing that I see broken most often to the detriment of the paper.

Unhelpful words and phrases

The following words make it hard for me to read and understand sentences.

  • etc.
  •   … (except in mathematical contexts)
  • and/or, or any use of the backslash
  • &
  • vs. (write versus instead)
  • “utilize” (write *use* instead) – use the shortest, most common word that says what you mean
  • contractions with apostrophes (e.g., “don’t”)
  • “eg.“ (write e.g., instead)
  • commas go after “which,” but not “that” as modifiers of nouns
  • think carefully when adding or omitting a comma. Too many or too few hurt the sentence flow.
  • avoid all adverbs: “very”, “really” especially
  • negative + verb: e.g., “not enriched” should be “depleted.”
  • always use an Oxford comma: \`\`A, B, and C“ not \`\`A, B and C”
  • Don’t capitalize letters or words that don’t need to be capitalized;
  • Avoid hyphens unless you have a multi-word adjective <- see what I did there?
  • Avoid italics, bold, and every type of formatting that draws attention to words unnecessarily

Latex commands and formatting

  • to avoid that annoying space after a comma in math mode, add:
Sentence structure
  • Don’t write long sentences. Break up long ideas with periods, semicolons, or triple dashed phrases (e.g., “…, with which gene A—when measured in the unexposed samples—does not appear to interact”)
  • Prefer active and not passive voice
  • Use simple words, and simple sentence structures.

I do not know if it is possible to teach a person to write meaningful, clear sentences and paragraphs. I think the phrase that another collaborator said once that I repeat to myself often when writing papers is:

Words mean things.

It sounds simple, but it embodies the idea that you should not use a word that does not capture the object, idea, or action you are trying to convey to the reader. For example, “We collected GWAS data for 943 participants.” What does it mean to collect “genome-wide association study data”? Do you mean that you collected genotype data for these participants? If so, say that.

Paper structure and consistency

Logical flow is another hard concept to teach. Paragraphs read almost like proofs. Avoid writing things until all the required information leading up to that statement have been written.

Order of presentation of ideas is also a difficult and subjective area. I look at the section and subsection headers to see if there is logical flow to the whole document. These section and subsection names are very helpful to directing the reader as to what is coming and what is in that section, like code comments. These should also be as descriptive as possible without being unreadably long. Some writers advise to write complete sentences as the section names with the punchline:  “Differential expression results suggest widespread impact of exposure to statins.”

Consistency is a problem I find with nearly every paper I read. If you use the word “data” as a plural, keep it plural. If you refuse to add an -s to eQTL when it is a plural word (don’t do this, please), at least keep that consistent throughout the paper. If you label something “sex-biased eQTLs,” don’t call them “sex-differential eQTLs” later on. Consistency is important for understanding.

Detailed outline

I advise students to put together a paragraph-resolution outline of their paper before actually writing, including figures and potential caption first lines.

How should you do this? Look through the related work in the journal to which you are planning on submitting your manuscript. Often, there is a published paper or two that are very well written and organized. Without using any of the words or phrases that the other paper does (this is plagiarism) follow their organizational lead in terms of presentation of ideas and details presented; adapt to the context of your research. If you are writing a Methods paper, do not use the outline of a Research paper, and vice versa – paper type matters.

Order of writing

People have strong opinions on this, and here are mine.

  • Before anything, detailed outline. Have your advisor or a peer read this over to get feedback.
  • First, and as the paper evolves, Related Work. To write a paper, it is essential to understand and to formulate in words the context.
  • Second, and as you go, Methods. The moment you implement your method, write it out as it is running. You will forget and omit, or you will leave out important details if you don’t write as you go.
  • Third, and as they arise, Results. These will need to be edited from brain dump to concise, but that is fine.
  • Fourth, Abstract. It will change, but getting the scope of the paper written is important at this point.
  • Fifth, Discussion. Summarize paper briefly, then discuss clearly the limitations and next steps to this research.
  • Last, Introduction. I’m sure you are itching to write this. A well-written introduction can change the world. But misstarts on introductions can also make crafting the perfect final product hard. It hurts, but is often necessary, to completely erase an introduction written too early and start from scratch — I’ve had to do this many times. When I don’t do this, I often regret the final product.
Really finishing a document

You have sent your advisor the draft, received feedback, and are ready to submit! At this point, there is (I find) as many as 10 hours left of work before actually being able to submit a journal length paper; conference papers are somewhat easier.

Here is my general checklist (parts adapted from Dave Blei); some of this advice assumes you are using TeX.

  • Authors names and affiliations (out for double blind review, double-checked for journal)
  • Spell check!
  • Each bibliography entry should be two lines. (there are exceptions.)
  • Make the bibliography consistent, e.g., first initial and last name only. omit “Proceedings of Conference” and just say “Conference”, e.g., “Artificial Intelligence and Statistics”. Omit page numbers if they send you to a third line. Capitalize proper names in curly brackets like Bayes and Dirichlet and RNA.
  • Review every single bibliography reference for proper information, not missing authors, journal name is capitalized appropriately, etc.
  • Ensure that the colors, ordering, and inclusion of methods, experiments, and results are consistent across Methods, Figures, Tables, and Results.
  • Read over Methods again. Make sure that you could repeat each step without having to go to your code. Also make sure that this is boring recipe book writing, and not motivation or explanation (see How to write a Methods section).
  • Look for paragraphs that end in 1-3 orphan words and edit them to save a line. This makes the writing better and saves space. And its a nice (and random) way to edit your paper.
  • Ensure that all acronyms are defined before they are used, with exceptions (colloquial acronyms, e.g., DNA). Define three letter acronyms (TLAs) like that — don’t capitalize the words if it is not necessary, keep the acronym plural if it is in the words, and the TLA should be the part in the parentheses, not the words.
  • Captions should be clear and consistent; they should begin (or end) with a sentence saying what you want the reader to get out of them (more information in the FIGURES document).
  • use Ref. \[x\] for when you need to use citations as a noun. Alternatively use the author names, but this might take more space. But try to avoid using citations as a noun.
  • Instead of “Equation“, use ”Eq.“; Instead of “Figure” use “Fig.“; instead of “Table”, use “Tab.”
  • Write a draft of the cover letter (for journal articles). Ask for an example of one if you need to see what these look like.
  • Read over the formatting instructions for the journal or conference, including figures. Do exactly what they say. Except for: put figures inline, since, as a reviewer, this is always better.
  • Make sure each labeled equation is referenced in the document. Make sure each figure and table are referenced in the document at least once. Make sure the order they are referenced are the same as their numbering. Do the same for the supplemental data.
  • Make sure the supplemental data, code, etc. are all ready to go.
  • Have code ready to make public. Make it public.
  • Look up a set of people as reviewer suggestions for the paper. Clear this with your co-authors (and ask for their suggestions). Also think about potential reviewers with conflict of interests to exclude (I generally only exclude current advisors or collaborators, if they are obvious reviewer choices).
  • Read, reread, read again, read out loud
  • Spell check again!
  • Get a (suitably journal-anonymized) version ready for arXiv or BiorXiv, after discussing with your advisor.