The scientific writing process

(1) Establish preliminary structure

  • First, write the major headings appropriate for your target journal and paper type (e.g. Introduction, Methods, Results, Discussion).
  • List tentative subheadings. For example, under Methods, one might have Study design, Subjects, Intervention, Beck anxiety inventory, Image acquisition, Image analysis, Genome-wide association study, and Data analysis. If you have a Methods section, be sure to include every technique involved in the study. For results, most journals prefer that the subheadings indicate briefly what was found, rather than what was done. For example, Patients with XYZ polymorphism exhibited heightened anxiety phenotype.
  • For more narrative sections (e.g. Introduction and Discussion), write a series of topics or questions to be answered. These can be changed and reorganized later. For now, just get some on the pages.

Now you’re getting somewhere. No more blank page, and you’ve made some real progress. Pat yourself on the back, maybe even take a break.

(2) Fill in content

Even papers with a format other than the classical “Introduction, Methods, Results, Discussion” format (e.g. Brief Communication, Case Report, Letter to the Editor, Grant application, etc.) encompass the same kinds of content in some form. To save yourself a chore later, include citations as you go. But if you are in a “writing flow”, insert a reminder, like (ref) or, better a reminder that reminds you what you were thinking of (Wang lab paper on X). It can be helpful to paste full references into margin comments, or at least the doi links, so that it will be easier to produce your References section later.

  • The easiest place to start is the Methods because it is just factual information that you already know, or at least know where to find. You can start by pasting in protocols, if you want, and then revise them.
  • After the Methods, the Results should be the next easiest to fill in. State exactly what you found. Do not include background or methods.

*Avoiding common mistakes: The Results section should not include general background or methods.

  • The overarching theme for the Introduction is to open with general information and move into specific topics that are important for this paper. Start with an explanation of the central driving topic that the work addresses, such as disease characteristics or an explanation of a problem that your work is addressing (e.g. juvenile smoking, poisonous algal blooms, etc.). Next, tell your readers about specific information that led you to the present work (e.g. prior research, a new technology, the development of a model, etc.). The final Introduction paragraph (or two) should include your aims and/or hypotheses and how (very generally) your study addresses them. For example, you might say, we employed electroencephalography to examine brain responses to emotionally salient images, but you would not provide details about how the technique was performed or how the images were produced here.

*Avoiding common mistakes: In an I-M-R-D paper, DO NOT give away your results or conclusions in the Introduction section.

  • Discussion text should begin with a brief synopsis of the main findings (or things learned) from the present work. Next, the findings should be placed into context, which may include comparing them to prior relevant findings, explaining whether and how the findings fit (or not) with established hypotheses and or models. Customarily, the second-to-last paragraph should point out the limitations (weaknesses) of the work and how they might be addressed in the future. Finally, with the exception of extremely space-limited formats, there should be a concluding paragraph that states what the authors concluded from the work.

*Avoiding common mistakes: The Discussion is NOT a second Introduction. Do not make your readers re-read background from the Introduction. Life is too short.

*Avoiding common mistakes:The Discussion is NOT a supplemental Results section. Your readers should not be learning of any findings from the present study in the Discussion that weren’t mentioned in the Results.

  • The Abstract can be generated last by taking and reworking bits of content from the main text. Be sure to follow journal formatting instructions. For unstructured abstracts, you should (generally) have 1-2 sentences of background/aims/objectives, 1-4 sentences of methods, 1-5 sentences of results; and 1-2 sentences of interpretation/conclusions.

(3) Revise

Even papers with a format other than the classical I-M-R-D format (e.g. brief communications, case reports, letters to the Editor, etc.) encompass these kinds of content in some form. To the extent that is true, this advice can be generalized. If you have not done so already, now you will need to fill in the references.

You should expect to do multiple revisions. And you should take some time in between revision runs, at least a couple hours, preferably a night’s sleep.

When you discover areas that are missing information, if it is not a good time to fill in that information, use the margin comment tool to insert a reminder, or write the reminder directly in the text and highlight it to ensure you do no forget later.

Look for opportunities to remove duplicated information and information that is either too detailed or not directly relevant to your present experiments.

*Avoiding common mistakes: An original research article should not be a mini-review. To maintain logical flow and keep your reader focused on your objectives, be highly selective about the information you provide details about.

Happy writing. We are standing by to provide any support you may need along the way.

Before you begin

If you know the journal your paper, or your client’s paper, will be submitted to, you should look over an article of the same type from the target journal. In particular, pay careful attention to whether the journal encourages the use of first versus third person, active versus passive voice, past versus present tense, how the tables and figures are formatted, and length restrictions. 


Voice refers to whether a subject acts (active voice) or is acted upon (passive voice). Traditionally, scientific papers have been written primarily in a passive voice. For most journals, however, it has become acceptable and even encouraged to use active voice where passive voice would be awkward. It is especially common to use active voice syntax in the Results and Discussion sections, specifically when the author is distinguishing what they did relative to what others did, when the authors are distinguishing their view in a debate, or when the authors are describing a technological innovation developed in their own laboratory. Passive voice is more commonly used in the Abstract and Methods, with some journals explicitly discouraging its use.

Although papers are customarily heavy on passive voice, largely related to the convention of using the third person and creating a sense of objectivity, active voice is always preferred when it is feasible. For example, the active and direct ‘Group X did not differ from the control group’ is preferred to the passive ‘No significant difference was observed between Group X and the control group’. Making writing in the active voice a habit can take some practice, but it can make papers much clearer and more concise when used properly.


Past tenses are predominant in biological and medical papers reporting experiments conducted in a laboratory, in the field, or in a clinic. This convention is especially true in the Methods and Results: procedure x was performed and data y and z were observed. Present tenses are predominant in proof reports, such as in Applied Mathematics and Social Sciences, when the author is actually leading the reader through a thought demonstration: ‘Substituting constant k’ for formula f’, it can be seen that variable D becomes negligible’; ‘Hence, this demonstration that assumption A is invalid proves that hypothesis H is false’. Past perfect (have done) and present tenses are appropriate for explaining the status quo of knowledge: ‘Icon and colleagues have demonstrated the validity of this model in rodents and primates’; ‘The laparotomy approach is the gold standard for this procedure’; ‘The Earth is not flat’. Present perfect, present subjective, and future tenses are appropriate for examining implications and making recommendations: ‘Surgeons should be particularly mindful of this possibility when operating on patients with a BMI over 35’; ‘These findings will provide a basis for changing life as we know it’.

Remove ambiguity

There is something very satisfying about reading a clear and succinct presentation of ideas. Readers should not have to work to comprehend what the author is trying to say. One important example of this issue that should be fixed is the use of comparator terms without reference to what the subject is being compared. When terms such as “greater” and “lesser” (and –er words in general) are used, it should be explicitly stated greater than what. Likewise, it should be clear what statistical comparisons were done.

While it is grammatically acceptable to leave out some words– that is, in syntactical terms, to use elliptical phrasing– it can create confusion in technical writing, especially when there are multiple entities being related to one another. If a sentence could be interpreted in more than one way, then the missing words should be inserted.

Modifiers: Clauses, phrases, and appositives

An exhaustive discussion of all of the different types and subtypes of modifiers can be found in the Tameri Guide for Writers (or other grammar-dedicated resources). Here, I will speak of ‘modifiers’ as a group.

Text providing further explanation/definition of something within a sentence should, whenever it is possible, be immediately adjacent to the subject being described. This practice eliminates “dangling modifiers” (i.e. modifiers that are out of place and therefore confusing). When located at the beginning of a sentence (such as here), modifiers should be followed by a comma. In similar fashion, when located in the middle of a sentence (such as here), nonessential modifiers should be set off by commas before and after.The rule is that if the modifier could be removed and the sentence would still make the critical point then it is nonessential, and thus should be set off by commas. Commas are not needed if the modifier is essential to the critical point of the sentence. That being said, essential modifiers can often be replaced with a more succinct adjective or adverb. For example, “the students who work hard will earn good grades” would be better said as “hard-working students will earn good grades”.

Prepositional phrases, especially, should often be removed in favor of simple adjectives where possible, especially in sentences where there are strings of them. This process goes hand in hand with making one’s language more direct. For example, “increased expression of mRNA from XYZ gene of mammals was found” would be better as “mRNA expression of the mammalian XYZ gene was increased.”

If the author is trying to pack multiple modifiers into a sentence, it can be a great improvement to break out one or more of the modifiers to form separate sentences. Likewise, if the relationship between sentence components is not obvious, the sentence needs to be broken up to clearly communicate those relationships. In many cases, direct objects may need to become the subject of a new sentence to achieve this. If the relationship cannot be deciphered, insert a comment advising the author that they need to provide this information to make the sentence readily understandable.

Formal diction


Authors should come across as refined in writing published in professional publications. It is important to not overstate conclusions or the certainty of suggested explanations. When suggesting a potential mechanism or explanation, it is helpful to use “may” terminology, as well as terms such as putative, possible, proposed, likely, could be, etc. Likewise, when an author is debating a point, the language needs to be respectful and objective.

Use pronouns with care

Pronouns (it, this, that, those, these, etc.) should only be used when the nouns to which they are referring are obvious. If ever the intended noun is dubious, the object should be restated. For manuscripts being submitted to scientific journals and theses/dissertations, the best practice is to always specify a noun after this/that/those/these. For example, rather than saying “this suggests”, say “this finding suggests”.

Spell out contractions

Contractions (don’t, isn’t, can’t, etc.) simply DO NOT BELONG in (most) formal writing.

Do not split infinitives

In formal writing, the rule of keeping the infinitive intact should be heeded:


Questions should be rare (for emphasis) or avoided altogether in academic writing. Look for ways to reword questions as sentences. You can usually state what is unknown or what hypotheses/possibilities/uncertainties will be examined.


Semi-colons should only be used when using commas is too confusing. Whether you are using commas or semi-colons, all items in the list should be similarly conjugated. Although dropping the last comma in a list or series before the word “and” (a.k.a. serial comma or Oxford comma) is common, it can create confusion—especially if the items in the list are phrases that include the word “and” themselves.

Proper nouns

Proper nouns loose the capitalized status when they become adjectives: Parkinson disease -> parkinsonian gait.

Formalize colloquialisms

To maintain the level of formality appropriate for scientific discourse, revise colloquial expressions:

Useful words

If you ever have the sense that a part of speech is missing, but you cannot find the word consider these: item, entity, process, phenomenon, individual, each, eventuality, process, existence of, presence of, organism, unit, component, portion, presence/absence of, excess/dearth of, peak/nadir, etc. It can also help to put in missing there is/are, in which, that is/are, which is/are.

Combining compounds that relax DNA packing with intracellular signaling inhibitors may inhibit the growth of tumor cells by affecting their stem cell features

Medulloblastoma, the most common brain cancer in children, may arise from biological abnormalities in neural stem cells or neuronal precursors during embryonic development. Indeed, the clinical challenges of treatment resistance and tumor recurrence in patients with medulloblastomas appear to be related to the presence of cancer stem cells within medulloblastoma tumors.

Brazilian researchers working in the Cancer and Neurobiology Laboratory at the Federal University of Rio Grande do Sul (Universidade Federal do Rio Grande do Sul, UFRGS), its university hospital (Hospital de Clínicas de Porto Alegre, HCPA), and the Children’s Cancer Institute (Instituto do Câncer Infantil, ICI) in Porto Alegre, in collaboration with Canadian scientists working at the Hospital for Sick Children and the University of Toronto, analyzed gene expression in medulloblastoma tumors from patients. They demonstrated that all medulloblastoma tumor subtypes express two stem cell markers, namely the proto-oncogene protein BMI1 and the cell surface protein CD133. When DNA is in a tightly compacted chromatin state, the expression of genes that promote cell differentiation is reduced, thereby keeping cancer cells in a stem cell-like state. Accordingly, this team of researchers treated medulloblastoma cells with an epigenetic compound that inhibits histone deacetylase (HDAC) activity, leading to chromatin relaxation, and found that they could thereby reduce BMI1 and CD133 expression and hinder tumor cell viability.

Further analysis of tumor samples revealed that expression of these “stemness” markers appeared to be associated with activity of the mitogen-activated protein kinase (MAPK)/ERK intracellular signaling pathway. To test the importance of MAPK/ERK signaling in carcinogenesis, the researchers examined the effects of inhibiting MAPK/ERK in medulloblastoma cells. They found that MAPK/ERK inhibition reduced the cellular content of stemness markers and decreased cancer stem cell formation in culture. Importantly, these antitumor effects were potentiated when the tumor cells were exposed to HDAC inhibitors and MAPK/ERK inhibitors at the same time.

According to the lead author of the article reporting these findings, Dr. Mariane da Cunha Jaeger, “these findings suggest that combining HDAC and MAPK/ERK inhibitors may be a novel and effective approach to preventing medulloblastoma cell proliferation by altering the tumor stem cell phenotype”.

The study findings will be reported in an upcoming issue of the Journal of Molecular Neuroscience. Preprints of the report are available at Professor Rafael Roesler, senior author of the study, underscores that this work demonstrates how “integrating gene expression data from patient tumors with cell culture experiments can enable the identification of novel potential therapy combinations”.

Commenting on the research team’s research outlook in light of these promising findings, the ICI Research Director Dr. André T. Brunetto has said, “We are focusing on finding translational opportunities that can be explored in innovative clinical studies on childhood cancers”.

Media contact: Dr. Mariane da Cunha Jaeger, 5551-33318704, , Federal University of Rio Grande do Sul , Hospital de Clínicas de Porto Alegre, Instituto do Câncer Infantil, Hospital for Sick Children, University of Toronto


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