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Question types

Type

Purpose

Example

Descriptive

Document phenomena

"What are the characteristics of X?"

Comparative

Compare groups/conditions

"How does X differ between groups?"

Correlational

Examine relationships

"Is there a relationship between X and Y?"

Causal

Establish causation

"Does X cause Y?"

Exploratory

Generate hypotheses

"What factors might explain X?"

Refining your question

Start broad → Narrow progressively

Draft 1: "How does social media affect politics?"

Draft 2: "How does Twitter use affect political polarization?"

Draft 3: "How does exposure to partisan Twitter accounts affect

political attitude polarization among US adults?"

Draft 4: "Does increased exposure to ideologically homogeneous Twitter

feeds increase affective polarization among politically

engaged US adults aged 18-35?"

### Literature review strategy

Systematic literature search

Database selection by field

• Multidisciplinary: Web of Science, Scopus, Google Scholar

• Social Sciences: JSTOR, ProQuest, SSRN

• Communication: Communication Abstracts, ComAbstracts

• Health: PubMed, MEDLINE, CINAHL

• Education: ERIC

• Business: Business Source Complete

Search strategy template

1. Identify key concepts from research question

1. Generate synonyms for each concept

1. Combine with Boolean operators

Example for: "social media political polarization"

Concept 1: social media

• OR: Twitter, Facebook, Instagram, "social networking sites",

"online platforms", "digital media"

Concept 2: political

• OR: partisan, ideological, electoral, civic

Concept 3: polarization

• OR: division, extremism, "attitude change", radicalization

Combined search:

(Twitter OR Facebook OR "social media" OR "social networking")

AND (political OR partisan OR ideological)

AND (polarization OR division OR extremism)

Inclusion/exclusion criteria

Document your criteria:

• Publication date range: [X to present]

• Languages: [English only / multiple]

• Publication types: [Peer-reviewed only / include preprints]

• Geographic scope: [Global / specific countries]

• Methodologies: [All / specific approaches]

Managing your search

• Save searches to re-run later

• Export results to reference manager

• Track number of results at each stage

• Document date of each search

### Citation management

Zotero/reference manager integration patterns

For automated citation workflows

CITATION_STYLES = {

'apa7': 'American Psychological Association 7th edition',

'mla9': 'Modern Language Association 9th edition',

'chicago': 'Chicago Manual of Style 17th edition',

'harvard': 'Harvard Reference format',

'ieee': 'IEEE',

'vancouver': 'Vancouver (medicine)',

}

BibTeX entry template

BIBTEX_ARTICLE = """

@article{{{citekey},

author = {{{author}}},

title = {{{title}}},

journal = {{{journal}}},

year = {{{year}}},

volume = {{{volume}}},

number = {{{number}}},

pages = {{{pages}}},

doi = {{{doi}}}

}}

"""

Common citation patterns by context

CITATION_CONTEXTS = {

'introducing_concept': "According to Author (Year), ...",

'supporting_claim': "Research has shown that X (Author, Year; Author, Year).",

'contrasting': "While Author (Year) argues X, Author (Year) contends Y.",

'methodology_reference': "Following the method developed by Author (Year), ...",

'direct_quote': 'Author (Year) states that "exact quote" (p. X).',

}

## Paper structure and writing

### IMRaD structure (scientific papers)

Standard research paper sections

Abstract (150-300 words typically)

• Background (1-2 sentences)

• Purpose/objective (1 sentence)

• Methods (2-3 sentences)

• Results (2-3 sentences)

• Conclusions (1-2 sentences)

Introduction

Funnel structure:

1. Broad context - Why does this topic matter?

1. Narrow focus - What's the specific problem?

1. Gap identification - What don't we know?

1. Research question/hypothesis - What will you investigate?

1. Contribution preview - Why does this study matter?

Literature Review

Organize thematically, not chronologically:

1. Theme 1: Key findings, debates, gaps

1. Theme 2: Key findings, debates, gaps

1. Theme 3: Key findings, debates, gaps

1. Synthesis: How themes connect to your study

Methods

The reproducibility test: Could another researcher replicate your study from this section alone?

Include:

• Participants/sample (who, how selected, N)

• Materials/measures (what instruments, their validity)

• Procedure (step-by-step what happened)

• Analysis approach (statistical tests, qualitative methods)

• Ethical considerations (IRB, consent)

Results

Report, don't interpret:

• Present findings systematically

• Use tables/figures for complex data

• Report effect sizes, not just p-values

• Address each research question/hypothesis

Discussion

Reverse funnel structure:

1. Summary of key findings

1. Interpretation in context of literature

1. Theoretical implications

1. Practical implications

1. Limitations

1. Future research directions

1. Conclusion

### Academic writing style

Writing conventions

Voice and tense

Hedging language

Appropriate hedging (avoiding overclaiming):

• "This suggests that..." (not "This proves that...")

• "may be related to" (not "causes")

• "Results indicate..." (not "Results demonstrate conclusively...")

• "One possible explanation..." (not "The explanation...")

Transition words by function

Addition: furthermore, moreover, additionally, in addition

Contrast: however, nevertheless, conversely, in contrast

Cause/effect: therefore, consequently, as a result, thus

Example: for instance, specifically, to illustrate

Sequence: first, subsequently, finally, meanwhile

Summary: in summary, overall, in conclusion

Paragraphs

Each paragraph should:

1. Begin with a topic sentence

1. Contain one main idea

1. Include supporting evidence

1. Connect to adjacent paragraphs

1. Average 100-200 words (varies by field)

### Common writing problems

Issues to avoid

Wordiness

❌ "It is important to note that the results demonstrate..."

✅ "Results demonstrate..."

❌ "In order to investigate..."

✅ "To investigate..."

❌ "A total of 50 participants..."

✅ "Fifty participants..."

Weak verbs

❌ "The study was conducted by the researchers"

✅ "The researchers conducted the study"

❌ "There was a significant difference found"

✅ "We found a significant difference"

Vague language

❌ "Several studies have shown..."

✅ "Three studies (Author, Year; Author, Year; Author, Year) showed..."

❌ "The results were significant"

✅ "The results were statistically significant (p < .05, d = 0.45)"

Unnecessary jargon

• Define technical terms on first use

• Use simpler words when equally precise

• Consider your audience's expertise level

Citation problems

❌ Citing secondary sources without noting

✅ "(Author, Year, as cited in Author, Year)"

❌ String citations without synthesis

✅ Group citations that make the same point; distinguish those that differ

## Peer review and revision

### Responding to reviewers

Response letter template

Dear Editor and Reviewers,

Thank you for the thoughtful feedback on our manuscript titled "[Title]"

(Manuscript ID: [Number]). We have carefully considered all comments and

revised the manuscript accordingly. Below, we provide point-by-point

responses to each comment.

---

Reviewer 1

Comment 1.1

[Quote or paraphrase the reviewer's comment]

Response:

[Your response explaining what you did]

Changes made:

[Quote the specific changes with page/line numbers]

"New text here..." (p. X, lines XX-XX)

Comment 1.2

[Continue for each comment]

---

Reviewer 2

[Same format]

---

We believe these revisions have substantially strengthened the manuscript

and hope you will find it suitable for publication in [Journal Name].

Sincerely,

[Authors]

### Handling criticism

Types of reviewer feedback

Must address

• Methodological concerns

• Missing literature

• Unclear writing

• Logical gaps in argument

• Statistical errors

Negotiate carefully

• Requests for additional analyses

• Suggestions to restructure

• Disagreements on interpretation

Pushback appropriately

• Requests outside scope

• Misunderstandings of your argument

• Contradictory advice from reviewers

Response strategies

Agreement: "We thank the reviewer for this suggestion. We have [action]."

Partial agreement: "We appreciate this point. While [acknowledge validity], we [explain your approach]. However, we have [partial accommodation]."

Respectful disagreement: "We thank the reviewer for raising this issue. We have considered this carefully; however, [explanation]. We hope the reviewer will find this reasoning persuasive."

## Grant proposals

### Proposal structure (NSF/NIH style)

Standard grant components

Specific aims (1 page)

Opening paragraph: What's the problem? Why does it matter?

Gap statement: What's missing from current understanding?

Long-term goal: Your research program vision

Objective: What this specific project will accomplish

Central hypothesis: Your testable prediction

Aims: 2-4 specific, achievable objectives

Impact statement: Why funding this matters

Significance (2-3 pages)

• Importance of the problem

• Gaps in current knowledge

• How your work advances the field

• Potential impact if successful

Innovation (1 page)

• What's new about your approach?

• Conceptual innovation

• Methodological innovation

• Technical innovation

Approach (6-12 pages)

For each aim:

• Rationale

• Preliminary data (if any)

• Research design

• Methods

• Expected outcomes

• Potential problems and alternatives

• Timeline

Broader impacts

• Training opportunities

• Dissemination plans

• Benefits to society

• Diversity and inclusion

### Budget justification

Budget categories

Personnel

• PI salary and effort (% time)

• Co-investigators

• Postdocs (salary + benefits)

• Graduate students (stipend + tuition + benefits)

• Undergraduate researchers

• Technical staff

Equipment

• Items over $5,000 (check sponsor threshold)

• Justify necessity for project

Supplies

• Lab consumables

• Software licenses

• Participant payments

Travel

• Conference presentations

• Data collection sites

• Collaborator visits

Other direct costs

• Publication costs

• Participant incentives

• Transcription services

• Equipment maintenance

Indirect costs (F&#x26;A — facilities and administrative)

• Each institution negotiates an F&#x26;A rate with its cognizant federal agency.

• The rate applies to modified total direct costs (MTDC), not raw total

direct costs — exclude equipment >$5K, tuition, participant support,

subaward portions over $25K, and a few other categories per the

institution's negotiated agreement.

• R1 universities commonly negotiate 55-70% of MTDC; smaller institutions

often run lower. Always confirm the current rate with your sponsored

programs office before budgeting.

## Publishing strategy

### Journal selection

Evaluating journals

Quality indicators

• Impact factor (use cautiously)

• Acceptance rate

• Review time

• Time to publication

• Reputation in your field

• Indexing (Web of Science, Scopus)

Fit indicators

• Scope alignment

• Audience match

• Article type (empirical, theoretical, review)

• Open access route (see below)

Open access routes

• Gold OA — published OA in a fully OA journal; usually requires an

Article Processing Charge (APC), often $1,000-$3,000+.

• Green OA — closed-access journal but author self-archives an

accepted manuscript in a repository (institutional, arXiv, etc.) under

the publisher's allowed embargo.

• Diamond / Platinum OA — fully OA journal with no APC; supported

by a sponsor (society, university, consortium). Increasingly common

in social sciences and humanities.

• Hybrid — a closed-access journal that lets individual articles

go OA for an APC. Note: hybrid is excluded from Plan S compliance

and from many funder OA mandates — verify before paying an APC.

• Bronze — free to read but no formal OA license; the publisher

can revoke access. Treat as not-actually-OA for compliance purposes.

Funder mandates (US + Europe, as of 2026)

• OSTP Nelson Memo (US) — federally-funded research must be made

immediately publicly accessible upon publication, with no embargo.

Implementation deadline was end of 2025, so as of 2026 this is

in effect for all major US federal funders (NIH, NSF, DOE, NASA, etc.).

• Plan S (cOAlition S) — European funders (Wellcome, UKRI, ANR,

many others) require immediate Gold or Diamond OA, or Green OA

with no embargo and a CC-BY license. Hybrid is not compliant.

• Verify the funder's most recent policy before submission — accepted

routes shift, and some funders cap APCs.

Red flags (predatory journals)

• Aggressive email solicitation

• Rapid "peer review" (days)

• Unclear editorial board

• Not indexed in major databases

• "Pay to publish" with no clear OA model

• Poor website quality

Resources for vetting journals + ethics

• Think. Check. Submit. (thinkchecksubmit.org) — checklist for legitimacy.

• DOAJ (Directory of Open Access Journals) — vetted OA-journal index.

• Journal Citation Reports — paid Web of Science product for impact factor.

• Cabells Predatory Reports — subscription-based replacement for the

original Beall's List, which was taken down in 2017 (only stale mirrors

remain — don't rely on them as a current source of truth).

• Retraction Watch Database — searchable record of retractions and

publisher misconduct; useful for vetting authors and journals.

• COPE (Committee on Publication Ethics, publicationethics.org) —

authoritative guidelines for editors and authors on ethics and integrity.

• ICMJE (International Committee of Medical Journal Editors,

icmje.org/recommendations) — defines authorship criteria, conflict-of-

interest disclosure, and reporting standards used across many fields.

### Cover letter template

Dear Dr. [Editor's name],

We are pleased to submit our manuscript titled "[Full title]" for

consideration as a [article type] in [Journal Name].

Summary (2-3 sentences):

[What you did and what you found]

Significance (2-3 sentences):

[Why this matters for the journal's readership]

Fit statement:

[Why this journal specifically]

Declarations:

• This manuscript is original and not under consideration elsewhere

• All authors have approved the submission

• [Conflict of interest statement]

• [Funding acknowledgment]

Suggested reviewers (if requested):

1. [Name, affiliation, email] - Expert in [relevant area]

1. [Name, affiliation, email] - Expert in [relevant area]

1. [Name, affiliation, email] - Expert in [relevant area]

Reviewers to exclude (if any):

[Name] - [Brief, professional reason]

We look forward to your response.

Sincerely,

[Corresponding author name]

[Title, affiliation]

[Contact information]

## Preprints and persistent identifiers

### Preprint servers (post a working version, get cited earlier)

Preprints are author-submitted manuscripts posted before formal peer
review. Most journals now permit (or actively encourage) preprinting;
verify the target journal's policy before posting if you're unsure.

Server
Field
Notes

**arXiv** (arxiv.org)
Physics, math, CS, quantitative bio, econ, stats
Oldest, largest; moderation by section.

**SSRN** (ssrn.com)
Social sciences, law, econ, finance
Owned by Elsevier since 2016 — some authors prefer SocArXiv as an alternative.

**bioRxiv** (biorxiv.org)
Biology
Cold Spring Harbor Laboratory; widely cited.

**medRxiv** (medrxiv.org)
Health sciences, medicine
Light moderation for safety claims; do not preprint clinical-trial results without preregistration.

**EarthArXiv**
Earth, planetary, environmental sciences
Community-run via the OSF infrastructure.

**PsyArXiv**
Psychology + behavioral sciences
OSF-hosted.

**SocArXiv**
Sociology + social sciences
OSF-hosted; Elsevier-independent alternative to SSRN.

**EngrXiv**
Engineering
OSF-hosted.

**Why preprint:** Faster timestamp on priority claims, citable months
before journal acceptance, and broader feedback before final review.
(The 2026 OSTP Nelson Memo governs immediate public access to the
peer-reviewed version of federally-funded US research at publication
— it is not a preprint mandate. Preprinting is a separate, voluntary
choice that complements but doesn't satisfy Nelson Memo compliance.)

### Persistent identifiers — get an ORCID and use DOIs

- **ORCID iD** (orcid.org) — Free 16-digit identifier that
unambiguously links you across publishers, funders, and institutions.
Required by most major journals and funders. Connect it to your
CV, manuscripts, datasets, software, and grant applications.

- **DOI** (doi.org) — Persistent identifier for scholarly objects.
Assigned automatically by journals at acceptance; you can also mint
DOIs for your own datasets, code, posters, and preprints via Zenodo
(zenodo.org) or your institutional repository — useful for citing
non-journal outputs.

- **ROR** (ror.org) — Persistent identifier for research organizations,
used by funders and publishers to disambiguate institutional names.

## Research ethics

### Ethical considerations checklist

Before starting research

Human subjects

• [ ] IRB/ethics board approval obtained

• [ ] Informed consent procedures established

• [ ] Vulnerable populations identified and protected

• [ ] Privacy and confidentiality measures in place

• [ ] Data security plan established

• [ ] Risk/benefit ratio acceptable

Data management

• [ ] Data management plan created

• [ ] Secure storage arranged

• [ ] Sharing/archiving plans documented

• [ ] Retention period determined

• [ ] Destruction procedures established

Authorship

• [ ] Contribution criteria discussed (use ICMJE definition: substantial

contribution + drafting/revising + final approval + accountability)

• [ ] Author order agreed upon

• [ ] All contributors will meet authorship criteria

• [ ] Acknowledgments planned for non-author contributors

• [ ] CRediT taxonomy (credit.niso.org) roles assigned for each

author — most major journals now require or recommend CRediT,

which has 14 standardized contributor roles (Conceptualization,

Methodology, Software, Validation, Formal analysis, Investigation,

Resources, Data curation, Writing — original draft, Writing —

review &#x26; editing, Visualization, Supervision, Project administration,

Funding acquisition).

Conflicts of interest

• [ ] Financial conflicts identified

• [ ] Non-financial conflicts identified

• [ ] Disclosure plan established

Reproducibility

• [ ] Analysis plan pre-registered on OSF (osf.io) or AsPredicted

(aspredicted.org) before data collection — distinguishes

confirmatory from exploratory analyses and protects against

HARKing. Check whether the target journal accepts **Registered

Reports* (peer review of the design before* data collection,

with in-principle acceptance regardless of results) — this format

now exists at 350+ journals across psychology, biomedical, and

social sciences as of 2026.

• [ ] Code will be shared (consider a GitHub release + Zenodo DOI for

versioned, citable code archives)

• [ ] Data will be shared (FAIR principles; institutional repository,

Dryad, Figshare, or domain-specific repository as appropriate)

• [ ] Materials will be shared

### Avoiding research misconduct

Types of misconduct

Fabrication

• Making up data or results

• Never acceptable under any circumstances

Falsification

• Manipulating data, equipment, or processes

• Selectively omitting data to change conclusions

• Image manipulation beyond acceptable adjustment

Plagiarism

• Using others' words without attribution

• Self-plagiarism (reusing own published work without acknowledgment)

• Paraphrasing too closely

Other questionable practices

• P-hacking (running multiple analyses until significant)

• HARKing (hypothesizing after results known)

• Salami slicing (fragmenting one study into many papers)

• Gift/ghost authorship

• Selective reporting of results

## AI / LLM use in academic writing

LLM-assisted writing is the defining 2024-2026 ethics issue across
academic publishing. Every major journal, funder, and ethics body has
issued policy in this window — and policies are still tightening.
Treat anything below as the floor, not the ceiling: read your target
journal's current submission guidelines AND your funder's most recent
policy before submitting.

### What's universally prohibited (as of 2026)

- **LLM authorship.** ICMJE, COPE, Nature, Science, NEJM, Cell, JAMA,
Lancet, and the major university presses all explicitly prohibit
listing an LLM (ChatGPT, Claude, Gemini, etc.) as a co-author. LLMs
cannot meet the accountability and approval criteria authorship
requires. Use the acknowledgments section or a methods/disclosure
statement instead — never the author byline.

- **Generating fabricated citations.** LLMs are well-documented to
produce plausible-looking but fabricated DOIs, page numbers, and
even author/title combinations that don't exist. Every citation in
a manuscript must be verified against the source — the LLM-induced
fake-citation rate has been a top retraction trigger since 2023.

- **Generating data, results, or images.** Synthesizing experimental
data, fabricating figures, or using generative AI to "fill in"
results that weren't actually obtained is research misconduct under
COPE's definition.

- **Undisclosed substantial use.** Most journals require disclosure
of any LLM use beyond trivial spell-check/grammar assistance. Failing
to disclose meaningful use can be grounds for retraction.

### What's typically permitted (with disclosure)

- Idea brainstorming and outlining

- Language polishing and grammar correction

- Translation of your own writing

- Code generation for analyses (with explicit testing)

- Summarization of your own notes or transcripts

- Generating boilerplate sections (cover letters, IRB language)
that you then fact-check and own

### Disclosure language (template)

Most journals want a methods/acknowledgments statement that names the
tool, version (if available), and what it was used for. Example:

During the preparation of this work the author(s) used [tool name,
e.g., ChatGPT-5, Claude Opus 4.7, Gemini 3 Pro] in order to
[specific use, e.g., language polishing of the introduction; drafting
code for the cluster analysis in section 3.2]. After using this tool,
the author(s) reviewed and edited the content as needed and take(s)
full responsibility for the content of the publication.

Adjust to match the target journal's exact required wording — Elsevier,
Springer Nature, Wiley, Taylor & Francis, IEEE, and ACM each publish
their own preferred language.

### Disclosure checklist before submission

-  Read the target journal's AI/LLM policy in the current submission
guidelines (policies updated multiple times per year).

-  Read your funder's policy — some (Wellcome, NSF) have stricter
rules than the journal.

-  Add a disclosure statement using the journal's preferred language.

-  Verify every citation manually — do not trust LLM output for any
DOI, author list, page range, or quoted passage.

-  Verify every numerical claim, date, and named fact.

-  Re-read the full manuscript to ensure your voice and argument
structure dominate, not the LLM's.

-  If the LLM was used for code or analysis, re-run with seeds and
verify all reported numbers reproduce.

### Detection tools (limited reliability)

GPTZero, Turnitin AI Detection, Originality.ai, and similar tools have
documented high false-positive rates against non-native-English writers
and against legitimately human-written technical text — and high false-
negative rates against current models with light editing. **Pangram
Labs** (pangram.com) has published more rigorous benchmarks and tends
to outperform the older detectors at roughly equivalent settings, but
is still not a definitive arbiter and shares the same fundamental
limits when authors edit LLM output substantially. Detection output
should never be the sole basis for a misconduct finding; journals that
rely on it as a gatekeeping signal are increasingly walking that back.
Treat detector results as a flag for follow-up discussion with the
author, not as evidence on their own.

## Productivity and workflow

### Writing routine

Sustainable academic writing

Daily writing practice

• Write at same time daily (habit formation)

• Start with minimum viable goal (e.g., 30 minutes)

• Track progress (word counts, time)

• Protect writing time from meetings/email

Managing large projects

1. Break into smallest possible tasks

1. Set deadlines for each component

1. Schedule regular writing blocks

1. Build in buffer time

1. Get feedback early and often

Overcoming blocks

• Start with easiest section

• Write a "shitty first draft" (Anne Lamott)

• Use placeholders for citations/data

• Talk through ideas with colleague

• Change environment

• Return to outline/structure