AI Prompts for Research Scientists

"Outline a systematic literature review framework for the topic CRISPR-Cas9 gene editing for sickle cell disease treatment. Include: the research question using PICO format, suggested database search strategy (PubMed, Scopus, Web of Science) with specific search strings, recommended MeSH terms and Boolean operators, inclusion/exclusion criteria with justification, a PRISMA flow diagram structure, quality assessment tool recommendation (GRADE or Cochrane RoB), and how to organize findings thematically vs. chronologically. Include a timeline estimate for completing each phase."

"Draft a Specific Aims page for an NIH R01 grant application studying the role of gut microbiome composition in treatment response to immune checkpoint inhibitors in melanoma patients. Include: an opening paragraph establishing significance and urgency, a paragraph identifying the knowledge gap, the central hypothesis with preliminary data reference, three specific aims with brief approaches (1-2 sentences each), and a closing impact statement. Follow NIH formatting conventions (Arial 11pt, 1-inch margins) and keep it to exactly one page. Flag common reviewer criticisms to avoid."

"Create a decision guide for selecting the appropriate statistical test based on experimental design. Cover these scenarios: comparing two groups (paired vs unpaired, normal vs non-normal), comparing three or more groups (one-way and two-way ANOVA), correlation between two continuous variables, categorical data analysis (chi-square, Fisher's exact), repeated measures over time (mixed-effects models), and survival analysis (Kaplan-Meier, Cox regression). For each, specify the parametric test, non-parametric alternative, key assumptions to check, sample size considerations, and the appropriate effect size measure. Include a text-based decision tree."

"Draft a detailed methods section for a cell biology paper describing a Western blot experiment to measure protein expression levels of p53 and GAPDH (loading control) in HeLa cells treated with 10 micromolar Doxorubicin for 24 hours versus untreated controls. Include: cell culture conditions (media, supplements, passage number), treatment protocol, protein extraction buffer composition, BCA assay quantification, SDS-PAGE parameters (gel percentage, loading amount), transfer conditions (wet vs semi-dry, membrane type), blocking conditions, primary antibody details (clone, dilution, incubation), secondary antibody, detection method (ECL), and ImageJ densitometry quantification with normalization approach."

"Create a professional template for responding to peer reviewer comments on a journal manuscript revision. Include: the formatting structure (point-by-point with reviewer comments in italics, responses in regular text, changes highlighted in the manuscript), example language for 3 scenarios: (1) agreeing with a reviewer and describing changes made with page/line references, (2) partially agreeing and explaining what was changed vs. what was not and why, (3) respectfully disagreeing with supporting evidence and citations. Include tips for maintaining a constructive tone even with harsh reviews, and a cover letter template for the editor summarizing all major changes."

"Walk through a complete power analysis and sample size calculation for a two-group comparison experiment (treatment vs control) measuring a continuous outcome. Use these parameters: expected effect size (Cohen's d = 0.8), significance level (alpha = 0.05), desired power (0.80). Show: the mathematical basis for the calculation, what each parameter means in practical terms, how to estimate effect size from pilot data or literature, how to adjust for multiple comparisons (Bonferroni), the impact of dropout rates on required enrollment, and complete R code using the pwr package. Include a sensitivity table showing how sample size changes with different effect sizes."

"Create a framework for translating scientific abstracts and paper sections between languages while preserving technical accuracy. Cover: how to handle field-specific terminology that may not have direct translations, maintaining the formal academic register, preserving statistical reporting conventions, handling chemical nomenclature and gene names (which should not be translated), and ensuring citation formats remain correct. Demonstrate by translating this sample abstract into Spanish, then back-translate to English to verify accuracy: 'We report a novel CRISPR-Cas9 delivery system using lipid nanoparticles that achieved 87% editing efficiency in hepatocytes in vivo (n=24, p<0.001 vs. control).'"

"Create a comprehensive reproducibility checklist for a computational biology research project to complete before manuscript submission. Cover: code version control (Git branching strategy, meaningful commits), environment management (conda environment.yml or Docker with specific base images), data management following FAIR principles, random seed documentation for all stochastic processes, dependency pinning with exact versions, README documentation standards (installation, usage, expected outputs), notebook organization (numbered, clear markdown headers), automated testing for analysis pipelines (expected outputs for test data), and recommended repositories for code (GitHub + Zenodo DOI) and data (Dryad, Figshare, GEO). Format as a checkable list."

"Create a systematic framework for selecting the most appropriate journal to submit a research manuscript. Evaluation criteria: scope and audience fit, impact factor and CiteScore, open access options and APC costs, average review timeline (first decision), acceptance rate, indexing in major databases (PubMed, Scopus, WoS), editorial board reputation in the subfield, and preprint policy. Apply this framework to a paper on machine learning applications in drug discovery, suggesting 5 candidate journals ranked by fit with pros and cons for each. Include a decision matrix template researchers can reuse."

"Write a structured abstract (250 words max) for a hypothetical research paper: a randomized controlled trial investigating whether a 12-week Mediterranean diet intervention improved cognitive function in adults aged 60-75 with mild cognitive impairment. 120 participants (60 per group), the intervention group showed significant improvement in Montreal Cognitive Assessment scores (mean improvement 2.3 points, 95% CI 1.4-3.2, p<0.01) compared to controls (0.4 points). Include Background, Methods, Results, and Conclusions sections. Ensure the abstract can stand alone without the full paper and includes the trial registration number placeholder."

"Create a comprehensive guide for making publication-quality scientific figures. Cover: choosing the right chart type (when to use bar plots vs violin plots vs box plots vs heatmaps), color palette selection for colorblind accessibility (viridis, cividis), proper axis labeling and scaling conventions, when to use log scales, how to annotate statistical significance (ns, *, **, ***), multi-panel figure layout with consistent sizing, recommended resolution (300 DPI minimum) and file formats (vector PDF/SVG for line art, TIFF for images), and the 5 most common figure mistakes reviewers flag. Include Python matplotlib/seaborn code for a bar plot with error bars, a violin plot, and a heatmap."

"Draft a professional email to a professor at another university proposing a research collaboration. Context: you are a computational biologist with expertise in single-cell RNA sequencing analysis, and you want to collaborate with a lab that has generated a novel dataset of tumor microenvironment samples but lacks computational expertise. Cover: a brief introduction of your lab's relevant publications (2-3 specific papers), why their dataset is uniquely valuable for your analytical approach, what specific analyses you would contribute (cell type deconvolution, trajectory analysis, ligand-receptor interaction mapping), a proposed collaboration structure (co-first authorship, data sharing agreement terms), timeline, and a request for a 30-minute video call. Keep it under 300 words."