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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / LHC-MR), colocalization, fine-mapping with SuSiE / FOCUS, mediation, TWAS triangulation, cis-pQTL drug-target MR, effector-gene prioritization (L2G / PoPS / cS2G), and GenomicSEM common-factor GWAS. Use when triangulating causal inference across multiple complementary methods, prioritizing tissues via stratified LDSC, nominating or de-risking drug targets, mapping a lead SNP to a candidate effector gene, modeling shared genetic architecture across correlated traits, or producing a STROBE-MR-compliant publication-grade evidence battery from GWAS summary statistics.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF-to-FDR calibration (BF >6 ≈ FDR 0.05 from Hart 2017). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

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Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables, figure captions, callout boxes, and page headers/footers.

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Bulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE figures.

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Workflow for spatial transcriptomics preprocessing, domain detection, deconvolution, neighborhood analysis, and publication-ready maps.

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SEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and publication-quality PDF report generation via Typst templates. Triggers on "SEC", "size exclusion", "chromatography", "oligomer analysis", "protein assembly", "SEC report".

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Workflow for packaging analysis outputs into reproducible reports, clean tables, and publication-ready figure exports.

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Streams change data capture from PostgreSQL into Redpanda or Kafka using Redpanda Connect's postgres_cdc input, which reads the WAL through logical replication (pgoutput). Use when configuring postgres_cdc (formerly pg_stream), setting up wal_level=logical, replication slots, and publications, enabling an initial snapshot before streaming, or troubleshooting slot growth and WAL accumulation. Also covers Redpanda Enterprise destination features such as Iceberg Topics, Tiered Storage, and server-side Schema ID Validation, since postgres_cdc itself requires a Redpanda Enterprise license.

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Find and synthesize research papers, whitepapers, PDFs, technical reports, and academic sources with Firecrawl Research, using semantic paper search, related-paper expansion, and in-body verification over Firecrawl's paper index — largely biomedical and life-science literature from PubMed, bioRxiv, and medRxiv, plus arXiv preprints in CS, physics, and math. Use when the user wants a literature review, systematic review, survey of studies, paper summary, research landscape, or sourced synthesis from scholarly and industry publications, including clinical, drug, gene, disease, epidemiology, and public-health topics. Prefer this over a general web-research workflow whenever the evidence base is published papers rather than web pages.

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Keeps private and unapproved material out of a public build. Scans the built output (HTML, serialized component payloads, client JS and CSS chunks, static data routes, public files) against a private tier that always applies and a draft tier that applies in production. Gates work-in-progress so it shows in preview and is absent from production, and keeps sign-off in a ledger only the human writes. Use when a site or app publishes content that agents drafted or that came from private sources.

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MEMO-ONLY prior-work overlap advisory: surfaces the two ADVISORY taxonomy signals neither a tool nor a model can decide from the paper alone — ADV-TRIVIAL-COMBINATION (standard A+B+C / 缝合 stapling) and ADV-DUPLICATE-PUBLICATION (repackaged / duplicate submission). The executor RETRIEVES candidate prior work (DBLP fuzzy-title + boolean · WebSearch · WebFetch) from the paper's own title + contribution spans in the evidence ledger; TWO fresh cross-model codex reviewers (one per axis) LAY OUT the overlap side-by-side against each anchored contribution claim. It NEVER rules 'trivial' or 'duplicate' (that is a human judgment) and absence of a match is NOT evidence of originality. Emits novelty-duplication-advisory.memo.md + an info-only findings mirror; carries NO verdict weight — tools/adjudicate_findings.py lists it in ZERO_WEIGHT_SKILLS and caps it at info. Detect-only. Adapted from ARIS novelty-check, reframed from 'is MY idea novel' to 'here is the overlap a reviewer should weigh'. Triggers: "novelty advisory", "duplication check", "prior-work overlap", "is this stapling", "缝合", "查重", "重复发表", "duplicate submission".

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Analyzes an AI/ML publication — paper, preprint, article, technical blog post — and extracts what an enterprise AI engineer should do about it. Use when someone supplies a URL or document on RAG, embeddings, fine-tuning, prompt engineering, agents, or LLM deployment and asks "review this paper", "what do you make of this", "is this worth adopting", or "summarise the method and its limits". The subject matter must itself be machine learning.

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Select the right Python charting library (seaborn, matplotlib, graphviz) and produce publication-quality static visualizations. Use when creating charts, plots, graphs, diagrams, heatmaps, visualizations from data, or when choosing between matplotlib/seaborn/graphviz. Also triggers for network diagrams, flowcharts, dependency trees, state machines, and entity-relationship diagrams. For interactive browser-rendered charts or uploaded data exploration, defer to charting-vega-lite instead.

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Build and audit deterministic verification gates — a check that blocks a pipeline and can be shown to go red. Use when writing a calibration gate, CI check, validation script or pre-publication check for a numeric or empirical result; when a plausible-but-wrong value would survive review; when asking whether an existing test, linter rule or check could actually fail; and when a suite passes first try, passes suspiciously often, or was written by whatever produced the thing it checks. Triggers on "can this check fail", "known-bad", "negative control", "calibration gate", "sanity check my results", "is this test actually testing anything".

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Prepare a declared release target, or preview it with --dry-run. Derive its version and require authorization before publication.

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Prepare a declared release target, or preview it with --dry-run. Derive its version and require authorization before publication.

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Format CVs for academic positions with publications, grants, and teaching

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