Built with Claude: Life Sciences

What I built. Lazarus is an agent that takes a dead research repository that is open, cited, and no longer runnable, and turns it back into a callable…

Diffuse midline glioma is a paediatric brainstem cancer that is almost uniformly fatal: about ninety percent of children die within two years, and the first…

Hippocampus AI is the memory and reasoning engine for scientific discovery. Every experiment generates valuable knowledge, but that knowledge becomes…

I used Claude to train a protein language model that can generate an extremophilic version of any enzyme, maintaining its function, while allowing it to…

Many primates are sexually dichromatic — males and females are different colors. I wanted to know how that trait is built genetically, and how it evolved…

About Trialign is a patient-facing clinical trial matcher for oncology. A patient pastes a clinical note, uploads a record, or connects their EHR via SMART on…

Hi! I built Provinans, a tool that helps research teams reconcile datasets for longitudinal studies. This week I focused on endometrial pathology in…

Two open-source tools, built with Claude, that catch expensive biology failures early — on public data, as decision-support (never a diagnosis). The…

PYRIN-PLAQUE Digital Twin investigates whether MEFV/pyrin inflammasome biology can be separated from the saturated NLRP3 atherosclerosis story and mapped to…

INTEGRITY is a forensic scanner for life-science manuscripts. It validates every biological entity a paper names - gene symbols, cell lines, antibody RRIDs…

OocyteZero asks a concrete question behind a disease that affects up to 1 in 8 women: can today's DNA-reading AI models name the single causal base at an…

Most people's medical history is a pile of PDF lab reports — one per clinic, each in its own layout, none of them talking to each other. A single value tells…

We investigated whether a genome-scale CD4+ T-cell Perturb-seq screen contains reproducible regulatory architecture beyond ranked hits, statistical noise and…

▎ PaperTrail is a provenance-grade verification platform for clinical-evidence claims. Given a claim like "lecanemab caused brain swelling in 21.3% of…

Co-localization of signaling molecules to a stable cell-cell interface is a key prerequisite for signaling in systems such T cell activation. We had…

Traumatic brain injury and inherited genetic risk both raise the odds of Alzheimer's, but no one had shown they act through the same mechanism. Working only…

Problem. A biologist generates new data and wants to build on the published literature, increasingly with an AI scientist running the analysis. That raises…

Specimen Casebook is auditable data reconciliation for biodiversity collections. Herbarium and museum data managers digitize specimens whose sources disagree…

What it is. A trust-first interpreter for non-coding, regulatory DNA variants — the frontier where variant-of-uncertain-significance (VUS) calls mostly fail…

CellVerdict is a multi-method consensus annotator and trust layer for single-cell RNA-seq data. Cell-type annotation is the linchpin of every single-cell…

We set out to build a machine-learning classifier that predicts a clinically meaningful vaginal-microbiome state from a baseline metagenomic profile, using…

When two well-run papers disagree, it is rarely because one of them is wrong. Usually the reason is a methodological difference buried in the methods…

RegScope- Now available at https://auronideep777.github.io/RegScope/ https://github.com/auronideep777/RegScope The short version: RegScope is a small suite…

Verastar is a morning literature harness built by and for a busy vascular surgeon who can't read the hundreds of papers published in her field each month, yet…

Right now, 57 million people are living with dementia — one more begins to forget every three seconds. The best-evidenced tool for helping them relearn what…

Scientists in different roles ask the same question and need different answers. Ask about KRAS and a medicinal chemist wants crystal structures and warhead…

Spatial perturbation transcriptomics aims to measure how a genetically edited cell affects surrounding tissue. I investigated whether these effects form a…

CuraVar is a "show your work" assistant for classifying genetic variants. Claude reads the evidence and proposes which ACMG/AMP rules apply — each with a…

Strata is a living meta-analysis like tool for the teams who depend on evidence. A meta-analysis can pull scattered trial data into a single defensible…

Clinical datasets that could move research forward sit unused because two questions are hard to answer together: is this use consented, and is the data…

In one week, I turned a biological question into a journal-ready paper and reproducible biomarker. IMMUNA-CD4 is a compact 17-gene measure of immune aging in…

I ran my tool on published, peer-reviewed data from the Wilbrecht lab at Berkeley (DANDI:001340, dopamine in the nucleus accumbens during reward learning). 8…

I built an interactive analysis that separates cell-state composition from cell-intrinsic gene regulation in 1,714 acute-leukemia RNA-seq samples. Using an…

I took one disease from idea to an investable program in a week and then turned that workflow into open AI agents for any disease. It began with eosinophilic…

I built OmniGate, a tool that answers questions about real single-cell perturbation data in plain English, and shows its work. "Analyze" takes a question…

omicau (Omics Audit) is a reproducible, leakage-safe command-line tool, with an optional no-code web interface, that audits a multi-omic dataset before anyone…

I created PKU Commons, a framework for developing and maintaining a phenylalanine estimating app usable for both managing the dietary requirements of PKU as…

We built a directional readout of organelle dynamics. Standard analysis measures how much of an organelle is present - it can't separate a cell building an…

Project: We benchmarked whether Boltz-2 (an AlphaFold-class structure predictor) can substitute for a binding measurement, testing two complementary questions…

Conserved gene co-expression & regulatory networks across vertebrates — abstract One of the holy grails of biology is to understand how 1 genome can make all…

The research question. When a patient's troponin rises, the heart is injured — but why? Is it a Type I MI, a true infarction from an atherothrombotic plaque…

BiotechOS — an operating system for running a drug-discovery pipeline. What we built: A system that reads a drug program's real inbox — CRO emails, quotes…

To understand how Alzheimer’s disease reshapes the brain’s regulatory landscape cell type by cell type, I used Claude Science to analyze Droplet Paired-Tag…

I built Basecase, an AI-assisted genomic research workspace that connects natural-language questions directly to an interactive genome browser. The system…

Every approved atopic dermatitis (AD) drug blocks the type-2 pathway from the outside: injectable antibodies against extracellular cytokines. The frontier is…

Autoimmune drug discovery often fails when a gene that looks important in a cell experiment doesn't hold up in real people. We built a reproducible pipeline…

protocol-to-data turns a clinical trial protocol into a validated, analyzable synthetic SDTM dataset in one Claude-driven agentic loop. Drop in a protocol…

What I built. A deep generative single-cell model of the human immune system that simulates aging and rejuvenation at single-cell resolution, then reasons…

Immune checkpoint blockade (ICB) reactivates T cells to kill tumors and has transformed cancer treatment, but many patients don't respond. Most work on ICB…

In this project, we established an automated pipeline that seamlessly generates explicit-solvent molecular dynamics (MD) ensembles directly from SMILES…

I tested a specific, high-stakes question for disease genetics: can today's best sequence-to-function deep-learning models (AlphaGenome, Borzoi, and the…

Glioma Copilot helps a neuro-oncology clinician and, through them, the patient - decide whether a clinical trial fits this specific glioma patient. It is not…

Most drugs for autoimmune and inflammatory disease work by blocking a cytokine everywhere, all the time. That is effective, but it broadly dampens immunity…

Brakepoint is a genome-scale discovery engine for the next generation of cancer-immunotherapy drug targets. The best checkpoint drugs work by cutting the…

Living Protocol Copilot A grounded, safety-first copilot for wet-lab protocols What I built Living Protocol Copilot is a web application that transforms…

I built Clinical Digital Twin, an open-source R system (Shiny/plotly dashboard, plumber API, SQLite, and a Telegram bot powered by Claude) that gives…

Orphan Finder: reliability-aware target prediction for natural products, drug repurposing, and antimicrobial resistance. Roughly half of all approved drugs…

OPUS-ET-AGENT: agent-conducted cryo-electron tomography Cryo-electron tomography (cryo-ET) is the only technique that resolves macromolecules at…

Mosaic is an MCP server for preclinical target diligence. Our user — a comp-bio at a 10–30 person biotech, or a solo diligence consultant — gets asked "which…

What we investigated. We started from an asset rather than a disease: a genome-scale CD4⁺ T-cell Perturb-seq dataset (a CRISPR knockout screen read out in…

SALUS Zero is a clinical training simulator and bedside decision companion for medicine where nothing is available. Most of the world's children are treated…

NeoVUS is a point-of-care tool for NICU clinicians who hit a variant of uncertain significance (VUS) in a neonatal genomic report. Existing tools either rank…

Journals now require that Methods declare RRIDs for antibodies, authentication for cell lines, and animal-rigor reporting. Methods Verifier is the…

What I built. Verdikt is an AI agent that turns one input — a drug, gene, or aging-related target — into a transparent, confidence-scored decision brief. It…

What if a model could say the one word every drug-discovery pipeline needs but no other tool can utter — "unreachable"? Cell-state-reachability reframes…

Panoscope is a grounded interpretation layer over jazzPanda's spatial-transcriptomics output. A wet-lab biologist opens a cluster and asks in plain language…

Everyone builds bigger models to predict what a gene knockdown does. I asked the prior question: how much is even predictable? Using a genome-scale CRISPRi…

HISTORA is a non-diagnostic, agentic clinical-research navigator built with Claude Code for a clinical/translational researcher. Testing a hypothesis like…

Background & motivation Mesothelioma is an aggressive, asbestos-linked cancer of the pleura with poor prognosis and few effective therapies. It is…

Wayfinder is a hypothesis referee. Literature-based discovery (LBD) overproduces hypotheses and tests almost none — the critique that has dogged the field for…

morphoDE asks a deliberately simple question: where two cell types meet, the boundary bulges outward in some places and caves inward in others—do the cells on…

Early in a routine lab protocol, piranha acid is prepared, used, and its spent waste poured into an acid waste carboy. A step later, someone rinses sodium…

We tested a timely scientific question: Does the brain (neocortex) fundamentally compute predictions (so-called predictive coding)? Specifically, do neurons…

Proteins are spelled in a twenty-letter alphabet, and every one of those letters is an ordinary Roman letter. So English words — HEALTH, ELVIS, VEGAN — fall…

**What we investigated.** ML leaderboards present ranked models with narrow error bars, which reads as evidence of predictive strength. But a February 2026…

Most "AI made a discovery" claims collapse the moment someone asks for a control. I built the opposite: a self-falsifying engine that predicts the missing…

PlaqueQTL builds a cell-type-resolved eQTL resource for atherosclerotic plaque entirely from public single-cell RNA-seq — no new sequencing, no genotyping…

OnLabel is a self-verifying OTC medication-safety assistant for US consumers. Ask a chatbot "Can I take Tylenol and DayQuil together?" and it's often right on…

I built Stanza to chase a frustrating question: when a resistance mutation kills a cancer drug, can you get to a redesigned molecule in minutes instead of…

What I built: I built BioSurface Audit, a deterministic tool that verifies the claims in an AI‑assisted single‑cell / Perturb‑seq analysis. It takes an AI…

What I investigated: I used the EvE Bio "pharmome" — a single-laboratory dataset measuring 1,397 approved drugs against 256 human targets (kinases, GPCRs…

We mapped the causal control architecture of a human immune cell and used it to nominate druggable, disease-relevant targets. From the Marson-lab genome-scale…

Negaverse is a Python toolkit for generating biologically informed negative datasets for protein–protein interaction models. The same approach can later…

This is Throughline, a workbench built for patients and families suffering from a rare or chronic illness. For chronically ill individuals, the vast majority…

SpatialScribe is a self-serve copilot for imaging-based spatial transcriptomics (Xenium, CosMx, MERSCOPE, and whole-transcriptome Atera). A wet-lab scientist…

I used the genome-scale CD4+ T-cell Perturb-seq atlas from Marson/Pritchard labs as an empirical genotype-phenotype map to ask how the architecture of the…

PaedScale — a starting pediatric dose from adult pharmacokinetics, with a cited rationale Most drugs are never trialed in children, so when a kid needs one…

Cadence is an AI copilot for the Learn phase of the synthetic-biology Design–Build–Test–Learn (DBTL) cycle. Four Claude-powered agents run the loop end to…

ClinVal Validator is built for one named user: the clinical-AI researcher who has trained a medical-imaging model and needs to know whether the reported AUC…

The user I built for is a genetic counselor holding a variant of uncertain significance in a regulatory region. Roughly 40% of what a clinical exome returns…

Cell-Type-Resolved Chromatin Effects of AD/PD Variants: DNA Language Model vs. ChromBPNet. We asked whether a general DNA language model can rival the…

ShiftScope compares any two single-cell populations, measures how far apart they are, finds the genes driving the difference, and ranks which genes to test…

TransBench turns a clinician's bedside observation, written in plain words, into a grounded, testable, bench-ready computational experiment. It ships as an…

SecondLook is a trust layer for an AI basal cell carcinoma detector, built for a dermatopathologist, Mohs surgeon, or dermatologist reading skin-pathology…

HLA class I molecules sit at the center of a trade-off: the same allele that helps T cells kill a tumor may also raise autoimmune risk. We built engageability…

Citera is a trust layer for AI-generated clinical regulatory documents. Large language models can write documents that sound compliant, but in clinical…

Globally, over 15 million people are living with spinal cord injury. We built a cross-species contrast to surface CNS-regeneration targets the field has…

Aging research is rate-limited by long iteration loops; it may take years or decades to know if an intervention has any effect. However, recent research…

What I built. Perturb-seq Copilot — a no-code web app that takes a wet-lab immunologist from a processed single-cell CRISPR Perturb-seq count matrix to a…

Target selection is one of the earliest and most expensive decisions in drug discovery. TraceTarget is a drug target prioritization tool that scores gene…

Most immunogenomic models predict T-cell receptor–peptide binding. KSHAMA inverts this: given a primary human CD4⁺ T cell and a candidate genetic perturbation…

DeepPro-v2 is a multi-view, multi-backbone deep learning model for prokaryotic promoter prediction across 23 species. It aggregates five complementary genomic…

regulatr — cell-type-aware non-coding variant prioritization What we built. regulatr is a web tool that answers a question standard variant annotation can't…

I built the Claude Human Phenotype Project (HPP) Research Harness, a paper-calibrated, local-first research environment for private biomedical cohorts…

I set out to test whether the IL-23/IL-17 therapeutic paradox — the same pathway helping in one organ and harming in another — has a measurable…

PORTRAIT turns population health data into a per-patient passport - calibrated position, honest uncertainty, and what genuinely stands out - and refuses when…

EvolvingScholar is an AI "research trainee" that learns the way a real medical trainee does — mentor-guided and improving across a *sequence* of gene–disease…

Vellum is a glass-box agentic ICD-10 coder. Five Claude Opus roles read a hospital discharge summary, resolve each finding to a current code through live…

Basepair watches for one specific kind of preventable mistake. A patient's genetics can make a drug useless or dangerous. Clopidogrel does nothing for a…

Disease predisposition arises from complex, multivariate gene regulation, yet conventional approaches typically nominate a single target gene and fail to…

Octopus is a wet lab operating system. It turns a written protocol into a live, voice-guided run and an auditable report, so the experiment record is created…

Why it matters. It is frequently cited that roughly a third to half of all proteins bind a metal, and the metal is frequently what makes an enzyme an enzyme…

Traxome is a deterministic biomedical interpreter: it turns any symptom, gene, variant, or drug into a fully-sourced evidence dossier for patients…

PerturbGate is an open-data, reproducible pipeline that turns a genome-scale primary human CD4 T-cell Perturb-seq screen into evidence-gated mechanism…

We built An Agentic Interface Over Existing Wet Lab Equipment Most lab equipment today is very difficult for researchers to use. Every piece of…

What we built: A genome-scale CRISPRi Perturb-seq screen in primary human CD4⁺ T cells turned into a working target-discovery system — not just an analysis. A…

Evolution Arena is an interactive 3D WebGL survival game that turns evolutionary biology into something you can experience rather than simply read about. You…

Synthetic lethality is one of the cleanest routes to targeted cancer therapy, yet it remains understudied, and most cancer-screening data sits siloed behind…

MMC - the Mechanistic Model Compiler AI models that predict what happens when you switch off a gene have a problem: the good ones are black boxes, and they…

I built a well curated dataset and then used it to answer 8 key scientific questions. They were mainly around devising interaction footprints and…

I created a workbench where you can name a protein and specify an objective in simple terms, and the agent will then manage the entire campaign. After…

I carried out a research study, written up as a manuscript, on one of the hackathon's suggested datasets: a genome-scale atlas of what happens inside human…

SeqIntel turns a patent name into a validated sequence dossier, in minutes instead of hours. Biotech IP researchers face a slow, manual wall. A single AAV…

KatalistSeek — a grounded reasoning layer over fragmented enzyme/reaction databases. Curated knowledge databases about a biochemical pathway or enzyme are…

I asked whether tissue-specific AAV regulatory elements could be identified systematically from public single-cell chromatin data, and whether their…

Repertoire2Structure (R2S) is a multi agent pipeline, orchestrated by Claude, that turns a raw 10x single cell TCR repertoire into QC'd predicted TCR to…

SurvivalLadder is an open-source screening tool — ten Galaxy tools, a Snakemake pipeline, and a Shiny app, all calling one identical R analysis core — that…

Recent progress in mass spectrometers and softare drive protein identification from a single HeLa cell to more than 6000. However, how many false positives…

Molaro is a next-generation molecular dynamics environment built as a VS Code extension. Instead of shipping with a fixed set of visualizations and analyses…

Human accelerated regions (HARs) are widely interpreted as developmental enhancers, and human-specific substitutions are known to alter their enhancer…

We are two medical oncologists in London who code. We spend our clinics telling people with cancer that we have run out of options. This hackathon was a…

What I built: Ratify convenes diverse AI "labs" (each a small crew of persona-driven agents (a PI, members, and a critic)) running on different Claude…

I built a benchmark and a prompt-level "closed-world grounding" layer that measurably reduces hallucination when an LLM writes investigation summaries for…

We asked a simple question of a genome-scale CRISPRi Perturb-seq screen of primary human CD4+ T cells (Marson & Pritchard labs): which single-gene knockdown…

Determining whether a cancer patient responds to immunotherapy, detecting contamination in food and water, measuring mitochondrial membrane potential…

One-sentence summary: I rebuilt the SARS-CoV-2 host interactome from the Krogan lab's raw AP-MS data using a novel updatable confidence score that lets…

WHAT WE BUILT • OCTB (Optical Compatibility Test Bench) — try a camera/lens/light swap in software before buying hardware, and prove the instrument still…

Enormous AI spend goes into building biomedical knowledge graphs — and almost all of it is private or paywalled, rebuilt from scratch behind every company's…

I built BALL-RL: Bayesian Anchored Latent Learning for Reinforcement Learning, a framework for learning personalized treatment policies when the clinically…

What I built. TrialBridge is a two-sided clinical-trial feasibility layer for Brazil, built entirely with Claude Code — by a founder who has never written a…

Aitiome grades whether an environmental chemical has mechanistically-supported links to Parkinson's or Alzheimer's. Give it a chemical and it reconstructs the…

Cardiac models are routinely fit to an ECG and their conduction parameters reported, but a prior question is rarely asked: which of those parameters can an…

I built HAR-annotator, a glass-box pipeline for ranking Human Accelerated Regions — short stretches of DNA that stayed frozen across mammals for a hundred…

What I built Clinical trials fail for predictable reasons. The problem is that teams usually discover those reasons after months of work and millions of…

vcf2report turns a raw exome VCF + the patient's phenotype (HPO terms) into an auditable, clinical-grade ACMG variant report — locally, offline, in…

What I built. Clinical AI Eval Designer turns a clinical AI's intended use — the model, the patient population, the care setting, and the claim it makes…

Heart failure switches off OPLAH—a protective enzyme that clears a toxic metabolite—and no one had mapped where its known activator binds because OPLAH has no…

Myomatlas is an open, image-based decision-support tool for abnormal uterine bleeding, one of the most common and most under-addressed problems in women's…

Perturbation screens often rank genes by effect size, so a gene that changes many transcripts can be mistaken for one that actually controls cell state. We…

Most new drugs fail, and the most expensive mistake is made years before a trial begins: choosing the wrong target (the specific protein a drug is designed to…

Thirteen real BCG trials. Pooled risk ratio 0.49. AskBench refuses to call it one number. I² is 92.1%. No model in the loop. One command reproduces it. That…

ChannelScope builds standardized, provenance-tracked context-graph objects for multi-omic biology — the structured groundwork that purpose-specific "omic"…

I have found a principled way to recover known and find new drug targets using the t-cell perturbation data for any disease whilst highlighting the…

The same search that produces adversarial examples—driving a model’s prediction up by making small changes to its input—can be turned into a tool for…

AstroOmix is a Claude-powered research application for analysing space-biology data without overstating what limited datasets can support. Researchers can…

VPS - Variant Priority Score Current genetic-testing tools (ClinVar, InterVar, Franklin) can only classify variants that already exist in reference databases…

Exercise interventions offer profound systemic benefits, yet patient adherence remains a major clinical hurdle. Recent reports identify Lac-Phe…

Claymore is an autonomous experimentation platform that gives scientific laboratories a persistent intelligence layer capable of conducting research on their…

GeneGround is a claim-level grounding layer for AI-generated omics interpretations. I built it to address a core problem in AI-assisted biology: LLMs can…

Everyone building research agents runs into the same quiet question: once you have one, how should you set it up to do its best work? Usually the answer is a…

# Project description ## What we built / investigated We mined a genome-scale CRISPRi Perturb-seq atlas of about 22 million primary human CD4⁺ T cells to…

Drug-resistant infections kill ~1.27 million people a year, and the hard part isn't naming a resistance gene — it's finding the reversible opening resistance…

Atlas: every lab has a taste. AI threatens to homogenise scientific research: every lab asks the same models to run its literature search, summarise papers…

AGEFOLD — A CONVERSATIONAL AI TO DECODE THE BIOLOGY OF AGING WHAT WE BUILT AgeFold turns a massive structural-proteomics dataset into something anyone can…

Single-cell RNA-seq conclusions fail peer review on the statistics while the biology holds up. A standard pipeline treats 51,842 cells from four donors as…

The bottom line: An AI agent that reads why an approved cancer drug failed a tumor — then designs a new antibody–drug conjugate (ADC) engineered to dodge that…

What we built / investigated. We tackled pediatric urology's top-ranked research gap (https://doi.org/10.1016/j.jpurol.2026.106024) — defining clinically…

Germinal-center (GC) selection is almost always modeled along a single axis — antigen affinity. But B cells are also selected on a second axis: tolerance…

Structure-based machine learning has ridden one wave: AlphaFold made static structure cheap and universal, and models like FeatureDock, Boltz-2, and…

Protein conformational rates are hard to compute: the transitions are rare, so brute-force molecular dynamics almost never sees them. Importance sampling…

I built Lab Brain, a tool that turns any biomedical lab project — its code, slides, data, papers, and notes — into a shared knowledge base that both Claude…

This project presents a causal-structure-oriented, interpretable pipeline for modeling influenza (H3N2) antigenic distance from hemagglutination-inhibition…

I built Spacefarer Phenome, a genetics-first computational drug-discovery pipeline for spaceflight physiological stress, anchored on bone mineral density…

I built DN-Isoform Scout, an end-to-end computational proof of concept for discovering an underexplored class of cancer mechanisms: dominant-negative proteins…

Speciate is an automated pipeline that turns a TEM micrograph of gold nanoparticles into the three numbers a nanoparticle lab needs on every batch: mean size…

sc-referee automatically checks single-cell analyses for statistical mistakes that commonly slip through analysis and review. It targets known failure…

Anchor is a retrospective reproducibility agent for bioinformatics. Most scientific code can't be re-run months later because the analysis, its environment…

Which neurons die first in Alzheimer's, and why those? I investigated whether two markers of the selectively vulnerable entorhinal-cortex neurons that seed…

CADENCE makes Parkinson's disease trials smarter and more cost-effective. This AI-driven pipeline pinpoints the common, ancestry-specific risk alleles that…

AI-predicted protein interactomes from AlphaFold-Multimer are now published as catalogues of "high-confidence" complexes and mined for drug targets. But the…

Clinical geneticists interpreting a patient's DNA constantly hit "Variants of Uncertain Significance" (VUS): changes where the evidence isn't enough to call…

Complex revascularization — left main, multivessel, frailty — sits in genuine equipoise. Guidelines mandate a Heart Team, yet 20–24% of recommendations flip…

Clonal Compass is a single-cell immune-repertoire co-pilot for paired scRNA-seq + TCR-seq data. I built it for immunologists and computational biologists who…

We built the first world model of the cell — and, we believe, the first to unify all four of its axes into one shared state. Expression, morphology, spatial…

What I investigated My PhD work showed that inhibiting the p38 kinase in mouse models of breast cancer sensitizes tumors to immune checkpoint therapy, and…

VERITAS is an independent verifier for AI-generated single-cell findings. A copilot says "gene X is up in Alzheimer's." VERITAS re-runs that claim across…

Litmus reads a scientific paper and tells you how much to trust it before you build on it. You give it a DOI, some pasted text, or a PDF, and it breaks the…

Tanvi Sinha is an experimental cardiovascular biologist at UCSF. The computational work behind this project — single-cell genomics and training deep-learning…

I built the QSAR Cosmetics Skill for Claude & Claude Science to accelerate the safety assessment of cosmetic ingredients. The solution combines a curated…

BGCFlow is the standard pipeline for mining biosynthetic gene clusters (BGCs) across bacterial pangenomes, but its output is hard to interpret without expert…

GLP-1 drugs like Ozempic are among the world's most prescribed — and in 2023 regulators opened suicide investigations after adverse-event databases lit up…

What I built: GlycoTwin, an open mechanistic digital twin connecting a bioreactor knob to the antibody's Fc N-glycan — a quality attribute governing potency…

Anveshar is a reproducible research workbench for rare cancers, built to run from inside Claude Science. Rare cancers are individually rare but collectively…

This project analyzed an in-vivo single-cell CRISPR Perturb-seq screen of tumor-infiltrating CD8 T cells (Zhou et al. 2023, GEO GSE216909 — 16 samples, 180…

Cellarium is a tool for asking questions of the whole-cell model of E. coli from Macklin et al. (Science, 2020). That model tracks about 16,000 molecular…

A logic-gated target-discovery pipeline for triple-negative breast cancer (TNBC). I built a pipeline that finds combinations of targets rather than single…

claim-check — a reproducibility auditor for agentic single-cell analysis. When an AI agent analyzes Perturb-seq data, it writes up what it did in prose — but…

### What I built and investigated Regulatory-variant prediction models are commonly evaluated against massively parallel reporter assays, or MPRAs, as though…

We built The Human Branch: a Claude Code agent that drives Claude Science as a headless lab and enforces the scientific method in code, so it cannot fool…

We built dbCAN4-advanced, an end-to-end research and software platform for annotating fungal carbohydrate-active enzymes, or CAZymes. Existing dbCAN methods…

FluxForge is a disease-agnostic, Model Context Protocol (MCP) server that fuses primary literature, regulatory/PPI networks, and genome-scale metabolic…

MutationRx turns an unreliable computational method into a decision an oncology researcher can act on, by pairing physics with judgment. What we built. When…

AgingPrint is a perturbation-informed immune aging clock that decomposes CD4+ T cell aging into three independent biological programs: pro-aging…

PertEMA is a post-hoc, model-agnostic reliability layer for single-cell perturbation-effect predictors. Deep models that predict how a CRISPR perturbation…

Iaso helps clinicians and patients recognize and navigate interventional options for severe cancer pain that persists despite escalating medication. A…

**Agentic Chroma is an MCP server that gives an AI agent the role of a human operator at a Waters chromatography workstation.** From any MCP-capable Claude…

I'm a backend/infrastructure engineer at Uber with no wet-lab background. This week I used Claude Science and Claude Code to run a real analysis on the Zhu &…

Which pair of cell-surface proteins marks prostate cancer cells while sparing every healthy human cell type? Antigen-directed therapies are limited by…

G-perturb re-ranks drug targets from a genome-scale CD4+ T-cell Perturb-seq screen by whether each effect is dependable, not just by how large it is. A large…

Please check the final report on the GitHub repo! 1. What We Investigated and Built: Conventional CAR-T screens fail to replicate the complex, months-long in…

SVBench AI is a Claude verdict layer for structural-variant callers. One reviewer — Claude Opus 4.8 — reads each call's alignment image and genomic context…

I built PerturbScope, a dashboard that helps wet-lab biologists, clinician-scientists, and hybrid researchers turn large CRISPR Perturb-seq screens into…

Tumor mutational burden (TMB) is our best predictor of immune checkpoint blockade (ICB) response, yet it's only modestly accurate (AUC ~0.6) and reads DNA…

AI now designs synthetic enhancers meant to switch a gene on in one cell type and stay silent everywhere else. When one fires in the wrong cell, the…

Enactome is a connectome-constrained simulation platform that loads the BANC Drosophila connectome (composed of 158,262 neurons, 3,990,039 synapses), signs…

Clinibrium is a clinical decision-support co-pilot for the otoneurology clinic, developed with a subspecialist otolaryngologist. It triages a common complaint…

Labs buy pipetting robots and then barely use them, because using one means writing code. So scientists who can't code pipette by hand for hours, and a…

A lab protocol is a document. It describes every step, in order, and it is completely correct — but you have to follow it. You keep your own place, you…

We worked on the Arc Institute Virtual Cell Challenge: given a gene knockdown, predict how the cell’s expression profile changes. Scoring is official Arc…

We carry ~100x more microbial genes than human genes (~3.3M vs ~20,000), and we already know microbes signal to us in chemistry — SCFAs->GPR43, bile…

BioSkeptic is a red team for drug-discovery claims. You give it a target, a disease, and a direction; it checks that hypothesis against ~21 public biomedical…

Flow cytometry underpins immunology and clinical diagnostics, yet its analysis is still bottlenecked by manual gating inside fragmented, subscription-locked…

Louis is an MCP server + Slack bot that turns a genome-scale CD4⁺ T-cell CRISPRi Perturb-seq screen (Marson/Pritchard 2025) into a discovery-and-memory…

What I built / investigated. The project asks whether the rules of collective cell behavior can be recovered from snapshots alone. Cells respond to stimuli…

Most oncogenic drivers — transcription factors, chromatin modifiers, scaffolds, DNA-repair proteins — are "occupancy-undruggable": they have no pocket a…

Labs don't sample variants randomly. They measure hotspots, clinically observed positions, the ones the models argue about, and then compute a predictor's…

Aquiles — auditable, host-directed antiviral target triage for Aedes arboviruses What we built. Dengue, Zika and chikungunya have no approved antiviral…

I rebuilt nature's strongest molecular motor — the phi29 gp16 DNA-packaging ATPase — as a single programmable protein, entirely in silico. The motor is a…

The standard way to detect interacting proteins (a method called DCA) assumes both organisms evolved together on the same family tree. But humans and the…

The Gene Program Interpreter is a Claude Skill for context-aware interpretation of gene programs from Perturb-seq and single-cell data. Every experiment…

APOE genotype is fixed at birth, yet Alzheimer's appears decades later. We asked whether the fixed APOE ε2/ε4 plasma-protein substrate (Lu 2026) interacts…

Data Ingestor turns the hours a data curator spends hand-reformatting every CRO's differently-shaped Excel/CSV into a one-click review. The pain I keep…

Neuroscience MRI research is slowed by silent failures - proprietary MATLAB tooling, out-of-memory crashes, and hundreds of preprocessing steps that never…

Labs are about to have agents doing real work — planning assays, calling compute, triaging data, ordering supplies. But a lab record only counts if it's…

ParkScreen is a multimodal Parkinson's disease screening decision aid that fuses three task-matched user recordings — sustained vowels /i/o/u/ for phonation…

Motif is a molecular-biology workbench that runs inside Claude Science as a plugin. Instead of answering sequence questions with prose, it turns a request…

RegLens turns a noncoding variant into a cited, cell-type-specific mechanistic hypothesis — and tells you when it doesn't know. Annotation tools tell you…

Rhinalx is a local-first scientific decision intelligence system that preserves the reasoning behind research decisions, not just the records…

Litmuz is a claim-level verification layer for life-sciences research agents. An AI agent's memo is fluent and cited, but some claims are unsupported or…

Biology may already contain quantum sensors we have not learned to recognize. Nebula is a discovery physics engine built to search for them. Today’s protein…

I built Mechanome, a physics-first inference engine that recovers mechanical forces in cells from protein structure and microscopy. It predicts forces forward…

Our analysis combines monogenic immune-disease genes, evolutionary constraint, GWAS, and genome-scale CRISPRi perturb-seq in primary human CD4+ T cells…

Sera helps target-discovery biologists decide which screen hits to advance. It reconciles a CRISPRi mRNA screen against a protein screen: for each gene and…

I built OSSICRO, open-source software that assembles the FDA regulatory package a physician needs to get an investigational drug to a single patient through…

Science has always started with people with a question, an idea, and the work to turn it into a finding. Today, tools like Claude for Science help researchers…

We developed a computational method that converts two-channel saturation genome editing (SGE) screens, which measure both cell survival and mRNA abundance…

Adaptive-computation halting was built to save compute, easy inputs exit early and hard ones run longer. I used it the other way, as a measurement. My…

The motivating question AI agents can now execute science at a level that was unthinkable two years ago. So the scarce resource has moved. It is no…

I built plant-bench, an open, reproducible benchmark for plant genomics foundation models. The problem it solves: there are now several strong DNA sequence…

A pLDDT for perturbation biology. Foundation models don't reliably beat linear baselines at predicting perturbation effects (Ahlmann-Eltze, Huber & Anders…

Protein language models (PLMs) can identify pathogenic missense variants, but it is unclear how they internally make the predictions. Inspired by Anthropic’s…

citeval is a citation referee for the life-sciences literature. Given one scientific claim and the paper cited to support it, it decides whether the paper…

I built a cross-dataset integration pipeline to nominate novel, small-molecule-druggable glioblastoma (GBM) targets. Starting from DepMap CRISPR dependencies…

NOTE: Please read the manuscript in github. I also linked a demo you should check out! ##100–200-word summary: I built HumanVector, an auditable system that…

I investigated a failure mode of agentic science: as an agent forks approaches, revises an upstream step, and re-runs, a final result can quietly come to rest…

Chansu is named for Chán sū (蟾酥), the traditional Chinese medicine preparation derived from toad venom, from which bufalin, a bufadienolide (a class of…

A model writes a confident list of disease genes in a second. I checked those lists against a frozen human CD4+ T-cell CRISPRi screen the model can't…

Seqcolyte is an open-source, protocol-aware platform for sequencing quality control and root-cause diagnosis. I built a workflow in which Claude Code agents…

The information of available grant is fragmented and it is time consuming to check the criteria manually. Tarboard help to provide tailored information…

Evidence Engine is a mechanism-aware oncology evidence platform that answers the recurring BD/commercial question — "which indication should we pursue for…

Norn (https://norn-five.vercel.app/) is a variant-interpretation copilot for clinical geneticists. You paste in one genetic variant, an HGVS string, an rsID…

Spot is a tool which simplifies the plumbing that takes us from a perturb-seq dataset like the CD4 perturb-seq published by Zhu et al., and immediately gives…

## Project description — agent-eln ### What I built **agent-eln** is an AI-native lab operating system: a single git repo that unifies an Electronic Lab…

NeuroVas Copilot: An Interrogable 3D Aneurysm Reasoning Tool What we built Unruptured brain aneurysms present a difficult decision: treat now with clipping…

Research Overview Current research gap. Classical gene regulatory networks (GRNs) rest on prior knowledge or on simple co-expression, which leaves the network…

built two open-source tools that solve problems I kept seeing in computational biology. The first is BioBouncer. In bioinformatics, identifiers are…

Sourced is a provenance-first medication safety review tool for clinicians and pharmacists. It ingests a patient's context (clinical note, medications…

Persona is a persistent, always-on synthetic researcher for the biomedical literature. The problem: science publishes millions of papers a year, but the tools…

I built a transparent computational bridge from a genome-scale CD4⁺ T-cell Perturb-seq atlas (Marson–Pritchard CRISPRi, 4 donors, conditions Rest / Stim 8 h /…

Cells don't live by themselves. In a healthy organ or a diseased one, they sit in a sophisticated spatial arrangement and constantly talk to whoever is next…

Target to a designed binder in one week. The full immuno-oncology discovery arc — target ID, a genome-scale counter-screen, a 1.65M-edge network, a whole-body…

Biologists call a protein interaction map a hairball: hundreds of contacts, each one months of bench work, and no way to know which one matters. The field…

Rare-disease researchers can know that a variant is pathogenic yet still not know what to measure next. I investigated how often public functional evidence…

NeoFlex Synthetic Chromosome Designer turns a plain-language objective ("engineer yeast to utilise xylan") into a synthesis-ready synthetic neochromosome for…

I asked which RNA-splicing changes in liver cancer actually affect patient survival — and whether isoform switching correlated with survival rather than gene…

Vidalign is a local, GPU-first web workbench that puts behavior video and the rest of an experiment's data — sensor traces, operant/Med-PC hardware logs…

Sequence-to-expression "oracles" (Enformer, Borzoi, AlphaGenome, Evo2) and the generative-DNA designers built on them all aim to predict how cis-regulatory…

I built GEOscope, a discovery layer for NCBI GEO’s 288,904 public functional-genomics studies. GEO metadata is largely free text, so relevant datasets are…

Bayleaf is an AI-assisted decision gate for genomics quality control. The context needed to trust a run is usually scattered across tools that do not talk to…

**Project description** This repository is the **computational side** of a PhD thesis (Schimmer lab, U of T Medical Biophysics): *Identifying Variable…

NUDGE — an "honesty engine" for AI-driven science. Point it at a differentiable model of a biological system; it tells you which parameters you can…

I built an interactive fibrosis enhancer combining direct perturbation CRISPR screen data (perturbseq) and evolutionary signals

We built a reproducible discovery-to-target pipeline using a genome-scale CRISPRi Perturb-seq atlas of primary human CD4+ T cells (Marson 2025), scoring every…

Biological research is increasingly reliant on complex computational pipelines, often involving multiple steps of QCing, transforming, processing, ingesting…

What I built / investigated A degree-bias assessment for protein–protein interaction (PPI) ranking. The central question: when a PPI method ranks candidate…

We are always looking to find inspirations to regain a more regenerative and youthful states in medicine so we can treat patients with disease and injury by…

Most locally advanced rectal cancers are mismatch-repair proficient and have no molecularly-guided treatment. We asked whether drugs that already exist could…

What we built. We created a Real-World Evidence Methodologist — an AI specialist that acts as a built-in epidemiologist and causal-inference expert, sitting…

Keystone is a Claude-powered discovery engine for life sciences that verifies evidence before it reasons. Across four real disease programs — immunology (CD4+…

Manual labeling is the bottleneck of biosignal ML — every hour of EMG needs a human marking what the muscles were doing. We built a tool that removes the…

Genome-scale screens and GWAS both tell you which genes matter in disease — but not what to do about them. A knockdown that reverses pathology is a drug lead…

I create a dry-wet-agent loop operator system which is the loop Engineering . I think it is

What I built and investigated: A complete biomarker discovery pipeline for post-traumatic epilepsy (PTE) in a longitudinal rodent TBI model, covering…

What I built and investigated. GWAS have catalogued tens of thousands of trait-associated loci, but naming the causal effector gene — usually acting through a…

Lab Memory turns a scattered pile of a lab's files (papers, notebooks, protocols, ClinicalTrials.gov exports, CSVs, notes) into a queryable, cited memory…

I built an integrated, honestly-scored prioritization of gene-regulatory "master regulators" in primary human CD4+ T cells from the Marson/Pritchard 2025…

gpu-sceptre is an independent, from-scratch GPU implementation of SCEPTRE (Barry et al., 2021), the calibrated conditional-resampling test for single-cell…

abdev-suite — Project Description WHAT I BUILT AND INVESTIGATED I built abdev-suite, a pluggable in-silico platform for antibody developability assessment…

1. Project name ||The Tempo of Transformation — Post-Translational Timing Gates How Driver Mutations Spread Through the Colorectal Cancer Network|| Short…