New arrivals

effiedes /

EffieDes

Protein sequence design

★ 4 · Updated 3mo ago · Licence unknown

xuan13hao /

scPyviewer

scPyviewer: a Python-native interactive viewer from AnnData single-cell data

★ — · Updated unknown · Licence unknown

bioinfoliu /

DiDyNet

DiDyNet: a robust framework for differential dynamic network inference from longitudinal multi-omics data.

★ — · Updated unknown · Licence unknown

kangk1204 /

MLHeatmap

MLHeatmap: an interactive application for transcriptomic marker-panel discovery.

★ — · Updated unknown · Licence unknown

chiu-lab /

DEGEmbedR

An embedding-based framework enables statistical testing of gene-set function hypotheses inferred by large language models.

★ — · Updated unknown · Licence unknown

xuanruihuang /

CRISPR Escape Dilution

No description

★ — · Updated unknown · Licence unknown

wenlu-lab /

RADAgent

RADAgent: Automating RADseq Pipelines with Private Open-Source LLMs

★ — · Updated unknown · Licence unknown

ames943 /

batch-detector

Cohort Effects, Not Treatment Response, Dominate Public Immunotherapy Cohorts: Evidence from Microbiome and Tumor Genomic Data

★ — · Updated unknown · Licence unknown

gefengya /

MCKcat

Predicting Enzyme Turnover Numbers and Enabling Rational Enzyme Evolution.

★ — · Updated unknown · Licence unknown

weixin7112 /

DFN-kcr

DFN-kcr: a dual-branch deep learning model with attention-guided fusion for predicting lysine crotonylation sites in human non-histone proteins.

★ — · Updated unknown · Licence unknown

SibelKervanci /

kp-meropenem-tabtransformer

A leakage-aware genomic prediction pipeline for meropenem resistance in Klebsiella pneumoniae using transformer-based resistome representation learning.

★ — · Updated unknown · Licence unknown

Cathylixi /

NESS

Uncovering smooth structures in single-cell data with neighbor embeddings guided by predictability-computability-stability.

★ — · Updated unknown · Licence unknown

Valdes-Tresanco-MS /

gmx_MMPBSA

Free energy calculation for GROMACS

★ 327 · Updated 5d ago · GPL-3

ratschlab /

Virtual-ST Uncertainty

No description

★ — · Updated unknown · Licence unknown

kjenike /

panagram

Panagram reveals pangenome architectures underlying trait variation in plants and animals

★ — · Updated unknown · Licence unknown

kiharalab /

NuFold

NuFold RNA Structure Database: Large-Scale RNA Tertiary Structure Prediction with Confidence Metrics

★ — · Updated unknown · Licence unknown

4D-Lab /

frame

Fragment-Level Graph Encoding for Interpretable Molecular Property Prediction

★ — · Updated unknown · Licence unknown

Digital-Metabolic-Twin-Centre /

gpuGEM

gpuGEM: GPU-based linear optimisation of genome-scale metabolic models

★ — · Updated unknown · Licence unknown

lovetaro /

selectbench

On the Selectivity of Generative Models in Structure-Based Drug Design

★ — · Updated unknown · Licence unknown

kasawa1234 /

ProtGlycanDock

ProtGlycanDock: Towards Accurate Protein-Glycan Docking with Tailored Dataset, Benchmark and Model

★ — · Updated unknown · Licence unknown

daydayup-xq /

CellNet

No description

★ — · Updated unknown · Licence unknown

YuX-Ren /

STAMP-V1

No description

★ — · Updated unknown · Licence unknown

BlueWhaleLab /

PerturbEnergy

No description

★ — · Updated unknown · Licence unknown

bioinfodlsu /

DUMMEST

DUMMEST: A simpler and faster model for frameshift-aware alignment of a DNA sequence to a protein family

★ — · Updated unknown · Licence unknown

UgoLomoio /

scHFBiMamba

scHFBiMamba: a bidirectional Mamba autoencoder for cardiac disease-state classification from single-nucleus RNA-seq data

★ — · Updated unknown · Licence unknown

mianqiu00 /

DC-Flow

DC-Flow: Target-Conditioned Cyclic Peptide Design via Delayed-Coupling Flow Matching

★ — · Updated unknown · Licence unknown

octree-nn /

OctMole

OctMole: Multiscale 3D Molecular Generation with Hierarchical Spatial Flows

★ — · Updated unknown · Licence unknown

dauparas /

LigandMPNN

Computational design of protein conformational landscapes for metamorphic behavior

★ 647 · Updated 1y ago · MIT

DUAL-Xiao /

MolP2SBench

MolP2SBench: Do LLMs Really Reason from Molecular Properties to Structure?

★ — · Updated unknown · Licence unknown

bilemond /

ChemDiffAgent

Masked Diffusion Language Agents for Tool-Integrated Chemical Reasoning

★ — · Updated unknown · Licence unknown

Jia040223 /

MAST

MAST: Motif-Augmented Diffusion with Search Tree for Spectroscopic Molecular Structure Elucidation

★ — · Updated unknown · Licence unknown

PanosAntoniadis /

RAGenome

RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts

★ — · Updated unknown · Licence unknown

AndolfoG /

HRPv2

HRPv2: an automated and enhanced method for full-length homology-based R-gene prediction

★ — · Updated unknown · Licence unknown

khelverskovp /

Atom-JEPA

Atom-JEPA: Joint-Embedding Predictive Architecture for 3D Atomistic Systems

★ — · Updated unknown · Licence unknown

lokali /

CausalBind

CausalBind: Causal Modeling and Learning for Protein-Molecule Virtual Screening

★ — · Updated unknown · Licence unknown

0217ljh /

ColdDDI

ColdDDI: Evaluating Knowledge Utilization in Cold-Start Drug-Drug Interaction Prediction

★ — · Updated unknown · Licence unknown

rotskoff-group /

idiom

Disordered protein region language model

★ 26 · Updated 3w ago · MIT · Curieus

Lyu6PosHao /

RipplePLM

RipplePLM: Structural and Property Decoupling for Protein Mutation Effect Generation

★ — · Updated unknown · Licence unknown

Jiadalee /

Mirror-Score

Mirror-Score: Calibrated, Inference-only Scoring Exposes the Limits of Sequence-compatibility Ranking in D-peptide Design

★ — · Updated unknown · Licence unknown

AmbiModBench

No description

★ — · Updated unknown · Licence unknown

QDKStorm /

ProFiT

Flow-Matching-Based Protein Structure Tokenizer Made Efficient and Easy

★ — · Updated unknown · Licence unknown

Radisen-Panthera /

MoSPR

MoSPR: Histology-to-Gene Expression Prediction with Morpho-Spatial Macrostates and Low-Rank Molecular Programs

★ — · Updated unknown · Licence unknown

UBC-NLP /

GyroNovo

GyroNovo: Error-Guided Fragment Imputation with Mass-Aware Attention for \textit{De Novo} Peptide Sequencing

★ — · Updated unknown · Licence unknown

domenicoscaramozzino /

ENM-BD

No description

★ — · Updated unknown · Licence unknown

iobio-zjut /

TopoFlow

No description

★ — · Updated unknown · Licence unknown

azizilab /

SHERLOCK

No description

★ — · Updated unknown · Licence unknown

GabbyKoki /

Pop-Corn

No description

★ — · Updated unknown · Licence unknown

Hoecker-Lab /

mmpbsa-scoring

Predicting single mutation effects on binding affinity at protein-protein interfaces based on MMPBSA calculations

★ — · Updated unknown · Licence unknown

rhparry /

sRNAMap

sRNAMap: a lightweight, browser-based web application for small RNA mapping, analysis and visualisation

★ — · Updated unknown · Licence unknown

rbouckaert /

potts

A first order approximation of a joint Potts and phylogenetic model

★ — · Updated unknown · Licence unknown

limengran98 /

CellAudit

No description

★ — · Updated unknown · Licence unknown

topu-benchmark /

TopU-LBVS

TopU-LBVS: A Realistic Multi Target Benchmark for Ligand Based Virtual Screening

★ — · Updated unknown · Licence unknown

jz890 /

scFM Long-Tail Benchmark

No description

★ — · Updated unknown · Licence unknown

huang-laboratory /

EM3DFold

EM3DFold: accurate de novo protein and nucleic acid model building for cryo-EM maps using language model-powered deep learning

★ — · Updated unknown · Licence unknown

COMBINE-lab /

Gravlax

Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq

★ — · Updated unknown · Licence unknown

valsv

A single-cell RNA-seq catalog of ground truth gene coregulation

★ — · Updated unknown · Licence unknown

XieZikai /

RECOB

RECOB: Reliable Benchmarking of Experimental Optimization in Chemistry and Materials Science

★ — · Updated unknown · Licence unknown

welch-lab /

LIGER

Single-cell dataset integration and analysis

★ 432 · Updated 2mo ago · GPL-3

softnanolab /

BAGEL

Protein engineering via energy landscape exploration

★ 148 · Updated 2d ago · MIT

Intelligent-Drug-Discovery-Lab /

OmniSyn

Target-aware synthesizable molecule generation

★ 1 · Updated 2mo ago · Licence unknown

coleygroup /

shepherd2

No description

★ — · Updated unknown · Licence unknown

math-diff /

gromacs-gamd

Gaussian Accelerated Molecular Dynamics in GROMACS

★ — · Updated unknown · Licence unknown

gityuling /

RevPert

No description

★ — · Updated unknown · Licence unknown

montilab /

Signature Recontextualization

No description

★ — · Updated unknown · Licence unknown

mindflow-cn /

scDrugPerturb-Bench

No description

★ — · Updated unknown · Licence unknown

tesorai /

Cross-Modal Proteomics Pretraining

No description

★ — · Updated unknown · Licence unknown

jbezney61 /

PHAROS

No description

★ — · Updated unknown · Licence unknown

LucaOne /

LucaCell

No description

★ — · Updated unknown · Licence unknown

Balays /

DogMAG

Dog-wise canine gut metagenome assemblies with reconstructed bacterial genomes and viral candidates

★ — · Updated unknown · Licence unknown

szczurek-lab /

OmegAMP

Designing antimicrobials with programmable mechanism and safety

★ — · Updated unknown · Licence unknown

PhysiCelldFBA /

PhysiCelldFBA

PhysiCelldFBA: Linking single-cell genome-scale metabolism to spatially explicit multicellular dynamics

★ — · Updated unknown · Licence unknown

geun-woo-shin /

DRIFT-GITHUB-DRAFT-20260829

Division-resolved inference of flow and trajectories in proliferating cell populations

★ — · Updated unknown · Licence unknown

DiLiuLab /

dsRNA-brick

Programmable Self-Assembly of RNA Nanostructures with >100 Unique Components

★ — · Updated unknown · Licence unknown

neginrhm /

panAD-MONET

An Integrated Single-Nucleus Atlas Resolves Cell-Type-Specific Programs and Molecular Subtypes in Alzheimer's Disease

★ — · Updated unknown · Licence unknown

SweepLink

SweepLink: Joint Inference of Demography and Linked~Selection from Time-series Data

★ — · Updated unknown · Licence unknown

dbjzs /

MAPS

Unifying physical and molecular coordinate systems across modalities in spatial biology

★ — · Updated unknown · Licence unknown

ehsanestaji /

VariantFlow

VariantFlow: a selective-execution engine for efficient population genomic computation on large variant datasets

★ — · Updated unknown · Licence unknown

MGXlab /

FxTractor

High-throughput genomic feature extraction reveals environmental adaptations of prokaryotes

★ — · Updated unknown · Licence unknown

cumbof /

HyperSketch

HyperSketch: de Bruijn graph sketching for genomic similarity estimation with Hyperdimensional Computing

★ — · Updated unknown · Licence unknown

JacquemontLab /

gVCF2CNV

gVCF2CNV: a scalable pipeline for CNV detection from whole-genome sequencing data

★ — · Updated unknown · Licence unknown

IacopoPasseri /

MErlin

From code to natural language: MErlin - a multiomics toolkit for bacterial epigenomics delivered as Claude agent skill.

★ — · Updated unknown · Licence unknown

Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies

No description

★ — · Updated unknown · Licence unknown

smuskal /

PharmCast

PharmCast: rapid generation of three-dimensional pharmacophore fingerprints from two-dimensional structure without conformer generation

★ — · Updated unknown · Licence unknown

bigomics /

WGCNA+

WGCNA+: AI-powered WGCNA for Integration of Multi-Omics Data

★ — · Updated unknown · Licence unknown

EarlhamInst /

EISCA and EISTA

EISCA and EISTA: Full-Spectrum Pipelines for Single-Cell and Spatial Transcriptomics Analysis

★ — · Updated unknown · Licence unknown

BOTANIC-1

BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era

★ — · Updated unknown · Licence unknown

KChen-lab /

Monopogen

Single-Cell Indel Detection Enhances Genetic Ancestry and Cellular Lineage Analysis

★ — · Updated unknown · Licence unknown

Xuebin-Feng /

EMAP-SSN

EMAP-SSN: An Embedding- and Multiple-Alignment-Integrated Sequence Similarity Network Platform for Interactive Exploration of Protein Sequence Space

★ — · Updated unknown · Licence unknown

SeonghwanSeo /

AtlasFold

AtlasFold: Protein structure prediction with metagenomic-scale language models

★ — · Updated unknown · Licence unknown · Curieus

liusihang /

ESMCapsid

Capsid-specialized protein language models reveal higher-order viral architecture from sequence

★ — · Updated unknown · Licence unknown

dhnihaoya /

EvSpark

EvSpark: Lossless Speculative Decoding for Hybrid DNA Foundation Models

★ — · Updated unknown · Licence unknown

YangLabHKUST /

CellART

CellART: a unified framework for extracting single-cell information from high-resolution spatial transcriptomics

★ — · Updated unknown · Licence unknown

dannyxbergeron /

NANOCUTSIGHT

NANOCUTSIGHT: A NANOPORE-SEQUENCING APPROACH AND ANALYSIS PIPELINE TO ASSESS GENOME EDITING EFFICACY IN VARIOUS CELL POPULATIONS

★ — · Updated unknown · Licence unknown

j-ackierao /

scFLAME

scFLAME: a unified generative model for interpretable clustering, hierarchical structure discovery and marker-gene identification in single-cell RNA-seq data

★ — · Updated unknown · Licence unknown

roger-yh-zhao /

PRIS

A Unified Structure-Based Deep-Learning Framework for High-Throughput Screening of Protein-Binding RNAs

★ — · Updated unknown · Licence unknown

wolfsonliu /

bioq

bioq: a unified, agent-native command-line interface to a fleet of AI drug-discovery methods

★ — · Updated unknown · Licence unknown

ThorKlm /

PLI-parallax

Predicted and experimental protein-ligand coordinates with distance labels and evaluation splits

★ — · Updated unknown · Licence unknown

ha01994 /

TAPAS

TAPAS: Learned integration of AlphaFold3 confidence and geometric features for TCR-pMHC binding prediction

★ — · Updated unknown · Licence unknown

brooksbenard /

PhenoMapR

PhenoMapR: scalable mapping of sample phenotypes to single-cell, spatial, and bulk transcriptomics data

★ — · Updated unknown · Licence unknown

DigBioLab /

odin-multi

Specificity-driven protein binder design with Odin-Multi

★ — · Updated unknown · Licence unknown

biolab /

dictyExpress

dictyExpress: an integrated browser for bulk and single-cell Dictyostelium transcriptomics

★ — · Updated unknown · Licence unknown

AstraZeneca /

GenCDR

Generative Language Modeling for Antibody CDR Grafting and Alignment-driven De Novo Design

★ — · Updated unknown · Licence unknown

veg /

HyphAeon

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

★ — · Updated unknown · Licence unknown

CompGenomeLab /

GPCR Evolution Database

No description

★ — · Updated unknown · Licence unknown

c16267 /

spaCraft

spaCraft: calibrated power analysis and sample-size planning for multi-sample spatial transcriptomics

★ — · Updated unknown · Licence unknown

probalytiq /

GOlien tool

GOlien tool: fast and scalable GO term annotation of proteins using a Shannon-entropy k-mer model

★ — · Updated unknown · Licence unknown

Rijinna /

scOLAR

scOLAR: Ontology-Anchored Open-Set Annotation of Single-Cell RNA-seq Data

★ — · Updated unknown · Licence unknown

giovannellilab /

Geomosaic

Geomosaic: a flexible bioinformatics platform integrating complementary metagenomic analyses from sequencing reads to genomes

★ — · Updated unknown · Licence unknown

kenll99minecart /

SpectroVQ

SpectroVQ: Noise-Aware Compression of Proteomics Data via Vector-Quantized Deep Learning improves MS/MS data storage and Peptide Identification

★ — · Updated unknown · Licence unknown

AngieHinrichs /

viral-usher

Real-time accessible phylogenetics for every highly sampled virus

★ — · Updated unknown · Licence unknown

scrcdnai-max /

DNT: Diploid Genomic Foundation Model

No description

★ — · Updated unknown · Licence unknown

EBI-Metagenomics /

MAP

MAP: a comprehensive pipeline for mobilome annotation and cargo gene characterisation in prokaryotic (meta)genomic assemblies

★ — · Updated unknown · Licence unknown

tslinux /

VARION

VARION: A Network Propagation Framework for Individual Patient Somatic Mutation Interpretation in Cancer Molecular Subtyping

★ — · Updated unknown · Licence unknown

dsong-lab /

spAlignDE

spAlignDE unifies cross-sample and cross-modal spatial alignment with mismatch-aware differential expression

★ — · Updated unknown · Licence unknown

mcjian09 /

SpaCoEx

SpaCoEx: Sparse Gene Selection for Spatially Varying Co-expression in Spatial Transcriptomics

★ — · Updated unknown · Licence unknown

adamyhe /

pydreg

pydreg: a fast Python package for identifying active cis-regulatory elements from nascent transcription

★ — · Updated unknown · Licence unknown

GuoBioinfoLab /

OmniTCR

OmniTCR: a foundation model unifying T cell receptor recognition prediction and conditional sequence generation

★ — · Updated unknown · Licence unknown

Jay-baijie /

PANDA

PANDA: Protein All-atom Nested-tree Denoising Architecture for End-to-End Generation

★ — · Updated unknown · Licence unknown

dina-lab3D /

SABLE

A structural antibody benchmark for leakage-aware deep-learning evaluation

★ — · Updated unknown · Licence unknown

darkest-opson /

ABCP_finder

ABCP_finder: A Transformer Embedding-Based Prediction of Anti-Breast Cancer Peptides

★ — · Updated unknown · Licence unknown

PacificBiosciences /

isocall

Isocall enables scalable transcript identification from long-read RNA-sequencing data

★ — · Updated unknown · Licence unknown

jianlin-cheng /

TransBind2

TransBind2: Improving Transcription Factor-DNA Binding Prediction with Multimodal Data and Bidirectional Cross Attention

★ — · Updated unknown · Licence unknown

ddzzjj /

ImmuneLens

ImmuneLens: linking transcriptional states and TCR clonotypes through disentangled multimodal learning

★ — · Updated unknown · Licence unknown

iobio-zjut /

ForceFlowAb

ForceFlowAb: physics-aware mixture-of-experts flow matching model for antibody CDRs design

★ — · Updated unknown · Licence unknown

MALL-Lab /

PRECISION-paper

Heterogeneous graph neural networks with biological prior knowledge for interpretable drug repurposing in triple-negative breast cancer

★ — · Updated unknown · Licence unknown

therna

A massively parallel synthetic gene atlas for learning compact cis-regulatory grammar across cellular contexts

★ — · Updated unknown · Licence unknown

rahul2512 /

cgNA-plus

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

★ — · Updated unknown · Licence unknown

apexfold

Peptide structural plasticity is predictable from sequence and environment

★ — · Updated unknown · Licence unknown

liskinsk /

RheoScale 2.0

RheoScale 2.0: Revealing the Hidden Roles of Protein Positions via Substitution Patterns

★ — · Updated unknown · Licence unknown

hdlugas /

LevenMap

Novel biologically relevant small RNA-sequencing alignment tool LevenMap for alignment to database of non-coding RNAs

★ — · Updated unknown · Licence unknown

OTEAM-AI4S /

NACraft

NACraft: Programmatic nucleic-acid aptamer design via all-atom structure-model feedback

★ — · Updated unknown · Licence unknown

mooreneural /

Lacuna

Lacuna: Cryptic Binding Pocket Discovery via Conformational Ensemble Analysis

★ — · Updated unknown · Licence unknown

XjunLi /

DuetRNA

Base-and-Sugar Dual-Frame Flow Matching for RNA Co-Design

★ — · Updated unknown · Licence unknown

plantomicsgwas1-boop /

PlantOmicsGWAS

PlantOmicsGWAS: An end-to-end, reproducible framework for plant genome-wide association and genomic prediction using linear and pan-genome references

★ — · Updated unknown · Licence unknown

discoperon

Predicting the operon structure of the Mycococcus xanthus genome using the novel software DiscOperon

★ — · Updated unknown · Licence unknown

tbaker67 /

ResiRuler

ResiRuler: A Toolkit for Visualizing Residue-Residue Distances and Structural Changes in Biomolecular Models

★ — · Updated unknown · Licence unknown

molinfo-vienna /

NEAT-POCKET

Pocket-conditioned 3D molecule generation

★ 7 · Updated 6w ago · MIT

molecularmodelinglab /

SABLE

Agentic Bayesian synthesizable ligand exploration

★ 3 · Updated 8w ago · Apache

afermg /

JUMP-lite

Code and release documentation for JUMP-Lite, a compact, analysis-ready subset of the JUMP Cell Painting dataset for benchmarking cell-image representations.

★ 2 · Updated 6w ago · MIT

Luosanj /

VOICE

No description

★ — · Updated unknown · Licence unknown

whd1125 /

PopPert

No description

★ — · Updated unknown · Licence unknown

blazejba /

Monroe

Monroe: A Molecular Foundation Model for In-Context Probabilistic Inference

★ — · Updated unknown · Licence unknown

GAIR-NLP /

RIBOSPAN

RIBOSPAN: A Long-Context RNA Foundation Model for Versatile RNA Modeling

★ — · Updated unknown · Licence unknown

ecnuabmlab /

CIR-DDG

CIR-DDG: backbone-agnostic residual correction of antibody-antigen affinity changes with explicit cross-chain geometry

★ — · Updated unknown · Licence unknown

graeter-group /

backflip

Predicting directional flexibility in proteins

★ — · Updated unknown · Licence unknown

jiankliu /

DSQ

GPCR Ligand Bioactivity Prediction with Physics-Informed Dual-State Query Learning

★ — · Updated unknown · Licence unknown

BiodiversityExtinction /

PlainMap

PlainMap: a lightweight, restartable mapping pipeline for ancient and modern DNA

★ — · Updated unknown · Licence unknown

tansey-lab /

ScreenShot

ScreenShot: A Foundation Model for Few-Shot Combination Drug Screening

★ — · Updated unknown · Licence unknown

MengzhouLu /

RetroMPA

RetroMPA: A Molecular Property-Aware Auxiliary Framework for Enhancing Retrosynthesis Prediction

★ — · Updated unknown · Licence unknown

littlepeachs /

CoMPASS

CoMPASS: Collaborative Molecular Property Prediction via Adaptive Small-Large Model Synergy

★ — · Updated unknown · Licence unknown

kasurl /

LiFT

Language-Informed Flow Matching for Trend-Guided Structure-Based 3D Molecular Generation

★ — · Updated unknown · Licence unknown

developer-hq /

ProbeMatchDTI

ProbeMatchDTI: Probe-Driven Multi-Scale Biochemical Pattern Matching for Drug-Target Interaction Prediction

★ — · Updated unknown · Licence unknown

rssrwn /

Ensemble-Conditioned Molecular Design

No description

★ — · Updated unknown · Licence unknown

BaoJiee /

scKITE

No description

★ — · Updated unknown · Licence unknown

weitse-hsu /

MDArena

AI agent benchmark for MD workflows

★ 9 · Updated 2mo ago · MIT