Trends in Computational Metabolomics (2021–2025)

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

[ICLR'24] Symphony: Symmetry-Equivariant Point-Centered Spherical Harmonics for Molecule Generation

ChatMol

Code repository associated with our recent work: Spatial RNA-Sequencing of Microbiome-Host Interactions at One Micron Resolution

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex ima…

Genome modeling and design across all domains of life

SPAtial Transcriptomics resource for subCellular and High-throughput platforms

[𝐧𝐚𝐭𝐮𝐫𝐞 𝐦𝐚𝐜𝐡𝐢𝐧𝐞 𝐢𝐧𝐭𝐞𝐥𝐥𝐢𝐠𝐞𝐧𝐜𝐞] ImmunoStruct enables multimodal deep learning for immunogenicity prediction

Quantifying metabolism activity at the single-cell resolution

The official implementation of GenomeOcean.

A curated repository designed to serve as a comprehensive guide for researchers interested in the intersection of Transformer models and genomics. This repository compiles key academic papers that …

A unified framework for identifying multicellular niches and niche-regulated cell states from spatial transcriptomics data.

Pathology Imaging Characterization with Uncertainty-aware Rapid Evaluation (PICTURE)

RefMan - A Simple python-based reference manager

Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS (Nat Biotechnology)

Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly multiplexed immunohistochemistry data. Docs available here: ht…

Predicting tandem mass spectra from molecules

RNA Velocity generalized through dynamical modeling

MUSTANG: reference-free MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance

ExerkineMap **Virtual Physiome** — a computational framework for exercise-induced exerkine signaling across single cells, tissues, and organs.

A Latex style and template for paper preprints (based on NIPS style)