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Starred repositories
The complete FlowSOM package known from R, now available in Python!
Nature Methods: RNA foundation model (together with RhoFold)
Tandem Repeats Finder: a program to analyze DNA sequences
Yin, C., Chen, Y., & Yau, S. S. T. (2014). A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering. Journal of Theoretical Biology, 359, 18-28.
Benchmarking code accompanying the release of `bioemu`
Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning
clinfo / gromacs
Forked from gromacs/gromacsPublic/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2
Introductory tutorial on TPS, committor analysis, and (MS)TIS with OpenPathSampling
An open source Python framework for transition interface and path sampling calculations.
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
Slides for lecture "Leveraging existing biological data and making sense of it" part of DTU's Summer School on Synthetic Biology for Cell Factories
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Updated Jun 17, 2025
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Machine Learning Journal for Intermediate to Advanced Topics.
A PyTorch library for implementing flow matching algorithms, featuring continuous and discrete flow matching implementations. It includes practical examples for both text and image modalities.
Tools for fast and flexible genome assembly scaffolding and improvement
Official code repository for GATK versions 4 and up
Official implementation: Transcription factor prediction using protein 3D structures
This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.
Code for our work on Protein-DNA binding prediction using FMs+CrossAttention
A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.