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Starred repositories
Efficient pythonic random access to fasta subsequences
A VS Code extension to manage and monitor SLURM cluster jobs – view active jobs, browse history, cancel jobs, and submit new workloads directly from your editor.
predicting expression effects of human genome variants ab initio from sequence
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Extracted system prompts from Anthropic - Claude Fable 5, Opus 5, Claude Design, Claude Code. OpenAI - ChatGPT GPT-5.6-Sol, Codex. Google - Gemini 3.5 Flash, 3.1 Pro, Antigravity. xAI - Grok, Curso…
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Materials for short, half-day workshops
PaCMAP: Large-scale Dimension Reduction Technique Preserving Both Global and Local Structure
BulkFormer: A large-scale foundation model for human bulk transcriptomes
Research code accompanying AlphaGenome
A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner
Benchmark gene representations from different model families
Benchmarking gene embeddings on single, paired, and gene set tasks
PertAdapt: Unlocking Single-Cell Foundation Models for Genetic Perturbation Prediction via Condition-Sensitive Adaptation.
A Knowledge Graph for Relational Learning On Biological Data
Jupyter widget to interactively view molecular structures and trajectories
Collection of open source software projects in which members of the Faculty of Computer Science at TU Dresden are involved.
dN/dS methods to quantify selection in cancer and somatic evolution
A computational approach for identifying cancer driver genes by detecting three-dimensional clusters of somatic missense mutations in protein structures.
Learning pipeline to identify somatic SNVs under positive selection.
A deep-learning framework for multi-omics integration (RNA-seq, CNV, DNA methylation, etc.)