Lukas Heumos

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

Pertpy provides a modular framework for analyzing large-scale perturbation single-cell experiments, offering tools for metadata annotation and perturbation distance calculations.

scPortrait integrates single-cell images with proteomics and transcriptomics data to identify cancer-associated macrophage subpopulations and embed images into transcriptome atlases.

This paper introduces BioContextAI, an open-source initiative that provides standardized access to validated biomedical knowledge to improve the reliability of AI systems in biomedical research.

Spapros selects optimal probe sets for targeted spatial transcriptomics to improve cell type identification and spatial variation detection across multiple datasets.

The paper introduces nf-core/pangenome, a scalable and reference-unbiased pipeline for constructing pangenome graphs, achieving faster performance than PGGB on large datasets.

hadge combines hashing and genotype-based deconvolution methods to recover previously discarded cells in single-cell data.

Sfaira provides a data and model zoo for single-cell RNA-seq, enabling fast reuse of pre-trained models and datasets across human and mouse tissues.