PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization genomebiology.biomedcentral.com/articles/10.11… #Bioinformatics

SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization nature.com/articles/s4358… #Bioinformatics

Deciphering cell types by integrating scATAC-seq data with genome sequences nature.com/articles/s4358… #Bioinformatics

Genomic language model predicts protein co-regulation and function nature.com/articles/s4146… #Bioinformatics

Spike sorting with Kilosort4 nature.com/articles/s4159… #Bioinformatics

AlphaPept: a modern and open framework for MS-based proteomics nature.com/articles/s4146… #Bioinformatics

A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes genomebiology.biomedcentral.com/articles/10.11… #Bioinformatics

Unsupervised ensemble-based phenotyping enhances discoverability of genes related to left-ventricular morphology nature.com/articles/s4225… #DeepLearning

Leveraging large language models for predictive chemistry nature.com/articles/s4225… #LLM

AI-guided pipeline for protein–protein interaction drug discovery identifies a SARS-CoV-2 inhibitor embopress.org/doi/full/10.10… #AI

Identification of clinical disease trajectories in neurodegenerative disorders with natural language processing nature.com/articles/s4159… #NLP

Accurately clustering biological sequences in linear time by relatedness sorting nature.com/articles/s4146… #Bioinformatics

Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain academic.oup.com/nar/article/52… #Bioinformatics

Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data nature.com/articles/s4158… #Bioinformatics

PLMSearch: Protein language model powers accurate and fast sequence search for remote homology nature.com/articles/s4146… #Bioinformatics

BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies academic.oup.com/nar/article/52… #Bioinformatics

scGHOST: identifying single-cell 3D genome subcompartments nature.com/articles/s4159… #Bioinformatics

Prediction of tumor origin in cancers of unknown primary origin with cytology-based deep learning nature.com/articles/s4159… #Bioinformatics

Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data academic.oup.com/bioinformatics… #Bioinformatics

Improving microbial phylogeny with citizen science within a mass-market video game nature.com/articles/s4158… #CitizenScience