Awesome new work from @labschneeberger.bsky.social (with a small contribution from the Weigel lab). Experimentally observed mutational patterns in centromeres underpin a model that recapitulates intra-specific centromere divergence! www.biorxiv.org/content/10.1...

Pangenome-aware DeepVariant https://www.biorxiv.org/content/10.1101/2025.06.05.657102v1

Lossless Pangenome Indexing Using Tag Arrays www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/parsaeskanda...

New online! Predicting gene expression from DNA sequence using deep learning models

Parsing GTF and FASTA files using the eccLib Library www.biorxiv.org/content/10.1... 🧬🖥️🧪 gitlab.platinum.edu.pl/eccdna/eccLib

Vizitig: context-rich exploration of sequencing datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 gitlab.inria.fr/vizisoft/viz...

EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/PacificBiosc...

ICYMI: New online! Computational analysis of DNA methylation from long-read sequencing

The minda tool helps with SV benchmarking and merging by decomposing SVs into start and end records, supporting other types of SVs beyond primarily germine indels processed by truvari, SVanalyzer, SURVIVOR, Jasmine, etc. github.com/KolmogorovLa...

PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences arxiv.org/abs/2503.20766 🧬🖥️🧪 github.com/yana-safonov...

New online! Transcriptomics in the era of long-read sequencing

Generating multiple alignments on a pangenomic scale academic.oup.com/bioinformati... 🧬🖥️🧪 gitlab.com/qwerzuiop/pa...

deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model academic.oup.com/bib/article/... 🧬🖥️🧪 github.com/xiaoyan-wang...

CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/LouisPwr/Car...

1/35 New paper out! @jamesTstroud and I dive into why long-term studies are crucial for understanding evolution. They reveal processes impossible to detect in short timescales and capture rare events that transform our understanding of evolutionary dynamics. www.nature.com/articles/s41...

Learning the language of protein-protein interactions www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/VarunUllanat...

geneviewer - Gene Cluster Visualizations in R. Imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. github.com/nvelden/gene... #Rstats

The long, unsteady path to ecosystem recovery phys.org/news/2025-03...

This looks quite cool, latest paper from Frank Johannes on somatic mutations in trees: Branching architecture limits the rate of somatic mutation accumulation in trees doi.org/10.1101/2025...

We have a new paper out today, where, among other things, we find evidence that a locally adaptive chromosomal inversion likely trapped an even older inversion along its path to becoming the supergene it is today. onlinelibrary.wiley.com/doi/10.1111/...

Simulating 500 million years of evolution with a language model www.science.org/doi/10.1126/... 🧬🖥️🧪 github.com/evolutionary...

For those working with Hi-C data and the Arima workflow, we have rewritten the Arima tools using htslib to speed up the process. Any feedback is welcome: github.com/Genoscope-LB...

Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping https://www.biorxiv.org/content/10.1101/2025.02.11.637720v1 🧬🖥️🧪 https://github.com/SchriderLab/TEforest

Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1 🧬🖥️🧪 https://github.com/harvardinformatics/scrub-jay-genomics

Review: Foundation models in bioinformatics doi.org/10.1093/nsr/...