🚨 New preprint alert 🚨 We've generated a new gapless genome of Caenorhabditis brenneri🪱, one of the most diverse metazoans! We compared its genome and gene organizations with other nematodes with smaller population sizes. Check it out! https://t.co/y4LwypFRkT

I spent months illustrating how Transformers actually work. Not just what they do, but why they’re built this way. The history, design choices, and intuition behind every layer. From RNNs → Attention → Multi-Head → FFNs → Positional Encoding. Here's everything I wish I

scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution. #SingleCell #GeneExpression #Genomics #Transcriptomics #Epigenomics #Bioinformatics @naturemethods https://t.co/po0cmFRB9m

Pre-phasing long reads improves structural variant genotyping. #LongReads #Sequencing #ReadsPhasing #StructuralVariants #Genotyping #Genomics #Bioinformatics https://t.co/5DVdWnTc0d

GRiNS: a python library for simulating gene regulatory network dynamics https://t.co/iuTqGEPSYN

OrthoBrowser: Gene Family Analysis and Visualization https://t.co/lUysfxKYWz

G2PT: Genotype-to-Phenotype Transformer: Mechanistic genotype-phenotype translation using hierarchical transformers https://t.co/YVDTPZ3sY8

DiSC: a Statistical Tool for Fast Differential Expression Analysis of Individual-level Single-cell RNA-seq Data.#SingleCell #RNAseq #scRNAseq #DifferentialExpression #Bioinformatics https://t.co/oNSI5RDaID

Pangenome-aware DeepVariant https://t.co/zduXfPa8tH

ntSynt-viz: Visualizing synteny patterns across multiple genomes https://t.co/lcxxJRVaQ3 #biorxiv_genomic

sTELLeR: Detecting transposable elements in long read genomes https://t.co/flkjwSUEMP

A gentle introduction to pangenomics https://t.co/pbIzF1bySX

REPORTH: Determining orthologous locations of repetitive sequences between genomes https://t.co/aAYkBeBPDH #biorxiv_bioinfo

🚨 Excited to share this #preprint from my postdoc in the Lippman lab @CSHL, in collab. with @mike_schatz & many others! Using pan-genomics & pan-genetics across the Solanum genus 🍅🥔🍆 we reveal gene duplications 🧬 as contingencies in crop engineering.

Widely observed negative correlation between recombination rate and TE abundance is usually interpreted as recombination rate being the "cause," influencing the efficacy of selection purging TEs. Yet, our recent study "flipped" this causality! https://t.co/skk0F52uAP… (1/5)

Have you ever wondered whether modularity is the only driver of transcriptional network organization? Short answer, no! There are nuances to transcriptional networks, and together with @diogro and Julien Ayroles we explored some methods to find them:

Advertising this amazing tutorial that Rob Lanfear (no longer on this site) put together: "For phylo nerds interested in concordance and discordance: https://t.co/vhGOofgGWP"

DNA and RNA is not enough. Epigenetic state is necessary for drug development + basic biology. Understanding ATAC-seq data requires interactive + genome scale operations. We present a suite of interactive + publication-quality tools, in Python, to view chromatin accessibility.

How many genes for the starch-digesting enzyme amylase to you have? More than your non-agricultural ancestors. It may affect how many cavities you get. https://t.co/yrdGo1Xt44 @UCBerkeley @uthsc @Nature

Thanks to @vcallier for this nice write up covering our discovery of the cephalopod Z chromosome

Trackplot: A flexible toolkit for combinatorial analysis of genomic data https://t.co/CybnJmVjMQ