How do new centromeres evolve while staying compatible with the division machinery? Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore. 👉 doi.org/10.1038/s41586-025-09779-1

We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below: (TLDR; low-affinity motifs matter as pioneers!)

In #GENETICS, @alan-aw.bsky.social et al. introduce models for how individual variant effects in admixed individuals may be influenced by ancestry, contributing to work on the genetic architecture of complex traits and their implications for polygenic prediction. buff.ly/34ZvEil

Our method for genome size estimation from long-read overlaps is now published 🥳 academic.oup.com/bioinformati...

Join us Nov 18–20 for a Virtual Genome Annotation Workshop! Learn Linux, genome assembly, evidence-based annotation, & evaluation. No experience needed! 📅 10 AM – 2 PM ET 💻 MS Teams + recording 💰 $500 ($400 UConn) Register: bioinformatics.uconn.edu/cbc-workshops/ #GenomeAnnotation #Bioinformatics

This workshop is right around the corner. See the link for the rest of our upcoming workshop schedule.

Incredible new paper from @schacherer.bsky.social et al rdcu.be/eLcTH

My complex variant visualization tool SVTopo is now officially published in BMC Genomics! link.springer.com/article/10.1.... This tool allows HiFi users to view complex germline structural variation in intuitive and informative plots.

Now published! Our paper on: (1) Accurate sequencing of sperm at scale (2) Positive selection of spermatogenesis driver mutations across the exome (3) Offspring disease risks from male reproductive aging [1/n] www.nature.com/articles/s41...

I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months! Aardvark: Sifting through differences in a mound of variants GitHub: github.com/PacificBiosc... Some highlights in this thread: 1/N

Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

Advances in haplotype phasing and genotype imputation. #HaplotypePhasing #GenomeImputation @natrevgenet.nature.com www.nature.com/articles/s41...

Join us Oct. 28–30 for a Virtual ChIP-Seq / ATAC-Seq Workshop! 🧬 📅 10 AM – 2 PM EST 💻 Live on Zoom + recordings 💰 $500 ($400 UConn affiliates) Register: bioinformatics.uconn.edu/cbc-workshops/ #ChIPSeq #ATACSeq #Bioinformatics #Workshop

We published a detailed protocol for our Plate-CUT&Tag method on @protocolsio.bsky.social to accompany our recent preprint (www.biorxiv.org/content/10.1...) give it a try! Feedback welcome! dx.doi.org/10.17504/protocols.io.n2bvjed5wgk5/v1

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

Join us Sept. 16–18 for a Virtual Genome Assembly Workshop! 🧬 Learn sequencing, assembly & QC—all from your laptop. 📅 10 AM - 2 PM EST 💻 Live on MS Teams + recordings 💰 $500 ($400 UConn affiliates) Register: bioinformatics.uconn.edu/cbc-workshops/ #GenomeAssembly #Bioinformatics #Workshop

I suspected this during my first postdoc, when I was working with snATAC-seq data. Nice to see people doing the hard work! Multiple overlapping binding sites determine #transcription factor occupancy doi.org/10.1038/s415...

I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:

Excited to share our latest paper @natmethods.nature.com We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4). www.nature.com/articles/s41...

Excited to share our latest work with @simonbullock11.bsky.social! We looked at how diverse mRNAs get selected for subcellular localization and it turns out that a single protein can recognize different RNA elements using shared features that weren’t apparent before. www.biorxiv.org/content/10.1...

Spindle checkpoint can secure additional cheating time for selfish expanded centromeres cell.com/current-biol... @currentbiology.bsky.social @takashiakeralab.bsky.social

1/n Very excited to share our recent paper published on @ScienceAdvances where we dissect the gene regulatory landscape guiding mouse sex determination! science.org/doi/10.1126/... A huge well done to @IsabelleStevant.genomic.social.ap.brid.gy, Meshi and Elisheva who spearhead this project!

Noncanonical amino acids are efficiently incorporated into proteins by optimizing mRNA codon usage go.nature.com/3MDSSXQ rdcu.be/exfiH

Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state - @hagentilgner.bsky.social @liganlab.bsky.social go.nature.com/3IKlcJn

Fresh off the presses in @currentbiology.bsky.social : Is the deuterostome clade an artefact? www.sciencedirect.com/science/arti... We (yours truly, Paschalis Natsidis, Laura Piovani and co-leads Paschalia Kapli and @maxjtelford.bsky.social) set out to try to answer this question. Why? (1/12)

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context onlinelibrary.wiley.com/doi/10.1111/...

Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind

Vaccination schedules on the CDC website have already started changing under RFK Jr. So we published a guide to the evidence-based vaccine recommendations in place *before* all 17 members of the advisory panel were abruptly dismissed by the new admin. www.scientificamerican.com/article/see-... 🧪

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

Join us June 24–26 for a Virtual Single-Cell Transcriptomics Workshop! 🧬 Learn data processing, QC, clustering & integration using Python + R. 🕙 10 AM – 2 PM ET 💻 Zoom + recordings 💰 $500 ($400 UConn) Register: bioinformatics.uconn.edu/cbc-workshops/ #scRNAseq #Bioinformatics #Workshop

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

FYI: New online! RNA splicing — a central layer of gene regulation

Annalise Zouein's main PhD research paper is published today in Trends in Biotech. Building and using repetitive transcription factor-binding arrays to modulate gene regulation in mammalian cells. No RNA, no protein - just DNA doing the work! www.sciencedirect.com/science/arti...

Today, we’re announcing the preview release of ty, an extremely fast type checker and language server for Python, written in Rust. In early testing, it's 10x, 50x, even 100x faster than existing type checkers. (We've seen >600x speed-ups over Mypy in some real-world projects.)

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

A large-scale genomic study in Science of over 1500 individuals from 139 underrepresented Indigenous groups across northern Eurasia and the Americas sheds new light on the ancient migrations that shaped the genetic landscape of North and South America. Learn more: scim.ag/4mi1yUf

Spaces are still available in our upcoming genomics workshops! Join us for Variant Detection: May 20–22 and/or Genome Annotation, May 27-29 - Participants receive guided tutorials, live instruction, & daily recordings to support continued learning. bioinformatics.uconn.edu/cbc-workshops/

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

I’m very glad to share our recent publication @pnas.org , led by UnJin Lee from our lab at @rockefelleruniv.bsky.social : pnas.org/doi/10.1073/.... In this work, he 1) developed a method to efficiently compare single-cell RNA-seq data from rapidly evolving tissues across multiple species, and

Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1...

Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans https://www.biorxiv.org/content/10.1101/2025.05.04.652069v1

We quantify the aggregation of >100,000 random protein sequences to train CANYA, a convolution-attention hybrid neural network to predict aggregation from sequence. With @bennibolo.bsky.social www.science.org/doi/10.1126/...

Check out this great resource of single cell multiome data, cell annotations, regulatory DNA models of cell type resolved chromatin accessibility & comprehensive annotation of motifs & sequence syntax for multiple tissues in early human development 1/

Current methods for profiling #HistoneModifications require cell isolation & don't work with all tissue types. @jellevda.bsky.social &co adapt Targeted DamID (TaDa) to profile cell-type-specific #histone marks throughout the genome, in vivo, without cell isolation 🧪 @plosbiology.org plos.io/3Dw8sUD

🚨 Association between #HLA #genetics and #SARS-CoV-2 #infection in a large #real-#world #cohort 👉 #genes & #immunity @springernature.com www.nature.com/articles/s41...

Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...