Second day of Genome Informatics #GI2025 began with the session “Genome Assembly and Sequence Algorithms" Yun William Yu presented “Average-case Analysis of Seed-Chain-Extend under Random Mutations" genome.cshlp.org/content/33/7/1175 providing theoretical guarantees for the popular seed-chain-extend

Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory. List of talks and posters: meetings.cshl.edu/abstracts.as...

Excited to be at the Genome Informatics conference #GI2025 in Cold Spring Harbor Laboratory this week! I’ll be sharing my current work on using machine learning to improve the reliability of Metagenomics classification for analzing gut microbiota and soil samples. Let's connect!

🐝🦠 New paper: rdcu.be/eOf7A Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social

📆 Only 4 days left until the #RECOMB2026 abstract registration deadline! 📌 Authors who register abstracts can update their submissions until November 14. 👉 See submission guidelines: recomb.org/recomb2026/c...

The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social subulatepalpomere.com/2025/11/02/t...

We’re all so proud of Steven Tan! He’s a super talented undergraduate at JHU. Thanks to the incredible support of @benlangmead.bsky.social, I had the opportunity to help guide this work, and I really loved it. Many thanks also to @sinamajidian.bsky.social for his valuable collaboration and input.

Great new postdoc fellowship for foundational plant research. If you’re into genetics and genomics of plant reproductive evolution or adaptive convergence (incl in the cool and charismatic nightshades!) I’d be happy to talk about possible projects! www.simonsfoundation.org/grant/simons...

"We have named the package Basset, as an allusion to the extraordinary abilities of these hound dogs to learn a scent that they are subsequently able to detect and pursue." genome.cshlp.org/content/26/7... Kelley et al, Genome research 2016.

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology. I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

Final committee meeting... DONE. Defending in the first week of April, so if you're looking for postdocs or know someone who is, let me know!

Join our interdisciplinary online workshop on the Galaxy platform! Nov 6, 2025 | 13:30–16:05 (CET) Learn how to build reproducible data analysis workflows using Galaxy, a powerful, user-friendly platform. The session is intended for the Swiss rsrch community. Register forms.gle/Y3vxW1u62FLM...

Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓 Introducing: py2Dmol 🧬 (feedback, suggestions, requests are welcome)

Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications! www.nature.com/articles/s41...

It’s a tricky time of year to schedule meetings for international collaborations, some countries have already changed their clocks and ended daylight saving time, while others not. I guess I’ll just have to trust Google Calendar and Doodle to handle the time zone math for me!

Open position at the Swiss Institute of Bioinformatics: We are looking for a Director of the Center of Pathogen Bioinformatics apply.refline.ch/499599/0346/... I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

Our lab has published a couple of major papers in the past few months, which I would like to highlight in this thread! 🧵

Are you interested in Structural Variants? 🧬 Join our online course (1–3 Dec) to learn how to detect, compare, and annotate SVs from short & long @nanoporetech.com reads with @sedlazeck.bsky.social and Luis Paulin! 🚀 www.physalia-courses.org/courses-work...

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

2/6 Movi 2 uses length-based and threshold-based splitting to reduce the size of rows in the move structure. The threshold-splitting strategy compresses each threshold value to a single bit.

We are excited to announce APSPM 2026 - the SMBE Australasian Protein Structural Phylogenetics Meeting! 🗓️ 15-18 Feb. 2026 🌏 Brisbane, Australia 🔗 biosig.lab.uq.edu.au/strphy26/ 📄 Abstract submission: 28.11.2025 ✈️ Travel grant application: 28.11.2025 ✏️ Registration: 15.01.2026 #StrPhy26

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...

A lot of pressure on the different grant schemes, and pretty much independent of career stage.

🧬 Now published in Bioinformatics Advances: “Advances and challenges in understanding evolution through genome comparison.” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf223

We are pleased to announce the hg38 SpliceAI Wildtype tracks. These tracks show the scores for the genome sequence itself, without variants, from predicted splice donor and splice acceptor sites. More at bit.ly/spliceAIWt

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇

We're hiring! My team at @nygenome.org is looking for a statistical genetics postdoc to decipher functional architecture of complex diseases from cutting-edge CRISPR+scRNA-seq data, with @nevillesanjana.bsky.social lab. Happy to meet at #ASHG25, apply here jobs.silkroad.com/NYGenome/Car...

Hi #ASHG2025, the Lausanne team made it to Boston ! Excited to present our latest discoveries — come say hi and learn more about our research! @samuelmoix.bsky.social @rjhfmstr.bsky.social

Happy to share that Flashzoi is now published! We enhanced Borzoi with RoPE & FlashAttention for >3x faster training/inference & 2.4x reduction in memory usage. This brings large-scale genomic analysis and fine-tuning within reach of academic budgets. 📄: doi.org/10.1093/bioi...

ICYMI: New online: Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

Complex structural variant visualization with SVTopo (2025) BMC Genomics doi.org/10.1186/s128... Online viz: pacificbiosciences.github.io/SVTopo/#chr1...

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

10 new CS professors! 🥳 @anandbhattad.bsky.social @uthsav.bsky.social @gligoric.bsky.social @murat-kocaoglu.bsky.social @tiziano.bsky.social

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon: docs.google.com/document/d/1...

Genomics in Context Awards: collaborative research at the intersection of genomics, humanities, social sciences and bioethics wellcome.org/research-fun... Teams must include >1 researcher from life sciences & >1 researcher from humanities, social sciences and bioethics

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

How did animals repeatedly conquer land? 🌊➡️⛰️ We analysed ~1,000 gene repertoires (24M genes!) from all animal phyla to uncover how this happened. Work led by @gemmaeling.bsky.social & Klara Eleftheriadi, both first coauthors of this titanic effort! www.biorxiv.org/content/10.1...

Our new tool "X-Mapper: fast and accurate sequence alignment via gapped x-mers" now published on Genome Biology! Please try it if you work on DNA sequences :) github.com/mathjeff/Map... genomebiology.biomedcentral.com/articles/10....

What are folks using for calling genes these days in isolate genomes: PGAP, Bakta, or Prokka? This is for a 70% GC genome of a very novel lineage.

Advances in haplotype phasing and genotype imputation Quan Sun & Yun Li Nature Reviews Genetics 2025 www.nature.com/articles/s41...

Looking for scientists working with long-read transcriptomics technologies to join a COST action proposal. Contact us!!! @nanoporetech.com @pacbio.bsky.social

CADD: predicting the deleteriousness of variants throughout the human genome, 2019, NAR doi.org/10.1093/nar/... CADD v1.7, 2024, NAR doi.org/10.1093/nar/...

🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise. Until now, using AccuSNV. Herui Liao trained an ML model based on our previous meticulously called SNVs. www.biorxiv.org/content/10.1...

Very important initiative! This could really help facilitate increasing data sharing as well as appropriate attribution of data creation.

Whole-genome alignments revealed pennycress has nearly dichotomous genome compartmentalization: huge gene-poor pericentromeric regions (~300Mb; <1% genic) with frequent rearrangements and highly syntenic gene-rich chromosome arms (~150Mb; ~20% genic). What we call a "two-speed" genome structure. 3/

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1... Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date! Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!