Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

New preprint out by #RobertKoetsier, the first of his PhD project, on assessing the use of cross-species coexpression analysis to identify primary and secondary metabolic interactions in microbiomes: www.biorxiv.org/content/10.1...

Excited to share our EvANI benchmarking workflow, published in Briefings in Bioinformatics doi.org/10.1093/bib/... Computing average nucleotide identity (ANI) is neither conceptually nor computationally trivial. Its definition has evolved over years, with different meanings and assumptions (1/5)

#Seminar: Evidence-based genome #annotation with EviAnn 🗓️ Tuesday, Sep 23 - 15:00 CEST 🔗 www.erga-biodiversity.eu/post/efficie... Aleksey Zimin will introduce & demonstrate the use of #EviAnn -a new system for eukaryotic gene annotation. @ebpgenome.bsky.social @biogeneurope.bsky.social

Our department of Plant Molecular Biology at the University of Lausanne @unil.bsky.social is recruiting a Tenure-Track Assistant Professor in the field of Plant-Organism Interactions 🌱🐛🦠🍄! Application before November 30, 2025. See the official job ad for more details: tinyurl.com/mtxdcz6p

In a new preprint from @brianhie.bsky.social's lab, the team reports the first generative design of viable bacteriophage genomes. Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.

🧬 US genomics expert Paul Thomas joins SIB as Swiss-Prot co-director, with @alanbridge.bsky.social 🔍 Leader in gene function research; among the world’s most-cited scientists 📊 His arrival strengthens SIB’s role in generating trustworthy, AI-ready biological knowledge #UniProt #GeneOntology More 👇

The call for abstract for LEGEND is now open: legend2025.sciencesconf.org It will close on September 22nd (oral presentations) and October 1st (posters). Send us your best work on Machine Learning for Evolutionary Genomics and come discuss it with us in the French Alps next December!

2025 Machine Learning in Computational Biology (#MLCB) meeting starts TODAY (9/10) at 9:30a (EST) at the NY Genome Center in NYC! We have a great lineup of keynotes, contributed talks, and posters today and tomorrow Schedule: mlcb.org/schedule Join for free via livestream: m.youtube.com/@mlcbconf

The LSRF post-doc fellowship is open (due Oct 31)! The LSRF is a supportive and kind community. We *always* celebrate each other. On a personal level, they've always greeted me with open arms and an abundance of kindness. If you are thinking of applying and have questions, feel free to reach out!

A full day of computational biology at the BC2 conference with neural networks everywhere even where they didn't make so much sense to be used. Is it peak AI and its going to go down from here to be just a very useful data analysis/modelling approach?

Which tool should I use nowadays to identify pathogens in long-read DNA sequencing from human brain samples?

Very excited to share I’ll be starting my own group at University of Utah in the Department of Human Genetics in the new year! Reach out if you are interested! vollgerlab.com

Please take a moment to tell us how you use the Genome Browser: surveymars.com/q/mnb... Your feedback supports future improvements and our continued funding.

Logan rapidly accesses the tapestry of Life’s genetic diversity and can help solve global issues. To tackle the microplastic crisis, we searched Logan for new versions of the 213 known plastic-degrading enzymes. We identified 200+ million homologs 🤯, including new high-efficiency enzymes 🥤🔥

❗ I clearly consider this result as THE most important result achieved over this last decade for exploiting and democratizing genomic data. I think there will be a "before" and an "after" logan and logan-search github.com/IndexThePlan... logan-search.org Have a look at this thread

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Translon: a single term for translated regions www.nature.com/articles/s41...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp.... Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!

Join us for our next Kipoi Seminar with Hani Goodarzi, Arc Institute, UCSF @arcinstitute.org @ucsfcancer.bsky.social 👉Reading and writing the language of life 📅 Wed Sep 3, 5:30pmCET 🧬 kipoi.org/seminar 🦋 @kipoizoo.bsky.social

FINAL CALL! ⏰ Registration for the 1st Great Lakes Plant Science Conference closes this weekend – Sunday, August 31st at 11:59 p.m. ET. Join plant scientists from across the region Sept. 12–14 in Lansing, MI for #GLPSC2025. Don’t miss out! 🌱 Register now: research.msu.edu/glpsc2025

"I hope this email finds you well. I am writing to inquire about potential PhD opportunities in your lab, as I am deeply interested in your research on within-person microbial evolution and precision microbiome engineering.

Today is our 7th #bioinformatics Hackathon @bcmhgsc.bsky.social ! 120+ people from around the world attending! Super excited about all the new projects ! Thanks to @dcgenomics.bsky.social @dnanexus.bsky.social @gregor-research.bsky.social @smahtnetwrk.bsky.social @treangen.bsky.social !

Genome Informatics abstract deadline now Sept 8! h/t @benlangmead.bsky.social meetings.cshl.edu/meetings.asp...

A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing. www.uu.se/en/about-uu/...

Link mentions 2 positions specifically in Comparative Genomics, Depts. of animal science and entomology. Bill Murphy running the search. apply.interfolio.com/171886

🚀 Panacus v0.4.0 is out! Bringing more power, flexibility, and speed to your pangenome reports 🧬📊 👉 Upgrade now & explore: github.com/codialab/pan... #genomics #bioinformatics #pangenome #panacus

Headed to #ASHG25? Don’t miss HPRC’s workshop on the Human Pangenome: Data, Tools & Workflows. 📅 Oct 14 | 10AM–12PM Learn how to access data & use pangenome tools! www.ashg.org/product/ashg...

If you are a postdoc working on any topic related to environmental microbiology and are looking for exposure, the Thermal Biology Institute (tbi.montana.edu) has slots open for virtual talks via zoom this fall. Email me if you are interested! Seminars are most Mondays, 3-4 pm Mountain Time.

The Genome Informatics conference (@ Cold Spring Harbor Lab, Nov 5 - 8) abstract deadline is **today**. We welcome your submissions! Topics include: - PanGenomes - Genome Assembly & Seq. Algos. - Algorithmic Evo. Bio - Single Cell & Spatial Omics - Microbial Genomics - AI/ML & Integrative Omics 🙏🙏🙏

Save the Date #eccb2026: 31 August-4 September 2026 The 25th ECCB European Conference on Computational Biology will take place in Geneva, Switzerland, organized by @sib.swiss For more information: eccb2026.org 🧪

A solution to the indexing dilemma in large pangenomes, by Parsa Eskandar from UCSC: Lossless Pangenome Indexing Using Tag Arrays", offering a practical indexing layer to develop scalable aligners and downstream graph-based tools www.biorxiv.org/content/10.1... #wabi25

"Human readable compression of GFA paths using grammar-based code" being presented by Peter Heringer at #WABI25

Great talk by Vikram @vikramshivakumar.bsky.social on studying pangenomes and synteny visualization in #WABI25 Github: github.com/vikshiv/mume... First paper: genomebiology.biomedcentral.com/articles/10.... Second: www.biorxiv.org/content/10.1... #WABI2025

Is more genomic data always better? Not necessarily, the benefits may eventually plateau. Keynote talk by @benlangmead.bsky.social in #WABI2025 link.springer.com/article/10.1... FORGe: prioritizing variants for graph genomes

EdgeHOG: a method for fine-grained ancestral gene order inference at large scale www.nature.com/articles/s41...

Newly developed structure-based methods do not outperform standard sequence-based methods for large-scale phylogenomics academic.oup.com/mbe/article/...

How can we best infer horizontal gene transfer (HGT) in prokaryotes? Our new study finds a surprising winner: gene presence–absence patterns beat explicit phylogenetic approaches! 📄 Mishra & Lercher (2025), Mol Biol Evol 🔗 doi.org/10.1093/molb...

Pangenome-guided sequence assembly via binary optimisation www.biorxiv.org/content/10.1... "a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex regions without bias towards a single reference...a new tool kmer2node for aligning reads onto pangenome graphs

I love this diagram

Using google gemini with grounding for later reference? Make sure you download your links before they expire... :(

A computational screen for alternative genetic codes in over 250,000 genomes Yekaterina Shulgina, Sean R Eddy (2021) elifesciences.org/articles/71402

Long story short: we assemble 17 representative Arabidopsis thaliana genomes, exhaustively annotate NLRs with long read evidence & manual curation, and assay many measures of NLR diversity.

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...

The Sudmant lab at UC Berkeley is seeking a postdoc to work on a fully funded NIH project to understand differences in DNA repair and somatic mutation across the primate tree of life. Please spread widely to those who may be interested aprecruit.berkeley.edu/JPF05052

Dijkstra’s is not optimal anymore for finding shortest paths!? Breaking the Sorting Barrier for Directed Single-Source Shortest Paths arxiv.org/abs/2504.17033

My team has updated our free database of POSTDOC fellowships. This database contains 286 entries. For each entry, we provide a link, short description, deadline, amount, and eligibility criteria. Download this updated and expanded database here: research.jhu.edu/rdt/funding-...

Olivier's paper out now! We find that similarity metrics derived from AlphaFold structures & PLM embeddings can help identify pairs of paralogs with shared functions. Not always better than sequence identity, but not redundant with it, so combining them works best. academic.oup.com/nargab/artic...

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3