New postdoc opportunity in our team! Topic is computational analysis of (meta)genomic data to study evolution of plant-microbiome interactions. Part of the AEGIS consortium (aegisearth.bio/en). Apply here: www.wur.nl/en/vacancy/p... Please RT!

Postdoc on computational (meta)genomic analysis

Climate change is one of the greatest challenges for global food security, requiring new approaches to understand and harness the natural diversity that enables plants and their associated microbiomes...

wur.nl

1/ Excited to share our preprint ImpuT2T: a pangenome-based assembly patching tool ImpuT2T scaffolds draft human assemblies with a pangenome (HPRC2) and patches gaps by leveraging linkage disequilibrium and sequence identity between contigs and reference haplotypes Code: github.com/maojanlin/Im...

ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies

With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...

biorxiv.org

Amazing to see this online today! A very fun project over the past couple of years (made all the better by a great team of people to work with!)

Yulin Zhang@yulinzhang.bsky.social · 6d ago

Good news! Our paper (with @aabiddanda.github.io @sarahaj34.bsky.social @codushlaine.bsky.social and Priya Moorjani) is now officially online! www.science.org/doi/10.1126/...

📢 Genome Informatics 2026 (Hinxton UK + virtual, 2–4 Dec) is coming! Some confirmed speakers now listed: coursesandconferences.wellcomeconnectingscience.org/event/genome... Early-bird registration & bursary deadlines: 7 Sept. Abstract deadline: 5 Oct. Please submit your work & join us!

ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies https://www.biorxiv.org/content/10.64898/2026.07.27.741037v1

MADRe: Strain-level metagenomic classification through assembly-driven database reduction doi.org/10.1093/giga... Software: github.com/lbcb-sci/MADRe

Ver excited to share my just-published Darwin Review with @lh3lh3.bsky.social on population-scale long-read sequencing! royalsocietypublishing.org/rspb/article...

Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics

Abstract. Population-scale long-read DNA sequencing (PLRS) is rapidly reshaping our understanding of genomic variation in humans and non-model species. In

royalsocietypublishing.org

Accelign: a GPU-based library for accelerating pairwise sequence alignment doi.org/10.1186/s128...

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

Excited to share our now published paper @cp-cell.bsky.social highlighting advances in modeling the evolution of protein-protein interactions with MSA Pairformer. Big thanks to Zhidian Zhang, Olivia Tang, @eunbelivable.bsky.social @milot.bsky.social @martinsteinegger.bsky.social and @sokrypton.org!

Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer

Protein language models have excelled at modeling individual proteins, but extending these capabilities to protein complexes remains a major challenge. MSA Pairformer, a parameter-efficient protein la...

cell.com

Only 3 days left to submit an abstract for the Great Lakes Annual Meeting of Evolutionary Genomics! The abstract submission deadline is July 24; registration will remain open until August 10. GLAM will be held on August 15, at the University at Buffalo. The participation is capped at 100 people.

GLAM-Evogen 2026 Registration and Abstract Submission Portal

GLAM-Evogen will be held on August 15, 2026 at University at Buffalo, NY. We aim to bring together faculty and trainees from a range of backgrounds with a particular focus on work at the interface bet...

forms.gle

A DNA foundation model predicts osteoporosis risk genes without proximity bias www.biorxiv.org/content/10.6... They address the assumption underlying variant-to-gene methods: that the gene nearest to a non-coding variant is the most likely causal effector gene (eGene).

Why rammap can be faster: 1) AVX2/AVX512 for base alignment; 2) better memory management (minimap2 is okay but not the best); 3) more sophisticated multi-threading model with rayon; 4) SIMD-based chaining learned from mm2-fast.

New Nature Reviews Genetics paper out! How are graph-based pangenomes removing reference bias and opening up new possibilities in GWAS and rare- and common disease genetics? 🔗 nature.com/articles/s41576-026-00987-7 #pangenome #geneticdiversity #referencebias

Building and applying pangenome references to capture genetic diversity - Nature Reviews Genetics

Pangenomes are genome references that integrate sequences from multiple individuals into graph-based or multi-haplotype representations, capturing genetic variation beyond a single linear reference. H...

nature.com

I am starting my lab at the University of Geneva next January! Incredibly excited to soon be joining the MOCEL department as an Asst. Professor. The lab will use evolutionary cell biology to study chromosomes, centromeres & speciation 🧬🔬🌱 Intrigued, want to join or collaborate? 🔗 helsenlab.org

Helsen lab | chromosome and centromere evolution

The Helsen lab at the University of Geneva explores how centromeres and chromosomes evolve, diversify, and function across eukaryotes. Discover our latest publications, research team, and open positio...

helsenlab.org

1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

Navigating the pangenome coordinate system with Shredtools

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

biorxiv.org

Efficient algorithms for simulating sequences along a phylogenetic tree doi.org/10.1093/bioi...

Very happy to be presenting "Taxonomic classification using Kraken 2" in today's #ISMB2026 tutorial "Metagenomic sequence analysis using k-mer based methods": www.iscb.org/ismb2026/wha... In about 15 minutes!

We're hiring interns, research officers & postdocs at the A*STAR Genome Institute of Singapore. Projects: • RNA therapeutics—optimizing mRNA for drugs & vaccines • RNA drugs—structure prediction & small-molecule binding • World models for biology • Read error correction for cancer genomes HERRO2 2/3

We're recruiting! An open functional genomics postdoc position at @scilifelab-ngi.bsky.social / my lab / Robert Månsson lab. Top notch environment for technology and applications development in lovely Stockholm. Please spread the word or apply if interested: www.kth.se/lediga-jobb/...

JOB ALERT! I'm hiring two postdocs in Computational Genomics to join our lab in beautiful Gothenburg, Sweden. Please share and repost! CGRLab.github.io/research/

🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...

Pangenome-based human genome analysis improves trait association and genomic prediction

The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysi...

doi.org

Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg

Efficient evidence-based genome annotation with EviAnn

Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.

rdcu.be

Hi ocean -omics folks, someone (a while back) mentioned to me that they thought the Tara Oceans metagenome sequencing effort did some "blanks" sequencing - negative controls intended to get at contam & artifacts. I can't find any mention of them in papers tho. Can anyone help me find 'em? thx!

The microbiome as a biosensor? Here we show that metabarcoding and machine learning can predict seawater chemistry, plankton composition and eutrophication status. Hackathon project with Emma Bell, @garefelt.bsky.social, @ktjurdzinski.eurosky.social, Fernando Delgado et al. doi.org/10.1038/s432...

The marine microbiome can accurately predict its chemical and biological environment - Communications Earth & Environment

Microbial DNA profiles from seawater can act as biosensors of environmental conditions and ecosystem status, demonstrating the potential of metabarcoding and machine learning in marine monitoring and ...

doi.org

Join us for a community-driven tutorial on orthology, featuring developers of OrthoDB, OrthoFinder, InParanoid, MBGD, PANTHER, OMA and ... A special thanks to @wheelerlab.org and Evgenia Kriventseva for making this happen!

European Conference on Computational Biology@eccb-europe.bsky.social · 3mo ago

Orthology made practical 🧬 Compare genes across species and choose the right tools. Tutorial organized by: Natasha Glover, Sina Majidian and Stefano Pascarelli Register here: 👉 eccb2026.org/registration... #ECCB2026 #ComparativeGenomics

Applications now open for the UNIL Summer School on Modelling for Evolutionary Biology (31 Aug–5 Sep 2026, Lausanne)! For PhD & postdocs interested in formal approaches to evolutionary ecology (incl. social evo, life-history, species interactions). Scholarships available, Pls RP! shorturl.at/fo1GA

Last day of #biodiversity #bioinformatics summer school with @denbi.bsky.social & @sib.swiss - great presentation from Topic 4 Comparative #Genomics group

How? Mainly length-based + threshold-based row splitting in the move structure. Threshold splitting squeezes each threshold value down to a single bit. (2/6)