1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

Check out our new article if you are interested in disorder-mediated protein interactions, AlphaFold-based structural modeling and variant characterization: Https://rdcu.be/fw2oz Dx.doi.org/10.1038/s41594-026-01846-z

Variant characterization in the intrinsically disordered human proteome - Nature Structural & Molecular Biology

Proteome-wide prediction and structural modeling of disordered protein interaction interfaces advance characterization of disease-associated variants in disordered protein regions.

dx.doi.org

Every time I see a new method with fine tuning protein language models to predict any form of interaction my immediate reaction is skepticism and thinking of the effort it takes to test any new model for generalisation.

Huge congrats to the many authors who over MANY years worked on this (but especially @karaehunt.bsky.social , @trevorbrandt.bsky.social, Karina, @shaharsu.bsky.social and @remenecker.bsky.social. www.nature.com/articles/s41...

Rational design of disordered proteins for sequence–function investigation - Nature

GOOSE enables the design and testing of thousands of disordered protein region sequences to reveal distinct sequence-to-function relationships.

nature.com

Alex Holehouse@alexholehouse.bsky.social · 5mo ago

New (well, very old, but 100% updated) preprint: Rational design of disordered proteins for systematic sequence-to-function investigation Work done in collaboration with @shaharsu.bsky.social lab - check out the three (3) threads from the folks who did the work!

The Chen Lab @ EMBL Rome (current population: 1) is hiring! Looking for an experimental Lab Manager w/ a PhD and experience in molecular bio and mouse-based neuro research. Apply if you like: mouse behaviors, high-throughput sequencing, good coffee & ancient history tinyurl.com/48h66vfh

Lab Manager

The European Molecular Biology Laboratory (EMBL) is one of the world’s leading life science research organizations. With sites across Europe, EMBL fosters an international, collaborative, and inclusiv...

tinyurl.com

Frontier AI companies as biotech acquirers www.nature.com/articles/s41...

If I had to sum all the flight delays and time spent on a plane waiting to take off, I am sure that the single biggest share of it must be due to issues with the French air traffic controllers.

Our congratulations to Ludwig Princeton’s Michael Skinnider, winner of the 2026 ICTP-IBM Brahmagupta Artificial Intelligence Prize for Early Career Scientists, which celebrates applications of AI to science that promise to be of general benefit to society. bit.ly/4pAf87x

Review/perspective article by Diederik Laman Trip on some of his and our lab's thinking on how we can study human genetics across different levels. In particular around cell-type specific protein interactions, tissue organization and organ morphology. (paywall, shareable link rdcu.be/fvnpz)

Human genetics across levels of biological organization

Nature Reviews Genetics - Genetic variation influences biological processes across scales; however, deciphering how effects propagate from molecules to whole organisms remains a key challenge in...

rdcu.be

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

Can we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX

Ensembles of in silico structures enable T cell peptide-MHC binding prediction

Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data rem...

biorxiv.org

RSS is officially launched! This is the latest project to join OMSF and will focus on unlocking experimental data modeling at scale. Co-founded by the incomparable @alisiafadini.bsky.social!

Reciprocal Space Station@rs-station.bsky.social · 2w ago

1/ We're excited to announce that @rs-station.bsky.social is joining the Open Molecular Software Foundation @omsf.io!

New lab preprint - Deep learning models are most often difficult to interpret black box models. What if we engineer them with interpretation in mind? Dennis Gankin carefully studied so-called biologically inspired neural networks and found an interesting phenomenon www.biorxiv.org/content/10.6...

Leveraging multiplicity in biologically informed neural networks to uncover disease heterogeneity

Biologically inspired neural networks (BINNs) embed pathway, ontology, or protein-interaction structure directly into neural networks, promising interpretable disease prediction where hidden nodes map...

biorxiv.org

The dynamics of this AI race is changing. It was a 3 way race including 2 companies that are cautious about safety risks. Now it is some 5 USA and 2 Chinese, some open models, but on average much less is being done about risk mitigation. International cooperation and regulation seems critical now.

With @helucro.bsky.social, @mikelove.bsky.social and Robert Gentleman at the Ukrainian Biological Data Science Summer School

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

We have updated our preprint with a benchmark of 17 methods for structural annotation of MS/MS spectra: www.biorxiv.org/content/10.6...

Confronting spurious evaluations of computational methods in small molecule mass spectrometry

Mass spectrometry-based metabolomics detects thousands of small molecule-associated signals in biological samples, but the vast majority cannot be structurally identified. Mounting interest in this me...

biorxiv.org

Michael Skinnider@skinnider.bsky.social · 3mo ago

We have identified what we believe to be a critical issue in the way that computational methods for structural annotation of small molecule MS/MS spectra have historically been evaluated. Fortunately, there is a solution: www.biorxiv.org/content/10.6...

Join us in a fun, crazy and interesting interdisciplinary research project that combines protein biophysics, evolutionary genomics, biomolecular archaeology, and textile research to resolve species identity and post-translational modifications in the structural proteins collagen and keratin

Matthew Collins@matthewcollins.bsky.social · 3w ago

Copenhagen job alert 🚨 GLOBE (@ucph.bsky.social) is hiring a 21-mo Postdoc in #Bioinformatics & #ComputationalProteomics Work with @lindorfflarsen.bsky.social, @fridowelker.bsky.social, @brandtgroup.bsky.social & more mapping collagen/keratin diversity across 1000s of genomes. 📅 Deadline Aug 31

Can we program a kinase like a switch? Inspired by natural autoinhibitory complexes, we designed miniproteins against active- and inactive-like conformations of Focal Adhesion Kinase. Depending on the targeted state, the resulting binders either activated or inhibited the kinase.

Team science preprint, exploring the capabilities and limitations of Alphafold3 across different application areas, including protein-RNA, protein-lipid, ubiquitination,TCR and antibody recognition with @ninjani.bsky.social @labvanni.bsky.social @dgfeller.bsky.social www.biorxiv.org/content/10.6...

Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas

Structure prediction models have moved from single proteins to assemblies that include diverse biomolecules and their modifications. AlphaFold3 (AF3) and related models extended structural modelling v...

biorxiv.org

🚨 We're hiring! My new lab at EMBL Hamburg is looking for a Research Technician. I'm looking for someone excited by phages, metabolism, enzymes, structural biology and bacterial immunity—if you know the right person, please share this post!🧵⬇️ Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Research Technician (Osterman Group – Metabolism-driven immunity)

EMBL Hamburg / CSSB The European Molecular Biology Laboratory (EMBL) is Europe’s flagship life sciences organization, with more than 110 independent research groups across Heidelberg, Hamburg, Grenobl...

embl.wd103.myworkdayjobs.com

New preprint: Cell-type-resolved spatial proteogenomics, matched genome AND proteome of the same cells. The trick: the flowthrough we normally discard after loading peptides onto an Evotip contains genomic DNA at 85–95% yield. One tip, two molecular layers. www.biorxiv.org/content/10.6...

Cell-type-resolved spatial proteogenomics from matched genome and proteome of the same cells

The genome and proteome of the same cells are rarely measured together, which is especially consequential in cancer, where somatic mutations vary across clones and drive disease. We show that a single...

biorxiv.org

Happy to share that this beautiful work by @mudgal17.bsky.social in collaboration with the Weis lab @eth-dbiol.bsky.social, discovering a new membrane fusion mechanism in eukaryotes, is finally out in peer-reviewed form at @cp-molcell.bsky.social. www.cell.com/molecular-ce...

A conserved mechanism of membrane fusion in nuclear pore complex assembly

Fischer et al. uncover a fundamental mechanism of membrane fusion during nuclear pore complex (NPC) assembly. Brl1 and Brr6 form ring-shaped, membrane-remodeling complexes that interact and bridge the...

cell.com

Vanni Lab at UNIFR, Switzerland@labvanni.bsky.social · last yr.

Happy to share the latest work from the lab, led by @mudgal17.bsky.social‬, in collaboration with the Weis lab @ethzurich.bsky.social. How do nuclear membranes fuse during NPC assembly? We answer this question in our latest work, where we identify a new mechanism for membrane fusion… (1/13)

New preprint alert! We integrated plasma proteomics, whole-blood transcriptomics, machine learning and network propagation to dissect high-risk thrombotic primary antiphospholipid syndrome (APS). 🩸🧬https://www.medrxiv.org/content/10.64898/2026.06.26.26356680v1

Adding my 2 cents about using agents for scientific work, with a focus on what's dear for German academia: "Datenschutz" and independence from foreign influence. Plus some concrete examples on how to use and sandbox the excellent pi harness! www.microbial-pangenomes-lab.org/2026/07/08/A...

The @qedscience.bsky.social "impact" score generated a lot of discussion on ranking preprints, including ideas on multi-dimensional rankings that are user specific. Besides describing the ideas, we can now prototype them (with Claude in this case). Here is Salient salient-sgeu6fs5ua-uc.a.run.app

1/ 🧬🧪 New preprint! Do you actually need a biology-specific foundation model to predict how cells respond to perturbations? Surprising answer: a general-purpose tabular model - never trained on a single cell - matches or beats the specialists. 🧵 📄 doi.org/10.64898/2026.06.28.735106 @biohub

I would like to announce that I have recently started my own research group, the Pediatric Cancer Genomics Laboratory, at Institut de Recerca Sant Joan de Déu (IRSJD) - Fundació de Recerca Sant Joan de Déu.

An Atlas of Short Linear Motif-Mediated Human Protein-Protein Interactions https://www.biorxiv.org/content/10.64898/2026.07.03.735260v1