Rauf Salamzade

Toward a unified framework for determining conformational ensembles of disordered proteins - Nature Methods This Perspective establishes a comprehensive and practical framework to guide intrinsically disordered protein (IDP) ensemble determination, benchmarking and interpretation, as well as proposes a roadmap for IDP ensemble determination, uncertainty quantification and actionable benchmarking strategies.

Toward a unified framework for determining conformational ensembles of disordered proteins | Nature Methods https://www.nature.com/articles/s41592-026-03003-2

mvif 47

Happy Monday!
We can't wait to welcome #MVIF 47 speakers and YOU 🤩

Highlights
🇧🇪 Andrey Radev
🇮🇷 Zahra Nezamivand Chegini

Keynote
🇬🇧 Lindsay Hall (@halllab.bsky.social)

Talks
🇺🇸 Chris Robinson
🇨🇭 @lukasmalf.bsky.social

🇮🇷 Mohammad Salimi

Free registration: cassyni.com/s/mvif-47

Diagram representing the impacts of viruses on aqueous sediment geochemistry. Organic matter (OM) sinks to the sediments, which is cycled in the microbial community, as well as increasing abundance, diversity, activity, and degradation of OM. From this “microbial loop” recalcitrant dissolved organic matter (RDOM) and dissolved inorganic carbon (DIC) are stored in sediments. Carbon is also released into the atmosphere from the sediment, and viral infection transfers genes between hosts or releases exogenous DNA to be used by bacteria, potentially aiding in metabolic activity. Created in BioRender. Williams, J. (2026) https://BioRender.com/b4wqimp.

#MicrobiologyMonday: Marine sediments store vast amounts of carbon. By infecting and lysing microbes, viruses shape biogeochemical cycling from coastal zones to the deep sea and influence long-term carbon storage. Get the story in #AppEnvMicro: asm.social/2Qv

A new era for #ONT amplicon sequencing?
We show that #ONT #amplicon sequencing now achieves accuracy sufficient for #ASV resolution using standard Illumina-based pipelines. We validated this by sequencing identical amplicons on #ONT and #PacBio. @nanoporetech.com www.biorxiv.org/content/10.6...

Portrait of Elisabeth Bik @elisabethbik.bsky.social

Join us today @cudanlab.bsky.social

for a lecture & discussion with

Elisabeth Bik @elisabethbik.bsky.social

on "Errors and Misconduct in Biomedical Research Images"

🦠🔬🎨

16:00-18:00 Tallinn time UTC+2 🇪🇪🇪🇺🌍
(5 hours from this post).

Details & zoom: cudan.tlu.ee/events/2026-...

This! 👇

Our work on bacterial Schlafens in phage defense is out today @natmicrobiol.nature.com!

Check out the final version here:
rdcu.be/e7Bmz

We are looking for postdocs and students to expand our team! Official postings are coming soon.

Please reach out if you're interested!
#phage #phagesky #microsky

Peer review reliability is shockingly low. Meta-analyses show reviewer agreement barely above chance, and grant outcomes often depend more on who reviews than what's proposed. Our new preprint with Agnes Urban and Arjun Krishnan @compbiologist.bsky.social : papers.ssrn.com/sol3/papers.... 🧵 1/

New preprint on the limits of detecting higher-order interactions in microbial communities.
www.biorxiv.org/content/10.6...
We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.

In Our Time - Bacteriophages - BBC Sounds Melvyn Bragg and guests discuss how viruses can help us track and cure bacterial illnesses

🦠 “𝗧𝗵𝗲 𝘃𝗶𝗿𝘂𝘀𝗲𝘀 𝘁𝗵𝗮𝘁 𝗲𝗮𝘁 𝗯𝗮𝗰𝘁𝗲𝗿𝗶𝗮 𝗰𝗼𝘂𝗹𝗱 𝘀𝗮𝘃𝗲 𝘂𝘀 — 𝗯𝘂𝘁 𝗵𝗼𝘄?”

Historian @kirchhelle.bsky.social chats with 𝗠𝗮𝗿𝘁𝗵𝗮 𝗖𝗹𝗼𝗸𝗶𝗲 & 𝗝𝗮𝗺𝗲𝘀 𝗘𝗯𝗱𝗲𝗻 about revival of phage biology & phage therapy as antibiotics fail.

🎧 2024 BBC Radio 4 — listen worldwide:

www.bbc.co.uk/sounds/play/...

#phage #phagesky #microsky

#OnThisDay in 1938, American evolutionary biologist Lynn Margulis was born. Margulis is most known for developing and popularising the endosymbiotic theory, which explains how eukaryotic cells evolved organelles from simpler prokaryotic organisms that resided within another and became incorporated.

Lovely work driven by Lizzie Ledger in the group: a new but druggable mechanism by which Staphs produce biofilm using components of human serum. First polysaccharides, then protein, then eDNA, now lipids too!

bsky.app/profile/bior...

🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process.
www.biorxiv.org/content/10.6...

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

MKado: a toolkit for McDonald-Kreitman tests of natural selection https://www.biorxiv.org/content/10.64898/2026.03.02.709122v1

Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...

Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives.
www.nature.com/articles/s41...

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes

www.science.org/doi/10.1126/...

Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!

Linking below previous thread on our findings

An Enzyme System to Help Catalyze Bioproduction of Plastic | Joint Genome Institute By characterizing the structure and function of a methylthio-alkane reductase system, researchers could open avenues for using bacteria to produce ethylene and more.

By characterizing the structure and function of a methylthio-alkane reductase system, researchers could open avenues for using bacteria to produce ethylene and more. 🖥️ 🧬

Full story: https://jgi.doe.gov/user-science/science-stories/enzyme-system-help-catalyze-bioproduction-plastic

🚨 Registration is OPEN!
Join us for the 2026 Perlman Symposium on Antibiotic Discovery & Development
🗓 May 15, 2026 | ⏰ 9–5
📍 In-person or virtual (FREE!)
🔗 perlman.mmi.wisc.edu

Gut bacteria rewire fat tissue to burn more energy Study reveals how the gut microbiome and diet work together to transform white fat cells into energy-burning beige fat in mice.

New research from @thexavierlab.bsky.social finds that the gut microbiome fine-tunes fat tissue in mice in response to diet, converting it from energy-storing fat to more energy-burning fat when dietary protein is low.

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

Diversity and ecological roles of hidden viral players in groundwater microbiomes - Nature Communications Groundwater viruses are less well studied. Here, using large-scale sequencing, the authors uncover extensive, largely uncharacterized viral diversity in groundwater, showing that viruses infect domina...

New paper from @adjiep.bsky.social on viral impacts in groundwater at Nature Comms. Congratulations Adjie and team!

Read: www.nature.com/articles/s41...

#viruses #viromics #groundwater

Flexible paths to multicellularity Close relatives of animals can become multicellular if distinct individuals join together or if dividing cells remain attached. A species has been found to use both mechanisms.

This species can become multicellular using two mechanisms previously thought to be mutually exclusive

go.nature.com/4aTKdfF

🧫 Just out in Bioinformatics Advances: "AssiST: Convolutional neural network for analysis of antibiotic susceptibility testing" 

Read the full paper here:  https://doi.org/10.1093/bioadv/vbag063

Authors include: @carmenli.bsky.social, @amitchell.bsky.social

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

Structural insights into metallocluster trafficking in the nitrogenase assembly scaffold NifEN - Nature Catalysis Structural insights into the assembly of the complex nitrogenase cofactor are scarce. Now, cryo-EM and AlphaFold analyses of NifEN, which converts the precursor (L-cluster) to a mature cofactor (M-clu...

So excited to share our cryo-EM study of the nitrogenase cofactor assembly scaffold NifEN expressed in E. coli!
@ribbehulab.bsky.social @ucibiosci.bsky.social @natcatal.nature.com
www.nature.com/articles/s41...

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions.

We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.

Integrating the Microbiome Into Infection Ecology and Evolution in Wild Animals Parasites are a ubiquitous force in nature threatening wildlife populations and ecosystems. Interactions between hosts and their parasites are impacted by host-associated microbiomes, which are essen...

A nice collaboration from post-docs in my lab 😊 onlinelibrary.wiley.com/doi/full/10.... @jingdi.bsky.social @luismsilva.bsky.social @paradyseb.bsky.social @molecularecolup.bsky.social

A symbiotic origin of the ribosome? Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

"we propose that the protoribosome was a parasite (...). If this view is correct, then like the spliceosome in the stem eukaryote, a repurposed host-parasite interaction led to a dramatic change in cell biology at the base of the tree of life, in this case leading to the exit from an RNA world"