Rauf Salamzade
Interested in microbial ecology & evolution. Views are only my own. (he/him)
🎓: scholar.google.com/citations?hl=en&use…
👨💻: github.com/raufs
- Reposted by Rauf SalamzadeRegistration fee is only 175€, some of the invited speakers: Charles Rice, Yasmine Belkaid, Bonnie Bassler, Daniel Mucida, Joy Bergelson, Matthew Chang, Carolina Lucas, Jeff Barrick, Carolina Tropini, Roy Kishony and more... Save the date now!
- Reposted by Rauf Salamzademeetings.embo.org/event/26-mic... Announcing the 2026 EMBO course in Computational and Experimental Microbiomics, to be held at Bath. The course brings together experiments and bioinformatics to study host-microbe interactions and co-evolution. Register now, or at least by 11 May, if interested :)
- Reposted by Rauf SalamzadeWeekend read! Structural proteome unfolds insight into gut microbiome: Structure database of gut microbial proteins & structure-aware AI model for remote homolog detection. Reveals diversification of phage endolysins & bacterial enzymes in melatonin biosynthesis www.cell.com/cell-host-mi...
- Reposted by Rauf SalamzadeWhat happened before the last universal common ancestor? Pre-LUCA evolution is hard to study. In our new Cell Genomics Perspective we spotlight how paralogous proteins open a window onto the deepest chapters of evolution. 🧬🌍 Out today! --> www.cell.com/cell-genomic... @cellpress.bsky.social
- Reposted by Rauf SalamzadeNew blog post: ONT read QC strategies for assembly rrwick.github.io/2026/02/05/r... Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
- Reposted by Rauf Salamzade🧬🔬🎥 @science.org Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries | Science www.science.org/doi/10.1126/...
- Reposted by Rauf SalamzadeMapping of the viral shunt across widespread coccolithophore blooms using metabolic biomarkers | PNAS pnas.org/doi/abs/10.1073/pna…
- Reposted by Rauf SalamzadeWhat does competition for iron look like for pathogens in different environments? We had the chance to contribute to this great paper looking at Salmonella in the gut with the Cunrath Lab (UoStrasbourg). Salmonella relies on siderophore exploitation at low pH url: academic.oup.com/microlife/ar...
- Reposted by Rauf SalamzadeHow does catalysis emerge from non-catalytic domains? In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead. A striking case of catalysis evolving from binding.
- @claudele.bsky.social et al. studied the fundamental question of how enzymatic activity emerges by focusing on type B dihydrofolate reductases, suggesting DfrB domains evolved rudimentary catalysis from a binding capacity. 🔗 doi.org/10.1093/molbev/msaf215 #evobio #molbio
- Reposted by Rauf SalamzadeImportant study highlighting the need for rigorous quality control during sequencing and the value of analyzing sequence read depth variation in assemblies.
- Reposted by Rauf SalamzadeEven with the largest zoom on a classic compound optical system, scientists struggle to make sense of finer details. Microbiologists are turning to an unexpected source to clear things up: a moisture-absorbing material found in diapers. www.quantamagazine.org/expansion-mi...
- Reposted by Rauf SalamzadeAccurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
- Reposted by Rauf SalamzadeIt's increasingly clear that commensal viruses play important roles in human health, but how do you study them? Our review "Tools and approaches to study the human gut virome: from the bench to bioinformatics" is out today in mSystems! journals.asm.org/doi/10.1128/... @haleybiont.bsky.social
- Reposted by Rauf SalamzadeMany questions in biology aren’t about individual proteins...they’re about how proteins behave together. This week we launched CoSearch in SeqHub: a user-requested analysis that lets you explore where multiple proteins co-occur across 132,000 microbial genomes, in seconds.
- Reposted by Rauf Salamzade🦠 How do microbes arrive together, and why does it matter for #microbial #diversity? 👉 Read the paper: journals.plos.org/ploscompbiol... Published in @plos.org Computational Biology 🎉 Congratulations to authors Loïc Marrec & Sonja Lehtinen @sonjalehtinen.bsky.social @unil.bsky.social @sib.swiss
- Reposted by Rauf SalamzadeNew paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects. www.nature.com/articles/s44...
- Reposted by Rauf Salamzade
- Reposted by Rauf SalamzadeNew @kaggle.com competition, which I am happy to co-host Can you extract the metadata of mass-spec experiments from scientific papers? Thanks to the NSF National Synthesis Center for Emergence in the Molecular and Cellular Sciences (NCEMS) for sponsoring. www.kaggle.com/competitions...
- Reposted by Rauf SalamzadeHey y’all, New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae www.microbiologyresearch.org/content/jour...
- Reposted by Rauf SalamzadeFirst paper of my PhD @doerrlab.bsky.social is up! We characterized meropenem tolerance in Enterobacterales species, and then further dissected tolerance mechanisms in Klebsiella pneumoniae. journals.plos.org/plospathogen...
- Reposted by Rauf SalamzadeDoes anyone have experience with counter-selectable markers for Gram-negative bacteria besides sacB? It's been working poorly in our hands.
- Reposted by Rauf SalamzadeCongratulations to Eilidh Ward (first author and PhD student co-supervised by co-authors Julie Aspden, David Westhead and yours truly) on this lovely contribution - a method to visually inspect reads from novel open reading frames: doi.org/10.1093/bioa...
- Reposted by Rauf Salamzade#microsky #phagesky #phage #microbiomesky Molecular adhesins from gut #phages www.biorxiv.org/content/10.6...
- Reposted by Rauf SalamzadeSlim 5 can now simulate genomes with multiple chromosomes like autosomes, sex chromosomes, mitochondria and chloroplast dna academic.oup.com/mbe/article/...
- Reposted by Rauf SalamzadeCustomizing CRISPR–Cas PAM specificity with protein language models Paper: www.nature.com/articles/s41... (free: rdcu.be/e1YwG) Code: github.com/Profluent-AI... Web: protein2pam.profluent.bio
- Reposted by Rauf SalamzadeDiscovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence academic.oup.com/ismej/advanc... #jcampubs
- Reposted by Rauf SalamzadeA gift of an article from the inimitable Colin Kleanthous as he says a moving farewell to his laboratory. A brave, unrepentant and scientifically brilliant journey is described - please have a read, friends. www.jbc.org/article/S002...
- Reposted by Rauf Salamzade#ProtistsOnSky no 'swimming' by 𝘝𝘢𝘮𝘱𝘺𝘳𝘦𝘭𝘭𝘢, definitively no 'staying still'. just a relaxed walk towards the lunch...
- Do microbes get more food by swimming or staying still? Turns out both work, and cilia help them pull in nutrients no matter the strategy. buff.ly/vK3GmK5
- Reposted by Rauf SalamzadeIt is widely accepted that #T6SS -mediated intoxication occurs only on solid surfaces, where prolonged cell-cell interactions are forced, and not in liquid environments. But is this generalization true? Our new preprint says it isn't. A 🧵 ... biorxiv.org/content/10.6... 🦠
- Reposted by Rauf SalamzadeBacteriophages mobilize bacterial defense systems via lateral transduction #phage #virus #microecoevo www.science.org/doi/10.1126/...
- Reposted by Rauf SalamzadeDietary fiber should be considered an essential nutrient 👇 www.nature.com/articles/s43...
- Reposted by Rauf SalamzadeFirst results chapter from Kelly-Rose Tulley’s PhD is published. It was a great team effort to get this finished. This work supports previous results on S. coelicolor OrrA and suggests its function is highly conserved. #microsky #streptomyces 1/2
- Defining the OrrA regulon and its role in development and antibiotic production in Streptomyces venezuelae NRRL B-65442 biorxiv.org/content/10.64898/20…
- Reposted by Rauf Salamzade𝘌. 𝘤𝘰𝘭𝘪 chromosome replicationists take note 👇 tsutomu katayama's lab tackles one of the last remaining puzzles of DnaB loading by DnaA to 𝘰𝘳𝘪𝘊 after opening. for bi-directional replication, 𝘁𝘄𝗼 DnaB helicases have to be loaded (in case you forgot). thx for pointing this out, wiep 🙏 #MicroSky
Dynamic DnaA–DnaB interactions at oriC coordinate the loading and coupled translocation of two DnaB helicases for bidirectional replication url: academic.oup.com/nar/article/...
- Reposted by Rauf SalamzadeGroup I introns in tRNA genes of Patescibacteria | mSystems journals.asm.org/doi/full/10.1128/ms…
- Reposted by Rauf SalamzadeFungal extracellular vesicles mediate conserved cross-species communication and immunomodulation -in #mBio journals.asm.org/doi/10.1128/...
- Reposted by Rauf SalamzadeThe Pseudomonas aeruginosa PrrF sRNAs and PqsA promote biofilm formation at body temperature -in #JBacteriol journals.asm.org/doi/10.1128/...
- Reposted by Rauf SalamzadeI joined efforts with D.A. Lucassen, @cdiener.com @gibbological.bsky.social and T. Wilson and got a really nice paper out on how to best integrate modern dietary assessment technologies to improve the accuracy of the current tools. Have a look here 👇 www.nature.com/articles/s43...
- Reposted by Rauf SalamzadeOur new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!) Link: www.nature.com/articles/s41...
- Reposted by Rauf SalamzadeFermentation conditions outweigh phylogeny in shaping the metabolome of novel Micromonospora strains: an integrated genomics-metabolomics analysis | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...
- Reposted by Rauf SalamzadeNow published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...
- New preprint! How much does antibiotic use shape bacterial lineage dynamics, and how does that relate to the fitness costs/benefits of resistance determinants? All sorts of fun findings and a method that we hope will be broadly useful. See @dhelekal.bsky.social's thread and the preprint!
- Reposted by Rauf SalamzadeMy first paper from my undergraduate work is out today :)
- Chemical inhibition of a bacterial immune system Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. One compound, IP6C, improves phage-therapy against P. aeruginosa & is effective against Thoeris in polymicrobial communities www.cell.com/cell-host-mi...
- Reposted by Rauf SalamzadeQuickening the pace (of evolution). Spatial structure speeds up adaptation to antibiotics. Great work by Partha Chakraborty just out: doi.org/10.7554/eLif...
- Reposted by Rauf SalamzadeFoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
- Reposted by Rauf SalamzadePioneering work by the @kacarlab.bsky.social Ancestral state reconstruction, expression of ancient nitrogenases, measuring their isotope fractionation, reinterpretations of geobiological record. Super cool :)
- The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient #microbes shaped Earth’s #nitrogen cycle and offering a new experimental framework for probing early life. www.nature.com/articles/s41...
- Reposted by Rauf SalamzadeVery happy and proud that our paper “Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation” is out today in #NatureMicrobiology @natmicrobiol.nature.com Paper 👉 t1p.de/v42xb #microbiome #commensal #pathomechanism #T3SS #immune #health #IBD
- Reposted by Rauf SalamzadeNew paper by Saskia Wilmsen and me just came out BioEssays: A new classification framework to understand evolutionary transitions in individuality Please find the OA paper here: onlinelibrary.wiley.com/doi/10.1002/...
- Reposted by Rauf SalamzadeShimojilide, a Potent and Selective Antiproliferative Cyclic Lipopeptide from a Marine Cyanobacterium Okeania sp. | Organic Letters pubs.acs.org/doi/10.1021/...
- Reposted by Rauf SalamzadeFresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41... Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
- Reposted by Rauf SalamzadeCan proteins fold and function with half of the amino acid alphabet? Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved. A minimalist foundation for ancient biology and synthetic design. tinyurl.com/37t8br4v #ProteinDesign #OriginsOfLife
- Reposted by Rauf SalamzadeWhy should microbiologists be interested in historical infection remedies, and how can we best investigate them for antimicrobial discovery? Thoroughly enjoyed co-writing this Microbiology Primer with @tosinorababa.bsky.social www.microbiologyresearch.org/content/jour... #MicroSky #Ancientbiotics
