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Luis E. Valentin-Alvarado

@luisvalentin.bsky.social
610 followers 346 following 36 posts

HFSP Research Fellow studying microbes, mobile DNA & RNA-guided immune systems.

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Reposted by Luis E. Valentin-Alvarado
Innovative Genomics Institute @innovativegenomics.bsky.social · 17/09/2026
Before #CRISPR, there was VIPR — a tool viruses used to battle each other with a never-before-seen genetic coding system, uncovered by researchers in the Doudna Lab. Read more here: ow.ly/KblS50ZOxwQ #AI #LanguageModel #RNA
Terry Zhang, Peter Yoon, Kenneth Loi (left to right) wanted to make sure to include Trevor Docter (on the phone from Harvard).
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Reposted by Luis E. Valentin-Alvarado
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 31/08/2026
Sad news. Yonath was/is a legend indeed. Now there are only 4 living female @nobelprize.org laureates in chemistry. There are 20 living Nobel Prize winners just at Stanford right now.
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Ardem Patapoutian @ardemp.bskyverified.social · 19/08/2026
Discover all the wonderful ways you can join the @hhmi-science.bsky.social, with opportunities ranging from undergraduate students to senior investigators. There will be no upper limit on career-stage eligibility for the Investigator program!
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Julia Meltzer @juliameltzer.bsky.social · 13/08/2026
Excited to share what I've been working on with an incredible team! Visualisation of Asgard viruses on cell surfaces and vesicles, and a story of complex viral interactions. Preprint: www.biorxiv.org/content/10.6... @brendanburns999.bsky.social @belindaferrari.bsky.social @xabivc.bsky.social
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Kranzusch Lab @kranzuschlab.bsky.social · 12/08/2026
The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyB
nature.com
Shared principles of human and bacterial antiviral immunity - Nature
The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector...
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Malcolm White @mfwhite2.bsky.social · 11/08/2026
Tim Blower and I are guest editing a Biochemical Journal @biochemsoc.bsky.social themed collection on: The Prokaryotic Immune System It's now open for research submissions and we'd welcome submission of research and review articles. More info: portlandpress.com/biochemj/pag...
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Reposted by Luis E. Valentin-Alvarado
Simon Roux @simrouxvirus.bsky.social · 27/07/2026
Reminder, registration for the Viral EcoGenomics & Applications (VEGA) 26 symposium is open ! See jgi.doe.gov/work-with-us... for more information
jgi.doe.gov
VEGA Symposium | Joint Genome Institute
Berkeley, CA
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Reposted by Luis E. Valentin-Alvarado
alex jaffe @alexjaf.bsky.social · 21/07/2026
my first 'data descriptor'! hoping this one will be useful for folks interested in tracing the distribution of genomes/genes/proteins over physicochemical gradients in the (deep) marine water column.
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Luis E. Valentin-Alvarado @luisvalentin.bsky.social · 21/07/2026
😍😍😍
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Chung Hyun Cho @chc-evobio.bsky.social · 04/07/2026
Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...
biorxiv.org
Emergence of histone-based chromatin complexity in Asgard archaea
The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...
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Reposted by Luis E. Valentin-Alvarado
Kevin Forsberg @kvnforsberg.bsky.social · 02/07/2026
Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial and human exonucleases mediate interkingdom antiviral immunity
All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...
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Reposted by Luis E. Valentin-Alvarado
Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...
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The Banfield Lab @banfieldlab.bsky.social · 06/06/2026
Big congrats to Susan Mullen and coauthors on this new preprint. 🎉 We're excited to share this work exploring microbial dispersal and establishment across river water, groundwater, soil, and hyporheic zone environments in the East River watershed. Read the preprint: www.biorxiv.org/content/10.6...
biorxiv.org
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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 28/05/2026
hetro-di-mers are released now.
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Reposted by Luis E. Valentin-Alvarado
Dan Portik @dportik.bsky.social · 28/05/2026
Now live! Submit a 100 word proposal to win free #PacBio HiFi sequencing for #metagenomics. Long-read metagenomics is rapidly gaining traction and this is a great time to apply it to your research. programs.pacb.com/l/1652/2026-...
programs.pacb.com
2026 PacBio SMRT Grant | Metagenomics
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Andrew Roger @andrewjroger.bsky.social · 28/05/2026
1/ Our new paper in Systematic Biology "Modeling Site-and-Branch-Heterogeneity with GFmix" led by @cgpmcc.bsky.social describes improved ways to model compositional heterogeneity across both sites and branches—an important source of error in deep phylogenomics. doi.org/10.1093/sysb...
doi.org
Modeling Site-and-Branch-Heterogeneity with GFmix
Abstract. Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino a
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Molecular Biology and Evolution @molbioevol.bsky.social · 27/05/2026
@joshnhamm.bsky.social @ndombrowski.bsky.social @greening.bsky.social @luisvalentin.bsky.social et al. provide the first investigation into the enigmatic Terrarchaeota and insights into the evolution of high salt adaptation in Archaea. 🔗 doi.org/10.1093/molbev/msag091 #evobio #molbio #microbeSky
doi.org
New lineages provide insights into the convergent evolution of extreme salt adaptation within symbiotic Archaea
Abstract. Environmental genomics has led to the discovery of many new lineages of archaea, including “DPANN” (or Nanobdellati), comprising organisms with s
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Ben J Woodcroft @benjwoodcroft.bsky.social · 26/05/2026
Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social
sandpiper.qut.edu.au
sandpiper
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Malcolm White @mfwhite2.bsky.social · 22/05/2026
As an editor at the Biochemical Journal, I'd love to see more papers submitted in the areas of bacterial immune systems / CRISPR / archaeal molecular biology / nucleic acid processing enzymes
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Reposted by Luis E. Valentin-Alvarado
Ben J Woodcroft @benjwoodcroft.bsky.social · 20/05/2026
SingleM 0.21 is go - @ace-gtdb.bsky.social R232 reference database, less verbose logging, fixes, etc. Thanks @thepatientwait.bsky.social @aroneys.bsky.social @rossenzhao.bsky.social and on GitHun @EisenRa @magicprotoss @MCeciC
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Luis E. Valentin-Alvarado @luisvalentin.bsky.social · 19/05/2026
Congrats Joshua for this amazing work!!
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Cress Lab @cresslab.bsky.social · 30/04/2026
Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.
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J. Craig Venter Institute @jcvi.org · 30/04/2026
It is with great sadness that we announce J. Craig Venter has died. 🧪🧬 www.jcvi.org/media-center...
jcvi.org
J. Craig Venter, genomics pioneer and founder of JCVI and Diploid Genomics, Inc., dies at 79
La Jolla, California—April 29, 2026—The J. Craig Venter Institute (JCVI) announced that J. Craig Venter, Ph.D., the Institute’s founder, board...
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Reposted by Luis E. Valentin-Alvarado
David Monchaud @dmonchaud.bsky.social · 29/04/2026
Happy to take you behind the scenes of the discovery of 7 alternative #DNA structures: 𝘁𝗿𝗶𝗽𝗹𝗲𝘅, G-quadruplex (𝗚𝟰), 𝗶-𝗺𝗼𝘁𝗶𝗳, both 3- and 4-way 𝗗𝗡𝗔 𝗷𝘂𝗻𝗰𝘁𝗶𝗼𝗻𝘀, 𝗥-𝗹𝗼𝗼𝗽 and the left-handed duplex 𝗭-𝗗𝗡𝗔. Hope you'll enjoy this journey back in time! In @narjournal.bsky.social 👉 doi.org/10.1093/nar/...
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Doudna Lab @doudna-lab.bsky.social · 27/04/2026
We present VIPR, a phage-encoded RNA-guided system that recognizes DNA with a noncontiguous code unlike CRISPR. Tiny, programmable, possibly ancestral to CRISPR immunity; VIPR is built around a striking RNA-DNA-DNA triplex.
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Jamie Cate @jhdcate.bsky.social · 27/04/2026
The best thing since *before* sliced bread... VIPRs. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
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Tami Lieberman @contaminatedsci.bsky.social · 22/04/2026
Interested in a *staff computational scientist* position? We are looking for an experienced computational biologist (ideally with microbiology experience) to support published packages while also driving new research. Pay range $73k-$111k w excellent benefits. careers.peopleclick.com/careerscp/cl...
careers.peopleclick.com
Computational Biology Program Scientist
MIT - Computational Biology Program Scientist - Cambridge MA 02139
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Karolin Luger @nucleosomepolice.bsky.social · 15/04/2026
Finally published at long last (at least in the pre-view version). Explore the wild and woolly world of archaeal histones! Interactive archaeal histone graph incluced rdcu.be/fdFjv. Congratulations to first author Shawn Laursen
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Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
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Asher Leeks @asherleeks.bsky.social · 14/04/2026
The Social Lives of Viruses is coming to Vancouver, Canada, from 4th-8th August 2026! This is a free meeting dedicated to all aspects of virus-virus interactions & evolution. To apply: socialviruses.zoology.ubc.ca @sociovirology.bsky.social #socialviruses #evosky #lovevirology #virosky
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Ella Sieradzki @sieravirus.bsky.social · 09/03/2026
I'm hiring my first postdoc! Apply by 20/4/26, position #20443. Seeking an environmental microbiologist with experience in metagenomics (preferably viromics) and molecular biology. Experience with targeted metabolomics is a plus. international.au.dk/about/profil...
international.au.dk
Postdoc in Soil viral ecology - Vacancy at Aarhus University
Vacancy at Department of Agroecology - Plant Pathology and Microbiology, Aarhus University
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Noah Whiteman @nkwhiteman.bsky.social · 01/04/2026
If preparing figures please consider "colorblind friendly" approaches (www.nature.com/articles/d41...). I am missing the long-wave opsin, which manifests in strange ways: I can't discern red vs. black. This dichromacy is rare and severe, but ~300 million have more common forms addressed in link.
nature.com
Colour me better: fixing figures for colour blindness
Images can be made more accessible by choosing hues, shapes and textures carefully.
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Evan Groover @evangroover.bsky.social · 31/03/2026
Excited to see the major chapter of my PhD in print! We present a massively-parallel approach for screening CRISPR edits in plants to speed up agricultural test cycles + benchmark genomic LMs. Thanks to my fantastic co-authors and advisors. Link below!
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The Banfield Lab @banfieldlab.bsky.social · 30/03/2026
Congratulations @wshuai.bsky.social and co-authors! We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...
biorxiv.org
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Géraldine Laloux @lalouxlab.bsky.social · 20/11/2025
Apply now to attend the next EMBO Bacterial Networks meeting #EMBOBacNet 🗓️13-18 September 2026 📍Sant Feliu de Guixols, Spain 📝Program and registration info: meetings.embo.org/event/26-bac... 👩‍🔬Organised with co-chair @s-lab.bsky.social and ECR @coralietesseur.bsky.social #MicroSky
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Kelly Nguyen @kellythd-nguyen.bsky.social · 26/03/2026
Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍. www.science.org/doi/10.1126/... www.youtube.com/watch?v=gFE4...
youtube.com
Cryo-EM structure of yeast telomerase
YouTube video by MRC Laboratory of Molecular Biology
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PacBio @pacbio.bsky.social · 26/03/2026
Successful AI models are built on data that is high-quality, complete, and rich in biological context. Basecamp Research is using PacBio HiFi sequencing to move beyond fragmented snapshots and build a richer map of biology. Read the blog here: bit.ly/4svvj6N #PacBio #HiFisequencing #Genomics
bit.ly
How HiFi metagenomic sequencing is powering AI-driven discovery with Basecamp Research - PacBio
Basecamp Research’s recent selection of PacBio HiFi sequencing to support its Trillion Gene Atlas initiative highlights an important shift in biological AI.
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Daan Speth @daanspeth.bsky.social · 25/03/2026
We now provide environmental metadata for the GlobDB genomes! 🖥️🧬🦠 More info here: globdb.org/news 🧵
Marker gene phylogeny of ammonia oxidizing archaea genomes in the GlobDB annotated with their prevailing environmental categories
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Human Frontier Science Program @hfspo.bsky.social · 17/03/2026
HFSP Awards now have Grant DOIs, back to 1990! #DOI improves traceability, visibility, and connections between funding and research outcomes in the era of #OpenScience 🧪 #HFSP awardees: please include your grant DOI in publications and preprints! #ResearchFunding #sts
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Ewan Birney @ewanbirney.bsky.social · 16/03/2026
This is a step forwards into the world of accurate complex models by AI m, at scale, openly distributed. Excellent work by the consortium here !
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DEEMteam_Orsay @deemteam.bsky.social · 17/03/2026
Living patescibacterial (CPR) cells are a rare sight! Meet Strigamonas methylophilicida, a parasite of methylotrophic proteobacteria we just described in our latest paper: doi.org/10.1128/mbio...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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Artem Nemudryi @artemnemudryi.bsky.social · 09/03/2026
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
rdcu.be
Bacterial Schlafen proteins mediate phage defence
Nature Microbiology - This study highlights that Schlafens are ancient, mechanistically conserved immune effectors that mediate antiviral immunity in organisms ranging from humans to bacteria.
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Cameron Thrash @jcamthrash.bsky.social · 05/03/2026
Diversity, ecology, cell biology and evolution of the Asgard archaea www.nature.com/articles/s41... #jcampubs
nature.com
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...
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PacBio @pacbio.bsky.social · 02/03/2026
Want epigenetic information automatically included in your sequencing runs? HiFi sequencing detects 5mC and 6mA directly from native DNA and combines multiple passes of the same molecule to generate long reads with greater than 99.9% accuracy. See how: bit.ly/3YSPBdo #PacBio #HiFisequencing
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Inga Songailiene @ingasongailiene.bsky.social · 24/02/2026
1/5 Happy by a recent biorxiv pre-print about DARNA (PD-T7-3) anti-phage defense system. This system is activated by binding to ssDNA, presented by phage SSB, to cleave tRNA in the anti-codon loop. www.biorxiv.org/content/10.6...
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 18/02/2026
“The best that I can do in terms of making the next breakthrough or discovery is not to do it by myself, but to enable other scientists to do it” — Jennifer Doudna www.forbes.com/sites/amyfel...
forbes.com
Jennifer Doudna’s $1 Billion Plan To Bring Gene Editing To The Masses
Crispr’s ability to cut genetic code like scissors has just started to turn into medicines. Now, gene editing pioneer Jennifer Doudna wants to build an entire ecosystem to bring these treatments mains...
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James Lingford @jameslingford.bsky.social · 23/02/2026
Understanding how enzymes work: the journey to ensemble–function studies febs.onlinelibrary.wiley.com/doi/10.1111/... This is an exceptionally well written review on how enzymes work. Rather than the structure-function relationship, Herschlag & Du analyse the ensemble-function relationship
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