Luis E. Valentin-Alvarado
@luisvalentin.bsky.social
HFSP Research Fellow studying microbes, mobile DNA & RNA-guided immune systems.
Reposted by Luis E. Valentin-Alvarado
✨New preprint!
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
December 9, 2025 at 7:52 AM
✨New preprint!
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
Reposted by Luis E. Valentin-Alvarado
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
December 9, 2025 at 3:14 PM
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
Reposted by Luis E. Valentin-Alvarado
I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Systematic discovery of TIR-based immune signaling systems in bacteria
Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...
www.biorxiv.org
December 4, 2025 at 9:25 AM
I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Luis E. Valentin-Alvarado
📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
phd.pages.ista.ac.at
December 2, 2025 at 8:44 AM
📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
Reposted by Luis E. Valentin-Alvarado
Happy December!
Join #MVIF 44 – we will discuss diverse #microbiome topics:
human urinary, gut, oral and nasal microbiomes,
extreme environments, and
a new sequence alignment tool.
Join #MVIF 44 – we will discuss diverse #microbiome topics:
human urinary, gut, oral and nasal microbiomes,
extreme environments, and
a new sequence alignment tool.
It's Monday!
...and a new #MVIF program is out! 🤩
Free registration: cassyni.com/s/mvif-44
⭐️ Highlights:
🇺🇸 Vanessa Hale
🇰🇷 Jun Hyung Cha
⭐️ Keynote:
🇺🇸 Katherine Lemon @kathlemon.bsky.social
⭐️ Talks:
🇺🇸 Meenakshi Chakraborty
🇨🇳 Wei Shen @shenwei356.bsky.social
🇺🇸 Johanna Gutleben
...and a new #MVIF program is out! 🤩
Free registration: cassyni.com/s/mvif-44
⭐️ Highlights:
🇺🇸 Vanessa Hale
🇰🇷 Jun Hyung Cha
⭐️ Keynote:
🇺🇸 Katherine Lemon @kathlemon.bsky.social
⭐️ Talks:
🇺🇸 Meenakshi Chakraborty
🇨🇳 Wei Shen @shenwei356.bsky.social
🇺🇸 Johanna Gutleben
December 1, 2025 at 12:21 PM
Happy December!
Join #MVIF 44 – we will discuss diverse #microbiome topics:
human urinary, gut, oral and nasal microbiomes,
extreme environments, and
a new sequence alignment tool.
Join #MVIF 44 – we will discuss diverse #microbiome topics:
human urinary, gut, oral and nasal microbiomes,
extreme environments, and
a new sequence alignment tool.
Reposted by Luis E. Valentin-Alvarado
Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!
December 1, 2025 at 7:58 PM
Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!
Reposted by Luis E. Valentin-Alvarado
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
www.nature.com
November 28, 2025 at 4:43 PM
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Officially out!
Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications
Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...
www.nature.com
November 28, 2025 at 11:22 PM
Officially out!
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
www.nature.com
November 28, 2025 at 11:21 PM
Reposted by Luis E. Valentin-Alvarado
Now out in Science! Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In @vcushing.bsky.social's magnum opus, we use #cryoEM to figure out how the CDK-activating kinase recognises CDKs to fully activate them - a key step in cell cycle control.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Structural basis of T-loop–independent recognition and activation of CDKs by the CDK-activating kinase
Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation o...
www.science.org
October 16, 2025 at 7:17 PM
Now out in Science! Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In @vcushing.bsky.social's magnum opus, we use #cryoEM to figure out how the CDK-activating kinase recognises CDKs to fully activate them - a key step in cell cycle control.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Luis E. Valentin-Alvarado
omicsomics.blogspot.com/2025/10/pacb... $300 LongRead personal genome via PacBio
PacBio: $300 Genome Via Chemistry Update
ASHG is here in Boston, just down the street from Ginkgo's HQ. I'm in a new role in Ginkgo Automation, trying to convince the NGS world tha...
omicsomics.blogspot.com
October 14, 2025 at 2:35 PM
omicsomics.blogspot.com/2025/10/pacb... $300 LongRead personal genome via PacBio
Reposted by Luis E. Valentin-Alvarado
Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social
Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1
October 1, 2025 at 5:10 AM
Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social
Reposted by Luis E. Valentin-Alvarado
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 2, 2025 at 3:01 AM
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Reposted by Luis E. Valentin-Alvarado
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 2, 2025 at 3:25 AM
Reposted by Luis E. Valentin-Alvarado
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature
The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.
www.nature.com
October 1, 2025 at 4:05 PM
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
Reposted by Luis E. Valentin-Alvarado
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 1, 2025 at 5:57 PM
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Reposted by Luis E. Valentin-Alvarado
Our Department of Microbiology & Immunology at UCSF is running a faculty search this year for a new Assistant Professor! Please see the ad below for details. Searching for a great colleague, mentor, and scientist!
aprecruit.ucsf.edu/JPF05807
aprecruit.ucsf.edu/JPF05807
Microbiology and Immunology – Faculty Position (Ladder Rank) – Assistant Professor
University of California, San Francisco is hiring. Apply now!
aprecruit.ucsf.edu
September 25, 2025 at 5:51 PM
Our Department of Microbiology & Immunology at UCSF is running a faculty search this year for a new Assistant Professor! Please see the ad below for details. Searching for a great colleague, mentor, and scientist!
aprecruit.ucsf.edu/JPF05807
aprecruit.ucsf.edu/JPF05807
Reposted by Luis E. Valentin-Alvarado
Join us tomorrow if you can. Link below to register.
⏰ Last call! The human #microbiome webinar is tomorrow.
See how #PacBio HiFi sequencing delivers clarity with full-length 16S rRNA and shotgun metagenomics, revealing strain-level insights, novel taxa, and functional pathways.
Register now: bit.ly/46wBttB
See how #PacBio HiFi sequencing delivers clarity with full-length 16S rRNA and shotgun metagenomics, revealing strain-level insights, novel taxa, and functional pathways.
Register now: bit.ly/46wBttB
September 24, 2025 at 11:21 PM
Join us tomorrow if you can. Link below to register.
Reposted by Luis E. Valentin-Alvarado
New blog post!
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
Benchmark update: metaMDBG and Myloasm
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
September 23, 2025 at 1:53 AM
New blog post!
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
Reposted by Luis E. Valentin-Alvarado
The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!
jobs.colostate.edu/postings/165...
jobs.colostate.edu/postings/165...
Assistant Professor Plant-Microbe Interactions
We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...
jobs.colostate.edu
September 8, 2025 at 3:45 PM
The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!
jobs.colostate.edu/postings/165...
jobs.colostate.edu/postings/165...
Reposted by Luis E. Valentin-Alvarado
❤️❤️❤️ CSU. Fort Collins is a lovely place to live, and students / faculty are awesome. I should know, I taught there for 15 years! Apply!
The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!
jobs.colostate.edu/postings/165...
jobs.colostate.edu/postings/165...
Assistant Professor Plant-Microbe Interactions
We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...
jobs.colostate.edu
September 8, 2025 at 4:07 PM
❤️❤️❤️ CSU. Fort Collins is a lovely place to live, and students / faculty are awesome. I should know, I taught there for 15 years! Apply!
Reposted by Luis E. Valentin-Alvarado
This is the dept where I got my PhD! Hiring for microbiology!
🎙️ Job Announcement: Penn State is seeking an ASSISTANT PROFESSOR in MICROBIOLOGY (any subdiscipline) in the Department of Biochemistry and Molecular Biology.
Learn more and Join the Microbiome Jubilee: psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
Learn more and Join the Microbiome Jubilee: psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
Assistant Professor in Microbiology
APPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...
psu.wd1.myworkdayjobs.com
September 8, 2025 at 4:16 PM
This is the dept where I got my PhD! Hiring for microbiology!
Reposted by Luis E. Valentin-Alvarado
How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 5, 2025 at 10:13 AM
How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Luis E. Valentin-Alvarado
🦠Exciting PhD opportunity @ ETH Zürich!
Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments.
🗓 Start: Spring 2026
⏳ Deadline: 3 Oct 2025
👉 Apply: lnkd.in/eSPiy6vQ
Please 🔁
Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments.
🗓 Start: Spring 2026
⏳ Deadline: 3 Oct 2025
👉 Apply: lnkd.in/eSPiy6vQ
Please 🔁
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
September 3, 2025 at 5:46 PM
🦠Exciting PhD opportunity @ ETH Zürich!
Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments.
🗓 Start: Spring 2026
⏳ Deadline: 3 Oct 2025
👉 Apply: lnkd.in/eSPiy6vQ
Please 🔁
Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments.
🗓 Start: Spring 2026
⏳ Deadline: 3 Oct 2025
👉 Apply: lnkd.in/eSPiy6vQ
Please 🔁
Reposted by Luis E. Valentin-Alvarado
📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations.
www.biorxiv.org/content/10.1...
#microbesky #microbiomesky
www.biorxiv.org/content/10.1...
#microbesky #microbiomesky
Genomic and physiological characterization of 'Candidatus Methylocystis sumavensis', a novel acid-tolerant methanotroph from peatland
Methanotrophic bacteria in peatlands mitigate emissions of methane (CH4), a potent greenhouse gas. Yet, the identity, physiology, and adaptive traits of methanotrophs inhabiting acidic peatlands are s...
www.biorxiv.org
September 1, 2025 at 10:39 AM
📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations.
www.biorxiv.org/content/10.1...
#microbesky #microbiomesky
www.biorxiv.org/content/10.1...
#microbesky #microbiomesky