Franklin Nobrega
@fnobrega.bsky.social
Phage Biology, Bacterial defense systems, CRISPR-Cas, Microbial communities, Mucus interactions
http://www.fnobregalab.org
http://www.klebphacol.org
http://www.phage-collection.org
http://www.fnobregalab.org
http://www.klebphacol.org
http://www.phage-collection.org
Pinned
Franklin Nobrega
@fnobrega.bsky.social
· Jul 28
Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites
Zhang, Todeschini, and Wu et al. show that the bacterial defense system Kiwa senses
phage attachment at the membrane and assembles a transmembrane complex that halts
infection by blocking phage DNA re...
www.cell.com
Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription.
www.cell.com/cell/fulltex...
Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.
www.cell.com/cell/fulltex...
Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.
Reposted by Franklin Nobrega
Reposted by Franklin Nobrega
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
November 24, 2025 at 4:57 PM
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
Reposted by Franklin Nobrega
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:55 PM
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Reposted by Franklin Nobrega
PhD Opportunity: Advance UTI treatment with on-chip tech! 🔬🧫
Work at the microbiology-bioengineering interface with Hywel Morgan, @fnobrega.bsky.social and me.
Program EPSRC/MOD CISDnS CDT cisdns-cdt.ac.uk
Co-funded by IfLS Southampton
tinyurl.com/infoUTI
tinyurl.com/applyUTI
Deadline: 8 Dec 2025
Work at the microbiology-bioengineering interface with Hywel Morgan, @fnobrega.bsky.social and me.
Program EPSRC/MOD CISDnS CDT cisdns-cdt.ac.uk
Co-funded by IfLS Southampton
tinyurl.com/infoUTI
tinyurl.com/applyUTI
Deadline: 8 Dec 2025
Advancing urinary tract infection treatment through on-chip technological innovation at University of Southampton on FindAPhD.com
PhD Project - Advancing urinary tract infection treatment through on-chip technological innovation at University of Southampton, listed on FindAPhD.com
tinyurl.com
November 26, 2025 at 11:24 AM
PhD Opportunity: Advance UTI treatment with on-chip tech! 🔬🧫
Work at the microbiology-bioengineering interface with Hywel Morgan, @fnobrega.bsky.social and me.
Program EPSRC/MOD CISDnS CDT cisdns-cdt.ac.uk
Co-funded by IfLS Southampton
tinyurl.com/infoUTI
tinyurl.com/applyUTI
Deadline: 8 Dec 2025
Work at the microbiology-bioengineering interface with Hywel Morgan, @fnobrega.bsky.social and me.
Program EPSRC/MOD CISDnS CDT cisdns-cdt.ac.uk
Co-funded by IfLS Southampton
tinyurl.com/infoUTI
tinyurl.com/applyUTI
Deadline: 8 Dec 2025
Reposted by Franklin Nobrega
Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
BarTn7: Optimizing Bacterial Lineage Tracking at Sub-Species Resolution for Population Dynamics in Ecological and Evolutionary Studies
Communities of bacteria undergo population bottlenecks which are crucial to their population, ecological, and evolutionary dynamics. However, conventional amplicon sequencing cannot distinguish such d...
www.biorxiv.org
November 25, 2025 at 10:38 PM
Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Franklin Nobrega
Now online at @cp-cellhostmicrobe.bsky.social from co-first authors @erinedoherty.bsky.social & @jnoms.bsky.social
Work I co-led with @jnoms.bsky.social is now online at
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
Divergent viral phosphodiesterases for immune signaling evasion
Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to …
www.sciencedirect.com
November 25, 2025 at 9:14 PM
Now online at @cp-cellhostmicrobe.bsky.social from co-first authors @erinedoherty.bsky.social & @jnoms.bsky.social
Reposted by Franklin Nobrega
Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 24, 2025 at 7:23 PM
Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466
Reposted by Franklin Nobrega
KlebPhaCol paper is now out! Go check it out and see all that we offer.
And when ready, visit our website for more: www.klebphacol.org
And when ready, visit our website for more: www.klebphacol.org
November 22, 2025 at 6:19 PM
KlebPhaCol paper is now out! Go check it out and see all that we offer.
And when ready, visit our website for more: www.klebphacol.org
And when ready, visit our website for more: www.klebphacol.org
Reposted by Franklin Nobrega
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
A ubiquitin-like protein controls assembly of a bacterial type VIIb secretion system
Cryo-EM structure reveals how a ubiquitin-like protein orchestrates assembly of a bacterial weapon system.
www.science.org
November 21, 2025 at 7:05 PM
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
Reposted by Franklin Nobrega
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Daniela is a super-talented scientist seeking a postdoc in the US focused on women's health. Colleagues, she is brilliant, and I am very happy (and sad) to see her leave to further explore her research interests.
Thrilled to share the core of my PhD work, now published in NAR!
This project was a true collaborative effort across multiple teams, and it was a joy to bring it to life.
Huge thanks to everyone involved, and especially to @fnobrega.bsky.social for the incredible support and guidance 🙏🏻
🧵1/5
This project was a true collaborative effort across multiple teams, and it was a joy to bring it to life.
Huge thanks to everyone involved, and especially to @fnobrega.bsky.social for the incredible support and guidance 🙏🏻
🧵1/5
⭐ NAR Breakthrough! ⭐
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
November 22, 2025 at 10:19 PM
Daniela is a super-talented scientist seeking a postdoc in the US focused on women's health. Colleagues, she is brilliant, and I am very happy (and sad) to see her leave to further explore her research interests.
Reposted by Franklin Nobrega
📣 Applications are NOW OPEN for our International Undergraduate Summer School 2026
🗓️ 29 June - 22 August 2026
📍 John Innes Centre, NR4 7UH
⏰ Deadline: 16 January 2026
Find out more and apply: www.jic.ac.uk/training-car...
🗓️ 29 June - 22 August 2026
📍 John Innes Centre, NR4 7UH
⏰ Deadline: 16 January 2026
Find out more and apply: www.jic.ac.uk/training-car...
November 22, 2025 at 1:05 AM
📣 Applications are NOW OPEN for our International Undergraduate Summer School 2026
🗓️ 29 June - 22 August 2026
📍 John Innes Centre, NR4 7UH
⏰ Deadline: 16 January 2026
Find out more and apply: www.jic.ac.uk/training-car...
🗓️ 29 June - 22 August 2026
📍 John Innes Centre, NR4 7UH
⏰ Deadline: 16 January 2026
Find out more and apply: www.jic.ac.uk/training-car...
Reposted by Franklin Nobrega
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
November 20, 2025 at 8:40 PM
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Reposted by Franklin Nobrega
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:12 PM
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Reposted by Franklin Nobrega
⭐ NAR Breakthrough! ⭐
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
November 20, 2025 at 6:01 PM
⭐ NAR Breakthrough! ⭐
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
Reposted by Franklin Nobrega
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
November 19, 2025 at 6:17 PM
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
Reposted by Franklin Nobrega
⏳ Only 10 days left to apply for the professorship! Don’t miss this opportunity, apply now!
#Academia #Professorship #DeadlineAlert
#Academia #Professorship #DeadlineAlert
🎉We have announced a new professorship at the University of Gothenburg 🇸🇪 to celebrate our Crown Princess’s 50th birthday!
🌿Broad focus on biodiversity — from microbes to modelling
📢A fantastic opportunity for researchers working across scales and disciplines!
🔗 web103.reachmee.com/ext/I005/103...
🌿Broad focus on biodiversity — from microbes to modelling
📢A fantastic opportunity for researchers working across scales and disciplines!
🔗 web103.reachmee.com/ext/I005/103...
The Crown Princess Victoria Professorship in Biodiversity
Professorship in Biodiversity.
The University of Gothenburg hereby announces a unique and prestigious position – the
web103.reachmee.com
November 18, 2025 at 10:25 AM
⏳ Only 10 days left to apply for the professorship! Don’t miss this opportunity, apply now!
#Academia #Professorship #DeadlineAlert
#Academia #Professorship #DeadlineAlert
Reposted by Franklin Nobrega
Update to BacFighT6, with presets for easy exploration of complex behaviors:
sites.google.com/view/bacfight6
Try "battle royale" preset where prey (blue) produce capsule, attackers (red) move towards prey and feed on it, defenders (orange) retaliate!
Took a while to eliminate the reds!
sites.google.com/view/bacfight6
Try "battle royale" preset where prey (blue) produce capsule, attackers (red) move towards prey and feed on it, defenders (orange) retaliate!
Took a while to eliminate the reds!
November 17, 2025 at 10:39 PM
Update to BacFighT6, with presets for easy exploration of complex behaviors:
sites.google.com/view/bacfight6
Try "battle royale" preset where prey (blue) produce capsule, attackers (red) move towards prey and feed on it, defenders (orange) retaliate!
Took a while to eliminate the reds!
sites.google.com/view/bacfight6
Try "battle royale" preset where prey (blue) produce capsule, attackers (red) move towards prey and feed on it, defenders (orange) retaliate!
Took a while to eliminate the reds!
Reposted by Franklin Nobrega
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons
Abstract. Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibioti
academic.oup.com
November 17, 2025 at 3:44 PM
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Reposted by Franklin Nobrega
We are hiring!! Biological Sciences as UNC Charlotte has a broad search for a new assistant professor.
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Assistant Professor
Applicants should possess a Ph.D. in the biological sciences or related fields.Candidates are expected to document expertise in their specialty by a record of postdoctoral training, peer reviewed publ...
jobs.charlotte.edu
November 17, 2025 at 2:52 PM
We are hiring!! Biological Sciences as UNC Charlotte has a broad search for a new assistant professor.
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Reposted by Franklin Nobrega
Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 15, 2025 at 10:21 PM
Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Franklin Nobrega
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Reposted by Franklin Nobrega
Very pleased to plug our latest preprint, lead author @microberamon.bsky.social - fantastic collaboration with labs of Dario Carugo (Oxford) and Martha Clokie (Leicester) https:// - and others #UTISKy #UTI #IDSky #MicroSky www.biorxiv.org/content/10.1101/2025.11.12.688052v1 more below👇🧵
Effect of human urinary microenvironment and fluid flow on antibiotic and phage therapy efficacy against uropathogenic Escherichia coli
Urinary tract infections (UTI) remain a major global health burden, with high recurrence despite antibiotic treatment. The escalating prevalence of antimicrobial resistance further compromises therape...
www.biorxiv.org
November 13, 2025 at 9:20 AM
Very pleased to plug our latest preprint, lead author @microberamon.bsky.social - fantastic collaboration with labs of Dario Carugo (Oxford) and Martha Clokie (Leicester) https:// - and others #UTISKy #UTI #IDSky #MicroSky www.biorxiv.org/content/10.1101/2025.11.12.688052v1 more below👇🧵
Reposted by Franklin Nobrega
Are you a piano player?
Become part of a World Record Attempt and help support family-poverty charity, Love, Amelia
Read the BBC article below and then sign up at
tinyurl.com/KeysoftheCity
www.bbc.co.uk/news/article...
Become part of a World Record Attempt and help support family-poverty charity, Love, Amelia
Read the BBC article below and then sign up at
tinyurl.com/KeysoftheCity
www.bbc.co.uk/news/article...
How Sunderland musicians can break a piano world record
If you can play a piano, Sunderland Music City wants you to help them join the longest piano relay.
www.bbc.co.uk
November 15, 2025 at 9:57 AM
Are you a piano player?
Become part of a World Record Attempt and help support family-poverty charity, Love, Amelia
Read the BBC article below and then sign up at
tinyurl.com/KeysoftheCity
www.bbc.co.uk/news/article...
Become part of a World Record Attempt and help support family-poverty charity, Love, Amelia
Read the BBC article below and then sign up at
tinyurl.com/KeysoftheCity
www.bbc.co.uk/news/article...
Reposted by Franklin Nobrega
Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses https://www.biorxiv.org/content/10.1101/2025.11.13.688357v1
November 15, 2025 at 12:17 AM
Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses https://www.biorxiv.org/content/10.1101/2025.11.13.688357v1