Vyshakh R Panicker
@vyshakhrp.bsky.social
Computational ‘Microbiologist’ - Structural and evolutionary biology to study bacteria-phage coevolution| PhD student - Microbial Genomics Group, MCB, UJ
So glad to be part of this work!
Some cool biology and a very nice thread summing it up well! 🔥
Some cool biology and a very nice thread summing it up well! 🔥
What determines who a phage can infect?
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
June 26, 2025 at 3:21 PM
So glad to be part of this work!
Some cool biology and a very nice thread summing it up well! 🔥
Some cool biology and a very nice thread summing it up well! 🔥
Excited to share my research and network with other phage aficionados at the Danish Viruses of Microbes.
Please come by my poster on Thursday to chat about Klebsiella phage depolymerase evolution and more!
Please come by my poster on Thursday to chat about Klebsiella phage depolymerase evolution and more!
June 10, 2025 at 12:26 PM
Excited to share my research and network with other phage aficionados at the Danish Viruses of Microbes.
Please come by my poster on Thursday to chat about Klebsiella phage depolymerase evolution and more!
Please come by my poster on Thursday to chat about Klebsiella phage depolymerase evolution and more!
Reposted by Vyshakh R Panicker
EMBO is delighted to announce that this year the EMBO Gold Medal is awarded to Tanmay Bharat @tbharat-lab.bsky.social @mrclmb.bsky.social and David Bikard @dbikard.bsky.social @pasteur.fr for their remarkable contributions to the #LifeSciences.
www.embo.org/press-releas...
#award 🧪
www.embo.org/press-releas...
#award 🧪
EMBO Gold Medal 2025 awarded to Tanmay Bharat and David Bikard – Press releases – EMBO
Every year, EMBO awards the Gold Medal to group leaders in the early stages of their careers for their remarkable contributions to the life sciences in
www.embo.org
June 5, 2025 at 12:05 PM
EMBO is delighted to announce that this year the EMBO Gold Medal is awarded to Tanmay Bharat @tbharat-lab.bsky.social @mrclmb.bsky.social and David Bikard @dbikard.bsky.social @pasteur.fr for their remarkable contributions to the #LifeSciences.
www.embo.org/press-releas...
#award 🧪
www.embo.org/press-releas...
#award 🧪
Reposted by Vyshakh R Panicker
(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Prevalence of Group II Introns in Phage Genomes
Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...
www.biorxiv.org
May 24, 2025 at 7:20 PM
(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Vyshakh R Panicker
"Science is a method for testing claims about the natural world, not an immutable compendium of absolute truths. The fundamentalists, by ‘knowing’ the answers before they start...lie outside the domain of science–or of any honest intellectual inquiry." - Stephen Jay Gould (1991) 🧪
May 25, 2025 at 5:10 PM
"Science is a method for testing claims about the natural world, not an immutable compendium of absolute truths. The fundamentalists, by ‘knowing’ the answers before they start...lie outside the domain of science–or of any honest intellectual inquiry." - Stephen Jay Gould (1991) 🧪
Reposted by Vyshakh R Panicker
🧬🐄 NEW PREPRINT: Really happy to finally share the last big piece of work from my PhD!
Spoiler: Cows are great and so are their viromes 🧵1/13
www.biorxiv.org/content/10.1...
Spoiler: Cows are great and so are their viromes 🧵1/13
www.biorxiv.org/content/10.1...
Life-Stage Transitions Drive Distinct Gut Viral Communities in Dairy Cattle
Ruminant gut microbial communities profoundly influence host health and environmental impacts, yet their viral components remain poorly characterised across developmental transitions. Here, we analyse...
www.biorxiv.org
May 25, 2025 at 9:05 AM
🧬🐄 NEW PREPRINT: Really happy to finally share the last big piece of work from my PhD!
Spoiler: Cows are great and so are their viromes 🧵1/13
www.biorxiv.org/content/10.1...
Spoiler: Cows are great and so are their viromes 🧵1/13
www.biorxiv.org/content/10.1...
Reposted by Vyshakh R Panicker
Superbugs on the rise as antibiotics in livestock threatens global health
cosmosmagazine.com/news/antibio...
cosmosmagazine.com/news/antibio...
Superbugs on rise as antibiotics in animals threatens health
The billions of doses of antibiotics administered to farm animals are undermining our most vital medicines.
cosmosmagazine.com
May 3, 2025 at 6:35 PM
Superbugs on the rise as antibiotics in livestock threatens global health
cosmosmagazine.com/news/antibio...
cosmosmagazine.com/news/antibio...
Woah!
Never heard of Telomere phages before.
Never heard of Telomere phages before.
"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors”
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Telomere bacteriophages are widespread and equip their bacterial hosts with potent interbacterial weapons
Klebsiella host strains infected with telomere phages can grow to be the dominant lineage in mixed populations.
www.science.org
May 2, 2025 at 9:49 AM
Woah!
Never heard of Telomere phages before.
Never heard of Telomere phages before.
It was a great pleasure to give my first talk from my PhD at an International talk conference last week!
#AdvMicro2025 in Warsaw, Poland
#AdvMicro2025 in Warsaw, Poland
April 23, 2025 at 5:41 PM
It was a great pleasure to give my first talk from my PhD at an International talk conference last week!
#AdvMicro2025 in Warsaw, Poland
#AdvMicro2025 in Warsaw, Poland
Reposted by Vyshakh R Panicker
A wonderful interview with our @yalecvrc.bsky.social colleague Martin Schwartz! Where science is like art: learning to define your taste in questions
In today's episode of the Night Science Podcast we talk with Martin Schwartz from Yale about the importance of stupidity in science: while learning science makes you feel smart, true scientific discovery often involves feeling stupid, because it means venturing into the unknown.
April 21, 2025 at 11:42 PM
A wonderful interview with our @yalecvrc.bsky.social colleague Martin Schwartz! Where science is like art: learning to define your taste in questions
Reposted by Vyshakh R Panicker
🚨Super happy to see this preprint out!! Main part of Leyre’s PhD journey on the eCIS from Photorhabdus luminescens. Full structure using #cryoEM Check it out! 🎊
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states.
Contractile injection systems (CISs) are phage-tail-like nanosyringes that mediate bacterial interactions by puncturing target cell membranes. Within these systems, Photorhabdus Virulence Cassettes (P...
www.biorxiv.org
April 22, 2025 at 12:54 PM
🚨Super happy to see this preprint out!! Main part of Leyre’s PhD journey on the eCIS from Photorhabdus luminescens. Full structure using #cryoEM Check it out! 🎊
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Vyshakh R Panicker
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
April 16, 2025 at 7:14 AM
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
Reposted by Vyshakh R Panicker
My guidelines for exploratory data analysis
April 14, 2025 at 8:11 PM
My guidelines for exploratory data analysis
Reposted by Vyshakh R Panicker
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 9:07 PM
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Reposted by Vyshakh R Panicker
🧪🧬🔬 Postdoc in Computational Structural Biology at the @biozentrum.unibas.ch & @sib.swiss in Basel, Switzerland.
www.biozentrum.unibas.ch/open-positio...
The position is initially funded for 3 years, possibility to start immediately.
#StructurePrediction, #Bioinformatics, #Uniprot3D, #AI
www.biozentrum.unibas.ch/open-positio...
The position is initially funded for 3 years, possibility to start immediately.
#StructurePrediction, #Bioinformatics, #Uniprot3D, #AI
February 26, 2025 at 11:01 AM
🧪🧬🔬 Postdoc in Computational Structural Biology at the @biozentrum.unibas.ch & @sib.swiss in Basel, Switzerland.
www.biozentrum.unibas.ch/open-positio...
The position is initially funded for 3 years, possibility to start immediately.
#StructurePrediction, #Bioinformatics, #Uniprot3D, #AI
www.biozentrum.unibas.ch/open-positio...
The position is initially funded for 3 years, possibility to start immediately.
#StructurePrediction, #Bioinformatics, #Uniprot3D, #AI
Reposted by Vyshakh R Panicker
And now with the working link!
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
January 30, 2025 at 8:33 AM
And now with the working link!
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Vyshakh R Panicker
The data is the data, so don’t do an experiment unless you’re willing to accept evidence that goes against your hypothesis.
January 24, 2025 at 4:25 AM
The data is the data, so don’t do an experiment unless you’re willing to accept evidence that goes against your hypothesis.
Reposted by Vyshakh R Panicker
😮
Whoa! When a large language of life model generates a protein equivalent to ~500 million years of evolution.
@science.org
science.org/doi/10.1126/...
@science.org
science.org/doi/10.1126/...
Simulating 500 million years of evolution with a language model
More than three billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here we show that language models trained at scale on evolutionary data can gen...
science.org
January 17, 2025 at 2:32 AM
😮
Reposted by Vyshakh R Panicker
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Reposted by Vyshakh R Panicker
Top 4 things to know about doing science:
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things
January 13, 2025 at 1:52 AM
Top 4 things to know about doing science:
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things