@phoeberice.bsky.social
Interested in mobile DNA, molecular machines, structural biology
Reposted
I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.
October 24, 2025 at 5:44 PM
I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.
Might not be the best use of limited funds, depending on what the structurally-based quesiton was!
Or: Just determine the structures (using constructs as predicted by AlphaFold)! 😇
October 30, 2025 at 5:20 PM
Might not be the best use of limited funds, depending on what the structurally-based quesiton was!
Reposted
Congrats to @utah.edu's Wes Sundquist on the cool honor. Had a chance to chat with him a few times when I was in college and he just came off as such a smart and humble guy. attheu.utah.edu/facultystaff...
Wesley Sundquist named in the ‘TIME 100 Most Influential People of 2025’ list - @theU
The honor is in recognition of the biochemist’s research to understand the structure of HIV that led to the drug lenacapavir, which is nearly 100% effective against HIV.
attheu.utah.edu
April 25, 2025 at 10:33 PM
Congrats to @utah.edu's Wes Sundquist on the cool honor. Had a chance to chat with him a few times when I was in college and he just came off as such a smart and humble guy. attheu.utah.edu/facultystaff...
Really cool!
But Bluesky has flipped your picture over - it now shows positively supercoiled left-handed DNA :-(.
But Bluesky has flipped your picture over - it now shows positively supercoiled left-handed DNA :-(.
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
October 29, 2025 at 9:15 PM
Really cool!
But Bluesky has flipped your picture over - it now shows positively supercoiled left-handed DNA :-(.
But Bluesky has flipped your picture over - it now shows positively supercoiled left-handed DNA :-(.
Reposted
Happy to share a new publication on Mechanistic Coupling of Enzyme Activities at the Replisome in JBC. We #Traklab compare and contrast strategies used across organisms to coordinate the many enzymatic processes that occur during DNA replication. Hope it is helpful. doi.org/10.1016/j.jb...
October 24, 2025 at 6:12 PM
Happy to share a new publication on Mechanistic Coupling of Enzyme Activities at the Replisome in JBC. We #Traklab compare and contrast strategies used across organisms to coordinate the many enzymatic processes that occur during DNA replication. Hope it is helpful. doi.org/10.1016/j.jb...
Reposted
Scientists often engineer microbes, like E. coli, to make drugs and other molecules.
But what if, instead, we could isolate ALL the components of a cell into little vials and sell them? How much would, say, 1 liter of cells be worth?
The answer, it turns out, is about $600,000.
But what if, instead, we could isolate ALL the components of a cell into little vials and sell them? How much would, say, 1 liter of cells be worth?
The answer, it turns out, is about $600,000.
October 20, 2025 at 7:20 PM
Scientists often engineer microbes, like E. coli, to make drugs and other molecules.
But what if, instead, we could isolate ALL the components of a cell into little vials and sell them? How much would, say, 1 liter of cells be worth?
The answer, it turns out, is about $600,000.
But what if, instead, we could isolate ALL the components of a cell into little vials and sell them? How much would, say, 1 liter of cells be worth?
The answer, it turns out, is about $600,000.
This could be a metaphor for so many things in society, international relations, etc ...
public service message from the brave people who keep our building functioning. this is actually good advice. 'Please refrain from kicking malfunctioning building equipment in the future until a certified technician can attempt a more permanent repair.'
October 14, 2025 at 6:23 PM
This could be a metaphor for so many things in society, international relations, etc ...
Reposted
1/3 To those interested in microbial iron & metal transport: In 1992, the late JB Neilands (UCB), the pioneer in the study of Fe transport entrusted me with his collection of purified siderophores from a wide range of microbes—many of them unique chemical species that can no longer be reproduced
October 14, 2025 at 2:54 PM
1/3 To those interested in microbial iron & metal transport: In 1992, the late JB Neilands (UCB), the pioneer in the study of Fe transport entrusted me with his collection of purified siderophores from a wide range of microbes—many of them unique chemical species that can no longer be reproduced
Reposted
I don’t know who needs to hear this but the CDC is being eviscerated right now. America is not going to have any kind of outbreak response capacity after tonight. Americans’ health data is no longer secure. Say goodbye to federal public health in any capacity. It’s a disaster. We won’t recover.
October 11, 2025 at 3:05 AM
I don’t know who needs to hear this but the CDC is being eviscerated right now. America is not going to have any kind of outbreak response capacity after tonight. Americans’ health data is no longer secure. Say goodbye to federal public health in any capacity. It’s a disaster. We won’t recover.
Reposted
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
nyti.ms
October 8, 2025 at 11:29 PM
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
Reposted
🚨 Are you an alum from one of the 9 universities Trump is attempting to extort right now?
✍️ Sign this petition to defend your university, free speech, and democracy. I signed.
This is a time for courage, not capitulation.
#JustSayNo #Compact 🧪🧠🧬
(context in thread)
✍️ Sign this petition to defend your university, free speech, and democracy. I signed.
This is a time for courage, not capitulation.
#JustSayNo #Compact 🧪🧠🧬
(context in thread)
Trump attacks 9 universities: Sign the alumni petition to defend your school now
Are you an alum outraged by Trump's attacks on universities? Defend your school now by signing this alumni petition in support of these 9 universities as well as campus communities across America.
alumni.controlshift.app
October 3, 2025 at 7:27 PM
🚨 Are you an alum from one of the 9 universities Trump is attempting to extort right now?
✍️ Sign this petition to defend your university, free speech, and democracy. I signed.
This is a time for courage, not capitulation.
#JustSayNo #Compact 🧪🧠🧬
(context in thread)
✍️ Sign this petition to defend your university, free speech, and democracy. I signed.
This is a time for courage, not capitulation.
#JustSayNo #Compact 🧪🧠🧬
(context in thread)
Reposted
The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...
Technician III - Department of Microbiology
Position Summary This position will be in the lab of Dr. Joseph E. Peters in the Department of Microbiology. Research in the Peters’ lab broadly involves deciphering mechanisms in genome stability and...
cornell.wd1.myworkdayjobs.com
October 3, 2025 at 1:01 PM
The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...
Reposted
Interested in a tenure track position teaching and doing research with undergrads at a PUI? We are looking for a broadly-defined microbiologist who can teach Med Micro and Immunology. Apply at universityofscrantonjobs.com/postings/8308. Pls share widely to feeds (& on twitter if you still tweet)! 🦠
October 1, 2025 at 1:44 PM
Interested in a tenure track position teaching and doing research with undergrads at a PUI? We are looking for a broadly-defined microbiologist who can teach Med Micro and Immunology. Apply at universityofscrantonjobs.com/postings/8308. Pls share widely to feeds (& on twitter if you still tweet)! 🦠
If you've got kids in the Chicago area, come to the South Side Science Fest on Saturday!
southsidescience.event.uchicago.edu?utm_source=H...
southsidescience.event.uchicago.edu?utm_source=H...
South Side Science Festival – Where Science is for Everyone
southsidescience.event.uchicago.edu
October 1, 2025 at 5:58 PM
If you've got kids in the Chicago area, come to the South Side Science Fest on Saturday!
southsidescience.event.uchicago.edu?utm_source=H...
southsidescience.event.uchicago.edu?utm_source=H...
Reposted
First publication from our lab!
The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem
#CurrOpinMicrobiol from @lgbacteria.bsky.social
www.sciencedirect.com/science/arti...
#CurrOpinMicrobiol from @lgbacteria.bsky.social
www.sciencedirect.com/science/arti...
September 29, 2025 at 4:56 PM
First publication from our lab!
Reposted
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted
Does anyone know a gene in E. coli that duplicated "fairly recently", as to compare and contrast it's sequence divergence with that found in mobile elements?
#sciencesky #microsky
#sciencesky #microsky
September 15, 2025 at 8:26 AM
Does anyone know a gene in E. coli that duplicated "fairly recently", as to compare and contrast it's sequence divergence with that found in mobile elements?
#sciencesky #microsky
#sciencesky #microsky
Reposted
These are the most challenging times for early-career scientists and engineers.
My team is doing its bit to help by maintaining and even expanding our database of funding opportunities for early-career researchers.
We found 437 of them.
Download it freely here: research.jhu.edu/rdt/funding-...
My team is doing its bit to help by maintaining and even expanding our database of funding opportunities for early-career researchers.
We found 437 of them.
Download it freely here: research.jhu.edu/rdt/funding-...
August 11, 2025 at 11:54 AM
These are the most challenging times for early-career scientists and engineers.
My team is doing its bit to help by maintaining and even expanding our database of funding opportunities for early-career researchers.
We found 437 of them.
Download it freely here: research.jhu.edu/rdt/funding-...
My team is doing its bit to help by maintaining and even expanding our database of funding opportunities for early-career researchers.
We found 437 of them.
Download it freely here: research.jhu.edu/rdt/funding-...
reposting from a different social media site:
mobilednajournal.biomedcentral.com/editors-picks
Featuring cutting-edge work on TE evolution, function & regulation.
#TEs #MobileDNA
mobilednajournal.biomedcentral.com/editors-picks
Featuring cutting-edge work on TE evolution, function & regulation.
#TEs #MobileDNA
August 6, 2025 at 6:43 PM
reposting from a different social media site:
mobilednajournal.biomedcentral.com/editors-picks
Featuring cutting-edge work on TE evolution, function & regulation.
#TEs #MobileDNA
mobilednajournal.biomedcentral.com/editors-picks
Featuring cutting-edge work on TE evolution, function & regulation.
#TEs #MobileDNA
Reposted
Looking forward to this new installment of the Woods Hole Mobile DNA Meeting! Fantastic program, laid-back atmosphere, and gorgeous setting at the Marine Biological Laboratory ⛵️🪼🐋
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
August 5, 2025 at 8:47 PM
Looking forward to this new installment of the Woods Hole Mobile DNA Meeting! Fantastic program, laid-back atmosphere, and gorgeous setting at the Marine Biological Laboratory ⛵️🪼🐋
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
Reposted
I NEED to tell you the story of Tae Heung “William” Kim.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
July 31, 2025 at 11:35 AM
I NEED to tell you the story of Tae Heung “William” Kim.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
only 17??
🚨 BREAKING NEWS!
Seventeen Senate Dems just urged Zeldin to reinstate #EPA workers placed on leave in retaliation for signing the #DeclarationofDissent.
The Declaration of Dissent condemns the admin’s politicization, science rollbacks, and climate of fear at EPA.
(1/3)
Seventeen Senate Dems just urged Zeldin to reinstate #EPA workers placed on leave in retaliation for signing the #DeclarationofDissent.
The Declaration of Dissent condemns the admin’s politicization, science rollbacks, and climate of fear at EPA.
(1/3)
July 31, 2025 at 2:08 PM
only 17??
It also means that enormous time and energy is being wasted writing proposal instead of doing science.
The overall NIH system may need serious reform, but this is vandalism.
The overall NIH system may need serious reform, but this is vandalism.
i dont 'like' this one bit and in fact its as scary as all get-out. The change is here, and its not good.
The difference between 4th and 5th percentile is meaningless hair’s-breadth random fluctuation.
Proposals in that range at NCI are invariably exceptional, with immense potential health impact. Americans generally don’t understand the staggering level of effort and intellectual achievement here.
Proposals in that range at NCI are invariably exceptional, with immense potential health impact. Americans generally don’t understand the staggering level of effort and intellectual achievement here.
July 24, 2025 at 7:15 PM
It also means that enormous time and energy is being wasted writing proposal instead of doing science.
The overall NIH system may need serious reform, but this is vandalism.
The overall NIH system may need serious reform, but this is vandalism.
Our work expanding the Large Serine Integrase toolkit is finally out! We used alphafold-multimer to identify likely recombination directionality factors and tested them experimentally. Much credit to fantastic postdoc Heewhan Shin.
@heewhanshin.bsky.social
#Alphafold
#MobileGeneticElements
@heewhanshin.bsky.social
#Alphafold
#MobileGeneticElements
⭐NAR Breakthrough!⭐
AlphaFold2 predicted LSI–RDF interactions and experimentally validated several new functional pairs.
@phoeberice.bsky.social @femijohn.bsky.social
doi.org/10.1093/nar/...
#NARBreakthrough #SyntheticBiology #AlphaFold2 #GenomeEditing #ComputationalBiology
AlphaFold2 predicted LSI–RDF interactions and experimentally validated several new functional pairs.
@phoeberice.bsky.social @femijohn.bsky.social
doi.org/10.1093/nar/...
#NARBreakthrough #SyntheticBiology #AlphaFold2 #GenomeEditing #ComputationalBiology
July 24, 2025 at 4:26 PM
Our work expanding the Large Serine Integrase toolkit is finally out! We used alphafold-multimer to identify likely recombination directionality factors and tested them experimentally. Much credit to fantastic postdoc Heewhan Shin.
@heewhanshin.bsky.social
#Alphafold
#MobileGeneticElements
@heewhanshin.bsky.social
#Alphafold
#MobileGeneticElements