Lauren Cowley
@laurencowley.bsky.social
Senior Lecturer in Microbial Genomics and Bioinformatics at Milner Centre for Evolution, University of Bath
Reposted by Lauren Cowley
New #MicroSky study showing extensive transmission of #AMR E coli transmission in East Africa under One Health framework, led by Patrick Musicha www.sanger.ac.uk/news_item/an...
Antimicrobial resistant bacteria and genes move freely between people, animals and the environment
By analysing Escherichia coli (E. coli) genomes, researchers have shown that antimicrobial resistant bacteria and the genes that confer resistance move between bacterial hosts and across ecological co...
www.sanger.ac.uk
November 26, 2025 at 6:00 PM
New #MicroSky study showing extensive transmission of #AMR E coli transmission in East Africa under One Health framework, led by Patrick Musicha www.sanger.ac.uk/news_item/an...
Reposted by Lauren Cowley
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications
Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...
www.nature.com
November 25, 2025 at 10:40 AM
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
Reposted by Lauren Cowley
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 18, 2025 at 9:59 AM
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
Reposted by Lauren Cowley
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
November 3, 2025 at 10:04 AM
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
In case anyone who follows me on here lives in Bristol and loves beer, my husband is opening his brewery in a railway arch next to Temple Meads on Saturday 22nd November. Come down for a pint of crisp beer! Follow here www.instagram.com/unwinsbrewery/ for more details on the event and the concept
October 27, 2025 at 11:30 AM
In case anyone who follows me on here lives in Bristol and loves beer, my husband is opening his brewery in a railway arch next to Temple Meads on Saturday 22nd November. Come down for a pint of crisp beer! Follow here www.instagram.com/unwinsbrewery/ for more details on the event and the concept
Reposted by Lauren Cowley
(With apologies to Randall Munroe)
October 15, 2025 at 7:36 AM
(With apologies to Randall Munroe)
Reposted by Lauren Cowley
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Lauren Cowley
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 3:49 PM
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
Reposted by Lauren Cowley
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Reposted by Lauren Cowley
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
May 28, 2025 at 10:18 AM
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
Reposted by Lauren Cowley
My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.
May 28, 2025 at 3:07 PM
My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.
Reposted by Lauren Cowley
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 22, 2025 at 12:42 PM
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
Come to Newcastle this summer to hear about all the latest cool research in Genome Science www.genomescience.org.uk. The programme is hotting up! Get registering and see you there
Genome Science UK 2025
Newcastle University
www.genomescience.org.uk
May 28, 2025 at 11:58 AM
Come to Newcastle this summer to hear about all the latest cool research in Genome Science www.genomescience.org.uk. The programme is hotting up! Get registering and see you there
Reposted by Lauren Cowley
Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab
May 13, 2025 at 11:37 PM
Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab
Reposted by Lauren Cowley
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
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 10:27 PM
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
Reposted by Lauren Cowley
Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons
@shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
@shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
Filamentous cheater phages drive bacterial and phage populations to lower fitness
Many bacteria carry phage genome(s) in their chromosome (i.e., prophage), and this intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages ...
www.biorxiv.org
April 2, 2025 at 12:41 PM
Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons
@shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
@shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
Reposted by Lauren Cowley
Working with an interdisciplinary team, we have developed a website to communicate how the White House's proposed cuts to health research would cause losses of $16B and 68,500 jobs.
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
March 28, 2025 at 2:15 AM
Working with an interdisciplinary team, we have developed a website to communicate how the White House's proposed cuts to health research would cause losses of $16B and 68,500 jobs.
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
Reposted by Lauren Cowley
UK Genome Science 2025 is going live for this year - www.genomescience.org.uk - get registering!
Genome Science
9th - 11th July 2025, Newcastle University
www.genomescience.org.uk
March 28, 2025 at 10:11 AM
UK Genome Science 2025 is going live for this year - www.genomescience.org.uk - get registering!
Reposted by Lauren Cowley
If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc:
sanger.wd103.myworkdayjobs.com/WellcomeSang...
Incredibly exciting datasets on host-microbe interactions in the lung.
Pls RT and reach out if you are interested.
sanger.wd103.myworkdayjobs.com/WellcomeSang...
Incredibly exciting datasets on host-microbe interactions in the lung.
Pls RT and reach out if you are interested.
Postdoctoral Fellow - Computational
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
sanger.wd103.myworkdayjobs.com
March 12, 2025 at 4:53 PM
If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc:
sanger.wd103.myworkdayjobs.com/WellcomeSang...
Incredibly exciting datasets on host-microbe interactions in the lung.
Pls RT and reach out if you are interested.
sanger.wd103.myworkdayjobs.com/WellcomeSang...
Incredibly exciting datasets on host-microbe interactions in the lung.
Pls RT and reach out if you are interested.
Reposted by Lauren Cowley
Remember that Europe (@ebi.embl.org) has mirrored all these services and they will keep on running. They look and feel a bit different but do the same thing. I think @ewanbirney.bsky.social should be able to confirm.
www.europepmc.org
www.ebi.ac.uk/jdispatcher/...
www.europepmc.org
www.ebi.ac.uk/jdispatcher/...
February 6, 2025 at 7:29 PM
Remember that Europe (@ebi.embl.org) has mirrored all these services and they will keep on running. They look and feel a bit different but do the same thing. I think @ewanbirney.bsky.social should be able to confirm.
www.europepmc.org
www.ebi.ac.uk/jdispatcher/...
www.europepmc.org
www.ebi.ac.uk/jdispatcher/...
Reposted by Lauren Cowley
Really enjoying having @atjcagan.bsky.social in the @geneticscam.bsky.social who drew this fab piece at our recent research day. Contains some exciting teasers for our next awesome piece of work landing before Christmas! Thanks Alex!
December 7, 2024 at 12:35 PM
Really enjoying having @atjcagan.bsky.social in the @geneticscam.bsky.social who drew this fab piece at our recent research day. Contains some exciting teasers for our next awesome piece of work landing before Christmas! Thanks Alex!
Very exciting piece of work to be involved in, the stuff microbial GWAS dreams are made of! Please read @ksbakes.bsky.social excellent thread
bsky.app/profile/ksba...
bsky.app/profile/ksba...
Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2
1/n
1/n
December 19, 2024 at 9:12 PM
Very exciting piece of work to be involved in, the stuff microbial GWAS dreams are made of! Please read @ksbakes.bsky.social excellent thread
bsky.app/profile/ksba...
bsky.app/profile/ksba...
Jumped ship. hello blueworld.
December 19, 2024 at 8:34 PM
Jumped ship. hello blueworld.