π¦ π§ββοΈFrom bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
24.07.2025 18:22 β π 255 π 119 π¬ 9 π 11
We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.
See thread for more information and reach out!
22.07.2025 19:34 β π 93 π 100 π¬ 2 π 1
Congrats!
11.07.2025 19:00 β π 1 π 0 π¬ 0 π 0
PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
05.06.2025 08:09 β π 78 π 85 π¬ 2 π 5
The Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases!
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated π
03.06.2025 21:35 β π 49 π 60 π¬ 3 π 4
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.
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/
09.04.2025 21:07 β π 253 π 104 π¬ 11 π 4
Microbial Omics
A suite of bioinformatics tools for microbial genome and metagenome analysis.
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
08.04.2025 12:11 β π 177 π 74 π¬ 7 π 4
Reference-free variant calling with local graph construction with ska lo (SKA)
Abstract. The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant calling methods from who
Our extension to ska, 'ska lo' (for 'left-out') which can additionally, and still very quickly, find indels and SNPs closers than the k-mer distance is now out: academic.oup.com/mbe/advance-...
This addresses a long standing challenge for reference-free variant callers
04.04.2025 09:56 β π 23 π 16 π¬ 1 π 0
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
Today we report a new compendium of human gut microbiomes with >168,000 samples
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
22.01.2025 17:12 β π 198 π 77 π¬ 10 π 14
Congrats!
22.01.2025 13:22 β π 1 π 0 π¬ 0 π 0
Application review for the 2025 Gordon Research Conference on Microbial Population Biology begins on Jan 20. Maximize your chance of acceptance and $ support by submitting your application with a poster abstract before that date! Details: www.grc.org/microbial-po...
09.01.2025 22:49 β π 33 π 29 π¬ 0 π 0
Bright green spots are phages (viruses), bacteria are the faint rods in light blue.
We developed a microscopy-based techniqueπ¬ to measure attachment of viruses #phages to host cells. π¦
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
19.12.2024 22:10 β π 76 π 30 π¬ 3 π 2
The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology:
www.annualreviews.org/content/jour...
21.11.2024 15:27 β π 296 π 112 π¬ 11 π 5
A "starter pack" image for my Evolutionary Biologists pack
Seeing a bunch of new followers, so I just tidied up my Evolutionary Biologists starter packβmostly trying to represent folks' fields right, and get in some topical journals/societies
Hope it's useful, but I'd also love to see packs from other folks, to better cover the field
go.bsky.app/TUNHbNu
07.11.2024 21:17 β π 93 π 49 π¬ 7 π 3
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results wereβ¦surprising. 1/30
26.10.2024 17:45 β π 687 π 326 π¬ 27 π 62
Tried to put together a Microbial Evolution starter pack, but there were so many great people I didn't want to leave out it turned into 3 starter packs
Comment or DM me if you were missed or would like to be added!
A thread (1/3)
go.bsky.app/6pkuYhi
20.10.2024 21:56 β π 145 π 87 π¬ 27 π 7
Note - if you are interested in the amazing Lake Arrowhead Microbial Genomes meeting but cannot attend in person, there is a highly reduced cost virtual option to participate. See www.eventbrite.com/e/lake-arrow...
29.08.2024 15:03 β π 6 π 9 π¬ 0 π 0
π¨Im looking for postdocs to join me at Montana State!
One position will focus on phage-host-microbe interactions in Lyme disease
The other will sequence phage populations recovered from ticks/mice
Interested? Send me a CV & cover letter! Job ads soon
π§«π¦ π§ͺ
22.08.2024 23:22 β π 18 π 29 π¬ 0 π 0
gcplyr: an R package for microbial growth curve data analysis - BMC Bioinformatics
Background Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the deve...
Glad to see this out! gcplyr is an R package that makes it easy to wrangle and analyze microbial growth curve data. In the paper, I highlight what it adds compared to other software
(a new version is up too! update to get the latest features)
#microbiomesky #MicroSky π§¬π₯οΈπ¦ π¬
doi.org/10.1186/s128...
09.07.2024 19:18 β π 25 π 17 π¬ 0 π 0
Assistant Professor - Global Change Biology- Department of Integrative Biology
University of California, Berkeley is hiring. Apply now!
Job alert!! Join Integrative Biology at UC Berkeley. We are hiring an Assistant Professor in the area of global change biology with emphasis on the Ecology and Evolution of Host-Microbe Interactions (pathogens, mutualists, microbiomes).
aprecruit.berkeley.edu/JPF04476
08.07.2024 14:51 β π 58 π 92 π¬ 0 π 0
captcha image with 3x3 grid of animals featuring 3 elephants, 3 dogs with sunglasses, two mice, and a frog. test image at top is an elephant with a sign that reads "frog"
I didn't know I could enjoy a CAPTCHA test this much
28.06.2024 19:36 β π 1 π 0 π¬ 0 π 0
Check out our new paper in collaboration with Travis Wheeler's group out today in NAR Genomics & Bioinformatics! Editors choice!
VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes
#microsky
#phagesky
π§«π§ͺπ¬
doi.org/10.1093/narg...
04.04.2024 16:15 β π 17 π 8 π¬ 0 π 1
UC Berkeley Postdoc interested in the ecological and evolutionary impacts of bacteria-phage interactions.
Every which way but loose. Mostly #science and #evolution, also #sciencepolicy
Prof @Cambridge_Uni Genomic epidemiologist. #Shigella and #AMR enthusiast. Views own. http://gen.cam.ac.uk/baker-group also www.pdu.gen.cam.ac.uk also @pducambridge.bsky.social
Evolutionary microbiologist π§ͺπ§«π§ͺ Postdoc in Vaughn Cooperβs Lab at the University of Pittsburgh School of Medicine
Professor of Molecular Systems Biology, University of Cambridge
Evolutionary community ecologist interested in disease emergence. Work with environmental DNA, primates, bacteriophages. Like bicycles. Heading a junior research group at the Helmholtz Institute for One Health.
Assistant Professor at Yale. Fixing whatβs broken: climate change, pandemics, and global governance. Look, I made a hat: carlsonlab.bio / viralemergence.org / watch this space
Pathogen informatics and modelling http://bacpop.org
(Research group leader at EMBL-EBI - http://ebi.ac.uk/research/lees/)
Evolutionary biologist based in Oxford (currently βon tourβ)
Mathematician, writer, Cornell professor. All cards on the table, face up, all the time. www.stevenstrogatz.com
Just another LLM. Tweets do not necessarily reflect the views of people in my lab or even my own views last week. http://rajlab.seas.upenn.edu https://rajlaboratory.blogspot.com
Assistant Professor Tufts University
Phage-driven evolution of the Vaginal Microbiome
staff writer at The Atlantic, covering science. former microbiologist / forever cat enthusiast. (she/her) SIGNAL: @katherinejwu.12
I love molecules microbes make and mass spectrometry. I can spend hours looking at MS/MS with the dream we can annotate every molecule.
Evolutionary biologist, photographer, NSF PO. Views are my own and do not represent those of my employer or the United States.
youtube.com/@xprinceps, https://www.facebook.com/profile.php?id=61577139550412, matthewherron.net
Associate Professor at Roswell Park Comprehensive Cancer Center. GPCRs and gene regulation in pancreatic cancer. Posts are mine.
I am a marine conservation biologist studying sharks and a science writer. Posts are about science and the environment, science communication, and more! He/him
Genome Scientist. Studies how DNA makes humans, mice, plants, microbes. At Lawrence Berkeley National Lab and Joint Genome Institute. Views are my own.
U.S. Senator, Massachusetts. She/her/hers. Official Senate account.
Community ecologist at Stanford University
https://profiles.stanford.edu/tadashi-fukami