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Patrick Bradley

@bradleyph.bsky.social
1.1K followers 258 following 4 posts

Asst. Prof of Microbiology at Ohio State. Specialist in human microbiomes and bioinformatics. Tweets reflect my own opinions (i.e. not OSU's). He/him/his 🏳️‍🌈🧑‍🔬

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Reposted by Patrick Bradley
Jeremy Berg @jeremymberg.bsky.social · 27/05/2026
I heard from several sources yesterday that NIH is planning to release a Request for Information (RFI) that apparently will include this: Scores and percentiles for NIH grant applications will not be shared with applicants although they will be provided to NIH program officers and staff. 1/3
static.klipy.com
Huh Kermit
ALT: Huh Kermit
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Laurie Belcher @lauriebelch.bsky.social · 26/05/2026
We’re hiring for OrthoFinder! Great role for someone who enjoys scientific software development: Python, data analysis, workflows, Git, scalability, and making tools nicer to use. Comparative genomics or open-source bioinformatics experience would be a lovely bonus. my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 18/02/2026
Anaerobic riboflavin degradation by human gut Lachnospiraceae www.biorxiv.org/content/10.64898/20…
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Steven Salzberg @stevensalzberg.bsky.social · 16/01/2026
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
embl.org
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
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Patrick Bradley @bradleyph.bsky.social · 17/01/2026
Extremely belated as this is the first time I've signed in in a while, but thank you so much Daan for doing this! Really opens up a lot of phylogenetic analyses that can be done with this cool new database.
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Ilnam Kang @ilnamkang.bsky.social · 09/04/2025
I really enjoyed reading this paper.(1/3) Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes doi.org/10.1093/bioa... #MicroSky
doi.org
Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes
AbstractMotivation. Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic pote
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Dave Baltrus 🦦 @surtlab.bsky.social · 03/02/2025
Posting the first section of the ASM bylaws below. The last line says that they are committed to promoting inclusive diversity with equity access and
The bylaws of the American microbiology society. The last line of “purpose” says they are committed to promoting inclusive diversity with equity access and accountability
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Nature Reviews Genetics @natrevgenet.nature.com · 08/01/2025
NEW ONLINE! New online! A phylogenetic approach to comparative genomics
go.nature.com
A phylogenetic approach to comparative genomics
Nature Reviews Genetics, Published online: 08 January 2025; doi:10.1038/s41576-024-00803-0Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests.…
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Micah G. Allen @micahgallen.com · 02/12/2024
Would you like to see @biorxivpreprint.bsky.social add a share to blue sky button?! I know I would! Share this post to let @richardsever.bsky.social @erictopol.bsky.social and others at bioarxiv know!
A screenshot of a paper on bioarxiv illustrating the lack of blue sky share button!
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Mike Blazanin @mikeblazanin.bsky.social · 09/07/2024
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 🧬🖥️🦠🔬 doi.org/10.1186/s128...
doi.org
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...
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Alex Crits-Christoph @acritschristoph.bsky.social · 27/02/2024
Here we describe the nitty gritty behind our toolkit assembly for screening pooled genetic tools to identify those that work for non-model bacteria. Made available through @addgene.bsky.social: www.addgene.org/kits/cultiva...
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Dr. Michael D. L. Johnson @copperbae.bsky.social · 13/02/2024
#NSURP2024 share broadly 😀
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Zhiru Liu @zzzhiru.bsky.social · 14/02/2024
Excited (and relieved!) to share that my 1st paper in grad school finally came out in PLOS Biology! We were motivated by a very basic question: how fast, really, do bacteria exchange DNA in the human gut? (1/n)
t.co
Dynamics of bacterial recombination in the human gut microbiome
Recombination is a ubiquitous force in bacterial evolution, but its dynamics are poorly characterized in many natural populations. This study presents a metagenomic approach for quantifying the landsc...
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Tami Lieberman @contaminatedsci.bsky.social · 11/02/2024
My favorite story from the Staph GRC last summer, from Tamia Harris-Tyron's group, is now up on biorxiv. Testosterone activates agr pathway (quorum sensing pathway that activates virulence factors) in S aureus!
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Tami Lieberman @contaminatedsci.bsky.social · 11/01/2024
Pleased that grad student Jacob Baker's tour de force analysis of intraspecies dynamics in the skin microbiome -- including >4,000 isolates of 2 species from 8 families carefully clustered into lineages and analyzed is now up.
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big lou @thetallblonde.bsky.social · 04/01/2024
please please tell your friends and loved ones about test2treat.org — a completely free site. they offer free tests, and FREE TREATMENT. no insurance needed. literally did not enter any insurance or payment info and i got a paxlovid script in an hour. please share. huge h/t to @eboldy.bsky.social ♥️
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Tuuli Lappalainen @tuuliel.bsky.social · 05/01/2024
Six weeks left until the abstract deadline for Biology of Genomes at CSHL #BoG24! We have a stellar lineup of keynotes and discussion leaders (=~invited speakers), and look forward to another brilliant meeting in May 7-11. Abstract submission & info: meetings.cshl.edu/meetings.asp...
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Ameet Pinto @watermicrobe.bsky.social · 04/01/2024
for folks in grad programs, what are key barriers that may affect your ability to regularly attend seminars organized as part of routine department seminar series?
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Sara Mitri @saramitri.bsky.social · 05/12/2023
Our department is recruiting a tenure-track Assistant Professor on microbial interactions linked to the NCCR Microbiomes nccr-microbiomes.ch Don't miss this opportunity to join a friendly, dynamic department in a city with hard-to-beat quality of life. Apply tinyurl.com/4k2mevax by Jan 31!
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Nandita Garud @nanditagarud.bsky.social · 14/11/2023
We are delighted to share our work on “Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history”! www.biorxiv.org/content/10.1... Please check out the full tweet thread and GIF here: twitter.com/nanditagarud...
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Rachel N. Arey @rnareylab.bsky.social · 14/11/2023
New PI slack was an incredible and often sanity saving resource for me in the early days, and still great now. I encourage New PIs to join!
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Michael Manhart @michaelmanhart.bsky.social · 14/11/2023
For microbiologists seeking faculty jobs: Rutgers has 4+ faculty searches in microbiology right now! Please share widely and see below for details and links on the individual positions 1/5
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Alison Feder @alisonfeder.bsky.social · 07/11/2023
We're hiring in computational biology! UW Genome Sciences has been a stellar place to start a computational lab - fantastic students, colleagues, and opportunities for collaboration with cutting-edge experimentalists and clinicians. Seattle is a great place to live too. Please circulate our ad!
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Kristen DeAngelis 🏳️‍🌈🏳️‍⚧️🍉 @kristenobacter.bsky.social · 19/09/2023
Come work with us in Microbiology at UMass Amherst! We're hiring a microbial immunologist. More info here --> careers.umass.edu/amherst/en-u... Apply by the November 13, 2023 to ensure consideration! Learn more about us here: www.micro.umass.edu #microsky #jobs 🧪🦠🧫
micro.umass.edu
Department of Microbiology at UMass Amherst
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Fabrice Jean-Pierre @fabricejpierre.bsky.social · 22/09/2023
Faculty position opening at Université de Montréal 👇🏾 Assistant or Associate Professor position in Bacteriology in the Department Microbiology, Infectious diseases & Immunology. Please share!
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Michele LeRoux @micheleleroux.bsky.social · 22/09/2023
The Molecular Microbiology department at Washington University in St Louis School of Medicine is recruiting at the Assistant Professor level! Come be a #newPI with me in this stellar research environment and fantastic microbiology community. facultyopportunities.wustl.edu/apply/Postin...
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Nandita Garud @nanditagarud.bsky.social · 19/10/2023
I am looking for a graduate student and a postdoc to join my group! We are a computational group working on understanding evolution in natural populations with a large emphasis on the microbiome. Please get in touch by dm or email! garud.eeb.ucla.edu
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Michael Love @mikelove.bsky.social · 14/09/2023
This preprint describes tidyomics, a community-led effort to enable application of grammar from tidyverse to omics data in Bioconductor. I've been greatly impressed with the crowd-sourcing of issues via GitHub Projects. preprint: www.biorxiv.org/content/10.1... github: github.com/tidyomics
schematic of code used to move between different Bioconductor containers supported by tidyomicsschematic of how common grammar can be applied to different Bioconductor data objects
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Elinor Karlsson @elinork.bsky.social · 13/09/2023
2nd Bluesky post … faculty search! Genomics and Comp Bio dept @ UMass Chan Med School academicjobsonline.org/ajo/jobs/25641 pop genomics, imaging, stat. genetics, machine learning aka cool science w big data. Collab & supportive environment where you can innovate & make discoveries. Join us!
academicjobsonline.org
University of Massachusetts Chan Medical School, Program in Bioinformatics and Integrative Biology
Full service online faculty recruitment and application management system for academic institutions worldwide. We offer unique solutions tailored for academic communities.
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Chemjobber @chemjobber.bsky.social · 13/09/2023
Cheeky Scientist is a bad company that should be stopped. Academic friends, please contact your department/school's career services and ask them to stop booking Isaiah Hankel or his company. 🧪academicsky Congrats @cofford.bsky.social for this important article: www.science.org/content/arti...
Sara describes what transpired as an aggressive sales pitch that played heavily on her anxiety about unemployment. The representative made her an offer: Cheeky Scientist’s Diamond Program, an online mentoring package, for a little over half what he said was the standard retail price of $9998—provided she sign up immediately. He had a solution for financing, too: a high-interest loan he could help her apply for through another company, there and then. Under pressure, Sara says, she signed up, but regretted it as soon as she was off the call. She contacted Cheeky Scientist within hours to request a cancellation. Now, she’s saddled with thousands of dollars of debt and is no closer to reclaiming her money—despite not using the company’s services.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2023
Our work on clustering the 214M AlphaFold protein structure was published in @Nature. We identified 2.3M clusters using our fast structure cluster algorithm and analysed its annotations, evolution and novel domains. Work with Pedro Beltrao. 1/n 📄 www.nature.com/articles/s41... 💾 cluster.foldseek.com
nature.com
Clustering-predicted structures at the scale of the known protein universe - Nature
The novel Foldseek clustering algorithm defines 2.30 million clusters of AlphaFold structures, identifying remote structural similarity of human immune-related proteins in prokaryotic species.
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Jason Stajich @hyphaltip.bsky.social · 14/09/2023
UMaine hiring Assistant Professor of Microbiology umaine.hiretouch.com/job-details?...
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Tami Lieberman @contaminatedsci.bsky.social · 14/09/2023
Looking forward to this event next week!
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Daan Speth @daanspeth.bsky.social · 11/09/2023
Seems like a super useful tool! 🖥️🧬🦠 "A fast comparative genome browser for diverse bacteria and archaea" preprint: www.biorxiv.org/content/10.1101/202… webserver: fast.genomics.lbl.gov/cgi/search.cgi
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Anne-Ruxandra Carvunis @carvunis.bsky.social · 11/09/2023
Please RT: multiple fully funded postdoc positions available to work on systems approaches for detecting and characterizing microproteins from an evolutionary and physiological perspective. Computational experience required. Email me your CV to start a discussion!
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Drew Steen @drewsteen.bsky.social · 11/09/2023
Three - count 'em! - faculty positions open at U Tennessee Microbiology! 1.) TT Assoc/Full prof: Plant/microbe interactions apply.interfolio.com/131119 2.) TT Ass't prof: Immunology apply.interfolio.com/130937 3.)TT Ass't prof: Micro. physiology apply.interfolio.com/130406
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Sheril Kirshenbaum @sheril.bsky.social · 09/09/2023
Beatrix Potter is best remembered for the tales of Peter Rabbit, but she also studied science. Potter examined beetles, butterflies, plants, eggs, shells, rocks, fossils & fungi. She wrote & illustrated a scientific paper but as a Victorian era woman, she couldn’t present it at the Linnean Society.
Potter aged fifteen with her springer spaniel, Spot. Source: WikipediaDrawings by Potter of a ground beetle, Credit: Victoria and Albert Museum, London, via Frederick Warne & Co Ltd
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