Patrick Bradley
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bradleyph.bsky.social
Patrick Bradley
@bradleyph.bsky.social
1.1K followers 220 following 2 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
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
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
doi.org
April 9, 2025 at 7:28 AM
Reposted by Patrick Bradley
surtlab.bsky.social
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
February 3, 2025 at 11:55 AM
Reposted by Patrick Bradley
natrevgenet.nature.com
NEW ONLINE! New online! A phylogenetic approach to comparative genomics
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.…
go.nature.com
January 8, 2025 at 1:58 PM
Reposted by Patrick Bradley
micahgallen.com
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!
December 2, 2024 at 12:10 PM
Reposted by Patrick Bradley
mikeblazanin.bsky.social
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...
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...
doi.org
July 9, 2024 at 7:18 PM
Reposted by Patrick Bradley
acritschristoph.bsky.social
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...
February 27, 2024 at 1:17 PM
Reposted by Patrick Bradley
copperbae.bsky.social
#NSURP2024 share broadly 😀
nsurp.bsky.social National Summer Undergraduate Research Project @nsurp.bsky.social · Feb 13
Applications for 2024 are now OPEN! Please share widely amongst your networks! Mentee (undergrad) app: etap.nsf.gov/award/407/op...
Mentor (grad student/post doc/faculty) app: uarizona.co1.qualtrics.com/jfe/form/SV_...
February 13, 2024 at 10:11 PM
Reposted by Patrick Bradley
zzzhiru.bsky.social
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)
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...
t.co
February 14, 2024 at 12:00 AM
Reposted by Patrick Bradley
contaminatedsci.bsky.social
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!
February 11, 2024 at 2:45 PM
Reposted by Patrick Bradley
contaminatedsci.bsky.social
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.
January 11, 2024 at 2:34 PM
Reposted by Patrick Bradley
thetallblonde.bsky.social
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 ♥️
nytimes.com The New York Times @nytimes.com · Jan 4
As Covid rises again, killing about 1,500 Americans each week, researchers are trying to understand why so few high-risk patients are taking Paxlovid, a medicine that is stunningly effective in preventing severe illness and death from the disease.
Paxlovid Cuts Covid Death Risk. But Those Who Need It Are Not Taking It.
With Covid deaths rising to about 1,500 per week, researchers question why Paxlovid use has remained low among high-risk patients.
www.nytimes.com
January 4, 2024 at 8:08 PM
Reposted by Patrick Bradley
tuuliel.bsky.social
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...
January 5, 2024 at 1:22 PM
Reposted by Patrick Bradley
watermicrobe.bsky.social
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?
January 4, 2024 at 1:29 AM
Reposted by Patrick Bradley
saramitri.bsky.social
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!
December 5, 2023 at 4:32 PM
Reposted by Patrick Bradley
nanditagarud.bsky.social
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...
November 14, 2023 at 9:29 PM
Reposted by Patrick Bradley
rnareylab.bsky.social
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!
whelanfj.bsky.social Fiona J Whelan @whelanfj.bsky.social · Nov 9
I started my group in 2020, in lockdown, without induction/mentorship bc of the chaos of the pandemic. New PI slack single-handedly kept me sane & grounded, & reminded me I wasn't alone. If you're a new PI, this article is great;my #1 tip is to join this amazing community newpislack.wordpress.com. 🧪
Five ways in which rookie lab leaders can get up to speed
An array of spreadsheets, courses and online resources are available to support principal investigators leading their first research groups. An array of spreadsheets, courses and online resources are ...
www.nature.com
November 14, 2023 at 4:19 PM
Reposted by Patrick Bradley
michaelmanhart.bsky.social
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
November 14, 2023 at 11:37 PM
Reposted by Patrick Bradley
alisonfeder.bsky.social
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!
maitreya.bsky.social Maitreya Dunham @maitreya.bsky.social · Oct 31
UW Genome Sciences is hiring a new Assistant Professor working in computational biology! apply.interfolio.com/135108
November 7, 2023 at 11:21 PM
Reposted by Patrick Bradley
kristenobacter.bsky.social
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 🧪🦠🧫
Department of Microbiology at UMass Amherst
www.micro.umass.edu
September 19, 2023 at 1:06 PM
Reposted by Patrick Bradley
fabricejpierre.bsky.social
Faculty position opening at Université de Montréal 👇🏾

Assistant or Associate Professor position in Bacteriology in the Department Microbiology, Infectious diseases & Immunology.

Please share!
September 21, 2023 at 11:46 PM
Reposted by Patrick Bradley
micheleleroux.bsky.social
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...
September 22, 2023 at 2:08 PM
Reposted by Patrick Bradley
nanditagarud.bsky.social
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
October 19, 2023 at 5:52 PM
Reposted by Patrick Bradley
mikelove.bsky.social
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 tidyomics schematic of how common grammar can be applied to different Bioconductor data objects
September 14, 2023 at 12:48 PM
Reposted by Patrick Bradley
elinork.bsky.social
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!
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.
academicjobsonline.org
September 13, 2023 at 8:50 PM
Reposted by Patrick Bradley
chemjobber.bsky.social
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.
September 13, 2023 at 10:52 PM