Patrick Bradley

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

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

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

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.…

NEW ONLINE! New online! A phylogenetic approach to comparative genomics

A screenshot of a paper on bioarxiv illustrating the lack of blue sky share button!

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!

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 🧬🖥️🦠🔬

doi.org/10.1186/s128...

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...

#NSURP2024 share broadly 😀

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...

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)

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!

"My husband thought that your room is very empty, so you might like a little weasel" still pops into my brain periodically

oh my god, it's soooo good

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.

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 ♥️

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...

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?

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!

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...

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!

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

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!

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 🧪🦠🧫

Faculty position opening at Université de Montréal 👇🏾

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

Please share!

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...

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

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

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

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!

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.

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...

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.

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

UMaine hiring Assistant Professor of Microbiology umaine.hiretouch.com/job-details?...

Looking forward to this event next week!