Alert! The abstract deadline for the Microbial Pathogenesis & Host Response meeting has been extended to July 7 meetings.cshl.edu/meetings.asp...

Course materials from the most recent iteration of the Statistical Analysis of Genome-scale Data course at @cshlnews.bsky.social. seandavi.github.io/RBiocBook/ Thanks to many contributors and to several years' worth of students. Always a work-in-progress...

/2 Per @statnews.com: At [NHGRI], the entire comms office was eliminated Tu, along w/the offices of policy, science education, procurement, & the whole division of management.. Bonham’s dismissal leaves the institute w/o anyone in charge or able to offer the final sign-off on issuing new grants.

They've put Christine Grady, chief of the department of bioethics at the NIH’s Clinical Center on admin leave. I've worked w/her a lot. A WONDERFUL bioethicist (& person—a saint!). Fired for personal reasons? She's Fauci's wife. They have no shame.

What are they doing? And why? @dahlialithwick.bsky.social

Given the recent and ongoing service interruptions in PubMed, National Library of Medicine, NIH Reporter, etc., I put together a status page that covers a few key resources and some NIH institute pages. stats.uptimerobot.com/Zrqh8AhvKn Let me know what other sites you'd like to see added.

Francis Collins, the NIH Director for 12 years, led the Human Genome Project and other NIH efforts for 32 years, resigned today. Key words from his resignation letter www.nytimes.com/2025/03/01/u...

Anyone else finding that ncbi.nlm.nih.gov and related subdomains are down right now?

The @bioconductor.bsky.social Zenodo community accepts any contributions related to or Bioconductor. It is a great way to share software, of course, but also slides, talks, posters, workflows, etc. All contributions to zenodo get a doi. zenodo.org/communities/...

📣 GBCC2025 Abstracts & Registration Open! Join us June 23-26, 2025, at Cold Spring Harbor Lab for the first Galaxy & Bioconductor Community Conference. 🗓 Abstract Deadline: April 1 🔗 Submit/Register: gbcc2025.org #GBCC2025 #Bioconductor #DataScience #OpenSource

@msftresearch.bsky.social and @carnegiemellon.bsky.social published a study examining self-reported reductions in cognitive effort and confidence among knowledge workers utilizing #AI. Not the complete picture, but provides insight, challenges, and opportunities. www.microsoft.com/en-us/resear...

scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1 🧬🖥️🧪 https://github.com/bowang-lab/scGPT-spatial

The data at statecancerprofiles.cancer.gov are a valuable source of information about nationwide #cancer incidence and mortality. To address the lack of an API or data download, we have generated data extracts for dashboards, data integration, #epidemiology research, etc. github.com/seandavi/sta...

In case folks are interested in contacting their congresspeople about the NIH indirect cuts with some estimates of what they would mean for institutions in their state, here are some estimates based on published F&A rates and funding ... let me know if you want a particular state

We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...

#macos in #docker. github.com/dockur/macos #mswindows in #docker. github.com/dockur/windows

Application of ChatGPT in #oncology #research analyzed 91k US cancer crowdfunding stories and found that over one-third reported medical or social hardships like housing or food insecurity, with few meeting fundraising goals. jamanetwork.com/journals/jam...

Six years on, github.com/seandavi/awe... is still going strong. Contributions welcome. Fastest growing category recently has been spatial transcriptomics. #compbio #singlecell #transcriptomics #genomics #awesome-list

This is wild and futuristic. A virtual lab comprised of multiple A.I. (5) agents designed potent nanobodies vs SARS-CoV-2 with minimal human oversight. t.co/09smMPwHCY

This paper argues that online spaces become ghost towns because it's too easy to lurk without contributing, and that asking people to regularly re-commit—or the incoming messages start getting muted—reverses the trend. arxiv.org/abs/2410.23267 It works! #cscw2024 paper by @popowski.bsky.social .

A large-scale audit of dataset licensing & attribution in #AI text datasets. rdcu.be/dZzux Dataset licenses are frequently missing or wrong on popular dataset hosting sites. Interactive Data Provenance Explorer: dataprovenance.org #DataTransparency #AIethics #MachineLearning

A framework for sharing of clinical and genetic data for precision medicine applications https://www.nature.com/articles/s41591-024-03239-5 🧬🖥️ https://github.com/G2Lab/PrecisionChain

The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks https://www.nature.com/articles/s41592-024-02406-3 (read free: https://rdcu.be/dSWrr) 🧬🖥️ https://github.com/husonlab/splitstree6

Mapping cellular interactions from spatially resolved transcriptomics data https://www.nature.com/articles/s41592-024-02408-1 (read free: https://rdcu.be/dSTC5) Spacia software: https://github.com/yunguan-wang/Spacia 🧬🖥️