Sean Davis
@seandavi.bsky.social
Reposted by Sean Davis
Alert! The abstract deadline for the Microbial Pathogenesis & Host Response meeting has been extended to July 7 meetings.cshl.edu/meetings.asp...
Microbial Pathogenesis & Host Response
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
June 23, 2025 at 8:24 PM
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...
seandavi.github.io/RBiocBook/
Thanks to many contributors and to several years' worth of students. Always a work-in-progress...
The RBioc Book
A collection of chapters more than a book, but….
seandavi.github.io
June 24, 2025 at 5:50 PM
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...
seandavi.github.io/RBiocBook/
Thanks to many contributors and to several years' worth of students. Always a work-in-progress...
Reposted by Sean Davis
/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.
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.
April 2, 2025 at 4:18 AM
/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.
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.
Reposted by Sean Davis
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.
Fired for personal reasons? She's Fauci's wife.
They have no shame.
April 2, 2025 at 4:13 AM
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.
Fired for personal reasons? She's Fauci's wife.
They have no shame.
Reposted by Sean Davis
What are they doing? And why? @dahlialithwick.bsky.social
March 2, 2025 at 1:15 PM
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.
stats.uptimerobot.com/Zrqh8AhvKn
Let me know what other sites you'd like to see added.
March 2, 2025 at 11:55 AM
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.
stats.uptimerobot.com/Zrqh8AhvKn
Let me know what other sites you'd like to see added.
Reposted by Sean Davis
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...
www.nytimes.com/2025/03/01/u...
March 1, 2025 at 6:07 PM
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...
www.nytimes.com/2025/03/01/u...
Anyone else finding that ncbi.nlm.nih.gov and related subdomains are down right now?
National Center for Biotechnology InformationTwitterFacebookLinkedInGitHubNCBI Insights BlogTwitterFacebookYoutube
ncbi.nlm.nih.gov
March 1, 2025 at 5:45 PM
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/...
zenodo.org/communities/...
February 24, 2025 at 9:29 PM
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/...
zenodo.org/communities/...
Reposted by Sean Davis
📣 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
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
GBCC2025
Cold Spring Harbor Laboratory (CSHL), New York June 23-26, 2025
gbcc2025.org
February 11, 2025 at 10:01 PM
📣 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
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...
www.microsoft.com/en-us/resear...
February 11, 2025 at 5:38 PM
@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...
www.microsoft.com/en-us/resear...
Reposted by Sean Davis
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
February 10, 2025 at 7:30 PM
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...
GitHub - seandavi/state-cancer-profile-scraper: Bulk access and download state cancer profiles data
Bulk access and download state cancer profiles data - seandavi/state-cancer-profile-scraper
github.com
February 11, 2025 at 12:02 AM
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...
Reposted by Sean Davis
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
February 8, 2025 at 2:14 PM
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
Reposted by Sean Davis
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...
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...
www.cell.com
January 22, 2025 at 5:31 PM
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...
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...
jamanetwork.com/journals/jam...
Natural Language Processing–Assessed Unmet Medical and Social Needs
This cross-sectional study uses a large natural language processing model to examine unmet medical and social needs based on cancer-related fundraising stories in the US.
jamanetwork.com
November 14, 2024 at 1:53 PM
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...
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
#compbio #singlecell #transcriptomics #genomics #awesome-list
GitHub - seandavi/awesome-single-cell: Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. - seandavi/awesome-single-cell
github.com
November 13, 2024 at 7:25 PM
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
#compbio #singlecell #transcriptomics #genomics #awesome-list
Reposted by Sean Davis
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
November 13, 2024 at 3:24 PM
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
Reposted by Sean Davis
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
.
It works! #cscw2024 paper by @popowski.bsky.social
.
Commit: Online Groups with Participation Commitments
In spite of efforts to increase participation, many online groups struggle to survive past the initial days, as members leave and activity atrophies. We argue that a main assumption of online group de...
arxiv.org
November 1, 2024 at 5:56 PM
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
.
It works! #cscw2024 paper by @popowski.bsky.social
.