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Sean Davis

@seandavi.bsky.social
75 followers 13 following 20 posts
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Reposted by Sean Davis
Victor J. Torres @torreslab.bsky.social · 23/06/2025
Alert! The abstract deadline for the Microbial Pathogenesis & Host Response meeting has been extended to July 7 meetings.cshl.edu/meetings.asp...
meetings.cshl.edu
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.
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Sean Davis @seandavi.bsky.social · 24/06/2025
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
The RBioc Book
A collection of chapters more than a book, but….
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Reposted by Sean Davis
Hank Greely @hankgreely.bsky.social · 02/04/2025
/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.
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Reposted by Sean Davis
Hank Greely @hankgreely.bsky.social · 02/04/2025
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.
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Reposted by Sean Davis
NotAnInfluencer @scigeek69.bsky.social · 02/03/2025
What are they doing? And why? @dahlialithwick.bsky.social
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Sean Davis @seandavi.bsky.social · 02/03/2025
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.
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Reposted by Sean Davis
Eric Topol @erictopol.bsky.social · 01/03/2025
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...
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Sean Davis @seandavi.bsky.social · 01/03/2025
Anyone else finding that ncbi.nlm.nih.gov and related subdomains are down right now?
ncbi.nlm.nih.gov
National Center for Biotechnology InformationTwitterFacebookLinkedInGitHubNCBI Insights BlogTwitterFacebookYoutube
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Sean Davis @seandavi.bsky.social · 24/02/2025
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/...
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Reposted by Sean Davis
Bioconductor @bioconductor.bsky.social · 11/02/2025
📣 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
gbcc2025.org
GBCC2025
Cold Spring Harbor Laboratory (CSHL), New York June 23-26, 2025
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Sean Davis @seandavi.bsky.social · 11/02/2025
@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...
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Reposted by Sean Davis
Stephen Turner @stephenturner.us · 10/02/2025
scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪 github.com/bowang-lab/scGPT-spatial
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Sean Davis @seandavi.bsky.social · 11/02/2025
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.com
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
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Sean Davis @seandavi.bsky.social · 08/02/2025
ai.nejm.org/doi/full/10....
ai.nejm.org
The Burden of Reviewing LLM-Generated Content
Large language models (LLMs) in health care aim to reduce the cognitive and administrative burden for health care professionals. Yet the accuracy and completeness of LLM-generated material is still...
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Sean Davis @seandavi.bsky.social · 08/02/2025
ai.nejm.org/doi/full/10....
ai.nejm.org
A Cross-Sectional Study of GPT-4–Based Plain Language Translation of Clinical Notes to Improve Patient Comprehension of Disease Course and Management
The 21st Century Cures Act provides patients with access to their clinical notes, but most patients, particularly those with limited health literacy, have difficulty understanding and utilizing the...
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Reposted by Sean Davis
Erin Kane @dianamonkey.bsky.social · 08/02/2025
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
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Sean Davis @seandavi.bsky.social · 08/02/2025
www.nature.com/articles/d41...
nature.com
‘Despair is not an option’ — how scientists can help protect federal research
Government scientists in the US must be clear-eyed and continue to serve the public.
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Sean Davis @seandavi.bsky.social · 08/02/2025
www.nature.com/articles/d41...
nature.com
How are researchers using AI? Survey reveals pros and cons for science
Despite strong interest in using artificial intelligence to make research faster, easier and more accessible, researchers say they need more support to navigate its possibilities.
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Reposted by Sean Davis
Samantha Graham @samanthagraham.bsky.social · 22/01/2025
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...
cell.com
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...
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Sean Davis @seandavi.bsky.social · 18/11/2024
www.nature.com/articles/s41...
nature.com
A foundation model for joint segmentation, detection and recognition of biomedical objects across nine modalities - Nature Methods
BiomedParse is a foundation model for image analysis that uses a joint learning approach to jointly conduct segmentation, detection and recognition and offer state-of-the-art performance across a wide...
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Sean Davis @seandavi.bsky.social · 14/11/2024
#macos in #docker. github.com/dockur/macos #mswindows in #docker. github.com/dockur/windows
github.com
GitHub - dockur/macos: OSX (macOS) inside a Docker container.
OSX (macOS) inside a Docker container. Contribute to dockur/macos development by creating an account on GitHub.
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Sean Davis @seandavi.bsky.social · 14/11/2024
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
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.
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Sean Davis @seandavi.bsky.social · 13/11/2024
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
github.com
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
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Reposted by Sean Davis
Eric Topol @erictopol.bsky.social · 13/11/2024
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
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Reposted by Sean Davis
Michael Bernstein @mbernst.bsky.social · 01/11/2024
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 .
arxiv.org
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...
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Sean Davis @seandavi.bsky.social · 08/11/2024
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
rdcu.be
A large-scale audit of dataset licensing and attribution in AI
Nature Machine Intelligence - The Data Provenance Initiative audits over 1,800 text artificial intelligence (AI) datasets, analysing trends, permissions of use and global representation. It exposes...
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Reposted by Sean Davis
Stephen Turner @stephenturner.us · 03/09/2024
A framework for sharing of clinical and genetic data for precision medicine applications www.nature.com/articles/s41591-024-… 🧬🖥️ github.com/G2Lab/PrecisionChain
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Reposted by Sean Davis
Stephen Turner @stephenturner.us · 04/09/2024
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks www.nature.com/articles/s41592-024-… (read free: rdcu.be/dSWrr) 🧬🖥️ github.com/husonlab/splitstree6
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Reposted by Sean Davis
Stephen Turner @stephenturner.us · 04/09/2024
Mapping cellular interactions from spatially resolved transcriptomics data www.nature.com/articles/s41592-024-… (read free: rdcu.be/dSTC5) Spacia software: github.com/yunguan-wang/Spacia 🧬🖥️
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Sean Davis @seandavi.bsky.social · 05/09/2024
www.nature.com/articles/s41...
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Sean Davis @seandavi.bsky.social · 31/08/2024
www.nature.com/articles/s42...
nature.com
A large-scale audit of dataset licensing and attribution in AI - Nature Machine Intelligence
The Data Provenance Initiative audits over 1,800 text artificial intelligence (AI) datasets, analysing trends, permissions of use and global representation. It exposes frequent errors on several major...
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