Lightnews — Scholar-powered news

Reposted by Sean Davis

Victor J. Torres @torreslab.bsky.social · Jun 23

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

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Sean Davis @seandavi.bsky.social · Jun 24

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...

The RBioc Book

A collection of chapters more than a book, but….

seandavi.github.io

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Reposted by Sean Davis

Hank Greely @hankgreely.bsky.social · Apr 2

/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 · Apr 2

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

scigeek69.bsky.social @scigeek69.bsky.social · Mar 2

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

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Sean Davis @seandavi.bsky.social · Mar 2

Added. Thanks, @trishaclare.bsky.social. For folks unfamiliar with eRA Commons (public.era.nih.gov), it is the online system that allows users to manage grants for the National Institutes of Health (NIH). While it is down, the NIH grants process will be further curtailed.

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Sean Davis @seandavi.bsky.social · Mar 2

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 · Mar 1

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 · Mar 1

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

Sean Davis @seandavi.bsky.social · Feb 24

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 · Feb 11

📣 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

Cold Spring Harbor Laboratory (CSHL), New York June 23-26, 2025

gbcc2025.org

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Sean Davis @seandavi.bsky.social · Feb 11

@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...

Reposted by Sean Davis

Stephen Turner @stephenturner.us · Feb 10

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

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Sean Davis @seandavi.bsky.social · Feb 11

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

Sean Davis @seandavi.bsky.social · Feb 8

ai.nejm.org/doi/full/10....

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...

ai.nejm.org

Sean Davis @seandavi.bsky.social · Feb 8

ai.nejm.org/doi/full/10....

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...

ai.nejm.org

Reposted by Sean Davis

Erin 🦇🎃EEK🎃🦇 Kane @dianamonkey.bsky.social · Feb 8

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 · Feb 8

www.nature.com/articles/d41...

‘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.

www.nature.com

Sean Davis @seandavi.bsky.social · Feb 8

Thanks for the shout out. The real heros are the folks who submit data and the dedicated folks at NCBI GEO and NLM who maintain the data resources. We are reminded that such resources are not to be taken for granted....

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Sean Davis @seandavi.bsky.social · Feb 8

www.nature.com/articles/d41...

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.

www.nature.com

Reposted by Sean Davis

Samantha Graham @samanthagraham.bsky.social · Jan 22

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

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Sean Davis @seandavi.bsky.social · Nov 18

www.nature.com/articles/s41...

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...

www.nature.com

Sean Davis @seandavi.bsky.social · Nov 14

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

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

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.

github.com

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Sean Davis @seandavi.bsky.social · Nov 14

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...

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

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Sean Davis @seandavi.bsky.social · Nov 14

I've embraced these new technologies as both a student (aren't we all?) and an educator (of adults), encouraging students to experiment, share their experiences transparently, and understand that active learning can take many forms. Not all candy canes and roses, but this stuff is here to stay.