10 years ago today @casey.greenelab.com launched our review "Opportunities and obstacles for deep learning in biology and medicine" greenelab.github.io/deep-review/. It was a widely collaborative project written on GitHub, which lead to the creation of manubot.org.

How to do science that matters: Computational biologist @casey.greenelab.com on purpose-driven open science practices Read the interview here: go.nature.com/4uWAQoe

Supporting things because they are open is odd. Fund the practices that move science fastest. Open often wins on the merits, which is the whole point. I cannot rule out that there may have been some hot takes in this interview.

Richard Sever@richardsever.bsky.social · 2mo ago

“My interest isn't really open science; it's high-quality, rigorous science..often that happens to be open.” Sense from @casey.greenelab.com that aligns with how serious scientists see research and the idea it should be "open as possible, closed as necessary" www.springernature.com/gp/researche...

We built a thing ✨ Check it out:

Open Source for Science Fund@os4science.org · 3mo ago

Today we're launching the Open Source for Science Fund, a new multi-donor philanthropic fund by Renaissance Philanthropy, seeded by @biohub.org and @wellcometrust.bsky.social, with support from @kavlifoundation.org and @researchsoftware.bsky.social 🧵 os4science.org/news/open-so...

Emerging evidence from the gut–lung axis: antibiotic-driven microbiome disruption may reduce type-17 immune tone in the lungs long after treatment, with implications for infection susceptibility and immune balance.

Amoxicillin induces gut dysbiosis leading to long term suppression of type-17 immune tone in the lungs

T-helper (Th)-17 lymphocytes are central mediators of adaptive type 17 immunity. Decreased type-17 signaling increases severity of infections in humans and mice. However, detrimental effects of excessive type 17 responses in autoimmune and other inflamm...

cudbmi.info

Sean Davis & I are hiring a postdoc to work on turning massive public biological data collections into reusable engines for discovery. #ML / #AI + large-scale omics + open software Details + apply: cu.taleo.net/careersectio... seandavi.github.io | thekrishnanlab.org @cubiomedinfo.bsky.social

Happy to share this new, very intentional chapter. I have left UCLA after 14 years to join the University of Colorado Anschutz as Professor of Biomedical Informatics and Neurosurgery and the inaugural Marsico Chair in Excellence in Functional Precision Medicine/n news.cuanschutz.edu/dbmi/cu-ansc...

CU Anschutz Recruits National Leader to Launch Functional Personalized Medicine Initiative

CU Anschutz welcomes Alice Soragni to launch a Functional Personalized Medicine Initiative using rapid tumor organoid testing to guide treatment decisions.

news.cuanschutz.edu

This fall, the Data Lab is hitting the road to present some of our tools and projects during these exciting events. Here’s where you can find us! 🧵

Happy upcoming Pioneer Award Application Day to all who celebrate. I was mentioning that the best review comment I've ever gotten came from the related DP2 (New Innovator) mechanism. Enjoy this throwback to #GrantReviewGreatstHits as the deadline gets closer! May you all do better than I've done!

"I want to vibe code the genome" —the illustrious @casey.greenelab.com as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...

Beyond AlphaFold: how AI is decoding the grammar of the genome

Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.

nature.com

CU Anschutz 🤝UCLA We were thrilled to host @alice.soragnilab.com from UCLA at @cuanschutz.bsky.social. She’s teaming up with @casey.greenelab.com to drive innovation and improve patient outcomes. This collaboration is a powerful example of how partnerships accelerate scientific discovery.

What is the point of published abstracts?? Does anyone find them useful for anything? As if we don't already have enough clutter in the literature 😳

Now up in #BOSC2025 is our Ed Board Member @monimunozto.bsky.social talking about the AI/ML readiness of biomedical data through the Bridge2AI project #ISMBECCB2025 #ISMB2025

Study 50K cancer transcriptomes through deep learning. data: figshare.com/articles/da... paper www.biorxiv.org/content/10....

This Q&A with @casey.greenelab.com provides a nice summary of the current state of #ArtificialInteligence in healthcare, future developments on the horizon, and the potential opportunities and pitfalls of these technologies - for both providers and patients.

AI in Healthcare: Results Over Hype

What is AI in healthcare? How is my doctor using AI? An artificial intelligence expert explains how healthcare is uses AI for patients, medical research.

news.cuanschutz.edu

Bioinformatics is one of the areas covered in this US-Africa Frontiers of Science, Engineering, and Medicine Symposium. Feb 2026. Applications open through July 31, 2025: www.nationalacademies.org/event/45168_...

AI isn’t here to replace your doctor—it’s here to help them spend more time with you. @casey.greenelab.com explains how @cuanschutz.bsky.social researchers are using AI to improve patient care, streamline hospital operations, and build trust through transparency and real-world results.

AI in Healthcare: Results Over Hype

What is AI in healthcare? How is my doctor using AI? An artificial intelligence expert explains how healthcare is uses AI for patients, medical research.

news.cuanschutz.edu

Thread: Multi-omics sounds cool—until you actually try it. Here's are the nuances. 1/ You’ve got RNA-seq. Methylation. Proteomics. Time to “integrate” the data. But how? And why? Let’s break it down.

✴️ Request for proposals! ✴️ @navigation.org is funding focused gatherings to tackle key challenges in Open Science. We support meetings that define solvable problems and quickly move ideas toward implementation. Deadline: June 15, 2025 os.nav.fund/meeting-fund #OpenScience

✴️ REQUEST FOR PROPOSALS! ✴️ @navigation.org is seeking bold projects at the intersection of AI and Open Science. We support innovative applications that make science more transparent, efficient, and trustworthy. Deadline: July 15, 2025. os.nav.fund/ai-for-os/ #openscience #AIforScience

Life-saving treatments exist because of decades of research, but cuts to NIH-funded research put that progress at risk. When the unthinkable happens, will the care we need still be there? We must protect this lifeline. #StandUpForScience @casey.greenelab.com @annagreene.bsky.social

Science Under Threat in the United States: Research turns hope into reality

Two scientists describe how an acute myeloid leukemia diagnosis underscores the need for continued federal support for research and access to care.

buff.ly

Me too!!

Chrystal Starbird@drstarbird.bsky.social · last yr.

Just want to say again I’m grateful for the people doing their best to hold it down at the NIH despite the chaos and uncertainty. I see you 🙌🏾

Last year, I was surprisingly diagnosed with AML. Attacks on science that we currently face threaten future scientific discoveries that can benefit individuals' health. This should scare us all. Read more about my story and thoughts on this below (with @casey.greenelab.com).

Science Under Threat in the US Research turns hope into reality by @annagreene.bsky.social & @casey.greenelab.com Two scientists describe how an acute myeloid leukemia diagnosis underscores the need for continued federal support for research and access to care. elifesciences.org/articles/106...

We recently announced new ways to participate in the Open #SingleCell #PediatricCancer Atlas (OpenScPCA) project. Researchers who contribute their expertise may become eligible for a grant! Keep reading for more details about the unique 2025 grant categories. 🧵

Excited to see my dissertation work published in Cancer Research @theaacr.bsky.social 🎉! A big thank you to my chair, Jen Doherty and committee including @casey.greenelab.com for their mentorship on this project! Check out the highlights of our study below if interested 🧬😀

Huntsman Cancer Institute@huntsmancancer.bsky.social · last yr.

New research finds ovarian cancer mutations are nearly identical across populations, with key differences that may impact treatment. This study highlights the importance of diversity in cancer genomics and could help refine treatment strategies for all patients. bit.ly/4bHpifC

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Today, we're launching the Arc Virtual Cell Atlas, a growing resource for computation-ready single-cell measurements. arc-website-git-ben-virtual-cell-atlas-tool-arc-institute.vercel.app/news/news/ar...

Arc Virtual Cell Atlas launches, combining data from over 300 million cells | Arc Institute

Arc Institute today launched the Arc Virtual Cell Atlas, a growing resource for computation-ready single-cell measurements, starting with data from over 300 million cells. The initial release of the A...

arc-website-git-ben-virtual-cell-atlas-tool-arc-institute.vercel.app

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...

cell.com

We did a thing! Read below if you want to learn more :)

Ran Blekhman@blekhman.bsky.social · 2y ago

Today we report a new compendium of human gut microbiomes with >168,000 samples By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria Now out in Cell: www.cell.com/cell/fulltex...