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Casey Greene

@casey.greenelab.com
4.8K followers 479 following 83 posts

Chair of the Department of Biomedical Informatics at the University of Colorado School of Medicine. Research: transcriptomics, machine learning, public data - pick two of three. He/him. Views mine, not employer's.

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Reposted by Casey Greene
Anthony Gitter @anthonygitter.bsky.social · 02/08/2026
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.
https://github.com/greenelab/deep-review/commit/e1529c48fe2dd83c81cc91a09d3b80fdf40e16bbWe examine applications of deep learning to a variety of biomedical problems—patient classification, fundamental biological processes, and treatment of patients—and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art.
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Nature Reviews Genetics @natrevgenet.nature.com · 11/06/2026
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
How to do science that matters: Computational biologist @casey.greenelab.com on purpose-driven open science practices
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Casey Greene @casey.greenelab.com · 10/06/2026
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.
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Dario Taraborelli @dartar.bsky.social · 04/05/2026
We built a thing ✨ Check it out:
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CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 24/04/2026
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.
cudbmi.info
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...
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Arjun Krishnan @compbiologist.bsky.social · 07/04/2026
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
cu.taleo.net
Post-Doctoral Fellow
Click the link provided to see the complete job description.
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Soragni:Lab @alice.soragnilab.com · 10/02/2026
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...
news.cuanschutz.edu
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.
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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 08/09/2025
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! 🧵
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Casey Greene @casey.greenelab.com · 30/08/2025
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!
Negative grant review: "This is not a research application, it's a rambling discourse about contemporary issues in bioinformatics"
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Michael Hoffman @michaelhoffman.bsky.social · 18/08/2025
"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...
nature.com
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.
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CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 15/08/2025
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.
Two people on the Anschutz Health Sciences Building patio on a cloudy day at the CU Anschutz Medical Campus. They are overlooking Denver and the mountains
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Georgia Tomova @georgiatomova.bsky.social · 23/07/2025
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 😳
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GigaScience Journal @gigascience.bsky.social · 21/07/2025
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
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Ming Tommy Tang @tommytang.bsky.social · 02/07/2025
Study 50K cancer transcriptomes through deep learning. data: figshare.com/articles/da... paper www.biorxiv.org/content/10....
figshare.com
A deep profile of gene expression across 18 human cancers
Data for "A deep profile of gene expression across 18 human cancers"
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Casey Greene @casey.greenelab.com · 04/06/2025
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_...
Screenshot of US-Africa Frontiers of Science Engineering and Medicine webpage.
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Colorado Clinical and Translational Sciences Institute (CCTSI) @cctsi.bsky.social · 03/06/2025
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.
news.cuanschutz.edu
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.
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Ming Tommy Tang @tommytang.bsky.social · 19/05/2025
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.
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Karthik Ram @karthik.io · 02/05/2025
✴️ 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
os.nav.fund
Open Science Meeting Fund 2025
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Karthik Ram @karthik.io · 25/04/2025
✴️ 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
os.nav.fund
AI for Open Science - Request for Proposals
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eLife @elife.bsky.social · 03/04/2025
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
buff.ly
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.
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Audrey Hendricks @audreyhendricks.com · 27/03/2025
Me too!!
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Anna Greene @annagreene.bsky.social · 26/03/2025
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).
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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 17/03/2025
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. 🧵
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Richard Sever @richardsever.bsky.social · 11/03/2025
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
openrxiv.org
Homepage - openRxiv
openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.
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Arc Institute @arcinstitute.org · 25/02/2025
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-website-git-ben-virtual-cell-atlas-tool-arc-institute.vercel.app
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...
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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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Casey Greene @casey.greenelab.com · 22/01/2025
We did a thing! Read below if you want to learn more :)
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Ran Blekhman @blekhman.bsky.social · 22/01/2025
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...
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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Abhinay Ramaprasad @abhinay.bsky.social · 10/01/2025
We have got a website now! Shout-out to @casey.greenelab.com for their well-documented lab website template that offers super flexibility to make a website that is "our own". With plenty of ChatGPT assist, this was a fun project! www.parafugelab.com
parafugelab.com
ParaFuGe Lab
Parasite Functional Genetics Laboratory. We are a team of researchers interested in understanding how malaria parasites live and multiply within red blood cells. Our research focuses on identifying th...
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Casey Greene @casey.greenelab.com · 06/01/2025
Interesting find from ~20 years ago - fuzzy axolotls were first invented by Mahony et al, 2004 (Figure 2) pubmed.ncbi.nlm.nih.gov/15070404/
pubmed.ncbi.nlm.nih.gov
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models - PubMed
While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software deve...
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J. Brian Byrd @jbrianbyrd.bsky.social · 04/01/2025
Why use synthetic data? One rationale: because personal health data are highly protected and sensitive As @casey.greenelab.com and I and others have written, like oil, privacy can be gone, in contrast to data which are reusable: www.nature.com/articles/s41... #PSB25
nature.com
Responsible, practical genomic data sharing that accelerates research - Nature Reviews Genetics
Data sharing can maximize the benefit and reach of genomics research. However, sharing must occur in a responsible manner, particularly when there are privacy risks to human participants. In this Revi...
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Casey Greene @casey.greenelab.com · 22/12/2024
I started a list of CU Anschutz associated accounts and people. FYI in case you want to follow - not sure if I'm doing this right: bsky.app/profile/did:...
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Christian Mosimann @chrmosimann.bsky.social · 21/12/2024
Showing visitors the surroundings - F1 as tour guide at Barr Lake, where the Bald Eagles roam. 🦅 #Colorado
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CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 21/12/2024
Explore research from Yanjun Gao, PhD, on LLMs’ capabilities in understanding and representing structured electronic health record data for clinical prediction, which was accepted at the annual EMNLP meeting ▶️https://buff.ly/4a0tAOJ
Chats and graphics discussing LLMs
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AMIA @amia.org · 04/12/2024
We’re excited to join Bluesky! 🎉 Follow us for updates on advancing healthcare through informatics, upcoming events, and opportunities to connect with our community of professionals driving innovation in informatics. #AMIA #Informatics ##DataDrivenHealthcare
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CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 26/11/2024
A study from the Norman Lab at DBMI, published in @cellpressnews.bsky.social, shows that the KIR3DLI*114 allele, found in First Nations inhabitants of Oceania, could impact immunity. 🧬The team aims to use their research to address today's health disparities ▶️ buff.ly/3Zhbx2K
Image of a globe focuses on Australia and Oceania.
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Abhirupa Ghosh @abhirupaghosh.bsky.social · 03/12/2024
The postdocs (me and @evanbrenner.bsky.social ) enjoying the Holiday Selfie Station on day 1 of Byte Into Sweets, Holiday Edition at @cubiomedinfo.bsky.social | @cuanschutz.bsky.social
Holiday Selfie Station!Holiday Selfie Station!
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Heidi Rehm @heidirehm.bsky.social · 27/11/2024
We are delighted to announce this year's call for applications for the NHGRI-funded MGB T32 Postdoctoral Training Program in Precision and Genomic Medicine buff.ly/414Xajk Please RT or share w/ those who may be interested.
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Audrey Hendricks @audreyhendricks.com · 25/11/2024
I had so much fun visiting the BU Biostats Dept a couple weeks ago! What an amazing place! www.bu.edu/sph/news/art...
bu.edu
Audrey Hendricks (SPH'11) Receives 2023 Biostatistics Distinguished Alumni Award
Hendricks (SPH'11), whose research bridges biomedical science and statistical machine learning, is on a mission to advance inclusion in the sciences, from who joins the field to what questions are ask...
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CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 23/11/2024
This week's Tattered Cover session with Cathy Lozupone, PhD, and trainee Brook Santangelo was a hit! Their insightful talk on "The Role of the Intestinal Microbiome in Health" explored how our gut shapes our health. Learn more ▶️ buff.ly/4fZ4JfU
Two people sitting next to a screen featuring a series of different books about gut health in a bookstore setting.
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Casey Greene @casey.greenelab.com · 23/11/2024
What do you call a dumpling that sits in front of the house and watches folks walk by? A stoop dumpling.
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CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 22/11/2024
We had an amazing time exploring AI in cardiology with Mike Rosenberg, MD, during this week's Bytes to Bedside! From the latest #tech in clinical settings to the powerful potential use of #AI for method improvement, it's exciting to see how we're revolutionizing healthcare.
Person presenting on AI in front of a screen that reads, "DBMI Seminar"
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CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 20/11/2024
Explore how DBMI is revolutionizing care where it matters most: at the bedside ▶️ bit.ly/4hZwkzm
CU Anschutz Health Sciences Building at dusk
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 20/11/2024
Has anyone discovered/invented a better mechanism for follow-backs, something like checkboxes with a "select-all" option? It's amazing to see the community growing here but clicking follow-back on hundreds of people who I'd sincerely like to be following-back is a daunting task!
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University of Colorado Anschutz @cuanschutz.bsky.social · 12/11/2024
The largest academic health center in the Rocky Mountain region is excited to officially be on Bluesky! Follow us for the latest #healthscience news and breakthroughs straight from #CUAnschutz experts. Learn more about who we are, here: cuanschutz.edu
The CU Anschutz Medical Campus is photographed from afar, under the glow of a sunset.
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Charles Brenner, PhD @charlesmbrenner.bsky.social · 16/11/2024
i’m from the hypothesis-based side of compbio and genomics currently seeing what happens when you block electron flow into mitochondria #NAD #raredisease #metabolism
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Casey Greene @casey.greenelab.com · 15/11/2024
My understanding of this post is #evolving.
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