Casey Greene
@casey.greenelab.com
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.
Reposted by Casey Greene
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! 🧵
September 8, 2025 at 3:52 PM
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!
August 30, 2025 at 2:09 PM
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!
Reposted by Casey Greene
"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...
—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.
www.nature.com
August 18, 2025 at 9:42 PM
"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...
—the illustrious @casey.greenelab.com
as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...
Reposted by Casey Greene
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.
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.
August 15, 2025 at 8:25 PM
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.
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.
Reposted by Casey Greene
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 😳
July 23, 2025 at 2:00 PM
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 😳
Reposted by Casey Greene
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
July 21, 2025 at 4:27 PM
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
Reposted by Casey Greene
Study 50K cancer transcriptomes through deep learning. data: figshare.com/articles/da...
paper www.biorxiv.org/content/10....
paper www.biorxiv.org/content/10....
A deep profile of gene expression across 18 human cancers
Data for "A deep profile of gene expression across 18 human cancers"
figshare.com
July 2, 2025 at 2:15 PM
Study 50K cancer transcriptomes through deep learning. data: figshare.com/articles/da...
paper www.biorxiv.org/content/10....
paper www.biorxiv.org/content/10....
Reposted by Casey Greene
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
June 20, 2025 at 7:23 PM
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.
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_...
www.nationalacademies.org/event/45168_...
June 4, 2025 at 1:24 PM
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_...
www.nationalacademies.org/event/45168_...
Reposted by Casey Greene
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
June 3, 2025 at 3:33 PM
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.
Reposted by Casey Greene
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.
1/
You’ve got RNA-seq.
Methylation.
Proteomics.
Time to “integrate” the data.
But how? And why?
Let’s break it down.
May 19, 2025 at 1:21 PM
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.
1/
You’ve got RNA-seq.
Methylation.
Proteomics.
Time to “integrate” the data.
But how? And why?
Let’s break it down.
Reposted by Casey Greene
✴️ 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
@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
Open Science Meeting Fund 2025
os.nav.fund
May 2, 2025 at 9:23 PM
✴️ 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
@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
Reposted by Casey Greene
This is a lovely thread of self-introductions from members of the compbio/genomics crowd on BlueSky. It feels a bit more friendly and warm than a starter pack
There are so many people moving over that I'm sure I'm missing folks. Can we make a #compbio / #genomics intro thread to get reacquainted?
I'm at the University of Colorado. I often say that if you pick two of three from #transcriptome, #ML, and #publicdata, my lab is probably interested.
I'm at the University of Colorado. I often say that if you pick two of three from #transcriptome, #ML, and #publicdata, my lab is probably interested.
April 27, 2025 at 2:07 AM
This is a lovely thread of self-introductions from members of the compbio/genomics crowd on BlueSky. It feels a bit more friendly and warm than a starter pack
Reposted by Casey Greene
✴️ 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
AI for Open Science - Request for Proposals
os.nav.fund
April 25, 2025 at 4:54 PM
✴️ 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
Reposted by Casey Greene
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
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
April 3, 2025 at 3:12 PM
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
When the unthinkable happens, will the care we need still be there? We must protect this lifeline.
#StandUpForScience @casey.greenelab.com @annagreene.bsky.social
Reposted by Casey Greene
Me too!!
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 🙌🏾
March 27, 2025 at 11:00 PM
Me too!!
Reposted by Casey Greene
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...
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...
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.
elifesciences.org
March 26, 2025 at 3:57 PM
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).
Reposted by Casey Greene
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. 🧵
March 17, 2025 at 4:11 PM
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. 🧵
Reposted by Casey Greene
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 🧬😀
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
March 11, 2025 at 6:19 PM
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 🧬😀
Reposted by Casey Greene
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
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.
openrxiv.org
March 11, 2025 at 1:20 PM
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
Reposted by Casey Greene
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
February 25, 2025 at 2:03 PM
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...
Reposted by Casey Greene
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...
We did a thing! Read below if you want to learn more :)
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...
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...
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 5:41 PM
We did a thing! Read below if you want to learn more :)
Reposted by Casey Greene
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...
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...
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 5:12 PM
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...
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...
Reposted by Casey Greene
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
www.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...
www.parafugelab.com
January 10, 2025 at 11:42 AM
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
www.parafugelab.com