Reposted by Casey GreeneAnthony Gitter @anthonygitter.bsky.social · 02/08/202610 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. 192
Reposted by Casey GreeneNature Reviews Genetics @natrevgenet.nature.com · 11/06/2026How to do science that matters: Computational biologist @casey.greenelab.com on purpose-driven open science practices Read the interview here: go.nature.com/4uWAQoe 032
Casey Greene @casey.greenelab.com · 10/06/2026Supporting 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. 14230
Reposted by Casey GreeneDario Taraborelli @dartar.bsky.social · 04/05/2026We built a thing ✨ Check it out: 095
Reposted by Casey GreeneCU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 24/04/2026Emerging 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.infoAmoxicillin induces gut dysbiosis leading to long term suppression of type-17 immune tone in the lungsT-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... 011
Reposted by Casey GreeneArjun Krishnan @compbiologist.bsky.social · 07/04/2026Sean 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.socialcu.taleo.netPost-Doctoral FellowClick the link provided to see the complete job description. 053
Reposted by Casey GreeneSoragni:Lab @alice.soragnilab.com · 10/02/2026Happy 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.eduCU Anschutz Recruits National Leader to Launch Functional Personalized Medicine InitiativeCU Anschutz welcomes Alice Soragni to launch a Functional Personalized Medicine Initiative using rapid tumor organoid testing to guide treatment decisions. 4119330
Reposted by Casey GreeneChildhood Cancer Data Lab @cancerdatalab.bsky.social · 08/09/2025This 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! 🧵 101
Casey Greene @casey.greenelab.com · 30/08/2025Happy 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! 3452
Reposted by Casey GreeneMichael 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.comBeyond AlphaFold: how AI is decoding the grammar of the genomeScientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools. 12210
Casey Greene @casey.greenelab.com · 19/08/2025Day 3 of vibe coding the genome: velociraptors now code review pull requests.media.tenor.coma man is dancing with dinosaurs in the backgroundAlt: A man is fending off dinosaurs in Jurassic Park 172
Reposted by Casey GreeneCU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 15/08/2025CU 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. 041
Reposted by Casey GreeneGeorgia Tomova @georgiatomova.bsky.social · 23/07/2025What 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 😳 11194
Reposted by Casey GreeneGigaScience Journal @gigascience.bsky.social · 21/07/2025Now 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 176
Reposted by Casey GreeneMing Tommy Tang @tommytang.bsky.social · 02/07/2025Study 50K cancer transcriptomes through deep learning. data: figshare.com/articles/da... paper www.biorxiv.org/content/10....figshare.comA deep profile of gene expression across 18 human cancers Data for "A deep profile of gene expression across 18 human cancers" 172
Casey Greene @casey.greenelab.com · 02/07/2025FYI I'm pretty sure this one ended up getting published after peer review here: www.nature.com/articles/s41...nature.comDeep profiling of gene expression across 18 human cancers - Nature Biomedical EngineeringUsing unsupervised deep learning to generate low-dimensional latent spaces for gene-expression data can unveil biological insight across cancers. 131
Casey Greene @casey.greenelab.com · 04/06/2025Bioinformatics 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_... 051
Reposted by Casey GreeneColorado Clinical and Translational Sciences Institute (CCTSI) @cctsi.bsky.social · 03/06/2025AI 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.eduAI in Healthcare: Results Over HypeWhat is AI in healthcare? How is my doctor using AI? An artificial intelligence expert explains how healthcare is uses AI for patients, medical research. 011
Reposted by Casey GreeneMing Tommy Tang @tommytang.bsky.social · 19/05/2025Thread: 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. 3174
Casey Greene @casey.greenelab.com · 10/05/2025media.tenor.coma cartoon of homer simpson and his family in a car with the words are we there yetALT: a cartoon of homer simpson and his family in a car with the words are we there yet 020
Reposted by Casey GreeneKarthik 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 #OpenScienceos.nav.fundOpen Science Meeting Fund 2025 22015
Reposted by Casey GreeneKarthik 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 #AIforScienceos.nav.fundAI for Open Science - Request for Proposals 01821
Reposted by Casey GreeneeLife @elife.bsky.social · 03/04/2025Life-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.socialbuff.lyScience Under Threat in the United States: Research turns hope into realityTwo scientists describe how an acute myeloid leukemia diagnosis underscores the need for continued federal support for research and access to care. 152
Reposted by Casey GreeneAnna Greene @annagreene.bsky.social · 26/03/2025Last 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). 097
Reposted by Casey GreeneChildhood Cancer Data Lab @cancerdatalab.bsky.social · 17/03/2025We 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. 🧵 163
Reposted by Casey GreeneRichard Sever @richardsever.bsky.social · 11/03/2025Big 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/nopenrxiv.orgHomepage - openRxivopenRxiv 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. 552558846
Reposted by Casey GreeneArc Institute @arcinstitute.org · 25/02/2025Today, 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.appArc Virtual Cell Atlas launches, combining data from over 300 million cells | Arc InstituteArc 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... 13917
Reposted by Casey GreeneSamantha Graham @samanthagraham.bsky.social · 22/01/2025We’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.comIntegration of 168,000 samples reveals global patterns of the human gut microbiomeThe 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... 310044
Casey Greene @casey.greenelab.com · 22/01/2025We did a thing! Read below if you want to learn more :) 1141
Reposted by Casey GreeneRan Blekhman @blekhman.bsky.social · 22/01/2025Today 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.comIntegration of 168,000 samples reveals global patterns of the human gut microbiomeThe 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... 1020376
Reposted by Casey GreeneAbhinay Ramaprasad @abhinay.bsky.social · 10/01/2025We 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.comparafugelab.comParaFuGe LabParasite 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... 251
Casey Greene @casey.greenelab.com · 06/01/2025It might be under-recognized that Mahony et al's foundational 2004 research on fuzzy axolotls has laid the groundwork for the fuzzy axolotl handler job - more from ZipRecruiter: www.ziprecruiter.com/Salaries/fuz... 010
Casey Greene @casey.greenelab.com · 06/01/2025More on fuzzy axolotls here: bsky.app/profile/shau... 110
Casey Greene @casey.greenelab.com · 06/01/2025Interesting 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.govGene prediction using the Self-Organizing Map: automatic generation of multiple gene models - PubMedWhile 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... 251
Reposted by Casey GreeneJ. Brian Byrd @jbrianbyrd.bsky.social · 04/01/2025Why 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... #PSB25nature.comResponsible, practical genomic data sharing that accelerates research - Nature Reviews GeneticsData 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... 132
Casey Greene @casey.greenelab.com · 22/12/2024I 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:... 040
Reposted by Casey GreeneChristian Mosimann @chrmosimann.bsky.social · 21/12/2024Showing visitors the surroundings - F1 as tour guide at Barr Lake, where the Bald Eagles roam. 🦅 #Colorado 0191
Reposted by Casey GreeneCU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 21/12/2024Explore 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 031
Reposted by Casey GreeneAMIA @amia.org · 04/12/2024We’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 115311
Reposted by Casey GreeneCU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 26/11/2024A 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 051
Reposted by Casey GreeneAbhirupa Ghosh @abhirupaghosh.bsky.social · 03/12/2024The 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 095
Casey Greene @casey.greenelab.com · 02/12/2024@vincerubinetti.bsky.social would it help to get an issue filed or this is an issue with the underlying tech stack? 010
Reposted by Casey GreeneHeidi Rehm @heidirehm.bsky.social · 27/11/2024We 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. 0156