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 😳

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....

Deep profiling of gene expression across 18 human cancers - Nature Biomedical Engineering Using unsupervised deep learning to generate low-dimensional latent spaces for gene-expression data can unveil biological insight across cancers.

FYI I'm pretty sure this one ended up getting published after peer review here: www.nature.com/articles/s41...

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.

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.

Screenshot of US-Africa Frontiers of Science Engineering and Medicine webpage.

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 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.

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.

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.

Wow! Congratulations :)

✴️ 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

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

✴️ 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

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.

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

Me too!!

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).

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 🧬😀

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

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...

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...

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...

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 :)

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...

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...

Woo! True credit to @vincerubinetti.bsky.social :)

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...

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

It 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...

More on fuzzy axolotls here: bsky.app/profile/shau...

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...

Interesting find from ~20 years ago - fuzzy axolotls were first invented by Mahony et al, 2004 (Figure 2) pubmed.ncbi.nlm.nih.gov/15070404/

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...

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

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:...