New review on context-specificity and disease genetics from @ygilad.bsky.social and me: authors.elsevier.com/sd/article/S...

My lab is recruiting postdocs in AI/ML for genetics & genomics through the Malone Postdoctoral Fellows program. Apply by Jan 30! Lots of other great labs across the Malone Center as well.

JHU Malone Center for Engineering in Healthcare@jhumceh.bsky.social · 10mo ago

Looking for a postdoc opportunity in computational & engineering applications in medicine & health care? Apply to the Malone Fellows Program and work with mentors in genomics, AI/data science, robotics, human-computer interaction, augmented/virtual reality, & more. Deadline coming up: Jan 31, 2025

Loving the “Pitch a problem” session at the Johns Hopkins Symposium on Engineering in Healthcare. Lots of animated conversations! @jhumceh.bsky.social

Baltimore and Hopkins friends - remember to join us for the Malone Center Symposium Monday Dec 8 in the Glass Pavilion: Human + AI: Redefining the Standard of Care in Medicine

JHU Malone Center for Engineering in Healthcare@jhumceh.bsky.social · 10mo ago

Be sure to stop the 2025 Johns Hopkins Research Symposium on Engineering in Healthcare for our exhibition halls, collaboration and networking opportunities, and remarks from @alexisbattle.bsky.social, Chien-Ming Huang, and @moberst.bsky.social! Register now: 2025-malone-symposium.eventbrite.com

My kid just casually referred to the “starboard” side of his shoe. He’s going to be so sad for sailing camp to end and school to start.

Congratulations @stephaniehicks.bsky.social on being named an ASA Fellow! So well deserved! 🎉

Such a fun Battle lab retreat this week, with state of the lab updates, lightning talks, AI tools discussion, a meditation session, games, and general merriment. What a great group!

Now up, led by Ashton Omdahl! Our method GLEANR finds shared genetic factors across lots of GWAS, and handles spurious correlation driven by cohort overlap. Neat examples of factors driving related traits with enrichment in different cell types / developmental stages.

The American Journal of Human Genetics@ajhgnews.bsky.social · last yr.

📣New from @alexisbattle.bsky.social & co! 📄Sparse matrix factorization robust to sample sharing across GWASs reveals interpretable genetic components

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs: probgen2026.github.io Please help spread the news.

We have released a new annotation-informed PRS method with a preprint and code available, check it out!

Josh Weinstock@joshweinstock.bsky.social · last yr.

Really excited to share our new PRS method, developed with @aprilkim.bsky.social and @alexisbattle.bsky.social ! Our approach is to use a lot of recently developed functional annotations to better estimate the weights of the SNPs. www.medrxiv.org/content/10.1...

Excited to announce new Malone Center Seed Grants in three focus areas: collabs with Nursing, collabs with Surgery, and focusing on Precision Medicine.

JHU Malone Center for Engineering in Healthcare@jhumceh.bsky.social · last yr.

We are pleased to announce the first round of our 2025 Seed Grant Awards! 🌱 Learn more about the funded projects below:

Excited to share a blogpost summarizing challenges, opportunities & reflections from a course @hopkinsengineer.bsky.social co-taught with @alexisbattle.bsky.social (and huge support from Seraj Grimes!) at the intersection of #deeplearning #genetics #genomics 🧪 🧬 💻 stephaniehicks.com/blog/course-...

I'm excited to share I'll be starting a faculty position at Boston Children's Hospital in the Computational Health Informatics Program (CHIP) this October!!

Heading to Minneapolis next week to share this work at STATGEN2025!

Mingyuan "Merlin" Li@supmerlin.bsky.social · last yr.

1/n 🚨Very excited to share our recent work!🚨 To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro. www.biorxiv.org/content/10.1...

Our new work testing nicotine, alcohol, and caffeine exposure across many cell types at once, including their modulation of eQTLs. Take a look!

Mingyuan "Merlin" Li@supmerlin.bsky.social · last yr.

1/n 🚨Very excited to share our recent work!🚨 To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro. www.biorxiv.org/content/10.1...

Power enabled by creative use of public data! We called genotypes from thousands of ATAC-seq samples to run one of the largest chromatin accessibility QTL analyses ever- our results now online with Genome Biology rdcu.be/efKlI, led by Brandon Wenz and Yuan He. GWAS/eQTL overlap, TF binding and more.

Check out our work on rare SVs using long read sequencing, led by Tanner Jensen and @bohanni.bsky.social, now online in @genomeresearch.bsky.social. With @mikeschatz.bsky.social, @mwheelermd.bsky.social, and @sbmontgom.bsky.social

Bohan Ni@bohanni.bsky.social · 2y ago

Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...

There’s a lot of amazingly brilliant scientists and staff about to enter the job market. Hope people take advantage of that and give them a place to land. You won’t regret it

Fortunes at the Battle lab lunar near year celebration were on brand. Love the lab. Watch out for confounders this year everyone, and happy new year.

Congratulations to Malone affiliate Casey Overby Taylor on receiving a 2025 Presidential Early Career Award for Scientists and Engineers! Learn more about the research she’s being recognized for here below.

Casey Overby Taylor receives Presidential Early Career Award

Taylor is part of a select group of scientists and engineers to receive a 2025 PECASE award.

malonecenter.jhu.edu

Our study is up! Context-specificity galore -- we explore genetic regulation of gene expression across many cell types and temporal states simultaneously in an efficient experimental system + scRNA-seq:

Josh Popp@jmpopp.bsky.social · 2y ago

Excited to see our study on genetic regulation in heterogeneous differentiating cultures out in final form! www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6

Biology of Genomes 2025 is coming up: - meeting dates: May 6 - 10, 2025 - abstract deadline: Feb 14, 2025 We hope to see you there for another great meeting with a fantastic speaker lineup! meetings.cshl.edu/meetings.asp...

Biology of Genomes

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu

Did you know that Claude Shannon’s PhD thesis was on genetics? “An algebra for theoretical genetics”, MIT 1940. The bibliography has just six entries including Fisher and Haldane.

Check out our new work led by @ashton_omdahl discussing matrix factorization across GWAS, accounting for sample overlap. Factors with varying polygenicity, enrichment for cell type / developmental stage... Ashton is speaking at #biodata24 today! www.biorxiv.org/content/10.1...

Sparse matrix factorization of GWAS summary statistics robust to sample sharing improves detection and interpretation of factors with diverse genetic architectures

Complex trait-associated genetic variation is highly pleiotropic. This extensive pleiotropy implies that multi-phenotype analyses are informative for characterizing genetic variation, as they facilita...

biorxiv.org

Now online at Genome Biology! We developed a method for learning latent contexts for eQTL effects, applicable to single-cell or bulk studies, led by Ben Strober: rdcu.be/dwGzY

We inferred coexpression networks from over 95K RNA-seq samples from recount3, check out what we found www.biorxiv.org/content/10.1... on heritability, context-specificity, and more. Led by Prashanthi Ravichandran.

Aggregation of recount3 RNA-seq data improves the inference of consensus and tissue-specific gene co...

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org