Alexis Battle

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.

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

2025 Symposium The 9th Annual Johns Hopkins Research Symposium on Engineering in Healthcare: Human + AI: Redefining the Standard of Care in Medicine.

malonecenter.jhu.edu/2025-symposi...

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

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 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!

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

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!

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

This project was originally conceived and begun in collaboration with Casey Brown, who was then Brandon's PhD advisor. It is bittersweet to see this project completed. His memory is with us.

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

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.

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.

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.

Looking forward to reading this, especially since you named it after cheese.

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:

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

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...

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.

Welcome!

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...

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...

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

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

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.