Alexis Battle
@alexisbattle.bsky.social
Professor at Johns Hopkins Biomedical Engineering and CS, Director Malone Center for Engineering in Healthcare, Research Director (Strategy and Partnerships) Data Science and AI Institute
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.
August 13, 2025 at 10:34 PM
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.
Reposted by Alexis Battle
Congratulations @stephaniehicks.bsky.social on being named an ASA Fellow! So well deserved! 🎉
August 7, 2025 at 1:24 AM
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!
August 2, 2025 at 2:00 PM
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.
📣New from @alexisbattle.bsky.social & co!
📄Sparse matrix factorization robust to sample sharing across GWASs reveals interpretable genetic components
📄Sparse matrix factorization robust to sample sharing across GWASs reveals interpretable genetic components
Sparse matrix factorization robust to sample sharing across GWASs reveals interpretable genetic components
We developed a computational method to identify genetic pathways shared among complex
traits that applies matrix factorization to decompose genetic associations across
hundreds of phenotypes. Our meth...
www.cell.com
July 28, 2025 at 7:47 PM
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.
Reposted by Alexis Battle
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.
probgen2026.github.io
Please help spread the news.
Home - ProbGen 2026
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probgen2026.github.io
June 6, 2025 at 5:52 PM
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.
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!
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...
www.medrxiv.org/content/10.1...
Polygenic prediction of phenotypes with a neural empirical Bayes approach
Polygenic risk scores (PRS) estimate the expected value of a phenotype based on individual genotypes. Although statistical approaches for calculating PRS have advanced considerably in recent years, fe...
www.medrxiv.org
July 22, 2025 at 9:31 PM
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.
We are pleased to announce the first round of our 2025 Seed Grant Awards! 🌱 Learn more about the funded projects below:
First round of 2025 Malone Seed Grant Awards announced
Six grants were awarded in partnership with the School of Nursing and the Department of Surgery, as well as in precision medicine.
malonecenter.jhu.edu
July 18, 2025 at 4:42 PM
Excited to announce new Malone Center Seed Grants in three focus areas: collabs with Nursing, collabs with Surgery, and focusing on Precision Medicine.
Reposted by Alexis Battle
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-...
stephaniehicks.com/blog/course-...
Translating the face-paced world of research in deep learning and genetics and genomics to the classroom – Stephanie C. Hicks, PhD
stephaniehicks.com
July 8, 2025 at 11:34 PM
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-...
stephaniehicks.com/blog/course-...
Reposted by Alexis Battle
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!!
June 2, 2025 at 11:40 PM
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!!
Reposted by Alexis Battle
Heading to Minneapolis next week to share this work at STATGEN2025!
May 17, 2025 at 9:23 PM
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!
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...
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...
May 5, 2025 at 8:31 PM
Our new work testing nicotine, alcohol, and caffeine exposure across many cell types at once, including their modulation of eQTLs. Take a look!
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.
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.
Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms
rdcu.be
March 31, 2025 at 1:23 PM
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.
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
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...
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
March 26, 2025 at 3:57 PM
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
Reposted by Alexis Battle
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
February 14, 2025 at 11:41 PM
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.
January 29, 2025 at 5:01 PM
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.
Reposted by Alexis Battle
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
January 27, 2025 at 4:59 PM
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.
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:
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
www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6
Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures
Popp et al. generate dozens of cell types from 53 human iPSC lines in order to characterize
the dynamic genetic regulation of gene expression across early stages of cellular
differentiation. Accessing...
www.cell.com
December 5, 2024 at 4:20 PM
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:
Reposted by Alexis Battle
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...
- 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
December 3, 2024 at 7:21 PM
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...
- 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.
November 27, 2024 at 3:44 AM
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...
www.biorxiv.org
November 14, 2024 at 4:46 PM
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
January 24, 2024 at 12:01 AM
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
www.biorxiv.org
January 22, 2024 at 1:57 PM
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.