Lightnews — Scholar-powered news

Alexis Battle @alexisbattle.bsky.social · Aug 13

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.

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Reposted by Alexis Battle

Michael Love @mikelove.bsky.social · Aug 7

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

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Alexis Battle @alexisbattle.bsky.social · Aug 2

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!

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Alexis Battle @alexisbattle.bsky.social · Jul 28

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 · Jul 28

📣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

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

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Reposted by Alexis Battle

Yun S. Song @yun-s-song.bsky.social · Jun 6

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.

Home - ProbGen 2026

Your Site Description

probgen2026.github.io

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Alexis Battle @alexisbattle.bsky.social · Jul 22

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

Josh Weinstock @joshweinstock.bsky.social · Jul 22

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...

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

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Alexis Battle @alexisbattle.bsky.social · Jul 18

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 · Jul 18

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

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Reposted by Alexis Battle

Stephanie Hicks @stephaniehicks.bsky.social · Jul 8

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-...

Translating the face-paced world of research in deep learning and genetics and genomics to the classroom – Stephanie C. Hicks, PhD

stephaniehicks.com

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Reposted by Alexis Battle

Ben Strober @bennystrobes.bsky.social · Jun 2

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!!

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Reposted by Alexis Battle

Mingyuan "Merlin" Li @supmerlin.bsky.social · May 17

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

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Alexis Battle @alexisbattle.bsky.social · May 5

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 · May 5

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...

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Alexis Battle @alexisbattle.bsky.social · Mar 31

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.

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Alexis Battle @alexisbattle.bsky.social · Mar 31

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.

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms

rdcu.be

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Alexis Battle @alexisbattle.bsky.social · Mar 26

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 · Mar 26

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

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Reposted by Alexis Battle

Ian Fingerman @fingerman.bsky.social · Feb 14

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

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Alexis Battle @alexisbattle.bsky.social · Jan 29

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.

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Reposted by Alexis Battle

JHU Malone Center for Engineering in Healthcare @jhumceh.bsky.social · Jan 27

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

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Alexis Battle @alexisbattle.bsky.social · Dec 12

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

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Alexis Battle @alexisbattle.bsky.social · Dec 5

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 · Dec 4

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

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

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Reposted by Alexis Battle

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · Dec 3

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

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Alexis Battle @alexisbattle.bsky.social · Nov 27

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.

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Alexis Battle @alexisbattle.bsky.social · Nov 15

Welcome!

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Alexis Battle @alexisbattle.bsky.social · Nov 14

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

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Alexis Battle @alexisbattle.bsky.social · Jan 24

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

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Alexis Battle @alexisbattle.bsky.social · Jan 22

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

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