@alexisjbattle

Professor of Biomedical Engineering at JHU. Director, Malone Center for Engineering Healthcare. Interim co-director, Data Science and AI Inst. ML/AI, genomics

 Baltimore, MD
battlelab.jhu.edu
Joined November 2012
  • Tweets886
  • Following429
  • Followers5.4K
30Media
Our updated work led by @ekernf01 explores gene expression forecasting including benchmarking existing methods and discussing why frustratingly simple baselines - even the mean or median (!), let alone linear predictors - have been hard to beat.
Eric Kernfeld@ekernf0114 Oct 2024
Today, I'm excited to present the second big chunk of my Ph.D. work. We are building a thorough assessment of the burgeoning field of gene expression forecasting. Something is deeply wrong.🧵 - Preprint: biorxiv.org/content/10.1101/… - Code: github.com/ekernf01/perturba…

A systematic comparison of computational methods for expression forecasting

Expression forecasting methods use machine learning models to predict how a cell will alter its transcriptome upon perturbation. Such methods are enticing because they promise to answer pressing...

biorxiv.org
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Alexis Battle retweeted
Hammad Farooq@Hammad_Farooq_Aug 28
Excited to share that I recently joined @JohnsHopkins as a 2026 Malone Postdoctoral Fellow in @alexisjbattle’s group! 🎉 I’m thankful to @JHUMCEH for this opportunity and excited to explore new research directions at the intersection of AI, biology, and human genetics.
JHU Malone Center for Engineering in Healthcare@JHUMCEHAug 6
We’re pleased to announce our latest cohort of Malone Postdoctoral Fellows, Hammad Farooq and Fatima Sadjadpour! Learn more about these exceptional postdoctoral researchers’ past and upcoming work here: malonecenter.jhu.edu/welcomi…
Headshots of Hammad Farooq and Fatima Sadjadpour.

ALT Headshots of Hammad Farooq and Fatima Sadjadpour.

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Looking for a postdoc opportunity in computational & engineering applications in medicine & healthcare? Apply to the Malone Fellows Program and work with mentors in genomics, AI/data science, robotics, HCI, AR/VR, & more. Deadline coming up: Jan 31, 2025 malonecenter.jhu.edu/malone-…

Malone Fellows Program

malonecenter.jhu.edu
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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 @alexisjbattle and @MichaelOberst! Register now: 2025-malone-symposium.eventb…
Human + AI: Redefining the Standard of Care in Medicine. Morning & Afternoon Exhibition Halls, Pitch a Problem, Roundtable Discussions.

ALT Human + AI: Redefining the Standard of Care in Medicine. Morning & Afternoon Exhibition Halls, Pitch a Problem, Roundtable Discussions.

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Alexis Battle retweeted
Eric Kernfeld@ekernf0122 Nov 2025
The second major chunk of my Ph.D. is now online in Genome Biology! Brief recap: 🧵 genomebiology.biomedcentral.…

A comparison of computational methods for expression forecasting

Genome Biology - Diverse machine learning methods promise to forecast gene expression changes in response to novel genetic perturbations. However, these methods’ accuracy is not well...

link.springer.com
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Our work on mapping the germline determinants of clonal hematopoiesis without known driver point mutations, led with Marios Arvanitis + @alexisjbattle is now up at @NatureComms nature.com/articles/s41467-0… See 🧵below for more context

Genetic determinants and genomic consequences of non-leukemogenic somatic point mutations

Nature Communications - Here the authors develop a novel statistical method for quantifying mutation burden from whole genome sequencing data and use it to discover the genetic, genomic, and...

nature.com
Josh Weinstock@josh_weinstock28 Aug 2024
Thrilled to share our work on the germline, transcriptomic, and phenotypic correlates of clonal hematopoiesis without known point mutations in NHLBI TOPMed. Work led with Marios Arvanitis (not on Twitter/X) and @alexisjbattle medrxiv.org/content/10.1101/…
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Read about how @deniswirtz and his colleagues are using AI and multiscale imaging to reveal how tumors grow and spread across populations; a tool to better develop new treatments for cancer. inbt.jhu.edu/johns-hopkins-r…
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This is such an exciting project! Huge thanks to @Wenhe_Lin_ @popp_josh @radhikajangi Olivia Allen, Jonathan Burnett, and to @mstephens999 @Y_Gilad @alexisjbattle for their mentorships! Check out our preprint for more! biorxiv.org/content/10.1101/…

Disease-associated loci share properties with response eQTLs under common environmental exposures

Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To...

biorxiv.org
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#MLCB2025 will be Sept 10-11 at @nygenome in NYC! Paper deadline June 1st & in-person registration will open in May. Join our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RT!
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Help - I have had a paper stuck at @GenomeBiology for many months in strange state "Revisions Being Processed for Author" - I have emailed the handling editor and the board and gotten crickets. Help! Or any suggestions?
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Our study led by @popp_josh is up! Context-specific genetic regulation of gene expression in heterogeneous differentiating cultures.
Cell Genomics@CellGenomics2 Dec 2024
Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures dlvr.it/TGXTN5

Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differe...

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. Access...

cell.com
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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! biorxiv.org/content/10.1101/…

Sparse matrix factorization of GWAS summary statistics robust to sample sharing improves detection...

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

biorxiv.org
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Looking for a postdoc in machine learning, data science, AI? We are launching a postdoc program at JHU! Candidates in foundations/methods or applications welcome! Please share/RT! (For my friends & followers, yes this includes genomics and health applications)
Johns Hopkins Data Science and AI Institute@HopkinsDSAI13 Nov 2024
We’re thrilled to announce the #HopkinsDSAI Postdoctoral Fellowship Program! We’re looking for candidates across all areas of data science and AI, including science, health, medicine, the humanities, engineering, policy, and ethics. Apply today! ai.jhu.edu/postdoctoral-fell…
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Going on the faculty market this year? JHU is hiring at all levels. #ASHG2024 #ASHG24 folks in computational genomics, you could fit in here, contact me if interested!
Johns Hopkins Data Science and AI Institute@HopkinsDSAI7 Nov 2024
We're hiring! Faculty of all ranks across the fields of data science and AI. Come be a part of this historic investment in data science and AI. Join us today! @JHUCompSci @JHUECE @JohnsHopkinsAMS Check out all open positions: ai.jhu.edu/careers-for-facul…

Johns Hopkins Data Science and AI Institute Faculty Careers

We’re making an unprecedented investment in people Hiring 80 new tenure-track faculty specializing in data science and AI. Faculty positions are now open across multiple disciplines and offer...

ai.jhu.edu
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We also have relevant faculty positions in BME, my primary department: apply.interfolio.com/157516 - Biomedical Data Science apply.interfolio.com/157489 - Epigenomics
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Looking for a unique postdoc opportunity? We (my lab and other great faculty) are looking for postdocs under our Malone Fellows Program -- comp bio, AI/ML for genomics, comp health folks please apply! #ASHG2024 #ASHG24 folks, I'm here if you'd like to chat about opportunities.
JHU Malone Center for Engineering in Healthcare@JHUMCEH31 Oct 2024
🚨 Applications for the Malone Fellows Program are open! 🚨 Seeking postdoc researchers in: Comp. medicine & bioinformatics Precision med ML/AI for healthcare Systems modeling & optimization Medical robotics AR/VR, HCI, & devices Mobile health Learn more: malonecenter.jhu.edu/malone-…

Malone Fellows Program

malonecenter.jhu.edu
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Excited to share my ongoing PhD work at #ASHG24 in Denver this year! Come check out poster 4011W to learn about how decomposing GWAS can characterize genetic components with distinct genetic architectures and our new accompanying software package. #genomics
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Check out Battle Lab member and recent alumni work at #ASHG2024 this week!
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At dinner last night, out with a table full of (awesome) women scientists, men literally came up to our table simply to say “I’m sorry”. Apparently felt compelled to apologize to women on behalf of the world.
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Looking forward to this talk in just a few minutes by @rajivmccoy #ASHG2024
Rajiv McCoy@rajivmccoy3 Nov 2024
Looking forward to ASHG this week! I will be presenting work led by @aabiddanda and @saracarioscia using data from >100,000 IVF embryos to discover genetic variants influencing meiotic recombination and aneuploidy at the opening session on Tuesday evening. #ASHG24 🧬🏔️
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Headed to Denver for #ASHG2024 #ASHG24. Find me if you want to chat about machine learning, genetics of gene expression, context-specific genetic effects in disease, rare variants, or job opportunities at JHU!
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