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2026
August
The registered report for our Signaling Pathway Reconstruction Analysis Streamliner benchmark and software is available. This project is in collaboration with Anna Ritz's lab.
July
Our latest prospective small molecule screening with the Boltz team is available.
May
Sabah Khondaker and Mahunan Degbelo join the lab for summer research projects. Welcome!
February
Our collaborative manuscript on chemical screening for tuberculosis inhibitors, led by Nathan Wlodarchak's lab, has been published.
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2025
November
The Protein Set Transformer manuscript, led by our collaborators in the Anantharaman lab, has been published.
Anthony and Hannah Wayment-Steele launch the Madison AI for Proteins community as part of the RISE AI Collaboration HQ.
Our Assay2Mol manuscript was presented at EMNLP 2025. Assay2Mol generates chemicals by retrieving relevant biochemical assays from PubChem to use as context.
Tapanmitra Ravi has joined the group for a rotation. Welcome Tapanmitra!
September
The journal versions of our manuscripts on biophysics-based protein language models and multi-omic pathway analysis have been published.
August
Our Chemical Language Model Linker method for text-based chemical generation has been published.
July
Our Assay2Mol preprint is available. Assay2Mol generates chemicals by retrieving relevant biochemical assays from PubChem to use as context.
Anthony participated in two collaborative machine learning projects: a workshop on benchmarking and evaluation in biology and a community challenge on ADMET assay property prediction.
May
Undergraduates Grace Li and Canek Llera join the lab for summer research projects. Welcome!
April
Our paper on predicting protein fitness with protein structure-based models was presented at the ICLR 2025 GEM workshop.
Anthony contributed to the Adaptyv EGFR Binder Competition preprint.
March
Anthony contributed to the text-guided protein design publication.
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2024
October
Our Chemical Language Model Linker preprint for text-based chemical generation is available.
September
Our commentary preprint "A renewed call for open artificial intelligence in biomedicine" is available.
July
Anthony contributed to the Protein Set Transformer preprint from the Anantharaman lab.
June
Our collaborative manuscript with new software for multi-omic pathway analysis in cancer is available on bioRxiv.
Undergraduates Sumedha Sanjeev and Daniel Nachreiner join the lab for summer research projects and graduate student John Peters joins for a rotation. Welcome!
May
Anthony co-authored a letter to the editor about the lack of AlphaFold3 code alongside its publication.
Sam presented our machine-learning-guided engineering of green fluorescent protein as a poster at the GEM workshop.
March
Our preprint presenting the Mutational Effect Transfer Learning framework for learning biophysics-based protein language models is available. This is a collaboration with the Romero lab.
January
We posted our preprint on representation learning for biological pathway graphs in collaboration with Frederic Sala.
Undergraduate Carol Sze joins the lab. Welcome Carol!
Graduate student Arnav Sharma joins the lab and former undergraduate lab member Neha Talluri has graduated and continues as a graduate student. Welcome!
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2023
November
Anthony has been named the Jeanne M. Rowe Chair.
October
Sam successfully defended his PhD dissertation! Congratulations!
September
Anthony contributed to a review on current and future directions in network biology.
August
Our study prospectively evaluating supervised learning predictions of bacterial protein interaction inhibitors in the billion chemical synthesize-on-demand Enamine REAL library has been published.
Graduate student Ryan Kassab joins the lab and former undergraduate lab member Nistha Panda continues as a graduate student. Welcome!
July
Daniel will present our extended abstract on representation learning for biological pathway graphs in collaboration with Frederic Sala at the ICML Workshop on Computational Biology.
We contributed network analysis to a collaborative study of AURKB's role in HIV-1 spread.
June
David successfully defended his PhD dissertation and is joining the Broad Institute! Congratulations!
March
Companion manuscripts on traditional and nucleic acid COVID-19 vaccines from our collaborative review have been published.
February
We contributed to a preprint that uses text prompts to generate protein sequences.
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2022
December
We contributed network analysis to a study of influenza virus host factors from the Mehle lab.
Chris will present our paper on predicting subcellular localization at the pathway level at the Pacific Symposium on Biocomputing.
Graduate student Yifan Deng joins the lab. Welcome Yifan!
October
The nucleic acid vaccines section of our collaborative COVID-19 review is availabe on arXiv.
September
We have been awarded collaborative NSF funding with the Romero and Lewis labs for machine learning-guided enzyme engineering.
August
The traditional vaccines section of our collaborative COVID-19 review is availabe on arXiv.
June
Our paper describing our Machine Learning for Biologists workshop has been published.
April
The latest section of our collaborative COVID-19 review on diagnostics is availabe on arXiv.
March
Chris successfully defended his PhD dissertation and is joining Harvard Medical School as a Curriculum Fellow! Congratulations!
Our collaborative quick tips for deep learning in biology have been published.
February
Graduate student Bryce Johnson and undergraduate Neha Talluri join the lab. Welcome Bryce and Neha!
Our manuscript presenting SINGE for single-cell gene regulatory network inference has been published.
Our preprint describing our Machine Learning for Biologists workshop is available on bioRxiv.
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2021
November
Our collaboration with the Romero lab to use neural networks to learn protein sequence-function relationships has been published.
October
Our preprint presenting experimental testing of a virtual chemical screen with over 1 billion chemicals is available on ChemRxiv.
Alyssa Adams joins the lab as a Morgridge Institute Postdoctoral Fellow co-advised by Karthik Anantharaman. Welcome Alyssa!
September
Our paper describing how we are using Manubot to coordinate a series of open, living COVID-19 reviews is now available on arXiv. It will be presented at the DISCO 2021 workshop.
July
Graduate student Daniel McNeela joins the lab. Welcome Daniel!
June
Margaret Elliott has joined the group for a summer research project. Welcome Margaret!
May
Anthony contributed to a new preprint Ten Quick Tips for Deep Learning in Biology.
April
Anthony's promotion to associate professor with tenure has been approved.
February
Our pathway parameter advising method for improving biological pathway reconstruction has been published.
The first of our review articles on COVID-19 is now available on arXiv. This one focuses on pathogenesis and is one part of a larger collaborative review written with Manubot.
January
Moayad successfully defended his PhD dissertation! Congratulations!
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2020
December
Our Sparse Signaling Pathway Sampling paper has been published in the ECCB 2020 proceedings.
November
We've contributed to two new preprints from collaborators: Bayes optimal drug discovery with Michael Newton's group and analysis of influenza host factors with the Mehle lab.
October
Our preprint with Phil Romero on using neural networks to learn protein sequence-function relationships from deep mutational scanning data is now on bioRxiv.
September
We were awarded an R01 grant from NIH NIGMS to develop machine learning methods for drug discovery with collaborators Michael Newton, Miron Livny, Spencer Ericksen, and Scott Wildman.
August
Thevaa successfully defended his PhD dissertation and is starting a postdoc with Ken Cheung! Congratulations!
May
Our Sparse Signaling Pathway Sampling preprint and software are now available.
January
Our Lag Penalized Weighted Correlation clustering algorithm has been published.
The CHTC GPU Lab now has a home page, and the first GPU hardware will be arriving to CHTC soon.
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2019
December
Atul successfully defended his PhD dissertation! Congratulations!
November
Our pathway parameter advising method for improving biological pathway reconstruction is available on bioRxiv.
October
We published our convolutional neural network approach for classifying T cell activity with the Skala lab.
Our study with the Coon lab predicting drug function labels from chemical structures has been published.
August
Our study on classifying T cell activity with convolutional neural networks has been posted as a bioRxiv preprint.
Our manuscript on selecting chemicals to characterize new kinase targets has been published.
June
Our manuscript Open collaborative writing with Manubot has been published. See the Manubot website to learn more about our GitHub-based writing platform and try it yourself.
May
Anthony and CHTC are leading a UW2020 project Enabling GPU-based Data Science.
April
Congratulations to Jay for winning a 2019 University Book Store Academic Excellence Award for his honors thesis on T cell classification!
March
Come to GLBIO 2019 to see the latest research from our group. We will present 4 talks and 3 posters.
January
Our SCINGE manuscript on gene regulatory network inference with single-cell RNA-seq is available on bioRxiv.
Shengchao presented early results on negative transfer in multi-task chemical bioactivity prediction at the AAAI 2019 student abstract program.
Our computational drug discovery team posted a bioRxiv preprint on selecting chemicals to characterize new kinase targets.
Ben Kaufman has joined the group for a rotation. Welcome Ben!
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2018
November
Our manuscript Practical model selection for prospective virtual screening has been published with software on GitHub.
We contributed to a drug function prediction study that is now available on bioRxiv.
September
Our Temporal Pathway Synthesizer manuscript has been published.
August
Congratulations to Shengchao, who graduated with his M.S. in Computer Sciences!
A preprint of our manuscript on open collaborative writing with Manubot is now available. See the latest verison here.
June
Our manuscript Practical model selection for prospective virtual screening is available on bioRxiv with software on GitHub.
May
We are excited to be part of the new John W. and Jeanne M. Rowe Center for Research in Virology at the Morgridge Institute.
Our yeast salt stress network inference paper in collaboration with the Gasch and Coon labs has been published in PLoS Computational Biology.
Congratulations to Jay Wang, who was awarded an Honors Senior Thesis Summer Research Grant!
April
Our review Opportunities and obstacles for deep learning in biology and medicine has been published along with a press release and Naturejobs blog about the open, collaborative writing process.
March
Thevaa's Lag Penalized Weighted Correlation for Time Series Clustering is available on bioRxiv and GitHub.
February
Congratulations to Chris Magnano, who was awarded a CIBM predoctoral fellowship!
The Disease Module Identification DREAM Challenge paper, which includes Aaron and Anthony as consortium members, has been posted on bioRxiv.
January
An updated version of Opportunities and obstacles for deep learning in biology and medicine is available on bioRxiv along with an article about the open, collaborative writing process.
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2017
December
Congratulations to Sam Gelman, who was awarded a PhRMA Foundation Pre-Doctoral Fellowship in Informatics!
October
Anthony answers a Blue Sky Science question about whether scientists could build a virtual brain and body for research.
Our Temporal Pathway Synthesizer manuscript is available on bioRxiv with software on GitHub.
September
We have been awarded NIH Commons Credits for cloud computing resources in support of our drug discovery research.
August
Our yeast salt stress signaling network paper in collaboration with the Gasch and Coon labs is available on bioRxiv.
Graduate student Sam Gelman joins the lab. Welcome Sam!
Our lab is moving some of our code to a GitHub organization. Our Software page contains a complete list of software.
May
Our open, collaborative preprint Opportunities and obstacles for deep learning in biology and medicine is available on bioRxiv.
April
Our UW2020 project on adaptive computational drug discovery was recently funded.
March
The Multi-PCSF software has been released on GitHub.
Our systems biology study of KSHV latent infection with collaborators at the University of Washington is available at PLoS Pathogens.
January
A postdoctoral fellow position is available in the Gitter Lab in collaboration with the Gasch Lab in genetics.