Press and blogs

News archive

  • August 2023

    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.

  • August 2023

    Graduate student Ryan Kassab joins the lab and former undergraduate lab member Nistha Panda continues as a graduate student. Welcome!

  • July 2023

    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.

  • July 2023

    We contributed network analysis to a collaborative study of AURKB's role in HIV-1 spread.

  • June 2023

    David successfully defended his PhD dissertation and is joining the Broad Institute! Congratulations!

  • February 2023

    We contributed to a preprint that uses text prompts to generate protein sequences.

  • December 2022

    Graduate student Yifan Deng joins the lab. Welcome Yifan!

  • October 2022

    The nucleic acid vaccines section of our collaborative COVID-19 review is available on arXiv.

  • September 2022

    We have been awarded collaborative NSF funding with the Romero and Lewis labs for machine learning-guided enzyme engineering.

  • August 2022

    The traditional vaccines section of our collaborative COVID-19 review is available on arXiv.

  • June 2022

    Our paper describing our Machine Learning for Biologists workshop has been published.

  • April 2022

    The latest section of our collaborative COVID-19 review on diagnostics is available on arXiv.

  • March 2022

    Chris successfully defended his PhD dissertation and is joining Harvard Medical School as a Curriculum Fellow! Congratulations!

  • March 2022

    Our collaborative quick tips for deep learning in biology have been published.

  • February 2022

    Graduate student Bryce Johnson and undergraduate Neha Talluri join the lab. Welcome Bryce and Neha!

  • February 2022

    Our manuscript presenting SINGE for single-cell gene regulatory network inference has been published.

  • February 2022

    Our preprint describing our Machine Learning for Biologists workshop is available on bioRxiv.

  • November 2021

    Our collaboration with the Romero lab to use neural networks to learn protein sequence-function relationships has been published.

  • October 2021

    Our preprint presenting experimental testing of a virtual chemical screen with over 1 billion chemicals is available on ChemRxiv.

  • October 2021

    Alyssa Adams joins the lab as a Morgridge Institute Postdoctoral Fellow co-advised by Karthik Anantharaman. Welcome Alyssa!

  • July 2021

    Graduate student Daniel McNeela joins the lab. Welcome Daniel!

  • June 2021

    Margaret Elliott has joined the group for a summer research project. Welcome Margaret!

  • May 2021

    Anthony contributed to a new preprint Ten Quick Tips for Deep Learning in Biology.

  • April 2021

    Anthony's promotion to associate professor with tenure has been approved.

  • February 2021

    Our pathway parameter advising method for improving biological pathway reconstruction has been published.

  • February 2021

    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 2021

    Moayad successfully defended his PhD dissertation and is joining as faculty at King Fahd University of Petroleum & Minerals! Congratulations!

  • December 2020

    Our Sparse Signaling Pathway Sampling paper has been published in the ECCB 2020 proceedings.

  • October 2020

    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 2020

    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 2020

    Thevaa successfully defended his PhD dissertation and is starting a postdoc with Ken Cheung! Congratulations!

  • May 2020

    Our Sparse Signaling Pathway Sampling preprint and software are now available.

  • January 2020

    Our Lag Penalized Weighted Correlation clustering algorithm has been published.

  • January 2020

    The CHTC GPU Lab now has a home page, and the first GPU hardware will be arriving to CHTC soon.

  • December 2019

    Atul successfully defended his PhD dissertation and will start a postdoc with Elana Fertig! Congratulations!

  • November 2019

    Our pathway parameter advising method for improving biological pathway reconstruction is available on bioRxiv.

  • October 2019

    We published our convolutional neural network approach for classifying T cell activity with the Skala lab.

  • October 2019

    Our study with the Coon lab predicting drug function labels from chemical structures has been published.

  • August 2019

    Our study on classifying T cell activity with convolutional neural networks has been posted as a bioRxiv preprint.

  • August 2019

    Our manuscript on selecting chemicals to characterize new kinase targets has been published.

  • April 2019

    Congratulations to Jay for winning a 2019 University Book Store Academic Excellence Award for his honors thesis on T cell classification!

  • March 2019

    Come to GLBIO 2019 to see the latest research from our group. We will present 4 talks and 3 posters.

  • January 2019

    Our SCINGE manuscript on gene regulatory network inference with single-cell RNA-seq is available on bioRxiv.

  • January 2019

    Ben Kaufman has joined the group for a rotation. Welcome Ben!

  • August 2018

    Congratulations to Shengchao, who graduated with his M.S. in Computer Sciences!

  • August 2018

    A preprint of our manuscript on open collaborative writing with Manubot is now available. See the latest version here.

  • May 2018

    Congratulations to Jay Wang, who was awarded a Honors Senior Thesis Summer Research Grant!

  • March 2018

    Thevaa's Lag Penalized Weighted Correlation for Time Series Clustering is available on bioRxiv and GitHub.

  • February 2018

    Congratulations to Chris Magnano, who was awarded a CIBM predoctoral fellowship!

  • December 2017

    Congratulations to Sam Gelman, who was awarded a PhRMA Foundation Pre-Doctoral Fellowship in Informatics!

  • October 2017

    Anthony answers a Blue Sky Science question about whether scientists could build a virtual brain and body for research.

  • September 2017

    We have been awarded NIH Commons Credits for cloud computing resources in support of our drug discovery research.

  • August 2017

    Graduate student Sam Gelman joins the lab. Welcome Sam!

  • March 2017

    Our systems biology study of KSHV latent infection with collaborators at the University of Washington is available at PLoS Pathogens.

  • December 2016

    Graduate student Aaron Baker joins the lab. Welcome Aaron!

  • September 2016

    Our paper on latent variable graphical models for transcriptional regulatory networks has been posted on arXiv.

  • September 2016

    The DREM source code has been migrated to GitHub and re-licensed as open source software.

  • August 2016

    Graduate students Moayad Alnammi and Shengchao Liu join the lab. Welcome!

  • May 2016

    Congratulations Chris and Jon on their recent graduations.

  • March 2016

    Anthony's NSF CAREER award "Inference in temporal signaling and transcriptional data" is funded (see the Morgridge Institute story).

  • December 2015

    Anthony and collaborator Michael Hoffmann are awarded UW-Madison Fall Competition support for computational drug discovery.

  • August 2015

    Graduate student Nafisah Islam joins the lab. Welcome Nafisah!

  • March 2015

    Graduate student Thevaa Chandereng joins the lab. Welcome Thevaa!

  • November 2014

    Graduate student Chris Magnano joins the lab. Welcome Chris!

  • August 2014

    Anthony Gitter begins the lab.