Lab Updates

  • 2022

    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.

  • 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!

  • 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.

  • 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!

  • 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 a 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.

  • 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.