Gitter Lab

Anthony contributed to a review on current and future directions in network biology.

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!

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.

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

Companion manuscripts on traditional and nucleic acid COVID-19 vaccines from our collaborative review have been published.

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

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!

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

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

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

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

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

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.

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.

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

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!

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.

Graduate student Daniel McNeela joins the lab. Welcome Daniel!

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

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

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

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.

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

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

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.

Our preprint with Phil Romero on using neural networks to learn protein sequence-function relationships from deep mutational scanning data is now on bioRxiv.

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.

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

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

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.

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

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

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.

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.

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.

Anthony and CHTC are leading a UW2020 project Enabling GPU-based Data Science.

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

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

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!

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.

Our Temporal Pathway Synthesizer manuscript has been published.

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 version here.

Our manuscript Practical model selection for prospective virtual screening is available on bioRxiv with software on GitHub.

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!

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.

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

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.

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.

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

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.

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

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.

Our open, collaborative preprint Opportunities and obstacles for deep learning in biology and medicine is available on bioRxiv.

Our UW2020 project on adaptive computational drug discovery was recently funded.

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.

A postdoctoral fellow position is available in the Gitter Lab in collaboration with the Gasch Lab in genetics.

Graduate student Aaron Baker joins the lab. Welcome Aaron!

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

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

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

Congratulations Chris and Jon on their recent graduations.

Omics Integrator has been published as a PLoS Computational Biology software paper and released on GitHub.

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

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

Graduate student Nafisah Islam joins the lab. Welcome Nafisah!

A SDREM software protocol has been published as a book chapter.

The Maximum Edge Orientation and SDREM source code has been migrated to GitHub.

Anthony's Morgridge Factor guest blog post describes our lab's cancer pathway research.

A beta version of the Omics Integrator software is available.

Anthony becomes a member of the UW Carbone Cancer Center Cancer Genetics Scientific Program.

Graduate student Thevaa Chandereng joins the lab. Welcome Thevaa!

Our MT-SDREM influenza paper is published in PLoS Computational Biology.

Graduate student Chris Magnano joins the lab. Welcome Chris!

Version 1.1.0 of the Maximum Edge Orientation software is released.

Collaborator Ali Sinan Köksal presents our pathway synthesis work at the RECOMB/ISCB Conference on Regulatory and Systems Genomics.

Anthony Gitter begins the lab.