Presentations

Talks

Talks and presentations by Anthony Gitter. Other lab members' talks are included in the section below.

  • Computationally expanding signaling pathways with temporal phosphoproteomic data.
    Princess Margaret Cancer Centre. September 26, 2019.
  • Synthesizing biological pathway graphs from node activation times.
    University of Illinois at Chicago. September 9, 2019.
  • Multi-dimensional bioinformatics analysis of head and neck cancers.
    Understanding HPV and Oral Cancer: from Vaccination to Cancer Treatment Approaches. August 16, 2019.
  • Machine learning to guide chemical screening in antimicrobial drug discovery.
    NIH Drug Discovery Interest Group seminar. May 9, 2019.
  • Synthesizing signaling pathways from temporal phosphoproteomic data.
    RECOMB 2019. May 8, 2019.
    Slides
  • Machine learning for integrative cancer genomics and drug discovery.
    UW-Madison Cancer Biology Seminar Series. October 24, 2018.
  • Imposing biological domain knowledge with graphs.
    National Cancer Institute. Interpretable deep learning for cancer research workshop. September 20, 2018.
  • Synthesizing signaling pathways from temporal phosphoproteomic data.
    Flatiron Institute. September 10, 2018.
  • Manubot: the manuscript bot for automated scholarly publishing.
    eLife open-source technology in publishing community call. June 28, 2018.
    Video
  • Synthesizing signaling pathways from temporal phosphoproteomic data.
    2018 SIAM Conference on Discrete Mathematics. June 5, 2018.
  • Practical model selection for virtual chemical screening.
    UW-Madison Center for Predictive Computational Phenotyping retreat. May 31, 2018.
    Video
  • HTCondor for machine learning in biology.
    HTCondor Week 2018. May 22, 2018.
    Slides (pptx, pdf)
  • Tomes of cancer genomes.
    Wisconsin Science Festival. Big Ideas for Busy People: Big Data Edition. November 4, 2017.
    Video
  • Sifting and winnowing protein targets with biological network analysis.
    University of Pennsylvania Systems Pharmacology and Translational Therapeutics Seminar Series. April 3, 2017.
  • Venturing beyond textbook signaling pathways with temporal phosphoproteomic data.
    UW-Madison Animal Genetics Seminar Series. September 20, 2016.
  • Identifying active pathways in viral infection and cancer.
    UW-Madison Molecular Virology Seminar Series. September 24, 2015.
  • Deciphering the cancer mutational landscape with pathway analysis.
    UW-Madison Genomic Sciences Training Program retreat. May 29, 2015.
  • Deciphering the cancer mutational landscape with pathway analysis.
    UW-Madison Cancer Biology Seminar Series. April 29, 2015.
  • Cancer's camouflage: Detecting the causes of cancer amid overwhelming randomness.
    Morgridge Institute for Research Discovery Seminar Series. April 17, 2015.
  • Linking the signaling cascades and dynamic regulatory networks controlling infection response.
    Salk Institute for Biological Studies. November 13, 2014.
  • Connecting the dots in protein interaction networks.
    UW-Madison Systems Information Learning Optimization seminar. October 22, 2014.
  • Venturing beyond textbook signaling pathways with temporal phosphoproteomic data.
    UW-Madison SysBio seminar. October 7, 2014.
  • Synthesizing signaling pathways from temporal phosphoproteomic data.
    UW-Madison Computation and Informatics in Biology and Medicine seminar. September 30, 2014.
  • Sharing information to reconstruct patient-specific pathways in heterogeneous diseases.
    Pacific Symposium on Biocomputing 2014. January 6, 2014.
  • Identifying proteins controlling key disease signaling pathways.
    21st Annual International Conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology (ISMB/ECCB 2013). July 22, 2013.
    Video
  • Linking signaling pathways and dynamic regulatory networks.
    Brown University pattern theory seminar. November 14, 2012.
  • Identifying the signaling cascades and regulatory mechanisms that control stress responses.
    6th Annual RECOMB Satellite on Systems Biology. November 17, 2010.
  • Redundancy in the Eukaryotic regulatory code explains differences between binding and knockout experiments.
    5th Annual RECOMB Satellite on Regulatory Genomics. November 1, 2008.
    Video, Proceedings

Posters, abstracts, and lab member talks

Lab members are highlighted in bold.

  • Network inference with Granger causality ensembles on single-cell transcriptomic data.
    Atul Deshpande, Li-Fang Chu, Ron Stewart, Anthony Gitter.
    Algorithms and Models for Single Cell Genomics Workshop 2019.
  • Loss-balanced task weighting to reduce negative transfer in multi-task learning.
    Shengchao Liu, Yingyu Liang, Anthony Gitter.
    Midwest Machine Learning Symposium 2019.
  • Parameter selection in biological pathway prediction with graphlet based similarity score.
    Chris Magnano, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2019.
  • Network inference with Granger causality ensembles on single-cell transcriptomic data.
    Atul Deshpande, Li-Fang Chu, Ron Stewart, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2019.
  • The ml4bio workshop: machine learning literacy for biologists.
    Fangzhou Mu, Chris Magnano, Debora Treu, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2019.
    Slides
  • Modeling the functional activity of protein sequence variants using graph convolutional neural networks.
    Sam Gelman, Zhiyuan Duan, Philip Romero, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2019.
  • Classifying T cell activity with convolutional neural networks.
    Zijie Wang, Alex J Walsh, Melissa C Skala, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2019.
  • Pathway-regularized matrix factorization.
    Aaron Baker, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2019.
  • Learning drug function from chemical structure.
    Jesse Meyer, Shengchao Liu, Ian Miller, Anthony Gitter, and Joshua Coon.
    Great Lakes Bioinformatics Conference 2019.
  • Loss-balanced task weighting to reduce negative transfer in multi-task learning.
    Shengchao Liu, Yingyu Liang, Anthony Gitter.
    Thirty-Third AAAI Conference on Artificial Intelligence, 2019.
  • Pathway-regularized matrix factorization.
    Aaron Baker, Anthony Gitter.
    26th Conference on Intelligent Systems for Molecular Biology, 2018.
    Video, Slides, Abstract, Software
  • Network inference from single-cell transcriptomic data using Granger causality.
    Atul Deshpande, Anthony Gitter.
    26th Conference on Intelligent Systems for Molecular Biology, 2018.
    Abstract
  • An adaptive computational pipeline to accelerate drug discovery.
    Julie C Mitchell, Moayad Alnammi, Spencer S Ericksen, Ching-Pei Lee, Shengchao Liu, Scott A Wildman, Huikun Zhang, Michael A Newton, Robert Nowak, Stephen Wright, Anthony Gitter, F Michael Hoffmann.
    Fields Institute Workshop on the Mathematics of Drug Design/Discovery, 2018.
  • Lag penalized weighted correlation for time series clustering.
    Thevaa Chandereng, Anthony Gitter.
    2018 Midwest Biopharmaceutical Statistics Workshop.
  • Improving subnetwork identification with pathway simulation.
    Aaron Baker, Anthony Gitter.
    10th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, 2017.
    Software
  • Time series clustering with lag penalized weighted correlation.
    Thevaa Chandereng, Anthony Gitter.
    Great Lakes Bioinformatics Conference (GLBIO) 2017.
  • Unexpected findings from 10,391 brain magnetic resonance imaging exams in research volunteers.
    P Rowley, A Field, E Simcock, T Chandereng, H Rowley.
    American Society of Neuroradiology 55th Annual Meeting, 2017.
  • Synthesizing signaling pathways from temporal phosphoproteomic data.
    Ali Sinan Köksal, Anthony Gitter, Kirsten Beck, Aaron McKenna, Saurabh Srivastava, Nir Piterman, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher.
    7th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, 2014.
    Video, Slides, Abstract
  • Identifying signaling pathways associated with medulloblastoma subtypes from "omic" data.
    Tenley C Archer, Anthony Gitter, Aviad Tsherniak, Nurcan Tuncbag, Tobias Ehrenberger, Paul A Northcott, Jacob Silterra, Stefan M Pfister, Pablo Tamayo, Jill P Mesirov, Ernest Fraenkel, Scott L Pomeroy.
    16th International Symposium on Pediatric Neuro-Oncology, 2014.
  • Machine reading for cancer panomics.
    Hoifung Poon, Anthony Gitter, Chris Quirk.
    Pacific Symposium on Biocomputing 2014.
    Abstract book
  • Identifying common and patient-specific pathways in heterogeneous diseases.
    Anthony Gitter, Nurcan Tuncbag, Andrea Pagnani, Carlo Baldassi, Alfredo Braunstein, Riccardo Zecchina, Ernest Fraenkel.
    MIT Center for Environmental Health Sciences 2013 Annual Poster Session.
  • Identifying signaling pathways associated with medulloblastoma subtypes from "omic" data.
    Tenley C Archer, Aviad Tsherniak, Nurcan Tuncbag, Anthony Gitter, Shyamal Dilhan Weeraratne, Jessica Pierre Francois, Pablo Tamayo, Jill Mesirov, Ernest Fraenkel, Scott L Pomeroy.
    American Association for Cancer Research Annual Meeting 2013.
  • Backup in gene regulatory networks explains differences between binding and knockout results.
    Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon, Ziv Bar-Joseph.
    6th Annual RECOMB Satellite on Regulatory Genomics, 2009.
    Proceedings
  • A customizable evaluation platform for biomedical information extraction systems.
    Graciela Gonzalez, Anthony Gitter, Craig Teegarden, Chitta Baral.
    ISCB Rocky Mountain Bioinformatics Conference, 2006.