Presentations

Talks

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

  • Zooming in to the biology behind benchmarking.
    CZI Virtual Cells Workshop: AI Modeling Benchmarking and Evaluation for Biology. September 25, 2024.
  • Unleashing the power of protein engineering with artificial intelligence.
    Throughput Computing 2024. July 11, 2024.
    Video
  • Predicting genetic variants' function with neural networks and protein interaction networks.
    UW-Madison Center for Genomic Science Innovation retreat. June 11, 2024.
  • Combining artificial intelligence and biophysics for protein engineering.
    8th annual Life Sciences Symposium. The Pennsylvania State University. May 17, 2024.
  • Machine learning in biology: protein engineering and beyond.
    UW-Madison Computational Biology, Ecology, & Evolution seminar. April 15, 2024.
  • AI in biomedicine: promises and pitfalls.
    Lightning talks and panel discussion with Anthony Gitter, Juan Caicedo, Ron Stewart.
    Morgridge Institute for Research. March 21, 2024.
    Video and summary
  • AI in biomedical health.
    Lightning talks and panel discussion with Anthony Gitter, Yin Li, Junjie Hu, Anoop Mayampurath, Vikas Singh.
    Exploring Artificial Intelligence @ UW-Madison. September 15, 2023.
  • Mutational Effect Transfer Learning for protein design with small datasets.
    3rd Next Generation Biocatalysis symposium. April 19, 2023.
  • Using machine learning to guide biological experiments: A collection of successes, failures, and unanswered questions.
    39th International Conference on Machine Learning. AI for Science workshop. July 23, 2022.
  • Multi-modal networks and integration.
    Anthony Gitter, Sara Gosline, Meng Jiang, Alex Pico, Sushmita Roy, Hanghang Tong.
    Workshop on Future Directions in Network Biology. June 13, 2022.
    Video, Slides
  • Machine learning to guide drug screening and protein engineering.
    UW-Madison Molecular Virology Seminar Series. May 5, 2022.
  • Machine learning to guide drug screening and protein engineering.
    University of Graz and Technical University of Graz DocDays. February 10, 2022.
  • AI & machine learning.
    Panel discussion with Matthew Friedel, Anthony Gitter, Iya Khalil.
    Wisconsin Biohealth Summit 2021. October 7, 2021.
  • Expanding signaling pathways by modeling temporal phosphorylation.
    Quantitative Sciences Seminar at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University. May 20, 2021.
  • Effectively exploring a billion chemicals for drug discovery.
    UW-Madison Department of Biostatistics & Medical Informatics seminar. October 23, 2020.
  • Cooking up cures with machine learning.
    Wisconsin Science Festival. Big Ideas for Busy People: Futurescape. October 15, 2020.
    Video
  • Seize the moment: adapting old tools for a novel coronavirus.
    Webinar with John Brubacher, Anthony Gitter, Brian Bockelman, Ben Cox, Katie Overmyer, Gabriella Gerhardt.
    Morgridge Institute for Research webinar. July 22, 2020.
    Video and summary
  • Overcoming COVID-19 and future pandemics: New tools to control viral threats.
    Webinar with Paul Ahlquist, Anthony Gitter, Brad Schwartz.
    Morgridge Institute for Research webinar. June 2, 2020.
    Video and transcript, News
  • Writing manuscripts on GitHub. Can automated software replace publishers?
    Panel discussion with Arfon Smith, Eric Hellman, Olga Botvinnik, Anthony Gitter, Halie Rando, Alexey Isavnin, Vincent Rubinetti, Casey Greene, Daniel Himmelstein.
    Open Publishing Fest. May 28, 2020.
    Video
  • 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.

  • Benchmarking pathway reconstruction with SPRAS.
    Neha Talluri, Sumedha Sanjeev, Daniel Nachreiner, Gabe Howland, Schwa Yeleti, Justin Hiemstra, Altaf Barelvi, Oliver Anderson, Anna Ritz, Anthony Gitter.
    16th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenges, 2024.
  • Prioritizing variants in Long QT syndrome with network analysis.
    Nistha Panda, Yuriy Sverchkov, Mark Craven, Anthony Gitter.
    16th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenges, 2024.
  • A biophysics-based protein language model for protein engineering.
    Sam Gelman.
    Cross Roads Speaker Series, 2024.
    Video
  • Prioritizing variants in Long QT syndrome with network analysis.
    Nistha Panda, Yuriy Sverchkov, Mark Craven, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2024.
  • Green fluorescent protein engineering with a biophysics-based protein language model.
    Sam Gelman, Bryce Johnson, Chase R Freschlin, Sameer D'Costa, Anthony Gitter, Philip Romero.
    Generative and Experimental Perspectives for Biomolecular Design Workshop at the 12th International Conference on Learning Representations, 2024.
    Extended abstract
  • SPRAS: a workflow for streamlining network-based pathway reconstruction of omic data.
    Neha Talluri, Yancheng Liu, Olivia Johnson, Ella Ngo, Zhiqian Xu, Altaf Barelvi, Oliver Anderson, Justin Hiemstra, Christopher Magnano, Adam Shedivy, Anna Ritz, Anthony Gitter.
    15th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenges, 2023.
  • Mutational Effect Transfer Learning for protein design.
    Sam Gelman.
    ML Protein Engineering Seminar Series, 2023.
    Video
  • Geometric deep learning for molecules and biological networks.
    Daniel McNeela.
    UW-Madison ML+X Seminar Series, 2023.
  • Adapting Manubot for open publishing in the COVID-19 infodemic.
    Halie M Rando, Simina M Boca, Lucy D'Agostino McGowan, Daniel S Himmelstein, Michael P Robson, Vincent Rubinetti, Ryan Velazquez, Casey S Greene, Anthony Gitter.
    30th Conference on Intelligent Systems for Molecular Biology, 2022.
  • PathwayMultiomics: pathway-regularized GPU-accelerated matrix factorization.
    David Merrell, Anthony Gitter.
    30th Conference on Intelligent Systems for Molecular Biology, 2022.
  • Pre-training on molecular simulations improves protein sequence-function modeling.
    Sam Gelman, Zhiyuan Duan, Sameer D'Costa, Kaustubh Amritkar, Bryce Johnson, Philip Romero, Anthony Gitter.
    30th Conference on Intelligent Systems for Molecular Biology, 2022.
  • Generating challenging negatives for contrastive learning in hyperbolic space.
    Daniel McNeela, Anthony Gitter, Frederic Sala.
    30th Conference on Intelligent Systems for Molecular Biology, 2022.
  • SPRAS: A workflow for streamlining network-based pathway reconstruction.
    Adam Shedivy, Nina Young, Christopher Magnano, Pramesh Singh, Tobias Rubel, Anna Ritz, Anthony Gitter.
    30th Conference on Intelligent Systems for Molecular Biology, 2022.
    Poster
  • Interpretability of network measures in host-virus protein interactions.
    Alyssa M Adams, Karthik Anantharaman, Anthony Gitter.
    30th Conference on Intelligent Systems for Molecular Biology, 2022.
  • Learning protein sequence-function relationships from high-throughput molecular simulations.
    Sam Gelman.
    HTCondor Week 2022.
    Video, Slides
  • Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus.
    Steven F Baker, Helene Meistermann, Manuel Tzouros, Aaron Baker, Sabrina Golling, Juliane Siebourg Polster, Mitchell P Ledwith, Anthony Gitter, Angelique Augustin, Hassan Javanbakht, Andrew Mehle.
    Viruses 2022 - At the Leading Edge of Virology Research.
  • An open-publishing response to the COVID-19 infodemic.
    Halie M Rando, Simina M Boca, Lucy D'Agostino McGowan, Daniel S Himmelstein, Michael P Robson, Vincent Rubinetti, Ryan Velazquez, COVID-19 Review Consortium, Casey S Greene, Anthony Gitter.
    Digital Infrastructures for Scholarly Content Objects 2021.
  • Bayes optimal informer sets for drug discovery.
    Michael A Newton, Peng Yu, Spencer S Ericksen, Anthony Gitter.
    Joint Statistical Meetings 2021.
  • Streamlining signaling pathway reconstruction.
    Chris S Magnano, Tobias Rubel, Adam Shedivy, Pramesh Singh, Anna Ritz, Anthony Gitter.
    Great Lakes Bioinformatics Conference 2021.
    Video, Slides, Abstract, Software
  • Bayes optimal informer sets for drug discovery.
    Peng Yu, Spencer S Ericksen, Anthony Gitter, Michael A Newton.
    ENAR 2021 Spring Meeting.
  • Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus.
    Steven F Baker, Helene Meistermann, Manuel Tzouros, Aaron Baker, Sabrina Golling, Juliane Siebourg Polster, Mitchell P Ledwith, Anthony Gitter, Angelique Augustin, Hassan Javanbakht, Andrew Mehle.
    7th ESWI Influenza Conference, 2020.
  • Open publishing and the COVID-19 infodemic.
    Halie M Rando, Ryan Velazquez, Lucy D'Agostino McGowan, Simina M Boca, Anthony Gitter, Casey S Greene, COVID-19 Literature Review Contributors.
    Cold Spring Harbor Laboratory Biological Data Science Conference, 2020.
  • Inferring signaling pathways with probabilistic programming.
    David Merrell, Anthony Gitter.
    19th European Conference on Computational Biology, 2020.
    Video
  • Inferring signaling pathways with probabilistic programming.
    David Merrell, Anthony Gitter.
    28th Conference on Intelligent Systems for Molecular Biology, 2020.
    Video, Abstract
  • Scaling ligand-based virtual screening to a larger purchasable chemical space.
    Moayad Alnammi, Shengchao Liu, Spencer S Ericksen, Gene E Ananiev, James L Keck, F Michael Hoffmann, Scott A Wildman, Anthony Gitter.
    ACS Spring 2020 National Meeting & Expo. Conference canceled.
  • Pathway-regularized matrix factorization.
    Aaron Baker.
    17th Annual Rocky Mountain Bioinformatics Conference, 2019.
  • Automating parameter selection to avoid implausible biological pathway models.
    Chris Magnano, Anthony Gitter.
    12th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, 2019.
  • 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.
  • 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.