Gitter Lab

Lab members are highlighted in bold. ^* denotes equal contribution.

Latest preprints

• Protein Set Transformer: A protein-based genome language model to power high diversity viromics.
  Cody Martin, Anthony Gitter, Karthik Anantharaman.
  bioRxiv, 2024.
• MPAC: a computational framework for inferring cancer pathway activities from multi-omic data.
  Peng Liu, David Page, Paul Ahlquist, Irene M Ong^*, Anthony Gitter^*.
  bioRxiv, 2024.
  MPAC Bioconductor package, Shiny app GitHub repository, Shiny app, MPAC Zenodo archive, Shiny app zenodo archive
• AlphaFold3 transparency and reproducibility.
  Stephanie A Wankowicz, Pedro Beltrao, Benjamin Cravatt, Roland Dunbrack Anthony Gitter, Kresten Lindorff-Larsen, Sergey Ovchinnikov, Nicholas Polizzi, Brian K Shoichet, James S Fraser.
  Zenodo, 2024. doi:10.5281/zenodo.11179893
  >1,000 endorsement signatures as of May 28, 2024.
  Nature editorial response
• SaprotHub: Making protein modeling accessible to all biologists.
  Jin Su, Zhikai Li, Chenchen Han, Yuyang Zhou, Yan He, Junjie Shan, Xibin Zhou, Xing Chang, Dacheng Ma, The OPMC, Martin Steinegger, Sergey Ovchinnikov, Fajie Yuan.
  bioRxiv, 2024.
  The Open Protein Modeling Consortium includes Anthony Gitter
• Biophysics-based protein language models for protein engineering.
  Sam Gelman, Bryce Johnson, Chase Freschlin, Sameer D'Costa, Anthony Gitter^*, Philip A Romero^*.
  bioRxiv, 2024.
  GitHub repository 1, GitHub repository 2, GitHub repository 3, GitHub repository 4, Zenodo software archive 1, Zenodo software archive 2, Zenodo software archive 3, Zenodo software archive 4, Zenodo datasets, Zenodo models
• Product manifold representations for learning on biological pathways.
  Daniel McNeela, Frederic Sala^*, Anthony Gitter^*.
  arXiv:2401.15478 [q-bio.QM], 2024.
  GitHub repository 1, GitHub repository 2, Software Heritage archive 1, Software Heritage archive 2
  Expansion of 2023 ICML Workshop on Computational Biology extended abstract.
• A text-guided protein design framework.
  Shengchao Liu, Yanjing Li, Zhuoxinran Li, Anthony Gitter, Yutao Zhu, Jiarui Lu, Zhao Xu, Weili Nie, Arvind Ramanathan, Chaowei Xiao, Jian Tang, Hongyu Guo, Anima Anandkumar.
  arXiv:2302.04611 [cs.LG], 2023.
  GitHub software repository, Hugging Face data

Journal and conference papers

• Current and future directions in network biology.
  Marinka Zitnik^*, Michelle M Li^*, Aydin Wells^*, Kimberly Glass, Deisy Morselli Gysi, Arjun Krishnan, T M Murali, Predrag Radivojac, Sushmita Roy, Anaïs Baudot, Serdar Bozdag, Danny Z Chen, Lenore Cowen, Kapil Devkota, Anthony Gitter, Sara J C Gosline, Pengfei Gu, Pietro H Guzzi, Heng Huang, Meng Jiang, Ziynet Nesibe Kesimoglu, Mehmet Koyuturk, Jian Ma, Alexander R Pico, Nataša Pržulj, Teresa M Przytycka, Benjamin J Raphael, Anna Ritz, Roded Sharan, Yang Shen, Mona Singh, Donna K Slonim, Hanghang Tong, Xinan Holly Yang, Byung-Jun Yoon, Haiyuan Yu, Tijana Milenković.
  Bioinformatics Advances. 4:1, 2024.
  Preprint
• Evaluating scalable supervised learning for synthesize-on-demand chemical libraries.
  Moayad Alnammi, Shengchao Liu, Spencer S Ericksen, Gene E Ananiev, Andrew F Voter, Song Guo, James L Keck, F Michael Hoffmann, Scott A Wildman, Anthony Gitter.
  Journal of Chemical Information and Modeling. 63:17, 2023.
  GitHub software repository, Zenodo software archive, Zenodo data, PubChem data, Preprint
• HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B.
  James W Bruce^*, Eunju Park^*, Chris Magnano, Mark Horswill, Alicia Richards, Gregory Potts, Alexander Hebert, Nafisah Islam, Joshua J Coon, Anthony Gitter, Nathan Sherer, Paul Ahlquist.
  PLoS Pathogens. 19:7, 2023.
  GitHub software repository, Zenodo software archive, Chorus data (login required)
• Bayes optimal informer sets for early-stage drug discovery.
  Peng Yu, Spencer Ericksen, Anthony Gitter, Michael A Newton.
  Biometrics. 79:2, 2023.
  GitHub software repository, Software Heritage archive, Preprint
• The coming of age of nucleic acid vaccines during COVID-19.
  Halie M Rando, Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J Lee, Nils Wellhausen, Amruta Naik, Jeremy P Kamil, COVID-19 Review Consortium, Anthony Gitter, Casey S Greene.
  mSystems. 8:2, 2023.
  One section of a larger collaborative review, Preprint
• Application of traditional vaccine development strategies to SARS-CoV-2.
  Halie M Rando, Ronan Lordan, Alexandra J Lee, Amruta Naik, Nils Wellhausen, Elizabeth Sell, Likhitha Kolla, COVID-19 Review Consortium, Anthony Gitter, Casey S Greene.
  mSystems. 8:2, 2023.
  One section of a larger collaborative review, Preprint
• Graph algorithms for predicting subcellular localization at the pathway level.
  Chris S Magnano, Anthony Gitter.
  Pacific Symposium on Biocomputing. 28, 2023.
  GitHub repository, Zenodo software archive, Preprint
• 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.
  PLoS Biology. 20:12, 2022.
  GitHub software repository, Zenodo software archive, RNA-seq data, Preprint
• An approachable, flexible and practical machine learning workshop for biologists.
  Chris S Magnano, Fangzhou Mu, Rosemary S Russ, Milica Cvetkovic, Debora Treu, Anthony Gitter.
  Bioinformatics. 38:Supplement_1, 2022.
  GitHub workshop content, GitHub software repository, PyPI package, Zenodo workshop content archive, Zenodo software archive, Preprint
• Ten quick tips for deep learning in biology.
  Benjamin D Lee, Anthony Gitter, Casey S Greene, Sebastian Raschka, Finlay Maguire, Alexander J Titus, Michael D Kessler, Alexandra J Lee, Marc G Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J Fertig, Alexandr A Kalinin, Brandon Signal, Benjamin J Lengerich, Timothy J Triche Jr., Simina M Boca.
  PLoS Computational Biology. 18:3, 2022.
  Manuscript GitHub repository, Manubot version of the manuscript, Preprint
• Network inference with Granger causality ensembles on single-cell transcriptomics.
  Atul Deshpande, Li-Fang Chu, Ron Stewart, Anthony Gitter.
  Cell Reports. 38:6, 2022.
  GitHub repository, Zenodo software archive, GitHub supplement, Zenodo supplement archive, Docker image, Preprint
  Selected for review by the biOverlay editors
• Neural networks to learn protein sequence–function relationships from deep mutational scanning data.
  Sam Gelman, Sarah A Fahlberg, Pete Heinzelman, Philip A Romero^*, Anthony Gitter^*.
  Proceedings of the National Academy of Sciences of the United States of America. 118:48, 2021.
  GitHub software repository, Zenodo software archive, Preprint
• Identification and development of therapeutics for COVID-19.
  Halie M Rando, Nils Wellhausen, Soumita Ghosh, Alexandra J Lee, Anna Ada Dattoli, Fengling Hu, James Brian Byrd, Diane N Rafizadeh, Ronan Lordan, Yanjun Qi, Yuchen Sun, Christian Brueffer, Jeffrey M Field, Marouen Ben Guebila, Nafisa M Jadavji, Ashwin N Skelly, Bharath Ramsundar, Jinhui Wang, Rishi Raj Goel, YoSon Park, COVID-19 Review Consortium, Simina M Boca, Anthony Gitter, Casey S Greene.
  mSystems. 6:6, 2021.
  One section of a larger collaborative review, Preprint
• Pathogenesis, symptomatology, and transmission of SARS-CoV-2 through analysis of viral genomics and structure.
  Halie M Rando, Adam L MacLean, Alexandra J Lee, Ronan Lordan, Sandipan Ray, Vikas Bansal, Ashwin N Skelly, Elizabeth Sell, John J Dziak, Lamonica Shinholster, Lucy D'Agostino McGowan, Marouen Ben Guebila, Nils Wellhausen, Sergey Knyazev, Simina M Boca, Stephen Capone, Yanjun Qi, YoSon Park, David Mai, Yuchen Sun, Joel D Boerckel, Christian Brueffer, James Brian Byrd, Jeremy P Kamil, Jinhui Wang, Ryan Velazquez, Gregory L Szeto, John P Barton, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, COVID-19 Review Consortium, Anthony Gitter, Casey S Greene.
  mSystems. 6:5, 2021.
  One section of a larger collaborative review, Correction, Preprint
• Dietary supplements and nutraceuticals under investigation for COVID-19 prevention and treatment.
  Ronan Lordan, Halie M Rando, COVID-19 Review Consortium, Casey S Greene.
  mSystems. 6:3, 2021.
  The COVID-19 Review Consortium includes Anthony Gitter
  One section of a larger collaborative review, Preprint
• Automating parameter selection to avoid implausible biological pathway models.
  Chris S Magnano, Anthony Gitter.
  npj Systems Biology and Applications. 7:12, 2021.
  GitHub software repository, Zenodo software archive, PyPI package, Preprint
• Inferring signaling pathways with probabilistic programming.
  David Merrell, Anthony Gitter.
  Bioinformatics. 36:Supplement_2, 2020.
  19th European Conference on Computational Biology (ECCB 2020) Proceedings.
  GitHub software repository, Zenodo software archive, Preprint
• Lag penalized weighted correlation for time series clustering.
  Thevaa Chandereng, Anthony Gitter.
  BMC Bioinformatics. 21, 2020.
  GitHub software repository, GitHub examples repository, CRAN package, Preprint
• Classifying T cell activity in autofluorescence intensity images with convolutional neural networks.
  Zijie J Wang, Alex J Walsh, Melissa C Skala, Anthony Gitter.
  Journal of Biophotonics. 13:3, 2020.
  GitHub repository, Zenodo software archive, Zenodo data, Preprint
• Learning drug functions from chemical structures with convolutional neural networks and random forests.
  Jesse G Meyer, Shengchao Liu, Ian J Miller, Joshua J Coon, Anthony Gitter.
  Journal of Chemical Information and Modeling. 59:10, 2019.
  GitHub repository, Zenodo software archive, Preprint
• Assessment of network module identification across complex diseases.
  Sarvenaz Choobdar^*, Mehmet E Ahsen^*, Jake Crawford^*, Mattia Tomasoni, David Lamparter, Junyuan Lin, Benjamin Hescott, Xiaozhe Hu, Johnathan Mercer, Ted Natoli, Rajiv Narayan, The DREAM Module Identification Challenge Consortium, Aravind Subramanian, Jitao D Zhang, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K Slonim, Julio Saez-Rodriguez, Lenore J Cowen, Sven Bergmann^*, Daniel Marbach^*.
  Nature Methods. 16:9, 2019.
  The DREAM Module Identification Challenge Consortium includes Aaron Baker and Anthony Gitter
  Our team's method description and code
  Preprint
• Predicting kinase inhibitors using bioactivity matrix derived informer sets.
  Huikun Zhang^*, Spencer S Ericksen^*, Ching-pei Lee^*, Gene E Ananiev, Nathan Wlodarchak, Peng Yu, Julie C Mitchell, Anthony Gitter, Stephen J Wright, F Michael Hoffmann, Scott A Wildman, Michael A Newton.
  PLoS Computational Biology. 15:8, 2019.
  GitHub repository, Zenodo software archive, Preprint
• Open collaborative writing with Manubot.
  Daniel S Himmelstein, Vincent Rubinetti, David R Slochower, Dongbo Hu, Venkat S Malladi, Casey S Greene, Anthony Gitter.
  PLoS Computational Biology. 15:6, 2019.
  Manuscript GitHub repository, Manubot version of the manuscript, Manubot website
  Selected as featured research by the editors of the PLOS Open Source Toolkit Channel
• Practical model selection for prospective virtual screening.
  Shengchao Liu^*, Moayad Alnammi^*, Spencer S Ericksen, Andrew F Voter, Gene E Ananiev, James L Keck, F Michael Hoffmann, Scott A Wildman, Anthony Gitter.
  Journal of Chemical Information and Modeling. 59:1, 2019.
  GitHub repository, Zenodo software archive, Zenodo data, PubChem data, Preprint
• Synthesizing signaling pathways from temporal phosphoproteomic data.
  Ali S Köksal, Kirsten Beck, Dylan R Cronin, Aaron McKenna, Nathan D Camp, Saurabh Srivastava, Matthew E MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter.
  Cell Reports. 24:13, 2018.
  External supplement, GitHub repository, Zenodo software archive, GitHub osmotic stress repository, Zenodo osmotic stress archive, PRIDE data, Preprint
• Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.
  Matthew E MacGilvray^*, Evgenia Shishkova^*, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J Coon, Audrey P Gasch.
  PLoS Computational Biology. 13:5, 2018.
  GitHub repository, Software Heritage archive, PRIDE data, Preprint
• Opportunities and obstacles for deep learning in biology and medicine.
  Travers Ching, Daniel S Himmelstein, Brett K Beaulieu-Jones, Alexandr A Kalinin, Brian T Do, Gregory P Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M Hoffman, Wei Xie, Gail L Rosen, Benjamin J Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M Cofer, Christopher A Lavender, Srinivas C Turaga, Amr M Alexandari, Zhiyong Lu, David J Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K Wiley, Marwin HS Segler, Simina M Boca, S Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S Greene.
  Journal of the Royal Society Interface. 15:141, 2018.
  Author order was determined with a randomized algorithm
  GitHub repository, Preprint
  A popular paper of 2017 in the Nature article 2017 in news: The science events that shaped the year
  Most downloaded bioRxiv preprint of 2017
  F1000Prime recommendation
• Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism.
  Zoi E Sychev, Alex Hu, Terri A DiMaio, Anthony Gitter, Nathan D Camp, William S Noble, Alejandro Wolf-Yadlin, Michael Lagunoff.
  PLoS Pathogens. 13:3, 2017.
  GEO data
• Network-based interpretation of diverse high-throughput datasets through the Omics Integrator software package.
  Nurcan Tuncbag^*, Sara JC Gosline^*, Amanda Kedaigle, Anthony R Soltis, Anthony Gitter, Ernest Fraenkel.
  PLoS Computational Biology. 12:4, 2016.
  Supporting website
• Multitask learning of signaling and regulatory networks with application to studying human response to flu.
  Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph.
  PLoS Computational Biology. 10:12, 2014.
  Supporting website
• Sharing information to reconstruct patient-specific pathways in heterogeneous diseases.
  Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer Chayes, Riccardo Zecchina, Ernest Fraenkel.
  Pacific Symposium on Biocomputing. 19, 2014.
  GitHub repository, Zenodo software archive
• Identifying proteins controlling key disease signaling pathways.
  Anthony Gitter, Ziv Bar-Joseph.
  Bioinformatics. 29:13, 2013.
  21st Annual International Conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology (ISMB/ECCB 2013) Proceedings.
  Supporting website
• Linking the signaling cascades and dynamic regulatory networks controlling stress responses.
  Anthony Gitter, Miri Carmi, Naama Barkai, Ziv Bar-Joseph.
  Genome Research. 23:2, 2013.
  Top ten paper award in regulatory and systems genomics.
  Supporting website, GEO data
• DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.
  Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph.
  BMC Systems Biology. 6:1, 2012.
  Supporting website
• A network-based approach for predicting missing pathway interactions.
  Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph.
  PLoS Computational Biology. 8:8, 2012.
  Supporting website, GEO data
• Studying and modelling dynamic biological processes using time-series gene expression data.
  Ziv Bar-Joseph, Anthony Gitter, Itamar Simon.
  Nature Reviews Genetics. 13:8, 2012.
• Computationally efficient measure of topological redundancy of biological and social networks.
  Réka Albert, Bhaskar DasGupta, Rashmi Hegde, Gowri Sangeetha Sivanathan, Anthony Gitter, Gamze Gürsoy, Pradyut Paul, Eduardo Sontag.
  Physical Review E. 84:3, 2011.
  Supporting website, Preprint
• Discovering pathways by orienting edges in protein interaction networks.
  Anthony Gitter, Judith Klein-Seetharaman, Anupam Gupta, Ziv Bar-Joseph.
  Nucleic Acids Research. 39:4, 2011.
  Featured article representing the top 5% of papers in terms of originality, significance, and scientific excellence.
  Supporting website
• 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.
  Molecular Systems Biology. 5:276, 2009.
  ArrayExpress data
• CBioC: Beyond a prototype for collaborative annotation of molecular interactions from the literature.
  Chitta Baral, Graciela Gonzalez, Anthony Gitter, Craig Teegarden, Amanda Zeigler, Geeta Joshi-Topé.
  Proceedings of the Life Sciences Society Computational Systems Bioinformatics Conference (CSB) 2007. Vol 6, pp 381-384, 2007.
  Archived supporting website

Workshop papers and extended abstracts

• 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. Extended abstract. 2024.
  Derived from Gelman 2024
• Mixed-curvature representation learning for biological pathway graphs.
  Daniel McNeela, Frederic Sala^*, Anthony Gitter^*.
  2023 ICML Workshop on Computational Biology. Extended abstract. 2023.
  GitHub repository, Software Heritage archive
• 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, Casey S Greene, Anthony Gitter.
  Proceedings of the Workshop on Digital Infrastructures for Scholarly Content Objects (DISCO 2021). 2021.
  One section of a larger collaborative review, Preprint
• Loss-balanced task weighting to reduce negative transfer in multi-task learning.
  Shengchao Liu, Yingyu Liang, Anthony Gitter.
  Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence. Student abstract. 2019.
  External appendix, GitHub repository, Software Heritage archive
• Integrating knowledge from biomedical literature: Normalization and evidence statements for interactions.
  Graciela Gonzalez, Luis Tari, Anthony Gitter, Robert Leaman, Shawn Nikkila, Ryan Wendt, Amanda Zeigler, Chitta Baral.
  Proceedings of the Second BioCreative Challenge Evaluation Workshop. 2007.

Book chapters

• The SDREM method for reconstructing signaling and regulatory response networks: Applications for studying disease progression.
  Anthony Gitter, Ziv Bar-Joseph.
  In Systems Biology of Alzheimer's Disease, Methods in Molecular Biology series. Vol 1303, pp 493-506, 2015.
  Supporting website
• Computational methods for analyzing dynamic regulatory networks.
  Anthony Gitter, Yong Lu, Ziv Bar-Joseph.
  In Computational Biology of Transcription Factor Binding, Methods in Molecular Biology series. Vol 674, pp 419-441, 2010.

Older preprints and other documents

• Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference.
  Anthony Gitter.
  Cell Systems. 15:8, 2024.
• Molecular and serologic diagnostic technologies for SARS-CoV-2.
  Halie M Rando, Christian Brueffer, Ronan Lordan, Anna Ada Dattoli, David Manheim, Jesse G Meyer, Ariel I Mundo, Dimitri Perrin, David Mai, Nils Wellhausen, COVID-19 Review Consortium, Anthony Gitter, Casey S Greene.
  arXiv:2204.12598 [q-bio.BM], 2022.
  One section of a larger collaborative review
• Single-cell RNA-seq pseudotime estimation algorithms.
  Anthony Gitter.
  GitHub repository, 2018. doi:10.5281/zenodo.1297422
  Zenodo archive
• Unsupervised learning of transcriptional regulatory networks via latent tree graphical models.
  Anthony Gitter^*, Furong Huang^*, Ragupathyraj Valluvan, Ernest Fraenkel^*, Animashree Anandkumar^*.
  arXiv:1609.06335 [q-bio.MN], 2016.

Theses

• Learning protein sequence-function relationships for protein engineering.
  Sam Gelman. Ph.D. thesis.
  University of Wisconsin-Madison, 2023.
• Probabilistic machine learning with omics data and biological prior knowledge.
  David Merrell. Ph.D. thesis.
  University of Wisconsin-Madison, 2023.
• Bringing high-throughput data analysis to biologists.
  Christopher S Magnano. Ph.D. thesis.
  University of Wisconsin-Madison, 2022.
• Iterative batched screening and active learning in drug discovery.
  Moayad Alnammi. Ph.D. thesis.
  University of Wisconsin-Madison, 2021.
• Exploration on deep drug discovery: Representation and learning.
  Shengchao Liu. M.S. thesis. TR1854.
  University of Wisconsin-Madison, 2018.
• Massively multitask deep learning for drug discovery.
  Jason Feriante. M.S. project report.
  University of Wisconsin-Madison, 2015.
• Identifying the signaling cascades and regulatory mechanisms that control stress responses.
  Anthony Gitter. Ph.D. thesis.
  Carnegie Mellon University, 2012.
• Constituent tree-based extraction and evaluation of protein-protein interactions from biomedical literature.
  Anthony Gitter. Undergraduate honors thesis.
  Arizona State University, The Barrett Honors College, 2007.