Publications

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

Preprints

• Classifying T cell activity in autofluorescence intensity images with convolutional neural networks.

  Zijie J Wang, Alex J Walsh, Melissa C Skala, Anthony Gitter.
  bioRxiv, 2019. doi:10.1101/737346
  GitHub repository, Zenodo data

• Network inference with Granger causality ensembles on single-cell transcriptomic data.

  Atul Deshpande, Li-Fang Chu, Ron Stewart, Anthony Gitter.
  bioRxiv, 2019. doi:10.1101/534834
  GitHub repository, Zenodo software archive

• Learning molecule drug function from structure representations and deep neural networks or random forests.

  Jesse G Meyer, Shengchao Liu, Ian J Miller, Anthony Gitter, Joshua J Coon.
  bioRxiv, 2018. doi:10.1101/482877
  GitHub repository

• Lag penalized weighted correlation for time series clustering.

  Thevaa Chandereng, Anthony Gitter.
  bioRxiv, 2018. doi:10.1101/292615
  GitHub repository

• Open community challenge reveals molecular network modules with key roles in 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, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K. Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann^*, Daniel Marbach^*.
  bioRxiv, 2018. doi:10.1101/265553
  The DREAM Module Identification Challenge Consortium includes Aaron Baker and Anthony Gitter
  Our team’s method description and code

Journal and conference papers

• 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, 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, 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
  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.
  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.
  Supporting website

• 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, 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,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.
  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.

Workshop papers

• 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.
  GitHub repository

• 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

• 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

• 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.