Anthony Gitter

36 papers A* 2Misc 1Journal 32Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data.
J. Chem. Inf. Model.
Hugo MacDermott-Opeskin, Jenke Scheen, Cas Wognum, Joshua T. Horton, Devany West, Alexander Matthew Payne, Maria A. Castellanos, Sean Colby, Edward J. Griffen, David Cousins, Jessica Stacey, Lauren Reid, Jasmin Cara Aschenbrenner, Daren Fearon, Blake Balcomb, Peter Marples, Charles W. E. Tomlinson, Ryan Lithgo, Andre S. Godoy, Max Winokan, Haim Barr, Noa Lahav, Michael Lavi, Shirley Duberstein, Galit Cohen, Gwendolyn Fate, Bruce Lefker, Ralph Robinson, Tamas Szommer, Nick Lynch, David D. L. Minh, Van Ngoc Thuy La, Lulu Kang, Kate Huddleston, Ryan Renslow, Mallory Tollefson, W. Patrick Walters, Cynthia Xu, Jonny Hsu, Julien St-Laurent, Honore Etsmoberg, Lu Zhu, Andrew Quirke, Mohamed Iliyas Abdul Haleem, Irfan Alibay, Gunjan Baid, Benjamin Birnbaum, Kevin P. Bishop, Hugo-Javier Bohórquez, Ashmita Bose, C. J. Brown, Jackson W. Burns, Lianjin Cai, Ruel Cedeno, Stephane de Cesco, Vladimir I. Chupakhin, Finlay Clark, Daniel J. Cole, Carles Corbi-Verge, Muhammad Danial, Alec Davi, Wim Dehaen, Niklas Piet Doering, Alexis Dougha, Marie-Pierre Dréanic, Bryce Eakin, Anatol Ehrlich, Rokas Elijosius, Jozef Fülöp, Anthony Gitter, Kenneth Goossens, Yaowen Gu, Teresa Head-Gordon, Laurent Hoffer, Johan Hofmans, Ellena Jiang, Benjamin Kaminow, Sina Khosravi, Asma Feriel Khoualdi, Eelke B. Lenselink, Zhirong Liu, Yue Liu, Sijie Liu, Yizhou Ma, Patrick Maher, Imke Mayer, Oscar Mendez-Lucio, Antonia S. J. S. Mey, Julien Michel, Floriane Montanari, Taoyu Niu, Ryusei Ogino, Ashok Palaniappan, Xiaolin Pan, Auro Patnaik, Long-Hung Dinh Pham, Luis Pinto, Justin Purnomo, Alex Rich, Lars L. Schaaf, Christoph Schran, Rajeev Kumar Singh, Mounika Srilakshmi, Satya Pratik Srivastava, Kunyang Sun, Zhaoxi Sun, Valerij Talagayev, Balamurugan Thirukonda Subramanian Balakrishnan, Ida Titus, Alexandre Tkatchenko, Wojtek Treyde, Giovanni Tricarico, Austin Tripp, Nopsinth Vithayapalert, Yingze Wang, Azmine Toushik Wasi, Steffen Wedig, Gerhard Wolber, Bofei Xu, Weijun Zhou, Frank von Delft, Alpha Lee, Karla Kirkegaard, Peter Sjö, James S. Fraser, John D. Chodera
2025 J jnl
A text-guided protein design framework.
Nat. Mac. Intell.
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
2025 A* conf
Assay2Mol: Large Language Model-based Drug Design Using BioAssay Context.
EMNLP
Yifan Deng, Spencer S. Ericksen, Anthony Gitter
2025 J jnl
Assay2Mol: large language model-based drug design using BioAssay context.
CoRR
Yifan Deng, Spencer S. Ericksen, Anthony Gitter
2025 J jnl
Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop.
CoRR
Elizabeth Fahsbender, Alma Andersson, Jeremy Ash, Polina Binder, Daniel Burkhardt, Benjamin Chang, Georg K. Gerber, Anthony Gitter, Patrick Godau, Ankit Gupta, Genevieve Haliburton, Siyu He, Trey Ideker, Ivana Jelic, Aly Khan, Yang-Joon Kim, Aditi Krishnapriyan, Jon M. Laurent, Tianyu Liu, Emma Lundberg, Shalin B. Mehta, Rob Moccia, Angela Oliveira Pisco, Katherine S. Pollard, Suresh Ramani, Julio Saez-Rodriguez, Yasin Senbabaoglu, Elana Simon, Srinivasan Sivanandan, Gustavo Stolovitzky, Marc Valer, Bo Wang, Xikun Zhang, James Zou, Katrina Kalantar
2025 J jnl
Chemical Language Model Linker: Blending Text and Molecules with Modular Adapters.
J. Chem. Inf. Model.
Yifan Deng, Spencer S. Ericksen, Anthony Gitter
2025 J jnl
Exploring zero-shot structure-based protein fitness prediction.
CoRR
Arnav Sharma, Anthony Gitter
2025 J jnl
MPAC: a computational framework for inferring pathway activities from multi-omic data.
Bioinform.
Peng Liu, David Page, Paul Ahlquist, Irene M. Ong, Anthony Gitter
2024 J jnl
Chemical Language Model Linker: blending text and molecules with modular adapters.
CoRR
Yifan Deng, Spencer S. Ericksen, Anthony Gitter
2024 J jnl
Product Manifold Representations for Learning on Biological Pathways.
CoRR
Daniel McNeela, Frederic Sala, Anthony Gitter
2023 J jnl
A Text-guided Protein Design Framework.
CoRR
Shengchao Liu, Yutao Zhu, Jiarui Lu, Zhao Xu, Weili Nie, Anthony Gitter, Chaowei Xiao, Jian Tang, Hongyu Guo, Anima Anandkumar
2023 J jnl
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries.
J. Chem. Inf. Model.
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
2022 J jnl
An approachable, flexible and practical machine learning workshop for biologists.
Bioinform.
Chris S. Magnano, Fangzhou Mu, Rosemary S. Russ, Milica Cvetkovic, Debora Treu, Anthony Gitter
2022 J jnl
Graph algorithms for predicting subcellular localization at the pathway level.
CoRR
Chris S. Magnano, Anthony Gitter
2022 J jnl
Ten quick tips for deep learning in biology.
PLoS Comput. Biol.
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
2021 — conf
An Open-Publishing Response to the COVID-19 Infodemic.
DISCO@JCDL
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
2021 J jnl
An Open-Publishing Response to the COVID-19 Infodemic.
CoRR
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
2021 J jnl
Neural networks to learn protein sequence-function relationships from deep mutational scanning data.
Proc. Natl. Acad. Sci. USA
Sam Gelman, Sarah A. Fahlberg, Pete Heinzelman, Philip A. Romero, Anthony Gitter
2021 J jnl
Ten Quick Tips for Deep Learning in Biology.
CoRR
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, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche Jr., Simina M. Boca
2020 J jnl
Inferring Signaling Pathways with Probabilistic Programming.
CoRR
David Merrell, Anthony Gitter
2020 J jnl
Inferring signaling pathways with probabilistic programming.
Bioinform.
David Merrell, Anthony Gitter
2020 J jnl
Lag penalized weighted correlation for time series clustering.
BMC Bioinform.
Thevaa Chandereng, Anthony Gitter
2019 J jnl
Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests.
J. Chem. Inf. Model.
Jesse G. Meyer, Shengchao Liu, Ian J. Miller, Joshua J. Coon, Anthony Gitter
2019 A* conf
Loss-Balanced Task Weighting to Reduce Negative Transfer in Multi-Task Learning.
AAAI
Shengchao Liu, Yingyu Liang, Anthony Gitter
2019 J jnl
Open collaborative writing with Manubot.
PLoS Comput. Biol.
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
2019 J jnl
Practical Model Selection for Prospective Virtual Screening.
J. Chem. Inf. Model.
Shengchao Liu, Moayad Alnammi, Spencer S. Ericksen, Andrew F. Voter, Gene E. Ananiev, James L. Keck, F. Michael Hoffmann, Scott A. Wildman, Anthony Gitter
2019 J jnl
Predicting kinase inhibitors using bioactivity matrix derived informer sets.
PLoS Comput. Biol.
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
2018 J jnl
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.
PLoS Comput. Biol.
Matthew E. MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch
2016 J jnl
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.
PLoS Comput. Biol.
Nurcan Tuncbag, Sara J. C. Gosline, Amanda J. Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel
2016 J jnl
Unsupervised learning of transcriptional regulatory networks via latent tree graphical models.
CoRR
Anthony Gitter, Furong Huang, Ragupathyraj Valluvan, Ernest Fraenkel, Animashree Anandkumar
2014 J jnl
Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu.
PLoS Comput. Biol.
Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph
2014 Misc conf
Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases.
Pacific Symposium on Biocomputing
Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer T. Chayes, Riccardo Zecchina, Ernest Fraenkel
2013 J jnl
Identifying proteins controlling key disease signaling pathways.
Bioinform.
Anthony Gitter, Ziv Bar-Joseph
2012 J jnl
A Network-based Approach for Predicting Missing Pathway Interactions.
PLoS Comput. Biol.
Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph
2012 J jnl
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.
BMC Syst. Biol.
Marcel H. Schulz, William E. Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph
2011 J jnl
A New Computationally Efficient Measure of Topological Redundancy of Biological and Social Networks
CoRR
Réka Albert, Bhaskar DasGupta, Anthony Gitter, Gamze Gürsoy, Rashmi Hegde, Pradyut Paul, Gowri Sangeetha Sivanathan, Eduardo D. Sontag