A New Computationally Efficient Measure of Topological Redundancy of Biological and Social Networks - Réka Albert; Bhaskar DasGupta; Anthony Gitter; Gamze Gürsoy; Rashmi Hegde; Pradyut Paul; Gowri Sangeetha Sivanathan; Eduardo D. Sontag (CoRR, 2011)

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 Syst. Biol., 2012)

A Network-based Approach for Predicting Missing Pathway Interactions. - Saket Navlakha; Anthony Gitter; Ziv Bar-Joseph (PLoS Comput. Biol., 2012)

Identifying proteins controlling key disease signaling pathways. - Anthony Gitter; Ziv Bar-Joseph (Bioinform., 2013)

Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases. - Anthony Gitter; Alfredo Braunstein; Andrea Pagnani; Carlo Baldassi; Christian Borgs; Jennifer T. Chayes; Riccardo Zecchina; Ernest Fraenkel (Pacific Symposium on Biocomputing, 2014)

Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu. - Siddhartha Jain 001; Anthony Gitter; Ziv Bar-Joseph (PLoS Comput. Biol., 2014)

Unsupervised learning of transcriptional regulatory networks via latent tree graphical models. - Anthony Gitter; Furong Huang; Ragupathyraj Valluvan; Ernest Fraenkel; Animashree Anandkumar (CoRR, 2016)

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. - Nurcan Tuncbag; Sara J. C. Gosline; Amanda J. Kedaigle; Anthony R. Soltis; Anthony Gitter; Ernest Fraenkel (PLoS Comput. Biol., 2016)

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 Comput. Biol., 2018)

Loss-Balanced Task Weighting to Reduce Negative Transfer in Multi-Task Learning. - Shengchao Liu; Yingyu Liang; Anthony Gitter (AAAI, 2019)

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 (J. Chem. Inf. Model., 2019)

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 (J. Chem. Inf. Model., 2019)

Open collaborative writing with Manubot. - Daniel S. Himmelstein; Vincent Rubinetti; David R. Slochower; Dongbo Hu; Venkat S. Malladi; Casey S. Greene; Anthony Gitter (PLoS Comput. Biol., 2019)

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 001; F. Michael Hoffmann; Scott A. Wildman; Michael A. Newton (PLoS Comput. Biol., 2019)

Inferring signaling pathways with probabilistic programming. - David Merrell; Anthony Gitter (Bioinform., 2020)

Lag penalized weighted correlation for time series clustering. - Thevaa Chandereng; Anthony Gitter (BMC Bioinform., 2020)

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 (DISCO@JCDL, 2021)

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; et al. (CoRR, 2021)

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 (Proc. Natl. Acad. Sci. USA, 2021)

An approachable, flexible and practical machine learning workshop for biologists. - Chris S. Magnano; Fangzhou Mu; Rosemary S. Russ; Milica Cvetkovic; Debora Treu; Anthony Gitter (Bioinform., 2022)

Graph algorithms for predicting subcellular localization at the pathway level. - Chris S. Magnano; Anthony Gitter (CoRR, 2022)

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; et al. (PLoS Comput. Biol., 2022)

A Text-guided Protein Design Framework. - Shengchao Liu; Yutao Zhu 001; Jiarui Lu; Zhao Xu 005; Weili Nie; Anthony Gitter; Chaowei Xiao; Jian Tang 005; Hongyu Guo; Anima Anandkumar (CoRR, 2023)

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 (J. Chem. Inf. Model., 2023)

Product Manifold Representations for Learning on Biological Pathways. - Daniel McNeela; Frederic Sala; Anthony Gitter (CoRR, 2024)

Chemical Language Model Linker: blending text and molecules with modular adapters. - Yifan Deng; Spencer S. Ericksen; Anthony Gitter (CoRR, 2024)

A text-guided protein design framework. - Shengchao Liu; Yanjing Li; Zhuoxinran Li; Anthony Gitter; Yutao Zhu 001; Jiarui Lu; Zhao Xu 005; Weili Nie; Arvind Ramanathan; Chaowei Xiao; Jian Tang 005; Hongyu Guo; et al. (Nat. Mac. Intell., 2025)

Exploring zero-shot structure-based protein fitness prediction. - Arnav Sharma; Anthony Gitter (CoRR, 2025)

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop. - Elizabeth Fahsbender; Alma Andersson; Jeremy Ash; Polina Binder; Daniel Burkhardt; Benjamin Chang 009; Georg K. Gerber; Anthony Gitter; Patrick Godau; Ankit Gupta; Genevieve Haliburton; Siyu He; et al. (CoRR, 2025)

Assay2Mol: large language model-based drug design using BioAssay context. - Yifan Deng; Spencer S. Ericksen; Anthony Gitter (CoRR, 2025)