| 2024 | ICML | Prospector Heads: Generalized Feature Attribution for Large Models & Data. | Gautam Machiraju, Alexander Derry, Arjun D. Desai, Neel Guha, Amir-Hossein Karimi, James Zou, Russ B. Altman, Christopher R, Parag Mallick |
| 2023 | ACL | Detecting Contradictory COVID-19 Drug Efficacy Claims from Biomedical Literature. | Daniel N. Sosa, Malavika Suresh, Christopher Potts, Russ B. Altman |
| 2021 | AMIA | Randomized user testing of recommender system clinical decision support. | Andre Kumar, Rachael C. Aikens, Jason Horn, Lisa Shieh, Mark A. Musen, Michael T. M. Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen |
| 2021 | PSB | Drug Response Pharmacogenetics for 200, 000 UK Biobank Participants. | Gregory McInnes, Russ B. Altman |
| 2020 | PSB | PGxMine: Text Mining for Curation of PharmGKB. | Jake Lever, Julia M. Barbarino, Li Gong, Rachel Huddart, Katrin Sangkuhl, Ryan Whaley, Michelle Whirl Carrillo, Mark Woon, Teri E. Klein, Russ B. Altman |
| 2020 | PSB | Pathway and Network Embedding Methods for Prioritizing Psychiatric Drugs. | Yash Pershad, Margaret G. Guo, Russ B. Altman |
| 2020 | PSB | A Literature-Based Knowledge Graph Embedding Method for Identifying Drug RepurposingOpportunities in Rare Diseases. | Daniel N. Sosa, Alexander Derry, Margaret G. Guo, Eric Wei, Connor Brinton, Russ B. Altman |
| 2019 | AMIA | Classifying Non-Small Cell Lung Cancer Histopathology Types and Transcriptomic Subtypes using Convolutional Neural Networks. | Kun-Hsing Yu, Feiran Wang, Gerald J. Berry, Christopher R, Russ B. Altman, Michael Snyder, Isaac S. Kohane |
| 2019 | RECOMB | GRep: Gene Set Representation via Gaussian Embedding. | Sheng Wang, Emily R. Flynn, Russ B. Altman |
| 2018 | AMIA | Unraveling the Molecular Basis of Lung Adenocarcinoma Dedifferentiation and Prognosis by Integrating Omics and Histopathology. | Kun-Hsing Yu, Gerald J. Berry, Daniel L. Rubin, Christopher R, Russ B. Altman, Michael Snyder |
| 2018 | PSB | Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome. | Emily K. Mallory, Ambika Acharya, Stefano E. Rensi, Peter J Turnbaugh, Roselie A. Bright, Russ B. Altman |
| 2018 | PSB | Improving the explainability of Random Forest classifier - user centered approach. | Dragutin Petkovic, Russ B. Altman, Mike Wong, Arthur Vigil |
| 2018 | PSB | GeneDive: A gene interaction search and visualization tool to facilitate precision medicine. | Paul Previde, Brook Thomas, Mike Wong, Emily K. Mallory, Dragutin Petkovic, Russ B. Altman, Anagha Kulkarni |
| 2017 | AMIA | Predicting Non-Small Cell Lung Cancer Diagnosis and Prognosis by Fully Automated Microscopic Pathology Image Features. | Kun-Hsing Yu, Ce Zhang, Gerald J. Berry, Russ B. Altman, Christopher R, Daniel L. Rubin, Michael Snyder |
| 2016 | AMIA | Usability of an Automated Recommender System for Clinical Order Entry. | Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman |
| 2016 | PSB | Dynamically Evolving Clinical Practices and Implications for Predicting Medical Decisions. | Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman |
| 2016 | PSB | Separating the Causes and Consequences in Disease Transcriptome. | Yong Fuga Li, Fuxiao Xin, Russ B. Altman |
| 2015 | PSB | A Twentieth Anniversary Tribute to PSB. | Darla Hewett, Michelle Whirl Carrillo, Lawrence E. Hunter, Russ B. Altman, Teri E. Klein |
| 2015 | PSB | Training the Next Generation of Quantitative Biologists in the Era of Big Data. | Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Kevin Bretonnel Cohen, Elizabeth Wethington, Carsten Grg, Lawrence E. Hunter, Spencer V. Muse, Predrag Radivojac, Jason H. Moore |
| 2014 | AMIA | "Doctors who ordered this also ordered..." Automated physician order recommendations and outcome predictions by data-mining electronic medical records. | Jonathan H. Chen, Russ B. Altman |
| 2014 | PSB | PATH-SCAN: A Reporting Tool for Identifying Clinically Actionable Variants. | Roxana Daneshjou, Zachary Zappala, Kimberly R. Kukurba, Sean M. Boyle, Kelly E. Ormond, Teri E. Klein, Michael Snyder, Carlos D. Bustamante, Russ B. Altman, Stephen B. Montgomery |
| 2014 | PSB | Building the Next Generation of Quantitative Biologists. | Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Lawrence E. Hunter, David A. Ross, James A. Foster, Jason H. Moore |
| 2013 | AMIA | Expanding the Autism Ontology to DSM-IV Criteria. | Omri Mugzach, Mor Peleg, Steven C. Bagley, Russ B. Altman |
| 2013 | AMIA | Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. | Bethany Percha, Russ B. Altman |
| 2012 | PSB | Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine. | Konrad J. Karczewski, Robert P. Tirrell, Pablo Cordero, Nicholas P. Tatonetti, Joel T. Dudley, Keyan Salari, Michael Snyder, Russ B. Altman, Stuart K. Kim |
| 2012 | PSB | Discovery and Explanation of Drug-Drug Interactions via Text Mining. | Bethany Percha, Yael Garten, Russ B. Altman |
| 2012 | PSB | Systems Pharmacogenomics-Bridging the Gap. | Marylyn D. Ritchie, Nancy J. Cox, Cheng Cheng, Scott Weiss, Teri E. Klein, Russ B. Altman |
| 2011 | PSB | Structural insights into Pre-Translocation Ribosome Motions. | Samuel Coulbourn Flores, Russ B. Altman |
| 2010 | PSB | Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application. | Adrien Coulet, Nigam H. Shah, Lawrence Hunter, Chitta Baral, Russ B. Altman |
| 2010 | PSB | Predicting RNA Structure by Multiple Template Homology Modeling. | Samuel Flores, Yaqi Wan, Rick Russell, Russ B. Altman |
| 2010 | PSB | Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug Relationships. | Yael Garten, Nicholas P. Tatonetti, Russ B. Altman |
| 2009 | AMIA | A General Framework for Dose Optimization. | Robert G. Turcott, Hersh Sagreiya, Euan A. Ashley, Russ B. Altman, Amar K. Das |
| 2009 | PSB | Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System. | Shai Shen-Orr, Ofir Goldberger, Yael Garten, Yael Rosenberg-Hasson, Patricia A. Lovelace, David L. Hirschberg, Russ B. Altman, Mark M. Davis, Atul J. Butte |
| 2008 | CIKM | Text mining for pharmacogenomics. | Russ B. Altman |
| 2008 | PSB | Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition. | Dariya S. Glazer, Randall J. Radmer, Russ B. Altman |
| 2005 | PSB | Preface. | Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein |
| 2004 | PSB | Preface. | Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein |
| 2003 | PSB | Preface. | Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein |
| 2003 | PSB | Special Paper - Introduction. | Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein |
| 2003 | PSB | Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures. | Mike P. Liang, Douglas L. Brutlag, Russ B. Altman |
| 2002 | AMIA | Using binning to maintain confidentiality of medical data. | Zhen Lin, Micheal Hewett, Russ B. Altman |
| 2002 | ISMB | Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models. | Daniel L. Rubin, Farhad Shafa, Diane E. Oliver, Micheal Hewett, Russ B. Altman |
| 2002 | PSB | Preface. | Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein |
| 2002 | PSB | Ontology Development for a Pharmacogenetics Knowledge Base. | Diane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, Russ B. Altman |
| 2002 | PSB | Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XML. | Daniel L. Rubin, Micheal Hewett, Diane E. Oliver, Teri E. Klein, Russ B. Altman |
| 2001 | KDD | Challenges for knowledge discovery in biology. | Russ B. Altman |
| 2001 | PSB | ViewFeature: Integrated Feature Analysis and Visualization. | D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, Teri E. Klein |
| 2001 | PSB | Including Biological Literature Improves Homology Search. | Jeffrey T. Chang, Soumya Raychaudhuri, Russ B. Altman |
| 2001 | PSB | Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases. | Allison Waugh, Glenn A. Williams, Liping Wei, Russ B. Altman |
| 2000 | AMIA | The new peer review. | Isaac S. Kohane, Russ B. Altman |
| 2000 | ISMB | Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains. | Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, Russ B. Altman |
| 1998 | AMIA | Bioinformatics in support of molecular medicine. | Russ B. Altman |
| 1998 | AMIA | MHCWeb: converting a WWW database into a knowledge-based collaborative environment. | Lawrence S. Hon, Neil F. Abernethy, Vladimir Brusic, Jenny Chai, Russ B. Altman |
| 1998 | AMIA | Updating a bibliography using the related articles function within PubMed. | Xuemin Liu, Russ B. Altman |
| 1998 | CHI | Graphical style sheets: towards reusable representations of biomedical graphics. | Ramon M. Felciano, Russ B. Altman |
| 1998 | ISMB | A Surface Measure for Probabilistic Structural Computations. | Jeanette P. Schmidt, Cheng Che Chen, Jonathan L. Cooper, Russ B. Altman |
| 1998 | RECOMB | The hierarchical organization of molecular structure computations. | Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman |
| 1997 | ISMB | Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data. | Russ B. Altman, Neil F. Abernethy, Richard O. Chen |
| 1997 | ISMB | RIBOWEB: Linking Structural Computations to a Knowledge Base of Published Experimental Data. | Richard O. Chen, Ramon M. Felciano, Russ B. Altman |
| 1996 | SC | Parallel Hierarchical Molecular Structure Estimation. | Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman |
| 1995 | ISMB | Characterizing Oriented Protein Structural Sites Using Biochemical Properties. | Steven C. Bagley, Liping Wei, Carol Cheng, Russ B. Altman |
| 1994 | ISMB | Finding an Average Core Structure: Application to the Globins. | Russ B. Altman, Mark Gerstein |
| 1994 | ISMB | Constraint Satisfaction Techniques for Modeling Large Complexes: Application to the Central Domain of 16S Ribosomal RNA. | Russ B. Altman, Bryn Weiser, Harry F. Noller |
| 1994 | SC | Parallel protein structure determination from uncertain data. | Cheng Che Chen, Jaswinder Pal Singh, William B. Poland, Russ B. Altman |
| 1994 | UAI | Probabilistic Constraint Satisfaction with Non-Gaussian Noise. | Russ B. Altman, Cheng Che Chen, William B. Poland, Jaswinder Pal Singh |
| 1993 | ISMB | Probabilistic Structure Calculations: A Three-Dimensional tRNA Structure from Sequence Correlation Data. | Russ B. Altman |
| 1993 | UAI | A Probabilistic Algorithm for Calculating Structure: Borrowing from Simulated Annealing. | Russ B. Altman |
| 1987 | AAAI | Partial Compilation of Strategic Knowledge. | Russ B. Altman, Bruce G. Buchanan |
| 1986 | AAAI | PROTEAN: Deriving Protein Structure from Constraints. | Barbara Hayes-Roth, Bruce G. Buchanan, Olivier Lichtarge, Mike Hewitt, Russ B. Altman, James F. Brinkley, Craig Cornelius, Bruce S. Duncan, Oleg Jardetzky |