Russ B. Altman

ORCID

Publication Activity (10 Years)

Years Active: 1986-2024
Publications (10 Years): 74

Top Venues

Publications

Kaixuan Huang, Yuanhao Qu, Henry Cousins, William A. Johnson, Di Yin, Mihir Shah, Denny Zhou, Russ B. Altman, Mengdi Wang, Le Cong
CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments. CoRR (2024)
Abdoul Jalil Djiberou Mahamadou, Aloysius Ochasi, Russ B. Altman
Data Ethics in the Era of Healthcare Artificial Intelligence in Africa: An Ubuntu Philosophy Perspective. CoRR (2024)
Daniel N. Sosa, Georgiana Neculae, Julien Fauqueur, Russ B. Altman
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery. J. Biomed. Semant. 15 (1) (2024)
Gautam Machiraju, Alexander Derry, Arjun D. Desai, Neel Guha, Amir-Hossein Karimi, James Zou, Russ B. Altman, Christopher Ré, Parag Mallick
Prospector Heads: Generalized Feature Attribution for Large Models & Data. CoRR (2024)
Abdoul Jalil Djiberou Mahamadou, Lea Goetz, Russ B. Altman
Individual Fairness Through Reweighting and Tuning. CoRR (2024)
Aloysius Ochasi, Abdoul Jalil Djiberou Mahamadou, Russ B. Altman
Justice in Healthcare Artificial Intelligence in Africa. CoRR (2024)
Lu Yang, Sheng Wang, Russ B. Altman
POPDx: an automated framework for patient phenotyping across 392 246 individuals in the UK Biobank study. J. Am. Medical Informatics Assoc. 30 (2) (2023)
Daniel N. Sosa, Rogier Hintzen, Betty Xiong, Alex de Giorgio, Julien Fauqueur, Mark Davies, Jake Lever, Russ B. Altman
Associating biological context with protein-protein interactions through text mining at PubMed scale. J. Biomed. Informatics 145 (2023)
Daniel N. Sosa, Malavika Suresh, Christopher Potts, Russ B. Altman
Detecting Contradictory COVID-19 Drug Efficacy Claims from Biomedical Literature. ACL (2) (2023)
Henry Cousins, Taryn Hall, Yinglong Guo, Luke Tso, Kathy T. H. Tzeng, Le Cong, Russ B. Altman
Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19. Bioinform. 39 (1) (2023)
Tianyun Liu, Shiyin Wang, Michael Wornow, Russ B. Altman
Construction of disease-specific cytokine profiles by associating disease genes with immune responses. PLoS Comput. Biol. 18 (4) (2022)
Daniel N. Sosa, Malavika Suresh, Christopher Potts, Russ B. Altman
Detecting Contradictory COVID-19 Drug Efficacy Claims from Biomedical Literature. CoRR (2022)
Daniel N. Sosa, Russ B. Altman
Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference. Briefings Bioinform. 23 (4) (2022)
Lu Yang, Sheng Wang, Russ B. Altman
POPDx: An Automated Framework for Patient Phenotyping across 392, 246 Individuals in the UK Biobank Study. CoRR (2022)
Margaret G. Guo, Daniel N. Sosa, Russ B. Altman
Challenges and opportunities in network-based solutions for biological questions. Briefings Bioinform. 23 (1) (2022)
Mike Wong, Paul Previde, Jack Cole, Brook Thomas, Nayana Laxmeshwar, Emily K. Mallory, Jake Lever, Dragutin Petkovic, Russ B. Altman, Anagha Kulkarni
Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive. J. Biomed. Informatics 117 (2021)
Daniel N. Sosa, Binbin Chen, Amit Kaushal, Adam Lavertu, Jake Lever, Stefano E. Rensi, Russ B. Altman
Repurposing biomedical informaticians for COVID-19. J. Biomed. Informatics 115 (2021)
Raphael J. L. Townshend, Martin Vögele, Patricia Suriana, Alexander Derry, Alexander Powers, Yianni Laloudakis, Sidhika Balachandar, Bowen Jing, Brandon M. Anderson, Stephan Eismann, Risi Kondor, Russ B. Altman, Ron O. Dror
ATOM3D: Tasks on Molecules in Three Dimensions. NeurIPS Datasets and Benchmarks (2021)
Emily R. Flynn, Annie Chang, Russ B. Altman
Large-scale labeling and assessment of sex bias in publicly available expression data. BMC Bioinform. 22 (1) (2021)
Andre Kumar, Rachael C. Aikens, Jason Horn, Lisa Shieh, Mark A. Musen, Michael Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen
Randomized user testing of recommender system clinical decision support. AMIA (2021)
Gregory McInnes, Russ B. Altman
Drug Response Pharmacogenetics for 200, 000 UK Biobank Participants. PSB (2021)
Lichy Han, Zahra N. Sayyid, Russ B. Altman
Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease. PLoS Comput. Biol. 17 (2) (2021)
Emily K. Mallory, Matthieu de Rochemonteix, Alexander Ratner, Ambika Acharya, Christopher Ré, Roselie A. Bright, Russ B. Altman
Extracting chemical reactions from text using Snorkel. BMC Bioinform. 21 (1) (2020)
Gregory McInnes, Rachel Dalton, Katrin Sangkuhl, Michelle Whirl Carrillo, Seung-been Lee, Philip S. Tsao, Andrea Gaedigk, Russ B. Altman, Erica L. Woodahl
Transfer learning enables prediction of CYP2D6 haplotype function. PLoS Comput. Biol. 16 (11) (2020)
Yash Pershad, Margaret G. Guo, Russ B. Altman
Pathway and Network Embedding Methods for Prioritizing Psychiatric Drugs. PSB (2020)
Andre Kumar, Rachael C. Aikens, Jason Hom, Lisa Shieh, Jonathan Chiang, David Morales, Divya Saini, Mark A. Musen, Michael T. M. Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen
OrderRex clinical user testing: a randomized trial of recommender system decision support on simulated cases. J. Am. Medical Informatics Assoc. 27 (12) (2020)
Kun-Hsing Yu, Feiran Wang, Gerald J. Berry, Christopher Ré, Russ B. Altman, Michael Snyder, Isaac S. Kohane
Classifying non-small cell lung cancer types and transcriptomic subtypes using convolutional neural networks. J. Am. Medical Informatics Assoc. 27 (5) (2020)
Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Marylyn D. Ritchie, Tiffany Murray, Teri E. Klein
Biocomputing 2021: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2021 PSB (2020)
Daniel N. Sosa, Alexander Derry, Margaret G. Guo, Eric Wei, Connor Brinton, Russ B. Altman
A Literature-Based Knowledge Graph Embedding Method for Identifying Drug RepurposingOpportunities in Rare Diseases. PSB (2020)
Sheng Wang, Emily R. Flynn, Russ B. Altman
Gaussian embedding for large-scale gene set analysis. Nat. Mach. Intell. 2 (7) (2020)
Jake Lever, Julia M. Barbarino, Li Gong, Rachel Huddart, Katrin Sangkuhl, Ryan Whaley, Michelle Whirl Carrillo, Mark Woon, Teri E. Klein, Russ B. Altman
PGxMine: Text Mining for Curation of PharmGKB. PSB (2020)
Raphael J. L. Townshend, Martin Vögele, Patricia Suriana, Alexander Derry, Alexander Powers, Yianni Laloudakis, Sidhika Balachandar, Brandon M. Anderson, Stephan Eismann, Risi Kondor, Russ B. Altman, Ron O. Dror
ATOM3D: Tasks On Molecules in Three Dimensions. CoRR (2020)
Wen Torng, Russ B. Altman
Graph Convolutional Neural Networks for Predicting Drug-Target Interactions. J. Chem. Inf. Model. 59 (10) (2019)
Yu-Chen Lo, Tianyun Liu, Kari M. Morrissey, Satoko Kakiuchi-Kiyota, Adam R. Johnson, Fabio Broccatelli, Yu Zhong, Amita Joshi, Russ B. Altman
Computational analysis of kinase inhibitor selectivity using structural knowledge. Bioinform. 35 (2) (2019)
Kun-Hsing Yu, Feiran Wang, Gerald J. Berry, Christopher Ré, Russ B. Altman, Michael Snyder, Isaac S. Kohane
Classifying Non-Small Cell Lung Cancer Histopathology Types and Transcriptomic Subtypes using Convolutional Neural Networks. AMIA (2019)
Jennifer L. Wilson, Mike Wong, Ajinkya Chalke, Nicholas Stepanov, Dragutin Petkovic, Russ B. Altman
PathFXweb: a web application for identifying drug safety and efficacy phenotypes. Bioinform. 35 (21) (2019)
Adam Lavertu, Russ B. Altman
RedMed: Extending drug lexicons for social media applications. J. Biomed. Informatics 99 (2019)
Sheng Wang, Emily R. Flynn, Russ B. Altman
GRep: Gene Set Representation via Gaussian Embedding. RECOMB (2019)
Wen Torng, Russ B. Altman
High precision protein functional site detection using 3D convolutional neural networks. Bioinform. 35 (9) (2019)
Kun-Hsing Yu, Gerald J. Berry, Daniel L. Rubin, Christopher Ré, Russ B. Altman, Michael Snyder
Unraveling the Molecular Basis of Lung Adenocarcinoma Dedifferentiation and Prognosis by Integrating Omics and Histopathology. AMIA (2018)
Emily K. Mallory, Ambika Acharya, Stefano E. Rensi, Peter J Turnbaugh, Roselie A. Bright, Russ B. Altman
Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome. PSB (2018)
Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ B. Altman
PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development. PLoS Comput. Biol. 14 (12) (2018)
Bethany Percha, Yuhao Zhang, Selen Bozkurt, Daniel L. Rubin, Russ B. Altman, Curtis P. Langlotz
Expanding a radiology lexicon using contextual patterns in radiology reports. J. Am. Medical Informatics Assoc. 25 (6) (2018)
Bethany Percha, Russ B. Altman
A global network of biomedical relationships derived from text. Bioinform. 34 (15) (2018)
Weizhuang Zhou, Russ B. Altman
Data-driven human transcriptomic modules determined by independent component analysis. BMC Bioinform. 19 (1) (2018)
Paul Previde, Brook Thomas, Mike Wong, Emily K. Mallory, Dragutin Petkovic, Russ B. Altman, Anagha Kulkarni
GeneDive: A gene interaction search and visualization tool to facilitate precision medicine. PSB (2018)
Lichy Han, Mateusz Maciejewski, Christoph Brockel, William Gordon, Scott B. Snapper, Joshua R. Korzenik, Lovisa Afzelius, Russ B. Altman
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease. Bioinform. 34 (6) (2018)
Dragutin Petkovic, Russ B. Altman, Mike Wong, Arthur Vigil
Improving the explainability of Random Forest classifier - user centered approach. PSB (2018)
Stefano E. Rensi, Russ B. Altman
Shallow Representation Learning via Kernel PCA Improves QSAR Modelability. J. Chem. Inf. Model. 57 (8) (2017)
Weizhuang Zhou, Lichy Han, Russ B. Altman
Imputing gene expression to maximize platform compatibility. Bioinform. 33 (4) (2017)
Kun-Hsing Yu, Ce Zhang, Gerald J. Berry, Russ B. Altman, Christopher Ré, Daniel L. Rubin, Michael Snyder
Predicting Non-Small Cell Lung Cancer Diagnosis and Prognosis by Fully Automated Microscopic Pathology Image Features. AMIA (2017)
Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Lester W. Mackey, Russ B. Altman
Predicting inpatient clinical order patterns with probabilistic topic models vs conventional order sets. J. Am. Medical Informatics Assoc. 24 (3) (2017)
Muthuraman Alagappan, Mary K. Goldstein, Steven M. Asch, Russ B. Altman, Jonathan H. Chen
Decaying Relevance of Clinical Data when Predicting Future Decisions. CRI (2017)
Wen Torng, Russ B. Altman
3D deep convolutional neural networks for amino acid environment similarity analysis. BMC Bioinform. 18 (1) (2017)
Lichy Han, Robert Ball, Carol A. Pamer, Russ B. Altman, Scott Proestel
Development of an automated assessment tool for MedWatch reports in the FDA adverse event reporting system. J. Am. Medical Informatics Assoc. 24 (5) (2017)
Jonathan H. Chen, Muthuraman Alagappan, Mary K. Goldstein, Steven M. Asch, Russ B. Altman
Decaying relevance of clinical data towards future decisions in data-driven inpatient clinical order sets. Int. J. Medical Informatics 102 (2017)
Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman
Usability of an Automated Recommender System for Clinical Order Entry. AMIA (2016)
Emily K. Mallory, Ce Zhang, Christopher Ré, Russ B. Altman
Large-scale extraction of gene interactions from full-text literature using DeepDive. Bioinform. 32 (1) (2016)
Yong Fuga Li, Fuxiao Xin, Russ B. Altman
Separating the Causes and Consequences in Disease Transcriptome. PSB (2016)
Anthony E. Solomonides, Russ B. Altman, Joshua C. Denny, Larry Ozeran, Jessica D. Tenenbaum
The Many Meanings of Precision Medicine. CRI (2016)
Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Lester W. Mackey, Russ B. Altman
Automated Organization of Electronic Health Record Data by Probabilistic Topic Modeling to Inform Clinical Decision Making. CRI (2016)
Russ B. Altman
Current Progress in Bioinformatics 2016. Briefings Bioinform. 17 (1) (2016)
Steven C. Bagley, Russ B. Altman
Computing disease incidence, prevalence and comorbidity from electronic medical records. J. Biomed. Informatics 63 (2016)
Steven C. Bagley, Marina Sirota, Richard O. Chen, Atul J. Butte, Russ B. Altman
Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput. Biol. 12 (4) (2016)
Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman
Dynamically Evolving Clinical Practices and Implications for Predicting Medical Decisions. PSB (2016)
Sara Hillenmeyer, Lea K. Davis, Eric R. Gamazon, Edwin H. Cook Jr., Nancy J. Cox, Russ B. Altman
STAMS: STRING-assisted module search for genome wide association studies and application to autism. Bioinform. 32 (24) (2016)
Jonathan H. Chen, Tanya Podchiyska, Russ B. Altman
OrderRex: clinical order decision support and outcome predictions by data-mining electronic medical records. J. Am. Medical Informatics Assoc. 23 (2) (2016)
Amanda Miguel, Jen Hsin, Tianyun Liu, Grace W. Tang, Russ B. Altman, Kerwyn Casey Huang
Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species. PLoS Comput. Biol. 11 (3) (2015)
Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Kevin Bretonnel Cohen, Elizabeth Wethington, Carsten Görg, Lawrence E. Hunter, Spencer V. Muse, Predrag Radivojac, Jason H. Moore
Training the Next Generation of Quantitative Biologists in the Era of Big Data. Pacific Symposium on Biocomputing (2015)
Bethany Percha, Russ B. Altman
Learning the Structure of Biomedical Relationships from Unstructured Text. PLoS Comput. Biol. 11 (7) (2015)
Weizhuang Zhou, Grace W. Tang, Russ B. Altman
High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE. J. Chem. Inf. Model. 55 (8) (2015)
Tianyun Liu, Russ B. Altman
Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. J. Chem. Inf. Model. 55 (7) (2015)
Darla Hewett, Michelle Whirl Carrillo, Lawrence E. Hunter, Russ B. Altman, Teri E. Klein
A Twentieth Anniversary Tribute to PSB. Pacific Symposium on Biocomputing (2015)
Omri Mugzach, Mor Peleg, Steven C. Bagley, Stephen J. Guter, Edwin H. Cook Jr., Russ B. Altman
An ontology for Autism Spectrum Disorder (ASD) to infer ASD phenotypes from Autism Diagnostic Interview-Revised data. J. Biomed. Informatics 56 (2015)
Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Lawrence E. Hunter, David A. Ross, James A. Foster, Jason H. Moore
Building the Next Generation of Quantitative Biologists. Pacific Symposium on Biocomputing (2014)
Grace W. Tang, Russ B. Altman
Knowledge-based Fragment Binding Prediction. PLoS Comput. Biol. 10 (4) (2014)
Jonathan H. Chen, Russ B. Altman
"Doctors who ordered this also ordered..." Automated physician order recommendations and outcome predictions by data-mining electronic medical records. AMIA (2014)
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
PATH-SCAN: A Reporting Tool for Identifying Clinically Actionable Variants. Pacific Symposium on Biocomputing (2014)
Andrey Rzhetsky, Steven C. Bagley, Kanix Wang, Christopher S. Lyttle, Edwin H. Cook Jr., Russ B. Altman, Robert D. Gibbons
Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability. PLoS Comput. Biol. 10 (3) (2014)
Russ B. Altman, Cheng Che Chen, William B. Poland, Jaswinder Pal Singh
Probabilistic Constraint Satisfaction with Non-Gaussian Noise CoRR (2013)
Omri Mugzach, Mor Peleg, Steven C. Bagley, Russ B. Altman
Expanding the Autism Ontology to DSM-IV Criteria. AMIA (2013)
Ryen W. White, Nicholas P. Tatonetti, Nigam H. Shah, Russ B. Altman, Eric Horvitz
Web-scale pharmacovigilance: listening to signals from the crowd. J. Am. Medical Informatics Assoc. 20 (3) (2013)
Guy Haskin Fernald, Russ B. Altman
Using Molecular Features of Xenobiotics to Predict Hepatic Gene Expression Response. J. Chem. Inf. Model. 53 (10) (2013)
Kai J. Kohlhoff, Vijay S. Pande, Russ B. Altman
K-Means for Parallel Architectures Using All-Prefix-Sum Sorting and Updating Steps. IEEE Trans. Parallel Distributed Syst. 24 (8) (2013)
Bethany Percha, Russ B. Altman
Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. AMIA (2013)
Nicholas P. Tatonetti, Joshua C. Denny, Russ B. Altman
. J. Am. Medical Informatics Assoc. 20 (3) (2013)
Russ B. Altman
A Probabilistic Algorithm for Calculating Structure: Borrowing from Simulated Annealing CoRR (2013)
Konrad J. Karczewski, Robert P. Tirrell, Pablo Cordero, Nicholas P. Tatonetti, Joel T. Dudley, Keyan Salari, Michael Snyder, Russ B. Altman, Stuart K. Kim
Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine. Pacific Symposium on Biocomputing (2012)
Nicholas P. Tatonetti, Guy Haskin Fernald, Russ B. Altman
A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J. Am. Medical Informatics Assoc. 19 (1) (2012)
Russ B. Altman
Introduction to Translational Bioinformatics Collection. PLoS Comput. Biol. 8 (12) (2012)
Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman
The state of the art in text mining and natural language processing for pharmacogenomics. J. Biomed. Informatics 45 (5) (2012)
Russ B. Altman
Editorial: Current progress in Bioinformatics 2012. Briefings Bioinform. 13 (4) (2012)
Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, Russ B. Altman
Using ODIN for a PharmGKB revalidation experiment. Database J. Biol. Databases Curation 2012 (2012)
Bethany Percha, Yael Garten, Russ B. Altman
Discovery and Explanation of Drug-Drug Interactions via Text Mining. Pacific Symposium on Biocomputing (2012)
Scott L. Delp, Joy P. Ku, Vijay S. Pande, Michael A. Sherman, Russ B. Altman
Simbios: an NIH national center for physics-based simulation of biological structures. J. Am. Medical Informatics Assoc. 19 (2) (2012)
Marylyn D. Ritchie, Nancy J. Cox, Cheng Cheng, Scott Weiss, Teri E. Klein, Russ B. Altman
Systems Pharmacogenomics-Bridging the Gap. Pacific Symposium on Biocomputing (2012)
Konrad J. Karczewski, Roxana Daneshjou, Russ B. Altman
Chapter 7: Pharmacogenomics. PLoS Comput. Biol. 8 (12) (2012)
Emidio Capriotti, Russ B. Altman
Improving the prediction of disease-related variants using protein three-dimensional structure. BMC Bioinform. 12 (S-4) (2011)
Samuel Coulbourn Flores, Michael A. Sherman, Christopher M. Bruns, Peter K. Eastman, Russ B. Altman
Fast Flexible Modeling of RNA Structure Using Internal Coordinates. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (5) (2011)
Samuel Coulbourn Flores, Russ B. Altman
Structural insights into Pre-Translocation Ribosome Motions. Pacific Symposium on Biocomputing (2011)

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Publication Activity (10 Years)

Top Topics

Top Venues

Russ B. Altman