Russ B. Altman
Orcid: 0000-0003-3859-2905Affiliations:
- Stanford University, CA, USA
According to our database1,
Russ B. Altman
authored at least 207 papers
between 1986 and 2024.
Collaborative distances:
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Bibliography
2024
CoRR, 2024
2023
Associating biological context with protein-protein interactions through text mining at PubMed scale.
J. Biomed. Informatics, September, 2023
POPDx: an automated framework for patient phenotyping across 392 246 individuals in the UK Biobank study.
J. Am. Medical Informatics Assoc., January, 2023
Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19.
Bioinform., January, 2023
Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers), 2023
2022
Construction of disease-specific cytokine profiles by associating disease genes with immune responses.
PLoS Comput. Biol., 2022
Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference.
Briefings Bioinform., 2022
Briefings Bioinform., 2022
2021
Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease.
PLoS Comput. Biol., 2021
Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive.
J. Biomed. Informatics, 2021
Large-scale labeling and assessment of sex bias in publicly available expression data.
BMC Bioinform., 2021
Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021
Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks 1, 2021
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
2020
PLoS Comput. Biol., November, 2020
Classifying non-small cell lung cancer types and transcriptomic subtypes using convolutional neural networks.
J. Am. Medical Informatics Assoc., 2020
OrderRex clinical user testing: a randomized trial of recommender system decision support on simulated cases.
J. Am. Medical Informatics Assoc., 2020
A Literature-Based Knowledge Graph Embedding Method for Identifying Drug RepurposingOpportunities in Rare Diseases.
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020
Biocomputing 2021: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2021
, 2020
2019
J. Chem. Inf. Model., 2019
J. Biomed. Informatics, 2019
Bioinform., 2019
High precision protein functional site detection using 3D convolutional neural networks.
Bioinform., 2019
Bioinform., 2019
Proceedings of the Research in Computational Molecular Biology, 2019
Classifying Non-Small Cell Lung Cancer Histopathology Types and Transcriptomic Subtypes using Convolutional Neural Networks.
Proceedings of the AMIA 2019, 2019
2018
PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development.
PLoS Comput. Biol., 2018
J. Am. Medical Informatics Assoc., 2018
Data-driven human transcriptomic modules determined by independent component analysis.
BMC Bioinform., 2018
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease.
Bioinform., 2018
GeneDive: A gene interaction search and visualization tool to facilitate precision medicine.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018
Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018
Unraveling the Molecular Basis of Lung Adenocarcinoma Dedifferentiation and Prognosis by Integrating Omics and Histopathology.
Proceedings of the AMIA 2018, 2018
2017
J. Chem. Inf. Model., August, 2017
Development of an automated assessment tool for MedWatch reports in the FDA adverse event reporting system.
J. Am. Medical Informatics Assoc., 2017
Predicting inpatient clinical order patterns with probabilistic topic models vs conventional order sets.
J. Am. Medical Informatics Assoc., 2017
Decaying relevance of clinical data towards future decisions in data-driven inpatient clinical order sets.
Int. J. Medical Informatics, 2017
3D deep convolutional neural networks for amino acid environment similarity analysis.
BMC Bioinform., 2017
Proceedings of the Summit on Clinical Research Informatics, 2017
Predicting Non-Small Cell Lung Cancer Diagnosis and Prognosis by Fully Automated Microscopic Pathology Image Features.
Proceedings of the AMIA 2017, 2017
2016
Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.
PLoS Comput. Biol., 2016
Computing disease incidence, prevalence and comorbidity from electronic medical records.
J. Biomed. Informatics, 2016
OrderRex: clinical order decision support and outcome predictions by data-mining electronic medical records.
J. Am. Medical Informatics Assoc., 2016
Large-scale extraction of gene interactions from full-text literature using DeepDive.
Bioinform., 2016
STAMS: STRING-assisted module search for genome wide association studies and application to autism.
Bioinform., 2016
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
Dynamically Evolving Clinical Practices and Implications for Predicting Medical Decisions.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
Proceedings of the Summit on Clinical Research Informatics, 2016
Automated Organization of Electronic Health Record Data by Probabilistic Topic Modeling to Inform Clinical Decision Making.
Proceedings of the Summit on Clinical Research Informatics, 2016
Proceedings of the AMIA 2016, 2016
2015
PLoS Comput. Biol., 2015
Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species.
PLoS Comput. Biol., 2015
High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE.
J. Chem. Inf. Model., 2015
Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach.
J. Chem. Inf. Model., 2015
An ontology for Autism Spectrum Disorder (ASD) to infer ASD phenotypes from Autism Diagnostic Interview-Revised data.
J. Biomed. Informatics, 2015
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015
2014
Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability.
PLoS Comput. Biol., 2014
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014
"Doctors who ordered this also ordered..." Automated physician order recommendations and outcome predictions by data-mining electronic medical records.
Proceedings of the AMIA 2014, 2014
2013
IEEE Trans. Parallel Distributed Syst., 2013
J. Chem. Inf. Model., 2013
J. Am. Medical Informatics Assoc., 2013
Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden <i>et al</i>.
J. Am. Medical Informatics Assoc., 2013
Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics.
Proceedings of the AMIA 2013, 2013
2012
The state of the art in text mining and natural language processing for pharmacogenomics.
J. Biomed. Informatics, 2012
A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports.
J. Am. Medical Informatics Assoc., 2012
Simbios: an NIH national center for physics-based simulation of biological structures.
J. Am. Medical Informatics Assoc., 2012
Database J. Biol. Databases Curation, 2012
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
2011
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding.
PLoS Comput. Biol., 2011
J. Am. Medical Informatics Assoc., 2011
Improving the prediction of disease-related variants using protein three-dimensional structure.
BMC Bioinform., 2011
Integration and publication of heterogeneous text-mined relationships on the Semantic Web.
J. Biomed. Semant., 2011
Bioinform., 2011
Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011
2010
Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance.
PLoS Comput. Biol., 2010
The utility of general purpose versus specialty clinical databases for research: Warfarin dose estimation from extracted clinical variables.
J. Biomed. Informatics, 2010
Independent component analysis: Mining microarray data for fundamental human gene expression modules.
J. Biomed. Informatics, 2010
J. Biomed. Informatics, 2010
An integrative method for scoring candidate genes from association studies: application to warfarin dosing.
BMC Bioinform., 2010
BMC Bioinform., 2010
Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug Relationships.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
2009
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.
BMC Bioinform., 2009
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
Bioinform., 2009
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
2008
IEEE ACM Trans. Comput. Biol. Bioinform., 2008
The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge.
Nucleic Acids Res., 2008
BMC Bioinform., 2008
Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition.
Proceedings of the Biocomputing 2008, 2008
Proceedings of the Proceeding of the 2nd International Workshop on Data and Text Mining in Bioinformatics, 2008
2007
PLoS Comput. Biol., 2007
J. Biomed. Informatics, 2007
Clustering protein environments for function prediction: finding PROSITE motifs in 3D.
BMC Bioinform., 2007
Extracting Subject Demographic Information From Abstracts of Randomized Clinical Trial Reports.
Proceedings of the MEDINFO 2007 - Proceedings of the 12th World Congress on Health (Medical) Informatics, 2007
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007
2006
PLoS Comput. Biol., 2006
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006
2005
Application of Information Technology: A Statistical Approach to Scanning the Biomedical Literature for Pharmacogenetics Knowledge.
J. Am. Medical Informatics Assoc., 2005
Research Paper: Using Petri Net Tools to Study Properties and Dynamics of Biological Systems.
J. Am. Medical Informatics Assoc., 2005
Challenges in Creating an Infrastructure for Physics-Based Simulation of Biological Structures.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
2004
White Paper: Training the Next Generation of Informaticians: The Impact of "BISTI" and Bioinformatics - A Report from the American College of Medical Informatics.
J. Am. Medical Informatics Assoc., 2004
Proceedings of the MEDINFO 2004, 2004
Modeling and Analyzing Biomedical Processes using Workflow/Petri Net Models and Tools.
Proceedings of the MEDINFO 2004, 2004
2003
WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures.
Nucleic Acids Res., 2003
Inclusion of Textual Documentation in the Analysis of Multidimensional Data Sets: Application to Gene Expression Data.
Mach. Learn., 2003
Recognizing Complex, Asymmetric Functional Sites in Protein Structures Using a Bayesian Scoring Function.
J. Bioinform. Comput. Biol., 2003
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).
Bioinform., 2003
Bioinform., 2003
Proceedings of The Twelfth Text REtrieval Conference, 2003
Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
2002
Qualitative models of molecular function: linking genetic polymorphisms of tRNA to their functional sequelae.
Proc. IEEE, 2002
J. Am. Medical Informatics Assoc., 2002
Nonparametric methods for identifying differentially expressed genes in microarray data.
Bioinform., 2002
Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XML.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002
Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002
Proceedings of the AMIA 2002, 2002
2001
Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances.
J. Comput. Biol., 2001
Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001
Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining, 2001
2000
Viewpoint: The Interactions Between Clinical Informatics and Bioinformatics: A Case Study.
J. Am. Medical Informatics Assoc., 2000
Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000
1999
J. Am. Medical Informatics Assoc., 1999
IEEE Intell. Syst., 1999
Using imperfect secondary structure predictions to improve molecular structure computations.
Bioinform., 1999
AI Mag., 1999
Biomolecular Structure Estimation: A Case Study of Irregular Hierarchical Parallelism.
Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific Computing, 1999
1998
J. Comput. Biol., 1998
Proceedings of the 5th International Workshop on Knowledge Represenation Meets Databases (KRDB '98): Innovative Application Programming and Query Interfaces, 1998
Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998
Proceedings of the CHI 98 Conference Summary on Human Factors in Computing Systems, 1998
Proceedings of the AMIA 1998, 1998
Proceedings of the AMIA 1998, 1998
1997
RIBOWEB: Linking Structural Computations to a Knowledge Base of Published Experimental Data.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997
Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997
1996
Comput. Appl. Biosci., 1996
Proceedings of the 1996 ACM/IEEE Conference on Supercomputing, 1996
1995
A probabilistic approach to determining biological structure: integrating uncertain data sources.
Int. J. Hum. Comput. Stud., 1995
Comput. Appl. Biosci., 1995
Reuse with PROTÉgÉ-II: From Elevators to Ribosomes.
Proceedings of the ACM SIGSOFT Symposium on Software Reusability, 1995
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995
1994
Proceedings of the UAI '94: Proceedings of the Tenth Annual Conference on Uncertainty in Artificial Intelligence, 1994
Proceedings of the Proceedings Supercomputing '94, 1994
Constraint Satisfaction Techniques for Modeling Large Complexes: Application to the Central Domain of 16S Ribosomal RNA.
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994
1993
A Probabilistic Algorithm for Calculating Structure: Borrowing from Simulated Annealing.
Proceedings of the UAI '93: Proceedings of the Ninth Annual Conference on Uncertainty in Artificial Intelligence, 1993
Probabilistic Structure Calculations: A Three-Dimensional tRNA Structure from Sequence Correlation Data.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993
1988
Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562.
J. Chem. Inf. Comput. Sci., 1988
1987
Proceedings of the 6th National Conference on Artificial Intelligence. Seattle, 1987
1986
Proceedings of the 5th National Conference on Artificial Intelligence. Philadelphia, 1986