Russ B. Altman

According to our database1, Russ B. Altman authored at least 172 papers between 1986 and 2018.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Other 

Links

On csauthors.net:

Bibliography

2018
Expanding a radiology lexicon using contextual patterns in radiology reports.
JAMIA, 2018

Data-driven human transcriptomic modules determined by independent component analysis.
BMC Bioinformatics, 2018

A global network of biomedical relationships derived from text.
Bioinformatics, 2018

A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease.
Bioinformatics, 2018

2017
Development of an automated assessment tool for MedWatch reports in the FDA adverse event reporting system.
JAMIA, 2017

Predicting inpatient clinical order patterns with probabilistic topic models vs conventional order sets.
JAMIA, 2017

Decaying relevance of clinical data towards future decisions in data-driven inpatient clinical order sets.
I. J. Medical Informatics, 2017

3D deep convolutional neural networks for amino acid environment similarity analysis.
BMC Bioinformatics, 2017

Imputing gene expression to maximize platform compatibility.
Bioinformatics, 2017

Decaying Relevance of Clinical Data when Predicting Future Decisions.
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 Computational Biology, 2016

Computing disease incidence, prevalence and comorbidity from electronic medical records.
Journal of Biomedical Informatics, 2016

OrderRex: clinical order decision support and outcome predictions by data-mining electronic medical records.
JAMIA, 2016

Large-scale extraction of gene interactions from full-text literature using DeepDive.
Bioinformatics, 2016

STAMS: STRING-assisted module search for genome wide association studies and application to autism.
Bioinformatics, 2016

Current Progress in Bioinformatics 2016.
Briefings in Bioinformatics, 2016

Separating the Causes and Consequences in Disease Transcriptome.
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

The Many Meanings of Precision Medicine.
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

Usability of an Automated Recommender System for Clinical Order Entry.
Proceedings of the AMIA 2016, 2016

2015
Learning the Structure of Biomedical Relationships from Unstructured Text.
PLoS Computational Biology, 2015

Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species.
PLoS Computational Biology, 2015

High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE.
Journal of Chemical Information and Modeling, 2015

Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach.
Journal of Chemical Information and Modeling, 2015

An ontology for Autism Spectrum Disorder (ASD) to infer ASD phenotypes from Autism Diagnostic Interview-Revised data.
Journal of Biomedical Informatics, 2015

Training the Next Generation of Quantitative Biologists in the Era of Big Data.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

A Twentieth Anniversary Tribute to PSB.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014
Knowledge-based Fragment Binding Prediction.
PLoS Computational Biology, 2014

Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability.
PLoS Computational Biology, 2014

Building the Next Generation of Quantitative Biologists.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

PATH-SCAN: A Reporting Tool for Identifying Clinically Actionable Variants.
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
K-Means for Parallel Architectures Using All-Prefix-Sum Sorting and Updating Steps.
IEEE Trans. Parallel Distrib. Syst., 2013

Using Molecular Features of Xenobiotics to Predict Hepatic Gene Expression Response.
Journal of Chemical Information and Modeling, 2013

Web-scale pharmacovigilance: listening to signals from the crowd.
JAMIA, 2013

Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al.
JAMIA, 2013

A Probabilistic Algorithm for Calculating Structure: Borrowing from Simulated Annealing
CoRR, 2013

Probabilistic Constraint Satisfaction with Non-Gaussian Noise
CoRR, 2013

Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics.
Proceedings of the AMIA 2013, 2013

Expanding the Autism Ontology to DSM-IV Criteria.
Proceedings of the AMIA 2013, 2013

2012
Chapter 7: Pharmacogenomics.
PLoS Computational Biology, 2012

Introduction to Translational Bioinformatics Collection.
PLoS Computational Biology, 2012

The state of the art in text mining and natural language processing for pharmacogenomics.
Journal of Biomedical Informatics, 2012

A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports.
JAMIA, 2012

Simbios: an NIH national center for physics-based simulation of biological structures.
JAMIA, 2012

Using ODIN for a PharmGKB revalidation experiment.
Database, 2012

Editorial: Current progress in Bioinformatics 2012.
Briefings in Bioinformatics, 2012

Systems Pharmacogenomics-Bridging the Gap.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Discovery and Explanation of Drug-Drug Interactions via Text Mining.
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
Fast Flexible Modeling of RNA Structure Using Internal Coordinates.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding.
PLoS Computational Biology, 2011

2010 Translational bioinformatics year in review.
JAMIA, 2011

Improving the prediction of disease-related variants using protein three-dimensional structure.
BMC Bioinformatics, 2011

Integration and publication of heterogeneous text-mined relationships on the Semantic Web.
J. Biomedical Semantics, 2011

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.
Bioinformatics, 2011

Bioinformatics challenges for personalized medicine.
Bioinformatics, 2011

Genome Analysis.
Bioinformatics [ISMB/ECCB], 2011

Structural insights into Pre-Translocation Ribosome Motions.
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 Computational Biology, 2010

The utility of general purpose versus specialty clinical databases for research: Warfarin dose estimation from extracted clinical variables.
Journal of Biomedical Informatics, 2010

Independent component analysis: Mining microarray data for fundamental human gene expression modules.
Journal of Biomedical Informatics, 2010

Using text to build semantic networks for pharmacogenomics.
Journal of Biomedical Informatics, 2010

An integrative method for scoring candidate genes from association studies: application to warfarin dosing.
BMC Bioinformatics, 2010

Content-based microarray search using differential expression profiles.
BMC Bioinformatics, 2010

Editorial: Current progress in Bioinformatics 2010.
Briefings in Bioinformatics, 2010

Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug Relationships.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Predicting RNA Structure by Multiple Template Homology Modeling.
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 Bioinformatics, 2009

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
Bioinformatics, 2009

Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

A General Framework for Dose Optimization.
Proceedings of the AMIA 2009, 2009

2008
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops.
IEEE/ACM Trans. Comput. Biology Bioinform., 2008

The Simbios National Center: Systems Biology in Motion.
Proceedings of the IEEE, 2008

The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge.
Nucleic Acids Research, 2008

MScanner: a classifier for retrieving Medline citations.
BMC Bioinformatics, 2008

M-BISON: Microarray-based integration of data sources using networks.
BMC Bioinformatics, 2008

Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition.
Proceedings of the Biocomputing 2008, 2008

Text mining for pharmacogenomics.
Proceedings of the Proceeding of the 2nd International Workshop on Data and Text Mining in Bioinformatics, 2008

2007
The International Society for Computational Biology 10th Anniversary.
PLoS Computational Biology, 2007

Biomedical informatics training at Stanford in the 21st century.
Journal of Biomedical Informatics, 2007

Clustering protein environments for function prediction: finding PROSITE motifs in 3D.
BMC Bioinformatics, 2007

Current progress in bioinformatics 2007.
Briefings in Bioinformatics, 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

Combining Simulation and Machine Learning to Recognize Function in 4D.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007

2006
Correction: Time to Organize the Bioinformatics Resourceome.
PLoS Computational Biology, 2006

Choosing Snps Using Feature Selection.
J. Bioinformatics and Computational Biology, 2006

Annual Progress in Bioinformatics 2006.
Briefings in Bioinformatics, 2006

Physics-based simulation of biological structures.
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006

2005
Time to Organize the Bioinformatics Resourceome.
PLoS Computational Biology, 2005

Biomedical term mapping databases.
Nucleic Acids Research, 2005

Application of Information Technology: A Statistical Approach to Scanning the Biomedical Literature for Pharmacogenetics Knowledge.
JAMIA, 2005

Research Paper: Using Petri Net Tools to Study Properties and Dynamics of Biological Systems.
JAMIA, 2005

Editorial: Annual progress in bioinformatics.
Briefings in Bioinformatics, 2005

Preface.
Proceedings of the Biocomputing 2005, 2005

Choosing SNPs Using Feature Selection.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 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.
JAMIA, 2004

Tools for loading MEDLINE into a local relational database.
BMC Bioinformatics, 2004

GAPSCORE: finding gene and protein names one word at a time.
Bioinformatics, 2004

Editorial: Building successful biological databases.
Briefings in Bioinformatics, 2004

Preface.
Proceedings of the Biocomputing 2004, 2004

A Resource to Acquire and Summarize Pharmacogenetics Knowledge in the Literature.
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
Complexities of Managing Biomedical Information.
OMICS, 2003

WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures.
Nucleic Acids Research, 2003

Inclusion of Textual Documentation in the Analysis of Multidimensional Data Sets: Application to Gene Expression Data.
Machine Learning, 2003

Recognizing Complex, Asymmetric Functional Sites in Protein Structures Using a Bayesian Scoring Function.
J. Bioinformatics and Computational Biology, 2003

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).
Bioinformatics, 2003

A literature-based method for assessing the functional coherence of a gene group.
Bioinformatics, 2003

MutDB: annotating human variation with functionally relevant data.
Bioinformatics, 2003

Edinburgh-Stanford TREC-2003 Genomics Track.
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

Special Paper - Introduction.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Preface.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

A Personalized and Automated dbSNP Surveillance System.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

Automatic Construction of 3D Structural Motifs for Protein Function Prediction.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
PharmGKB: the Pharmacogenetics Knowledge Base.
Nucleic Acids Research, 2002

Research Paper: Creating an Online Dictionary of Abbreviations from MEDLINE.
JAMIA, 2002

Emerging scientific applications in data mining.
Commun. ACM, 2002

Nonparametric methods for identifying differentially expressed genes in microarray data.
Bioinformatics, 2002

Modelling biological processes using workflow and Petri Net models.
Bioinformatics, 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

Ontology Development for a Pharmacogenetics Knowledge Base.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Preface.
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

Using binning to maintain confidentiality of medical data.
Proceedings of the AMIA 2002, 2002

2001
Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances.
Journal of Computational Biology, 2001

Challenges for Intelligent Systems in Biology.
IEEE Intelligent Systems, 2001

Missing value estimation methods for DNA microarrays.
Bioinformatics, 2001

Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

Including Biological Literature Improves Homology Search.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

ViewFeature: Integrated Feature Analysis and Visualization.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

Challenges for knowledge discovery in biology.
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.
JAMIA, 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

The new peer review.
Proceedings of the AMIA 2000, 2000

1999
Model Formulation: Automated Diagnosis of Data-Model Conflicts Using Metadata.
JAMIA, 1999

RiboWeb: An Ontology-Based System for Collaborative Molecular Biology.
IEEE Intelligent Systems, 1999

Using imperfect secondary structure predictions to improve molecular structure computations.
Bioinformatics, 1999

AI in Medicine: The Spectrum of Challenges from Managed Care to Molecular Medicine.
AI Magazine, 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
Hierarchical Organization of Molecular Structure Computations.
Journal of Computational Biology, 1998

Reuse, CORBA, and knowledge-based systems.
Int. J. Hum.-Comput. Stud., 1998

A curriculum for bioinformatics: the time is ripe.
Bioinformatics, 1998

The hierarchical organization of molecular structure computations.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

Sophia: Providing Basic Knowledge Services with a Common DBMS.
Proceedings of the 5th International Workshop on Knowledge Represenation Meets Databases (KRDB '98): Innovative Application Programming and Query Interfaces, 1998

A Surface Measure for Probabilistic Structural Computations.
Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

Graphical style sheets: towards reusable representations of biomedical graphics.
Proceedings of the CHI 98 Conference Summary on Human Factors in Computing Systems, 1998

Updating a bibliography using the related articles function within PubMed.
Proceedings of the AMIA 1998, 1998

MHCWeb: converting a WWW database into a knowledge-based collaborative environment.
Proceedings of the AMIA 1998, 1998

Bioinformatics in support of molecular medicine.
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
Constraining volume by matching the moments of a distance distribution.
Computer Applications in the Biosciences, 1996

Parallel Hierarchical Molecular Structure Estimation.
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

Using a measure of structural variation to define a core for the globins.
Computer Applications in the Biosciences, 1995

Reuse with PROTÉgÉ-II: From Elevators to Ribosomes.
SSR, 1995

Characterizing Oriented Protein Structural Sites Using Biochemical Properties.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

1994
Probabilistic Constraint Satisfaction with Non-Gaussian Noise.
Proceedings of the UAI '94: Proceedings of the Tenth Annual Conference on Uncertainty in Artificial Intelligence, 1994

Parallel protein structure determination from uncertain data.
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

Finding an Average Core Structure: Application to the Globins.
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.
Journal of Chemical Information and Computer Sciences, 1988

1987
Partial Compilation of Strategic Knowledge.
Proceedings of the 6th National Conference on Artificial Intelligence. Seattle, 1987

1986
PROTEAN: Deriving Protein Structure from Constraints.
Proceedings of the 5th National Conference on Artificial Intelligence. Philadelphia, 1986


  Loading...