Russ B. Altman - researchr alias

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2011

Biocomputing 2011: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, 3-7 January 2011Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein, editors, World Scientific Publishing, 2011.

2010 Translational bioinformatics year in reviewRuss B. Altman, Katharine S. Miller. jamia, 18(4):358-366, 2011. [doi]

Bioinformatics challenges for personalized medicineGuy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman. bioinformatics, 27(16):2323, 2011. [doi]

Genome AnalysisGuy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman. bioinformatics, 27(13):1741-1748, 2011. [doi]

Structural insights into Pre-Translocation Ribosome MotionsSamuel Coulbourn Flores, Russ B. Altman. psb 2011: 205-216 [doi]

Fast Flexible Modeling of RNA Structure Using Internal CoordinatesSamuel Coulbourn Flores, Michael Sherman, Christopher M. Bruns, Peter Eastman, Russ B. Altman. tcbb, 8(5):1247-1257, 2011. [doi]

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithmsKai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman. bioinformatics, 27(16):2321-2322, 2011. [doi]

2010

Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela, Hawaii, USA, 4-8 January 2010Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein, editors, World Scientific Publishing, 2010.

Editorial: Current progress in Bioinformatics 2010Russ B. Altman. bib, 11(1):1-2, 2010. [doi]

Using text to build semantic networks for pharmacogenomicsAdrien Coulet, Nigam H. Shah, Yael Garten, Mark A. Musen, Russ B. Altman. jbi, 43(6):1009-1019, 2010. [doi]

Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics ApplicationAdrien Coulet, Nigam H. Shah, Lawrence Hunter, Chitta Baral, Russ B. Altman. psb 2010: 485-487 [doi]

Independent component analysis: Mining microarray data for fundamental human gene expression modulesJesse M. Engreitz, Bernie J. Daigle Jr., Jonathan J. Marshall, Russ B. Altman. jbi, 43(6):932-944, 2010. [doi]

Content-based microarray search using differential expression profilesJesse M. Engreitz, Alexander A. Morgan, Joel Dudley, Rong Chen, Rahul Thathoo, Russ B. Altman, Atul J. Butte. bmcbi, 11:603, 2010. [doi]

Predicting RNA Structure by Multiple Template Homology ModelingSamuel Flores, Yaqi Wan, Rick Russell, Russ B. Altman. psb 2010: 216-227 [doi]

Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug RelationshipsYael Garten, Nicholas P. Tatonetti, Russ B. Altman. psb 2010: 305-314 [doi]

The utility of general purpose versus specialty clinical databases for research: Warfarin dose estimation from extracted clinical variablesHersh Sagreiya, Russ B. Altman. jbi, 43(5):747-751, 2010. [doi]

2009

Biocomputing 2009: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, 5-9 January 2009Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein, editors, 2009.

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full textYael Garten, Russ B. Altman. bmcbi, 10(S-2), 2009. [doi]

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural modelsMagdalena A. Jonikas, Randall J. Radmer, Russ B. Altman. bioinformatics, 25(24):3259-3266, 2009. [doi]

Proceeding of the 3rd International Workshop on Data and Text Mining in Bioinformatics, DTMBIO 2009, Hong Kong, China, November 6, 2009Doheon Lee, Russ B. Altman, Min Song, Jun Huan, editors, ACM, 2009.

Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune SystemShai Shen-Orr, Ofir Goldberger, Yael Garten, Yael Rosenberg-Hasson, Patricia A. Lovelace, David Hirschberg, Russ B. Altman, Mark M. Davis, Atul J. Butte. psb 2009: 439-450 [doi]

2008

Biocomputing 2008, Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, 4-8 January 2008Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein, editors, World Scientific, 2008.

Text mining for pharmacogenomicsRuss B. Altman. CIKM 2008: 1-2 [doi]

Combining Molecular Dynamics and Machine Learning to Improve Protein Function RecognitionDariya S. Glazer, Randall J. Radmer, Russ B. Altman. psb 2008: 332-343 [doi]

The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledgeTina Hernandez-Boussard, Michelle Whirl Carrillo, Joan M. Hebert, Li Gong, Ryan Owen, Mei Gong, Winston Gor, Feng Liu, Chuong Truong, Ryan Whaley, Mark Woon, Tina Zhou, Russ B. Altman, Teri E. Klein. nar, 36(Database-Issue):913-918, 2008. [doi]

M-BISON: Microarray-based integration of data sources using networksBernie J. Daigle Jr., Russ B. Altman. bmcbi, 9, 2008. [doi]

MScanner: a classifier for retrieving Medline citationsGraham L. Poulter, Daniel L. Rubin, Russ B. Altman, Cathal Seoighe. bmcbi, 9, 2008. [doi]

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein LoopsPeggy Yao, Ankur Dhanik, Nathan Marz, Ryan Propper, Charles Kou, Guanfeng Liu, Henry van den Bedem, Jean-Claude Latombe, Inbal Halperin-Landsberg, Russ B. Altman. tcbb, 5(4):534-545, 2008. [doi]

2007

Biocomputing 2007, Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3-7 January 2007Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein, editors, World Scientific, 2007.

Current progress in bioinformatics 2007Russ B. Altman. bib, 8(5):277-278, 2007. [doi]

Combining Simulation and Machine Learning to Recognize Function in 4DRuss B. Altman. bibm 2007: 3 [doi]

Biomedical informatics training at Stanford in the 21st centuryRuss B. Altman, Teri E. Klein. jbi, 40(1):55-58, 2007. [doi]

Extracting Subject Demographic Information From Abstracts of Randomized Clinical Trial ReportsRong Xu, Yael Garten, Kaustubh S. Supekar, Amar K. Das, Russ B. Altman, Alan M. Garber. medinfo 2007: 550-554 [doi]

Clustering protein environments for function prediction: finding PROSITE motifs in 3DSungroh Yoon, Jessica C. Ebert, Eui-Young Chung, Giovanni De Micheli, Russ B. Altman. bmcbi, 8(S-4), 2007. [doi]

2006

Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3-7 January 2006Russ B. Altman, Tiffany Murray, Teri E. Klein, A. Keith Dunker, Lawrence Hunter, editors, World Scientific, 2006.

Annual Progress in Bioinformatics 2006Russ B. Altman. bib, 7(3):209-210, 2006. [doi]

Physics-based simulation of biological structuresScott L. Delp, F. Clayton Anderson, Russ B. Altman. isbi 2006: 802-805 [doi]

Choosing Snps Using Feature SelectionTu Minh Phuong, Zhen Lin, Russ B. Altman. jbcb, 4(2):241-258, 2006. [doi]

2005

Biocomputing 2005, Proceedings of the Pacific Symposium, Hawaii, USA, 4-8 January 2005Russ B. Altman, Tiffany A. Jung, Teri E. Klein, A. Keith Dunker, Lawrence Hunter, editors, World Scientific, 2005.

PrefaceRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. psb 2005: [doi]

Editorial: Annual progress in bioinformaticsRuss B. Altman. bib, 6(1):4-5, 2005.

Challenges in Creating an Infrastructure for Physics-Based Simulation of Biological StructuresRuss B. Altman. csb 2005: 3 [doi]

Research Paper: Using Petri Net Tools to Study Properties and Dynamics of Biological SystemsMor Peleg, Daniel L. Rubin, Russ B. Altman. jamia, 12(2):181-199, 2005. [doi]

Choosing SNPs Using Feature SelectionTu Minh Phuong, Zhen Lin, Russ B. Altman. csb 2005: 301-309 [doi]

Application of Information Technology: A Statistical Approach to Scanning the Biomedical Literature for Pharmacogenetics KnowledgeDaniel L. Rubin, Caroline F. Thorn, Teri E. Klein, Russ B. Altman. jamia, 12(2):121-129, 2005. [doi]

Biomedical term mapping databasesJonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman. nar, 33(Database-Issue):289-293, 2005. [doi]

2004

2003

PrefaceRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. psb 2003: [doi]

Special Paper - IntroductionRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. psb 2003: 636-637 [doi]

Complexities of Managing Biomedical InformationRuss B. Altman. omics, 7(1):127-130, 2003. [doi]

Automated Construction of Structural Motifs for Predicting Functional Sites on Protein StructuresMike P. Liang, Douglas L. Brutlag, Russ B. Altman. psb 2003: 204-215 [doi]

Automatic Construction of 3D Structural Motifs for Protein Function PredictionMike P. Liang, Douglas L. Brutlag, Russ B. Altman. csb 2003: 613-614 [doi]

WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structuresMike P. Liang, D. Rey Banatao, Teri E. Klein, Douglas L. Brutlag, Russ B. Altman. nar, 31(13):3324-3327, 2003.

A Personalized and Automated dbSNP Surveillance SystemShuo Liu, Steve Lin, Mark Woon, Teri E. Klein, Russ B. Altman. csb 2003: 132-136 [doi]

MutDB: annotating human variation with functionally relevant dataSean D. Mooney, Russ B. Altman. bioinformatics, 19(14):1858-1860, 2003.

Edinburgh-Stanford TREC-2003 Genomics TrackMiles Osborne, Mark Cuminskey, Gail Sinclair, Matthew Smillie, Bonnie L. Webber, Jeffrey T. Chang, Nipun Mehra, Veronica Rotemberg, Russ B. Altman. trec 2003: 622-630 [doi]

Inclusion of Textual Documentation in the Analysis of Multidimensional Data Sets: Application to Gene Expression DataSoumya Raychaudhuri, Hinrich Schütze, Russ B. Altman. ml, 52(1-2):119-145, 2003. [doi]

A literature-based method for assessing the functional coherence of a gene groupSoumya Raychaudhuri, Russ B. Altman. bioinformatics, 19(3):396-401, 2003.

Recognizing Complex, Asymmetric Functional Sites in Protein Structures Using a Bayesian Scoring FunctionLiping Wei, Russ B. Altman. jbcb, 1(1):119-138, 2003. [doi]

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)Iwei Yeh, Peter D. Karp, Natalya Fridman Noy, Russ B. Altman. bioinformatics, 19(2):241-248, 2003.

2002

PrefaceRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. psb 2002: [doi]

Emerging scientific applications in data miningJiawei Han, Russ B. Altman, Vipin Kumar, Heikki Mannila, Daryl Pregibon. CACM, 45(8):54-58, 2002. [doi]

PharmGKB: the Pharmacogenetics Knowledge BaseMicheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, Teri E. Klein. nar, 30(1):163-165, 2002.

Ontology Development for a Pharmacogenetics Knowledge BaseDiane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, Russ B. Altman. psb 2002: 65-76 [doi]

Modelling biological processes using workflow and Petri Net modelsMor Peleg, Iwei Yeh, Russ B. Altman. bioinformatics, 18(6):825-837, 2002.

Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational modelsDaniel L. Rubin, Farhad Shafa, Diane E. Oliver, Micheal Hewett, Russ B. Altman. ismb 2002: 207-215

Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XMLDaniel L. Rubin, Micheal Hewett, Diane E. Oliver, Teri E. Klein, Russ B. Altman. psb 2002: 88-99 [doi]

2001

Challenges for Intelligent Systems in BiologyRuss B. Altman, Alfonso Valencia, Satoru Miyano, Shoba Ranganathan. expert, 16(6):14-20, 2001. [doi]

Challenges for knowledge discovery in biologyRuss B. Altman. kdd 2001: 2 [doi]

ViewFeature: Integrated Feature Analysis and VisualizationD. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, Teri E. Klein. psb 2001: 240-250 [doi]

Including Biological Literature Improves Homology SearchJeffrey T. Chang, Soumya Raychaudhuri, Russ B. Altman. psb 2001: 374-383 [doi]

Missing value estimation methods for DNA microarraysOlga G. Troyanskaya, Michael Cantor, Gavin Sherlock, Patrick O. Brown, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman. bioinformatics, 17(6):520-525, 2001.

Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological DatabasesAllison Waugh, Glenn A. Williams, Liping Wei, Russ B. Altman. psb 2001: 360-371 [doi]

Constrained Global Optimization for Estimating Molecular Structure from Atomic DistancesGlenn A. Williams, Jonathan M. Dugan, Russ B. Altman. jcb, 8(5):523-548, 2001.

2000

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, August 19-23, 2000, La Jolla / San Diego, CA, USAPhilip E. Bourne, Michael Gribskov, Russ B. Altman, Nancy Jensen, Debra A. Hope, Thomas Lengauer, Julie C. Mitchell, Eric D. Scheeff, Chris Smith, Shawn Strande, Helge Weissig, editors, AAAI, 2000.

Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis StrainsSoumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, Russ B. Altman. ismb 2000: 286-295

1999

AI in Medicine: The Spectrum of Challenges from Managed Care to Molecular MedicineRuss B. Altman. aim, 20(3):67-77, 1999.

Using imperfect secondary structure predictions to improve molecular structure computationsCheng-Che Chen, Jaswinder Pal Singh, Russ B. Altman. bioinformatics, 15(1):53-65, 1999.

Biomolecular Structure Estimation: A Case Study of Irregular Hierarchical ParallelismCheng-Che Chen, Jaswinder Pal Singh, Russ B. Altman. ppsc 1999:

1998

1997

Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal DataRuss B. Altman, Neil F. Abernethy, Richard O. Chen. ismb 1997: 15-24

RIBOWEB: Linking Structural Computations to a Knowledge Base of Published Experimental DataRichard O. Chen, Ramon M. Felciano, Russ B. Altman. ismb 1997: 84-87

1996

Constraining volume by matching the moments of a distance distributionCheng-Che Chen, Richard O. Chen, Russ B. Altman. bioinformatics, 12(4):319-326, 1996.

1995

1994

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, August 14-17, 1994, Stanford University, Stanford, California, USARuss B. Altman, Douglas L. Brutlag, Peter D. Karp, Richard H. Lathrop, David B. Searls, editors, AAAI, 1994.

Finding an Average Core Structure: Application to the GlobinsRuss B. Altman, Mark Gerstein. ismb 1994: 19-27

Probabilistic Constraint Satisfaction with Non-Gaussian NoiseRuss B. Altman, Cheng-Che Chen, William B. Poland, Jaswinder Pal Singh. uai 1994: 15-22 [doi]

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