Key Documents

NIH Biosketch available Online

Curriculum Vitae available Online

Russ B. Altman

Professor, Bioengineering
Professor, Medicine - Stanford Medical Informatics
Professor (By courtesy), Computer Science
Professor, Genetics
Member, Bio-X
Member, Cancer Center

Contact Information

Clinical Offices

Dept of Engineering 318 Campus Dr S170 Stanford, CA 94305
Telephone Work (650) 725-3394 Fax (650) 723-8544
Academic Offices

Personal Information
Email Russ.Altman@stanford.edu Tel (650) 725-0659, (650) 725-3394

Administrative Contact
Tiffany Murray Administrative Associate Email tiffany.murray@stanford.edu Tel Work 650-725-0659

Administrative Appointments

Chairman, Department of Bioengineering , (2007– present )
Director, Biomedical Informatics Training Program , (2000– present )
Member, Biomedical Library and Informatics Research Commitee Study Section (NIH) , (2002– 2005 )
President, International Society for Computational Biology , (2000– 2001 )

Honors and Awards

Fellow, American Institute for Medical and Biological Engineering (2007)
Fellow, American College of Physicians (1998)
U.S. Presidential Early Career Award for Scientists & Engineers, NIH (1997)
Post-Doctoral Fellowship, Howard Hughes Medical Institute (1991)
Award for Excellence in Graduate Teaching, Stanford Medical School (2000)
Fellow, American College of Medical Informatics (1998)

Professional Education

AB, Harvard College Biochemistry & Molecular Biology (1983)
PhD, Stanford University Medical Information Sciences (1989)
MD, Stanford University Medicine (1990)

Postdoctoral Advisees

Dorit Berlin, Emidio Capriotti, Samuel Flores, Laura Hodges, Kai Kohlhoff, Wei-Nchih Lee, Tianyun Liu, Victoria Nembaware

Graduate & Fellowship Program Affiliations

Community & International Work

Attending Physician, Medicine, Menlo Park, CA More »

Web Site Links

Home Page

Research Interests

I am interested in the application of computational technologies to problems in molecular biology of relevance to medicine. In particular, my laboratory focuses on three areas. First, we are interested in building structured information repositories to support biological research. Our first effort was the RiboWEB resource for supporting studies of the bacterial ribosome (http://riboweb.stanford.edu). Our latest effort is in the creation of a comprehensive pharmacogenomics knowledge base (http://www.pharmgkb.org/) that provides access to information relating genotype to phenotype (in particular, how variation in genetics leads to variation in response to drugs). Second, we are interested in the elucidation and analysis of three dimensional structures. We have projects for computing 3D molecular structures from sparse and noisy data, and for analyzing these structures to recognize and annotate active sites. We are interested in physics-based simulation of biological structures (http://simbios.stanford.edu/). Third, we are interested in computational methods for analyzing functional genomics information. We are focusing on the use of natural language processing techniques for extracting and summarizing information, and in the development of novel methods for analyzing microarray expression data. We are applying these technologies to the study of functional genomics.

Publications

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. RNA. 2009; 15 (2): 189-99
Estimation of the warfarin dose with clinical and pharmacogenetic data. Klein TE, Altman RB, Eriksson N, Gage BF, Kimmel SE, Lee MT, Limdi NA, Page D, Roden DM, Wagner MJ, Caldwell MD, Johnson JA. N Engl J Med. 2009; 360 (8): 753-64
Generating genome-scale candidate gene lists for pharmacogenomics. Hansen NT, Brunak S, Altman RB. Clin Pharmacol Ther. 2009; 86 (2): 183-9
Improving structure-based function prediction using molecular dynamics. Glazer DS, Radmer RJ, Altman RB. Structure. 2009; 17 (7): 919-29
Direct-to-consumer genetic testing: failure is not an option. Altman RB, Clin Pharmacol Ther. 2009; 86 (1): 15-7
Predicting RNA structure by multiple template homology modeling. Flores SC, Wan Y, Russell R, Altman RB. Pac Symp Biocomput. 2010; 216-27
Improving the prediction of pharmacogenes using text-derived drug-gene relationships. Garten Y, Tatonetti NP, Altman RB. Pac Symp Biocomput. 2010; 305-14
Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application. Coulet A, Shah N, Hunter L, Barral C, Altman RB. Pac Symp Biocomput. 2010; 485-7
Very important pharmacogene summary: sulfotransferase 1A1. Hildebrandt M, Adjei A, Weinshilboum R, Johnson JA, Berlin DS, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (6): 404-6
New feature: pathways and important genes from PharmGKB. Eichelbaum M, Altman RB, Ratain M, Klein TE. Pharmacogenet Genomics. 2009; 19 (6): 403
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. Garten Y, Altman RB. BMC Bioinformatics. 2009; 10 Suppl 2 S6
Towards a cytokine-cell interaction knowledgebase of the adaptive immune system. Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte AJ. Pac Symp Biocomput. 2009; 439-50
Platinum pathway. Marsh S, McLeod H, Dolan E, Shukla SJ, Rabik CA, Gong L, Hernandez-Boussard T, Lou XJ, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 563-4
Cytochrome P450 2D6. Owen RP, Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 559-62
Etoposide pathway. Yang J, Bogni A, Schuetz EG, Ratain M, Dolan ME, McLeod H, Gong L, Thorn C, Relling MV, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 552-3
Codeine and morphine pathway. Thorn CF, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 556-8
Antiestrogen pathway (aromatase inhibitor). Desta Z, Nguyen A, Flockhart D, Skaar T, Fletcher R, Weinshilboum R, Berlin DS, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 554-5
Very important pharmacogene summary ADRB2. Litonjua AA, Gong L, Duan QL, Shin J, Moore MJ, Weiss ST, Johnson JA, Klein TE, Altman RB. Pharmacogenet Genomics. 2009;
PharmGKB summary: very important pharmacogene information for angiotensin-converting enzyme. Thorn CF, Klein TE, Altman RB. Pharmacogenet Genomics. 2009;
Knowledge-Based Instantiation of Full Atomic Detail into Coarse Grain RNA 3D Structural Models. Jonikas MA, Radmer RJ, Altman RB. Bioinformatics. 2009;
Selective serotonin reuptake inhibitors pathway. Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2009;
Maternal-fetal and neonatal pharmacogenomics: a review of current literature. Blumenfeld YJ, Reynolds-May MF, Altman RB, El-Sayed YY. J Perinatol. 2009;
Efficient algorithms to explore conformation spaces of flexible protein loops. Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin-Landsberg I, Altman RB. IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec; 5 (4): 534-45
Interview: Russ Altman speaks to Shreeya Nanda, Commissioning Editor. Altman RB, Pharmacogenomics. 2008; 9 (6): 663-5
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. Nucleic Acids Res. 2008; 36 (11): e63
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G. Science. 2008; 320 (5874): 362-5
PharmGKB and the International Warfarin Pharmacogenetics Consortium: the changing role for pharmacogenomic databases and single-drug pharmacogenetics. Owen RP, Altman RB, Klein TE. Hum Mutat. 2008; 29 (4): 456-60
Robust recognition of zinc binding sites in proteins. Ebert JC, Altman RB. Protein Sci. 2008; 17 (1): 54-65
Combining molecular dynamics and machine learning to improve protein function recognition. Glazer DS, Radmer RJ, Altman RB. Pac Symp Biocomput. 2008; 332-43
An XML-based interchange format for genotype-phenotype data. Whirl-Carrillo M, Woon M, Thorn CF, Klein TE, Altman RB. Hum Mutat. 2008; 29 (2): 212-9
The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M, Gor W, Liu F, Truong C, Whaley R, Woon M, Zhou T, Altman RB, Klein TE. Nucleic Acids Res. 2008; 36 (Database issue): D913-8
Commentaries on "Informatics and medicine: from molecules to populations". Altman RB, Balling R, Brinkley JF, Coiera E, Consorti F, Dhansay MA, Geissbuhler A, Hersh W, Kwankam SY, Lorenzi NM, Martin-Sanchez F, Mihalas GI, Shahar Y, Takabayashi K, Wiederhold G. Methods Inf Med. 2008; 47 (4): 296-317
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. Wu S, Liang MP, Altman RB. Genome Biol. 2008; 9 (1): R8
Structural inference of native and partially folded RNA by high-throughput contact mapping. Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Proc Natl Acad Sci U S A. 2008; 105 (11): 4144-9
M-BISON: microarray-based integration of data sources using networks. Daigle BJ, Altman RB. BMC Bioinformatics. 2008; 9 214
PharmGKB: understanding the effects of individual genetic variants. Sangkuhl K, Berlin DS, Altman RB, Klein TE. Drug Metab Rev. 2008; 40 (4): 539-51
Text mining for biology--the way forward: opinions from leading scientists. Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A. Genome Biol. 2008; 9 Suppl 2 S7
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. Halperin I, Glazer DS, Wu S, Altman RB. BMC Genomics. 2008; 9 Suppl 2 S2
PharmGKB: an integrated resource of pharmacogenomic data and knowledge. Gong L, Owen RP, Gor W, Altman RB, Klein TE. Curr Protoc Bioinformatics. 2008; Chapter 14 Unit14.7
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Nat Protoc. 2008; 3 (9): 1395-401
Extracting subject demographic information from abstracts of randomized clinical trial reports. Xu R, Garten Y, Supekar KS, Das AK, Altman RB, Garber AM. Stud Health Technol Inform. 2007; 129 (Pt 1): 550-4
Using surface envelopes to constrain molecular modeling. Dugan JM, Altman RB. Protein Sci. 2007; 16 (7): 1266-73
Predicting allosteric communication in myosin via a pathway of conserved residues. Tang S, Liao JC, Dunn AR, Altman RB, Spudich JA, Schmidt JP. J Mol Biol. 2007; 373 (5): 1361-73
Clustering protein environments for function prediction: finding PROSITE motifs in 3D. Yoon S, Ebert JC, Chung EY, De Micheli G, Altman RB. BMC Bioinformatics. 2007; 8 Suppl 4 S10
Genetic nondiscrimination legislation: a critical prerequisite for pharmacogenomics data sharing. Altman RB, Benowitz N, Gurwitz D, Lunshof J, Relling M, Lamba J, Wieben E, Mooney S, Giacomini K, Weiss S, Johnson JA, McLeod H, Flockhart D, Weinshilboum R, Shuldiner AR, Roden D, Krauss RM, Ratain M. Pharmacogenomics. 2007; 8 (5): 519
Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. Proc Natl Acad Sci U S A. 2007; 104 (17): 7045-50
Coplanar and coaxial orientations of RNA bases and helices. Laederach A, Chan JM, Schwartzman A, Willgohs E, Altman RB. RNA. 2007; 13 (5): 643-50
The education potential of the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Owen RP, Klein TE, Altman RB. Clin Pharmacol Ther. 2007; 82 (4): 472-5
Current progress in bioinformatics 2007. Altman RB, Brief Bioinform. 2007; 8 (5): 277-8
The PharmGKB: integration, aggregation, and annotation of pharmacogenomic data and knowledge. Hodge AE, Altman RB, Klein TE. Clin Pharmacol Ther. 2007; 81 (1): 21-4
Biomedical informatics training at Stanford in the 21st century. Altman RB, Klein TE. J Biomed Inform. 2007; 40 (1): 55-8
PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Altman RB, Nat Genet. 2007; 39 (4): 426
Pharmacogenomics: The relevance of emerging genotyping technologies. Hernandez-Boussard T, Klein TE, Altman RB. MLO Med Lab Obs. 2006; 38 (3): 24, 26-30
The incidentalome: a threat to genomic medicine. Kohane IS, Masys DR, Altman RB. JAMA. 2006; 296 (2): 212-5
Integrating large-scale genotype and phenotype data. Hernandez-Boussard T, Woon M, Klein TE, Altman RB. OMICS. 2006; 10 (4): 545-54
Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. Laederach A, Shcherbakova I, Liang MP, Brenowitz M, Altman RB. J Mol Biol. 2006; 358 (4): 1179-90
Drug Targets for Plasmodium falciparum: a post-genomic review/survey. Yeh I, Altman RB. Mini Rev Med Chem. 2006; 6 (2): 177-202
A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. Rubin DL, Thorn CF, Klein TE, Altman RB. J Am Med Inform Assoc. 2005 Mar-Apr; 12 (2): 121-9
Choosing SNPs using feature selection. Phuong TM, Lin Z, Altman RB. Proc IEEE Comput Syst Bioinform Conf. 2005; 301-9
Health-information altruists--a potentially critical resource. Kohane IS, Altman RB. N Engl J Med. 2005; 353 (19): 2074-7
PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Thorn CF, Klein TE, Altman RB. Methods Mol Biol. 2005; 311 179-91
Structural characterization of proteins using residue environments. Mooney SD, Liang MH, DeConde R, Altman RB. Proteins. 2005; 61 (4): 741-7
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. RNA. 2005; 11 (3): 344-54
Finding haplotype tagging SNPs by use of principal components analysis. Lin Z, Altman RB. Am J Hum Genet. 2004; 75 (5): 850-61
Genetics. Genomic research and human subject privacy. Lin Z, Owen AB, Altman RB. Science. 2004; 305 (5681): 183
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Genome Res. 2004; 14 (5): 917-24
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Genome Res. 2004; 14 (3): 451-8
GAPSCORE: finding gene and protein names one word at a time. Chang JT, Schütze H, Altman RB. Bioinformatics. 2004; 20 (2): 216-25
Using surface envelopes for discrimination of molecular models. Dugan JM, Altman RB. Protein Sci. 2004; 13 (1): 15-24
Extracting and characterizing gene-drug relationships from the literature. Chang JT, Altman RB. Pharmacogenetics. 2004; 14 (9): 577-86
Tools for loading MEDLINE into a local relational database. Oliver DE, Bhalotia G, Schwartz AS, Altman RB, Hearst MA. BMC Bioinformatics. 2004; 5 146
A resource to acquire and summarize pharmacogenetics knowledge in the literature. Rubin DL, Carrillo M, Woon M, Conroy J, Klein TE, Altman RB. Stud Health Technol Inform. 2004; 107 (Pt 2): 793-7
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB. Nucleic Acids Res. 2003; 31 (13): 3324-7
MutDB: annotating human variation with functionally relevant data. Mooney SD, Altman RB. Bioinformatics. 2003; 19 (14): 1858-60
Complexities of managing biomedical information. Altman RB, OMICS. 2003; 7 (1): 127-9
Genetic sequence data for pharmacogenomics. Altman RB, Curr Opin Drug Discov Devel. 2003; 6 (3): 297-303
Microenvironment analysis and identification of magnesium binding sites in RNA. Banatao DR, Altman RB, Klein TE. Nucleic Acids Res. 2003; 31 (15): 4450-60
A personalized and automated dbSNP surveillance system. Liu S, Lin S, Woon M, Klein TE, Altman RB. Proc IEEE Comput Soc Bioinform Conf. 2003; 2 132-6
The computational analysis of scientific literature to define and recognize gene expression clusters. Raychaudhuri S, Chang JT, Imam F, Altman RB. Nucleic Acids Res. 2003; 31 (15): 4553-60
Large scale study of protein domain distribution in the context of alternative splicing. Liu S, Altman RB. Nucleic Acids Res. 2003; 31 (16): 4828-35
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. Proc Natl Acad Sci U S A. 2003; 100 (14): 8348-53
Investigating hypoxic tumor physiology through gene expression patterns. Denko NC, Fontana LA, Hudson KM, Sutphin PD, Raychaudhuri S, Altman R, Giaccia AJ. Oncogene. 2003; 22 (37): 5907-14
Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. Khambata-Ford S, Liu Y, Gleason C, Dickson M, Altman RB, Batzoglou S, Myers RM. Genome Res. 2003; 13 (7): 1765-74
A functional analysis of disease-associated mutations in the androgen receptor gene. Mooney SD, Klein TE, Altman RB, Trifiro MA, Gottlieb B. Nucleic Acids Res. 2003; 31 (8): e42
Defining bioinformatics and structural bioinformatics. Altman RB, Dugan JM. Methods Biochem Anal. 2003; 44 3-14
Automated construction of structural motifs for predicting functional sites on protein structures. Liang MP, Brutlag DL, Altman RB. Pac Symp Biocomput. 2003; 204-15
A literature-based method for assessing the functional coherence of a gene group. Raychaudhuri S, Altman RB. Bioinformatics. 2003; 19 (3): 396-401
Ribosomal dynamics inferred from variations in experimental measurements. Gabashvili IS, Whirl-Carrillo M, Bada M, Banatao DR, Altman RB. RNA. 2003; 9 (11): 1301-7
Indexing pharmacogenetic knowledge on the World Wide Web. Altman RB, Flockhart DA, Sherry ST, Oliver DE, Rubin DL, Klein TE. Pharmacogenetics. 2003; 13 (1): 3-5
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Yeh I, Karp PD, Noy NF, Altman RB. Bioinformatics. 2003; 19 (2): 241-8
Creating an online dictionary of abbreviations from MEDLINE. Chang JT, Schütze H, Altman RB. J Am Med Inform Assoc. 2002 Nov-Dec; 9 (6): 612-20
Ontology development for a pharmacogenetics knowledge base. Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE, Altman RB. Pac Symp Biocomput. 2002; 65-76
Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Rubin DL, Hewett M, Oliver DE, Klein TE, Altman RB. Pac Symp Biocomput. 2002; 88-99
Mining biochemical information: lessons taught by the ribosome. Whirl-Carrillo M, Gabashvili IS, Bada M, Banatao DR, Altman RB. RNA. 2002; 8 (3): 279-89
Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis. Kivi M, Liu X, Raychaudhuri S, Altman RB, Small PM. J Clin Microbiol. 2002; 40 (6): 2192-8
Modelling biological processes using workflow and Petri Net models. Peleg M, Yeh I, Altman RB. Bioinformatics. 2002; 18 (6): 825-37
Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models. Rubin DL, Shafa F, Oliver DE, Hewett M, Altman RB. Bioinformatics. 2002; 18 Suppl 1 S207-15
Using text analysis to identify functionally coherent gene groups. Raychaudhuri S, Schütze H, Altman RB. Genome Res. 2002; 12 (10): 1582-90
Nonparametric methods for identifying differentially expressed genes in microarray data. Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. Bioinformatics. 2002; 18 (11): 1454-61
Using binning to maintain confidentiality of medical data. Lin Z, Hewett M, Altman RB. Proc AMIA Symp. 2002; 454-8
Promises of text processing: natural language processing meets AI. Chang JT, Altman RB. Drug Discov Today. 2002; 7 (19): 992-3
RNAML: a standard syntax for exchanging RNA information. Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNA. 2002; 8 (6): 707-17
PharmGKB: the Pharmacogenetics Knowledge Base. Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB, Klein TE. Nucleic Acids Res. 2002; 30 (1): 163-5
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. Genome Res. 2002; 12 (1): 203-14
Challenges for biomedical informatics and pharmacogenomics. Altman RB, Klein TE. Annu Rev Pharmacol Toxicol. 2002; 42 113-33
Diversity of gene expression in adenocarcinoma of the lung. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. Proc Natl Acad Sci U S A. 2001; 98 (24): 13784-9
Constrained global optimization for estimating molecular structure from atomic distances. Williams GA, Dugan JM, Altman RB. J Comput Biol. 2001; 8 (5): 523-47
Whole-genome expression analysis: challenges beyond clustering. Altman RB, Raychaudhuri S. Curr Opin Struct Biol. 2001; 11 (3): 340-7
Missing value estimation methods for DNA microarrays. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Bioinformatics. 2001; 17 (6): 520-5
Basic microarray analysis: grouping and feature reduction. Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Trends Biotechnol. 2001; 19 (5): 189-93
Including biological literature improves homology search. Chang JT, Raychaudhuri S, Altman RB. Pac Symp Biocomput. 2001; 374-83
Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, Hewett M, Lin Z, Liu Y, Liu S, Oliver DE, Rubin DL, Shafa F, Stuart JM, Altman RB. Pharmacogenomics J. 2001; 1 (3): 167-70
Using meta computing tools to facilitate large-scale analyses of biological databases. Waugh A, Williams GA, Wei L, Altman RB. Pac Symp Biocomput. 2001; 360-71
The interactions between clinical informatics and bioinformatics: a case study. Altman RB, J Am Med Inform Assoc. 2000 Sep-Oct; 7 (5): 439-43
Biomedical computation at Stanford University: a larger umbrella for the future. Altman RB, MD Comput. 2000 Nov-Dec; 17 (6): 35-7
Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains. Raychaudhuri S, Stuart JM, Liu X, Small PM, Altman RB. Proc Int Conf Intell Syst Mol Biol. 2000; 8 286-95
Computational modeling of structural experimental data. Bada MA, Altman RB. Methods Enzymol. 2000; 317 470-91
Generating interactive molecular documentaries using a library of graphical actions. Pulavarthi P, Chiang R, Altman RB. Pac Symp Biocomput. 2000; 266-77
Principal components analysis to summarize microarray experiments: application to sporulation time series. Raychaudhuri S, Stuart JM, Altman RB. Pac Symp Biocomput. 2000; 455-66
Automated diagnosis of data-model conflicts using metadata. Chen RO, Altman RB. J Am Med Inform Assoc. 1999 Sep-Oct; 6 (5): 374-92
Are predicted structures good enough to preserve functional sites? Wei L, Huang ES, Altman RB. Structure. 1999; 7 (6): 643-50
Using imperfect secondary structure predictions to improve molecular structure computations. Chen CC, Singh JP, Altman RB. Bioinformatics. 1999; 15 (1): 53-65
Updating a bibliography using the related articles function within PubMed. Liu X, Altman RB. Proc AMIA Symp. 1998; 750-4
MHCWeb: converting a WWW database into a knowledge-based collaborative environment. Hon L, Abernethy NF, Brusic V, Chai J, Altman RB. Proc AMIA Symp. 1998; 947-51
Recognizing protein binding sites using statistical descriptions of their 3D environments. Wei L, Altman RB. Pac Symp Biocomput. 1998; 497-508
Hierarchical organization of molecular structure computations. Chen CC, Singh JP, Altman RB. J Comput Biol. 1998; 5 (3): 409-22
A surface measure for probabilistic structural computations. Schmidt JP, Chen CC, Cooper JL, Altman RB. Proc Int Conf Intell Syst Mol Biol. 1998; 6 148-56
Bioinformatics in support of molecular medicine. Altman RB, Proc AMIA Symp. 1998; 53-61
Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Wei L, Altman RB, Chang JT. Pac Symp Biocomput. 1997; 465-76
RNA secondary structure as a reusable interface to biological information resources. Felciano RM, Chen RO, Altman RB. Gene. 1997; 190 (2): GC59-70
Standardized representations of the literature: combining diverse sources of ribosomal data. Altman RB, Abernethy NF, Chen RO. Proc Int Conf Intell Syst Mol Biol. 1997; 5 15-24
RIBOWEB: linking structural computations to a knowledge base of published experimental data. Chen RO, Felciano R, Altman RB. Proc Int Conf Intell Syst Mol Biol. 1997; 5 84-7
Informatics in the care of patients: ten notable challenges. Altman RB, West J Med. 1997; 166 (2): 118-22
LPFC: an Internet library of protein family core structures. Schmidt R, Gerstein M, Altman RB. Protein Sci. 1997; 6 (1): 246-8
Conserved features in the active site of nonhomologous serine proteases. Bagley SC, Altman RB. Fold Des. 1996; 1 (5): 371-9
Images in clinical medicine. Knotted umbilical cord. Altman RB, Merino JE. N Engl J Med. 1996; 334 (9): 573
Constraining volume by matching the moments of a distance distribution. Chen CC, Chen RO, Altman RB. Comput Appl Biosci. 1996; 12 (4): 319-26
Computational methods for defining the allowed conformational space of 16S rRNA based on chemical footprinting data. Fink DL, Chen RO, Noller HF, Altman RB. RNA. 1996; 2 (9): 851-66
A programming course in bioinformatics for computer and information science students. Altman RB, Koza J. Pac Symp Biocomput. 1996; 73-84
Lamprey: tracking users on the World Wide Web. Felciano RM, Altman RB. Proc AMIA Annu Fall Symp. 1996; 757-61
An evaluation of the TransFER model for sharing clinical decision-support applications. Sujansky W, Altman R. Proc AMIA Annu Fall Symp. 1996; 468-72
Characterizing the microenvironment surrounding protein sites. Bagley SC, Altman RB. Protein Sci. 1995; 4 (4): 622-35
Methods for displaying macromolecular structural uncertainty: application to the globins. Altman RB, Hughes C, Gerstein MB. J Mol Graph. 1995; 13 (3): 142-52, 109-2
Average core structures and variability measures for protein families: application to the immunoglobulins. Gerstein M, Altman RB. J Mol Biol. 1995; 251 (1): 161-75
Using a measure of structural variation to define a core for the globins. Gerstein M, Altman RB. Comput Appl Biosci. 1995; 11 (6): 633-44
Characterizing oriented protein structural sites using biochemical properties. Bagley SC, Wei L, Cheng C, Altman RB. Proc Int Conf Intell Syst Mol Biol. 1995; 3 12-20
A survey of patient access to electronic mail: attitudes, barriers, and opportunities. Fridsma DB, Ford P, Altman R. Proc Annu Symp Comput Appl Med Care. 1994; 15-9
Extraction of SNOMED concepts from medical record texts. Oliver DE, Altman RB. Proc Annu Symp Comput Appl Med Care. 1994; 179-83
Towards a standard query model for sharing decision-support applications. Sujansky W, Altman R. Proc Annu Symp Comput Appl Med Care. 1994; 325-31
Probabilistic constraint satisfaction: application to radiosurgery. Altman RB, Tombropoulos R. Proc Annu Symp Comput Appl Med Care. 1994; 780-4
Finding an average core structure: application to the globins. Altman RB, Gerstein M. Proc Int Conf Intell Syst Mol Biol. 1994; 2 19-27
Constraint satisfaction techniques for modeling large complexes: application to the central domain of 16S ribosomal RNA. Altman RB, Weiser B, Noller HF. Proc Int Conf Intell Syst Mol Biol. 1994; 2 10-8
Probabilistic constraint satisfaction with structural models: application to organ modeling by radial contours. Altman RB, Brinkley JF. Proc Annu Symp Comput Appl Med Care. 1993; 492-6
Probabilistic structure calculations: a three-dimensional tRNA structure from sequence correlation data. Altman RB, Proc Int Conf Intell Syst Mol Biol. 1993; 1 12-20
A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. Liu Y, Zhao D, Altman R, Jardetzky O. J Biomol NMR. 1992; 2 (4): 373-88
The solution structures of Escherichia coli trp repressor and trp aporepressor at an intermediate resolution. Arrowsmith C, Pachter R, Altman R, Jardetzky O. Eur J Biochem. 1991; 202 (1): 53-66
Sequence-specific 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor. Arrowsmith CH, Pachter R, Altman RB, Iyer SB, Jardetzky O. Biochemistry. 1990; 29 (27): 6332-41
Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562. Brinkley JF, Altman RB, Duncan BS, Buchanan BG, Jardetzky O. J Chem Inf Comput Sci. 1988; 28 (4): 194-210
New strategies for the determination of macromolecular structure in solution. Altman RB, Jardetzky O. J Biochem. 1986; 100 (6): 1403-23
Quaternary structural changes in aspartate carbamoyltransferase of Escherichia coli at pH 8.3 and pH 5.8. Altman RB, Ladner JE, Lipscomb WN. Biochem Biophys Res Commun. 1982; 108 (2): 592-5