RUSS BIAGIO ALTMAN

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Pathway analysis of genome-wide data improves warfarin dose prediction
    Roxana Daneshjou
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    BMC Genomics 14:S11. 2013
  2. doi request reprint Personal genomic measurements: the opportunity for information integration
    R B Altman
    Departments of Bioengineering, Genetics, and Medicine, Stanford University, Stanford, California, USA
    Clin Pharmacol Ther 93:21-3. 2013
  3. doi request reprint Translational bioinformatics: linking the molecular world to the clinical world
    R B Altman
    Department of Bioengineering, Stanford University, Stanford, California, USA
    Clin Pharmacol Ther 91:994-1000. 2012
  4. pmc Integration and publication of heterogeneous text-mined relationships on the Semantic Web
    Adrien Coulet
    LORIA INRIA Nancy Grand Est, Campus Scientifique BP 239 54506 Vandoeuvre lès Nancy Cedex, France
    J Biomed Semantics 2:S10. 2011
  5. pmc Predicting drug side-effects by chemical systems biology
    Nicholas P Tatonetti
    Training Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
    Genome Biol 10:238. 2009
  6. pmc The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation
    Shirley Wu
    Program in Biomedical Informatics, Stanford University, Stanford, CA, 94305 USA
    Genome Biol 9:R8. 2008
  7. pmc Prediction of calcium-binding sites by combining loop-modeling with machine learning
    Tianyun Liu
    Department of Genetics, Stanford University, Stanford, CA, USA
    BMC Struct Biol 9:72. 2009
  8. pmc Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues
    Shirley Wu
    23andMe, 1390 Shorebird Way, Mountain View, CA, USA
    BMC Struct Biol 10:4. 2010
  9. pmc The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications
    Inbal Halperin
    Department of Genetics, 318 Campus Drive, Clark Center S240, Stanford, CA 94305, USA
    BMC Genomics 9:S2. 2008
  10. pmc MScanner: a classifier for retrieving Medline citations
    Graham L Poulter
    UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
    BMC Bioinformatics 9:108. 2008

Detail Information

Publications76

  1. pmc Pathway analysis of genome-wide data improves warfarin dose prediction
    Roxana Daneshjou
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    BMC Genomics 14:S11. 2013
    ....
  2. doi request reprint Personal genomic measurements: the opportunity for information integration
    R B Altman
    Departments of Bioengineering, Genetics, and Medicine, Stanford University, Stanford, California, USA
    Clin Pharmacol Ther 93:21-3. 2013
    ..Thus, the integration of population science with individual genomic measurements will enable the practice of personalized medicine...
  3. doi request reprint Translational bioinformatics: linking the molecular world to the clinical world
    R B Altman
    Department of Bioengineering, Stanford University, Stanford, California, USA
    Clin Pharmacol Ther 91:994-1000. 2012
    ..Translational bioinformatics spans these two fields; it involves the development of algorithms to analyze basic molecular and cellular data with an explicit goal of affecting clinical care...
  4. pmc Integration and publication of heterogeneous text-mined relationships on the Semantic Web
    Adrien Coulet
    LORIA INRIA Nancy Grand Est, Campus Scientifique BP 239 54506 Vandoeuvre lès Nancy Cedex, France
    J Biomed Semantics 2:S10. 2011
    ....
  5. pmc Predicting drug side-effects by chemical systems biology
    Nicholas P Tatonetti
    Training Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
    Genome Biol 10:238. 2009
    ..New approaches to predicting ligand similarity and protein interactions can explain unexpected observations of drug inefficacy or side-effects...
  6. pmc The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation
    Shirley Wu
    Program in Biomedical Informatics, Stanford University, Stanford, CA, 94305 USA
    Genome Biol 9:R8. 2008
    ..We built a library of models that shows good performance compared to other methods. In particular, SeqFEATURE demonstrates significant improvement over other methods when sequence and structural similarity are low...
  7. pmc Prediction of calcium-binding sites by combining loop-modeling with machine learning
    Tianyun Liu
    Department of Genetics, Stanford University, Stanford, CA, USA
    BMC Struct Biol 9:72. 2009
    ..Methods for recognizing functional sites in these missing loops would be useful for recovering additional functional information...
  8. pmc Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues
    Shirley Wu
    23andMe, 1390 Shorebird Way, Mountain View, CA, USA
    BMC Struct Biol 10:4. 2010
    ..Unfortunately, our ability to analyze these proteins is restricted by the limited catalog of known molecular functions and their associated 3D motifs...
  9. pmc The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications
    Inbal Halperin
    Department of Genetics, 318 Campus Drive, Clark Center S240, Stanford, CA 94305, USA
    BMC Genomics 9:S2. 2008
    ....
  10. pmc MScanner: a classifier for retrieving Medline citations
    Graham L Poulter
    UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
    BMC Bioinformatics 9:108. 2008
    ....
  11. pmc M-BISON: microarray-based integration of data sources using networks
    Bernie J Daigle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    BMC Bioinformatics 9:214. 2008
    ....
  12. pmc Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text
    Yael Garten
    Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA
    BMC Bioinformatics 10:S6. 2009
    ..Availability of full text articles as input into text mining engines is key, as literature abstracts often do not contain sufficient information to identify these pharmacogenomic associations...
  13. pmc Tools for loading MEDLINE into a local relational database
    Diane E Oliver
    Department of Genetics, Stanford University, Stanford, CA, USA
    BMC Bioinformatics 5:146. 2004
    ..Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers...
  14. pmc An integrative method for scoring candidate genes from association studies: application to warfarin dosing
    Nicholas P Tatonetti
    Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA, USA
    BMC Bioinformatics 11:S9. 2010
    ..We then define a summary score for each gene based on allele frequencies and train linear and logistic regression classifiers to predict drug response phenotypes...
  15. pmc Clustering protein environments for function prediction: finding PROSITE motifs in 3D
    Sungroh Yoon
    Computer Systems Laboratory, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 8:S10. 2007
    ..Toward that end, we have developed a method for clustering protein microenvironments in order to evaluate the potential for discovering novel sites that have not been previously identified...
  16. pmc Content-based microarray search using differential expression profiles
    Jesse M Engreitz
    Department of Bioengineering, Stanford University School of Medicine, CA, USA
    BMC Bioinformatics 11:603. 2010
    ....
  17. ncbi request reprint Genetic nondiscrimination legislation: a critical prerequisite for pharmacogenomics data sharing
    Russ B Altman
    Stanford University, Department of Genetics and Bioengineering, Clark S172, Stanford, CA 94305 5444, USA
    Pharmacogenomics 8:519. 2007
  18. pmc Direct-to-consumer genetic testing: failure is not an option
    R B Altman
    Department of Bioengineering, Stanford University, Stanford, California, USA
    Clin Pharmacol Ther 86:15-7. 2009
    ..Therefore, the key challenge is to set up social, educational, and technical means to support individuals who have access to their genome...
  19. pmc Commentaries on "Informatics and medicine: from molecules to populations"
    R B Altman
    Stanford University, Chair, Department of Bioengineering, Stanford, CA, USA
    Methods Inf Med 47:296-317. 2008
    ..To discuss interdisciplinary research and education in the context of informatics and medicine by commenting on the paper of Kuhn et al. "Informatics and Medicine: From Molecules to Populations"...
  20. pmc 2010 translational bioinformatics year in review
    Russ B Altman
    Department of Bioengineering, Stanford University School of Medicine, Stanford, California 94305 5444, USA
    J Am Med Inform Assoc 18:358-66. 2011
    ..At the same time, the infrastructure for the field has burgeoned. While acknowledging that, according to researchers, the members of this field tend to be overly optimistic, the authors predict a bright future...
  21. pmc Pharmacogenomics: will the promise be fulfilled?
    Russ B Altman
    Department of Bioengineering, Stanford University, 318 Campus Drive, S172, MC, 5444 Stanford, California 94305 5444, USA
    Nat Rev Genet 12:69-73. 2011
    ....
  22. doi request reprint Pharmacogenomics: "noninferiority" is sufficient for initial implementation
    R B Altman
    Department of Bioengineering, Stanford University, Stanford, California, USA
    Clin Pharmacol Ther 89:348-50. 2011
    ..In many cases, pharmacogenetic tests need only reach reasonable expectations of noninferiority (compared with current prescribing practices) to merit use...
  23. ncbi request reprint Biomedical informatics training at Stanford in the 21st century
    Russ B Altman
    Department of Genetics, Stanford University Medical Center, L 301 Stanford, CA 94305 5120, USA
    J Biomed Inform 40:55-8. 2007
    ..The core focus on research training-the development and application of novel informatics methods for biomedical research-keeps the program centered in the midst of this period of growth and diversification...
  24. ncbi request reprint Complexities of managing biomedical information
    Russ B Altman
    Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford, California 94305 5479, USA
    OMICS 7:127-9. 2003
  25. ncbi request reprint Genetic sequence data for pharmacogenomics
    Russ B Altman
    Stanford Medical Informatics, Department of Genetics, 251 Campus Drive MSOB X 215, Stanford, CA 94305 5479, USA
    Curr Opin Drug Discov Devel 6:297-303. 2003
    ..These surveys form the basis for determination of population frequencies, genetic linkage studies and association studies relating genotype with drug response phenotypes of interest...
  26. ncbi request reprint Challenges for biomedical informatics and pharmacogenomics
    Russ B Altman
    Stanford Medical Informatics, Stanford, California 94305 5479, USA
    Annu Rev Pharmacol Toxicol 42:113-33. 2002
    ..In this review, we summarize the current uses of informatics within pharmacogenomics and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the postgenomic era...
  27. pmc The interactions between clinical informatics and bioinformatics: a case study
    R B Altman
    Stanford University, Stanford, California 94305 5479, USA
    J Am Med Inform Assoc 7:439-43. 2000
    ..The author provides examples of technology transfer between clinical informatics and bioinformatics that illustrate how they complement each other...
  28. pmc Improving structure-based function prediction using molecular dynamics
    Dariya S Glazer
    Department of Genetics, Stanford University, Clark Center, Stanford, CA 94305, USA
    Structure 17:919-29. 2009
    ..Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods...
  29. pmc The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge
    Tina Hernandez-Boussard
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Nucleic Acids Res 36:D913-8. 2008
    ..These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data. PharmGKB is available at www.pharmgkb.org...
  30. pmc WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures
    Mike P Liang
    Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 31:3324-7. 2003
    ..A major application of WebFEATURE is in rapid annotation of function to structures in the context of structural genomics...
  31. ncbi request reprint Extracting and characterizing gene-drug relationships from the literature
    Jeffrey T Chang
    Department of Genetics, Stanford Biomedical Informatics, Stanford, CA 94305 5120, USA
    Pharmacogenetics 14:577-86. 2004
    ....
  32. ncbi request reprint Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
    Iwei Yeh
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Bioinformatics 19:241-8. 2003
    ..In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO...
  33. pmc Using pre-existing microarray datasets to increase experimental power: application to insulin resistance
    Bernie J Daigle
    Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 6:e1000718. 2010
    ..We envision SAGAT as a means to maximize the potential for biological discovery from subtle transcriptional responses, and we provide it as a freely available software package that is immediately applicable to any human microarray study...
  34. ncbi request reprint A personalized and automated dbSNP surveillance system
    Shuo Liu
    Department of Genetics, Stanford Medical Informatics, CA 94305 5479, USA
    Proc IEEE Comput Soc Bioinform Conf 2:132-6. 2003
    ..The system uses data warehousing, object model-based data integration, object-oriented programming, and a platform-neutral data access mechanism...
  35. pmc Using surface envelopes for discrimination of molecular models
    Jonathan M Dugan
    Department of Genetics, Informatics Laboratory, Stanford University, Stanford, California 94305, USA
    Protein Sci 13:15-24. 2004
    ..This correlation is stronger for molecular models with greater oblong character (as measured by the ratio of largest to smallest principal component)...
  36. ncbi request reprint Genetics. Genomic research and human subject privacy
    Zhen Lin
    Department of Genetics, Stanford University School of Medicine, CA 94305 5120, USA
    Science 305:183. 2004
  37. ncbi request reprint Nonparametric methods for identifying differentially expressed genes in microarray data
    Olga G Troyanskaya
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Bioinformatics 18:1454-61. 2002
    ..We systematically assess the performance of each method based on simulated and biological data under varying noise levels and p-value cutoffs...
  38. pmc Pharmacogenomics and bioinformatics: PharmGKB
    Caroline F Thorn
    Department of Genetics, Stanford University Medical Center, Stanford, CA 94305 5120, USA
    Pharmacogenomics 11:501-5. 2010
    ....
  39. ncbi request reprint GAPSCORE: finding gene and protein names one word at a time
    Jeffrey T Chang
    Department of Genetics, Stanford Medical Center, 300 Pasteur Drive, Lane L 301, Mail Code 5120, Stanford, CA 94305 5120, USA
    Bioinformatics 20:216-25. 2004
    ..Therefore, we have developed a new method, GAPSCORE, to identify gene and protein names in text. GAPSCORE scores words based on a statistical model of gene names that quantifies their appearance, morphology and context...
  40. pmc Efficient algorithms to explore conformation spaces of flexible protein loops
    Peggy Yao
    Computer Science Department, Stanford University, S240 Clark Center, 318 Campus Drive, Stanford, CA 94305, USA
    IEEE/ACM Trans Comput Biol Bioinform 5:534-45. 2008
    ..The sampling algorithms are implemented in a toolkit (LoopTK), which is available at https://simtk.org/home/looptk...
  41. ncbi request reprint Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models
    Daniel L Rubin
    Department of Genetics, Stanford Medical Informatics, MSOB X 215, Stanford, CA 94305 5479, USA
    Bioinformatics 18:S207-15. 2002
    ..As experimental and analytical methods change, and as biological knowledge advances, the data storage requirements and types of queries needed may also change...
  42. pmc A functional analysis of disease-associated mutations in the androgen receptor gene
    Sean D Mooney
    Stanford Medical Informatics, Department of Genetics, Stanford University, MSOB X 215, 251 Campus Drive, Stanford, CA 94305 5479, USA
    Nucleic Acids Res 31:e42. 2003
    ..Our method provides a means for assessing the significance of single nucleotide polymorphisms (SNPs) and cancer-associated mutations...
  43. doi request reprint PharmGKB: an integrated resource of pharmacogenomic data and knowledge
    Li Gong
    Genetics Department, Stanford University, Stanford, California, USA
    Curr Protoc Bioinformatics . 2008
    ..Workflow on how to use PharmGKB to facilitate design of the pharmacogenomic study is also described in this unit...
  44. pmc Using text analysis to identify functionally coherent gene groups
    Soumya Raychaudhuri
    Department of Genetics, Stanford Medical Informatics, University, Stanford, California 94305 5479, USA
    Genome Res 12:1582-90. 2002
    ..We also apply neighbor divergence to previously published gene expression clusters to assess its ability to recognize gene groups that had been manually identified as representative of a common function...
  45. pmc Clinical assessment incorporating a personal genome
    Euan A Ashley
    Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
    Lancet 375:1525-35. 2010
    ..The cost of genomic information has fallen steeply, but the clinical translation of genetic risk estimates remains unclear. We aimed to undertake an integrated analysis of a complete human genome in a clinical context...
  46. ncbi request reprint A resource to acquire and summarize pharmacogenetics knowledge in the literature
    Daniel L Rubin
    Department of Genetics, Stanford University, Stanford, CA 94305 5210, USA
    Stud Health Technol Inform 107:793-7. 2004
    ..This resource is growing, containing entries for 138 genes and 215 drugs of pharmacogenetics significance, and is a core component of PharmGKB, a pharmacogenetics knowledge base (http://www.pharmgkb.org)...
  47. pmc A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    Olga G Troyanskaya
    Department of Genetics, Stanford University School of Medicine, CA 94305, USA
    Proc Natl Acad Sci U S A 100:8348-53. 2003
    ..We found that by creating functional groupings based on heterogeneous data types, MAGIC improved accuracy of the groupings compared with microarray analysis alone. We describe several of the biological gene groupings identified...
  48. pmc Extending and evaluating a warfarin dosing algorithm that includes CYP4F2 and pooled rare variants of CYP2C9
    Hersh Sagreiya
    Stanford University, Stanford, California 94305 5444, USA
    Pharmacogenet Genomics 20:407-13. 2010
    ..We sought to analyze new factors involved in its dosing and to evaluate eight dosing algorithms, including two developed by the International Warfarin Pharmacogenetics Consortium (IWPC)...
  49. pmc Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery
    Iwei Yeh
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 14:917-24. 2004
    ..A total of 87.5% of proposed drug targets with biological evidence in the literature are chokepoint reactions. Therefore, identifying chokepoint enzymes represents one systematic way to identify potential metabolic drug targets...
  50. ncbi request reprint Modelling biological processes using workflow and Petri Net models
    Mor Peleg
    Stanford Medical Informatics, Stanford University, CA 94305, USA
    Bioinformatics 18:825-37. 2002
    ..To represent high-level processes in the context of their component functions, we have developed a graphical knowledge model for biological processes that supports methods for qualitative reasoning...
  51. ncbi request reprint MutDB: annotating human variation with functionally relevant data
    Sean D Mooney
    Department of Genetics, Stanford Medical Informatics, Stanford University, 251 Campus Drive, MSOB X 215 Stanford, CA 94305 5479, USA
    Bioinformatics 19:1858-60. 2003
    ..MutDB provides interactive mutation maps at the gene and protein levels, and allows for ranking of their predicted functional consequences based on conservation in multiple sequence alignments...
  52. pmc Microenvironment analysis and identification of magnesium binding sites in RNA
    D Rey Banatao
    Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, CA 94305, USA
    Nucleic Acids Res 31:4450-60. 2003
    ..We also identified potentially important, high scoring sites in the group I intron that are not currently annotated as Mg2+ binding sites. We note their potential function and believe they deserve experimental follow-up...
  53. pmc A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge
    Daniel L Rubin
    Section of Medical Informatics, MSOB X 215, Stanford, CA 94305, USA
    J Am Med Inform Assoc 12:121-9. 2005
    ..The goal of the authors was to develop an automated method to identify articles in Medline citations that contain pharmacogenetics data pertaining to gene-drug relationships...
  54. pmc PharmGKB: the Pharmacogenetics Knowledge Base
    Micheal Hewett
    Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford, CA 94305 5479, USA
    Nucleic Acids Res 30:163-5. 2002
    ..The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001...
  55. pmc The computational analysis of scientific literature to define and recognize gene expression clusters
    Soumya Raychaudhuri
    Department of Genetics and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 31:4553-60. 2003
    ..In both cases, we are able to rapidly define and identify the biologically relevant gene expression profiles without manual intervention. In both cases, we identified novel clusters that were not noted by the original investigators...
  56. pmc Using surface envelopes to constrain molecular modeling
    Jonathan M Dugan
    Department of Genetics, Stanford University, CA 94305 5120, USA
    Protein Sci 16:1266-73. 2007
    ....
  57. pmc Structural characterization of proteins using residue environments
    Sean D Mooney
    Department of Genetics, Stanford University, Stanford, California, USA
    Proteins 61:741-7. 2005
    ..S-BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors...
  58. pmc A literature-based method for assessing the functional coherence of a gene group
    Soumya Raychaudhuri
    Department of Genetics, Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford University, Stanford, CA 94305 5479, USA
    Bioinformatics 19:396-401. 2003
    ..NDPG finds functional coherence in 96, 92, 82 and 45% of the groups (at 99.9% specificity) in yeast, mouse, fly and worm respectively...
  59. pmc Robust recognition of zinc binding sites in proteins
    Jessica C Ebert
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Protein Sci 17:54-65. 2008
    ..Both the source code and a Web interface are available to the public at http://feature.stanford.edu/metals...
  60. pmc Mining biochemical information: lessons taught by the ribosome
    Michelle Whirl-Carrillo
    Stanford Medical Informatics, Stanford University, California 94305 5479, USA
    RNA 8:279-89. 2002
    ..We also conclude that development of automated modeling approaches would benefit from better annotations of experimental data for detection and interpretation of their significance...
  61. doi request reprint PharmGKB and the International Warfarin Pharmacogenetics Consortium: the changing role for pharmacogenomic databases and single-drug pharmacogenetics
    Ryan P Owen
    Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
    Hum Mutat 29:456-60. 2008
    ..PharmGKB has embraced the challenge of continuing to maintain its original mission while taking an active role in the formation of pharmacogenetic consortia...
  62. pmc Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature
    Soumya Raychaudhuri
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 12:203-14. 2002
    ..We conclude that statistical methods may be used to assign GO codes and may be useful for the difficult task of reassignment as terminology standards evolve over time...
  63. pmc Creating an online dictionary of abbreviations from MEDLINE
    Jeffrey T Chang
    Department of Genetics, Stanford Medical Informatics, Stanford, California 94305, USA
    J Am Med Inform Assoc 9:612-20. 2002
    ..Therefore, to create an automatically generated and maintained lexicon of abbreviations, we have developed an algorithm to match abbreviations in text with their expansions...
  64. pmc Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
    Magdalena A Jonikas
    Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
    Bioinformatics 25:3259-66. 2009
    ..Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications...
  65. pmc Finding haplotype tagging SNPs by use of principal components analysis
    Zhen Lin
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Am J Hum Genet 75:850-61. 2004
    ..We applied these methods to three experimental data sets and found that the PCA-based methods tend to select the smallest set of htSNPs to achieve a 90% reconstruction precision...
  66. pmc PharmGKB: understanding the effects of individual genetic variants
    Katrin Sangkuhl
    Department of Genetics, Stanford University, Stanford, California 94305 5120, USA
    Drug Metab Rev 40:539-51. 2008
    ..These features link variant genotypes to phenotypes, increase the breadth of pharmacogenomics literature curated, and visualize single-nucleotide polymorphisms on a gene's three-dimensional protein structure...
  67. ncbi request reprint PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base
    Caroline F Thorn
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Methods Mol Biol 311:179-91. 2005
    ..Registered users can access and download primary data to aid in the design of future pharmacogenetics and pharmacogenomics studies...
  68. ncbi request reprint Integrating large-scale genotype and phenotype data
    Tina Hernandez-Boussard
    Department of Genetics, Stanford University Medical School, Stanford, California, USA
    OMICS 10:545-54. 2006
    ..PharmGKB has confronted these challenges, and these experiences and solutions can benefit all genome communities...
  69. pmc SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    Rhiju Das
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    RNA 11:344-54. 2005
    ..Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu...
  70. pmc Large scale study of protein domain distribution in the context of alternative splicing
    Shuo Liu
    Department of Genetics, Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford, CA 94305 5479, USA
    Nucleic Acids Res 31:4828-35. 2003
    ....
  71. pmc Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay
    Shirin Khambata-Ford
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 13:1765-74. 2003
    ..This method promises to be a useful genome-wide function-based approach that can complement existing methods to look for promoters...
  72. pmc Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
    Magdalena A Jonikas
    Department of Bioengineering, Stanford University, California 94305, USA
    RNA 15:189-99. 2009
    ..thermophila group I intron, creating an integrated model of the entire molecule. Our software package is freely available at https://simtk.org/home/nast...
  73. ncbi request reprint Promises of text processing: natural language processing meets AI
    Jeffrey T Chang
    Department of Genetics, Stanford Medical Informatics, Stanford School of Medicine, MSOB X 215, 251 Campus Drive, Stanford, CA 94305, USA
    Drug Discov Today 7:992-3. 2002
  74. ncbi request reprint Indexing pharmacogenetic knowledge on the World Wide Web
    Russ B Altman
    Department of Genetics, Stanford Medical Informatics, Stanford University, Stanford, California, USA
    Pharmacogenetics 13:3-5. 2003
  75. pmc Eukaryotic regulatory element conservation analysis and identification using comparative genomics
    Yueyi Liu
    Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA
    Genome Res 14:451-8. 2004
    ..CompareProspector outperformed many other computational motif-finding programs, demonstrating the power of comparative genomics-based biased sampling in eukaryotic regulatory element identification...
  76. doi request reprint Interview: Russ Altman speaks to Shreeya Nanda, Commissioning Editor
    RUSS BIAGIO ALTMAN
    Pharmacogenomics 9:663-5. 2008
    b>Russ Biagio Altman is a professor of bioengineering, genetics, and medicine (and of computer science by courtesy) and chairman of the Bioengineering Department at Stanford University, CA, USA...

Research Grants20

  1. Annotating functional sites in 3D biological structures
    RUSS BIAGIO ALTMAN; Fiscal Year: 2010
    ..In particular, we will focus our new capabilities on three difficult function annotation challenges: ATP binding sites, phosphorylation sites, and metabolizing enzyme active sites. ..
  2. Annotating functional sites in 3D biological structures
    Russ Altman; Fiscal Year: 2007
    ..We will make the resulting models available on the Web for real-time structural annotation, and will distribute the software for open source development. ..
  3. Physics-based Simulation of Biological Structures(RMI)
    Russ Altman; Fiscal Year: 2007
    ..It will thus provide a critical piece of a national biomedical computing infrastructure. ..
  4. MODELING AND COMPUTING WITH UNCERTAIN STRUCTURES
    Russ Altman; Fiscal Year: 2002
    ..Therefore, we will leverage other efforts in malaria genomics within our laboratory by attempting to estimate structures and assess their function. ..
  5. Biomedical Computation Graduate Training at Stanford
    Russ Altman; Fiscal Year: 2007
    ..abstract_text> ..
  6. The PharmGKB: Catalyzing Research in Pharmacogenetics
    Russ Altman; Fiscal Year: 2007
    ....
  7. Annotating functional sites in 3D biological structures
    RUSS BIAGIO ALTMAN; Fiscal Year: 2010
    ..In particular, we will focus our new capabilities on three difficult function annotation challenges: ATP binding sites, phosphorylation sites, and metabolizing enzyme active sites. ..