David J States

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  2. pmc A mouse plasma peptide atlas as a resource for disease proteomics
    Qing Zhang
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 9:R93. 2008
  3. pmc MiSearch adaptive pubMed search tool
    David J States
    Department of Human Genetics, National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:974-6. 2009
  4. ncbi request reprint Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction
    Carlos Santos
    Bioinformatics Program, The University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 21:1653-8. 2005
  5. pmc Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    Damian Fermin
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    Genome Biol 7:R35. 2006
  6. ncbi request reprint Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
    Marcin Adamski
    University of Michigan, Ann Arbor, MI 48109 2218, USA
    Proteomics 5:3246-61. 2005
  7. ncbi request reprint Understanding distal transcriptional regulation from sequence, expression and interactome perspectives
    Arvind Rao
    Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    J Bioinform Comput Biol 8:219-46. 2010
  8. ncbi request reprint Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
    David J States
    University of Michigan, 100 Washtenaw Rd, Palmer Commons 2035B, Ann Arbor, Michigan 48109, USA
    Nat Biotechnol 24:333-8. 2006
  9. ncbi request reprint Using directed information to build biologically relevant influence networks
    Arvind Rao
    Electrical Engineering and Computer Science, Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    Comput Syst Bioinformatics Conf 6:145-56. 2007
  10. pmc SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
    Junguk Hur
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:838-40. 2009

Research Grants

  1. Training Program in Bioinformatics
    David States; Fiscal Year: 2007

Detail Information

Publications29

  1. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  2. pmc A mouse plasma peptide atlas as a resource for disease proteomics
    Qing Zhang
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 9:R93. 2008
    ..A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis...
  3. pmc MiSearch adaptive pubMed search tool
    David J States
    Department of Human Genetics, National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:974-6. 2009
    ..The user can optionally elect to include or exclude specific features and vary the importance of timeliness in the ranking...
  4. ncbi request reprint Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction
    Carlos Santos
    Bioinformatics Program, The University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 21:1653-8. 2005
    ..In this work we describe a natural language processing (NLP) system that is able to identify references to biological interaction networks in free text and automatically assembles a protein association and interaction map...
  5. pmc Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    Damian Fermin
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    Genome Biol 7:R35. 2006
    ....
  6. ncbi request reprint Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
    Marcin Adamski
    University of Michigan, Ann Arbor, MI 48109 2218, USA
    Proteomics 5:3246-61. 2005
    ..Recommendations of the PPP for future large-scale proteomics endeavors are described...
  7. ncbi request reprint Understanding distal transcriptional regulation from sequence, expression and interactome perspectives
    Arvind Rao
    Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    J Bioinform Comput Biol 8:219-46. 2010
    ....
  8. ncbi request reprint Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
    David J States
    University of Michigan, 100 Washtenaw Rd, Palmer Commons 2035B, Ann Arbor, Michigan 48109, USA
    Nat Biotechnol 24:333-8. 2006
    ....
  9. ncbi request reprint Using directed information to build biologically relevant influence networks
    Arvind Rao
    Electrical Engineering and Computer Science, Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    Comput Syst Bioinformatics Conf 6:145-56. 2007
    ..Apart from network inference, the proposed framework enables the exploration of specific interactions, not just those revealed by data...
  10. pmc SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
    Junguk Hur
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:838-40. 2009
    ..8% F-measure. SciMiner's literature mining performance coupled with functional enrichment analyses provides an efficient platform for retrieval and summary of rich biological information from corpora of users' interests...
  11. pmc Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer
    Rajasree Menon
    Center for Computational Medicine and Biology and Pediatric Endocrinology, University of Michigan, 100 Washtenaw Avenue, Palmer Commons, Ann Arbor, MI 48109, USA
    Cancer Res 69:300-9. 2009
    ..Our results show that, in a mouse model for human pancreatic cancer, novel and differentially expressed alternative splice isoforms are detectable in plasma and may be a source of candidate biomarkers...
  12. pmc Literature-based discovery of diabetes- and ROS-related targets
    Junguk Hur
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Med Genomics 3:49. 2010
    ..Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS...
  13. ncbi request reprint SAGA: a subgraph matching tool for biological graphs
    Yuanyuan Tian
    Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 23:232-9. 2007
    ..SAGA employs an indexing technique that allows it to efficiently evaluate queries even against large graph datasets...
  14. pmc Integrating and annotating the interactome using the MiMI plugin for cytoscape
    Jing Gao
    National Center for Integrative Biomedical Informatics, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:137-8. 2009
    ..Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI and links out to multiple data sources and tools. Community annotation of the interactome is supported...
  15. pmc Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function
    Yili Chen
    Bioinformatics Program, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
    PLoS Comput Biol 3:e63. 2007
    ..The approach thus successfully identifies many known c-MYC targets and suggests many novel sites. Our findings suggest that to identify c-MYC genomic targets, integration of different data sources helps to improve the accuracy...
  16. pmc Computationally identifying novel NF-kappa B-regulated immune genes in the human genome
    Rongxiang Liu
    Bioinformatics Program and the Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genome Res 13:654-61. 2003
    ..Our method of predicting gene function, based on characteristic patterns of transcription factor binding, evolutionary conservation, and expression studies, would be applicable to finding genes with other functions...
  17. ncbi request reprint Evolutionary-conserved gene expression response profiles across mammalian tissues
    Ji Chen
    Bioinformatics Program, University of Michigan, Ann Arbor, Michigan 48109, USA
    OMICS 11:96-115. 2007
    ....
  18. pmc Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling
    Rongxiang Liu
    Bioinformatics Program and the Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Genome Res 12:462-9. 2002
    ..Candidate promoters for many novel genes will be a useful resource in elucidating complex biological response mechanisms...
  19. pmc A bioinformatics analysis of the cell line nomenclature
    Sirarat Sarntivijai
    National Center for Integrative Biomedical Informatics and the Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 24:2760-6. 2008
    ..Annotation of microarray gene expression studies is used as a test case. The CLKB facilitates data exploration and comparison of different cell lines in support of clinical and experimental research...
  20. ncbi request reprint Using directed information to build biologically relevant influence networks
    Arvind Rao
    Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
    J Bioinform Comput Biol 6:493-519. 2008
    ..Additionally, we show that DTI can be used in conjunction with mutual information to infer higher-order influence networks involving cooperative gene interactions...
  21. pmc Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription
    Yili Chen
    Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109 5622
    Endocrinology 150:3645-54. 2009
    ..Together these analyses identify Bcl6 as a participant in GH-regulated gene expression and suggest an interplay between the repressor Bcl6 and the activator Stat5 in regulating genes, which contribute to GH responses...
  22. pmc GLay: community structure analysis of biological networks
    Gang Su
    Bioinformatics Program, University of Michigan, Ann Arbor, MI, USA
    Bioinformatics 26:3135-7. 2010
    ..High performance is achieved by dynamically linking highly optimized C functions to the Cytoscape JAVA program, which makes GLay especially suitable for decomposition, display and exploratory analysis of large biological networks...
  23. ncbi request reprint Profiles of growth hormone (GH)-regulated genes reveal time-dependent responses and identify a mechanism for regulation of activating transcription factor 3 by GH
    Jeffrey S Huo
    Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, 48109, USA
    J Biol Chem 281:4132-41. 2006
    ..These findings suggest that GH regulates transcription of Atf3 through a mechanism utilizing factors, such as C/EBPbeta, which bind to a novel C/EBP site...
  24. ncbi request reprint Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    Gilbert S Omenn
    Internal Medicine, University of Michigan, Ann Arbor, MI 48109 0656, USA
    Proteomics 5:3226-45. 2005
    ....
  25. ncbi request reprint Supplementary data need to be kept in public repositories
    Carlos Santos
    Nature 438:738. 2005
  26. pmc Cytoscape ESP: simple search of complex biological networks
    Maital Ashkenazi
    Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
    Bioinformatics 24:1465-6. 2008
    ..Availabiity: http://chianti.ucsd.edu/cyto_web/plugins/..
  27. ncbi request reprint A functional annotation of subproteomes in human plasma
    Peipei Ping
    Department of Physiology and Medicine, Division of Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
    Proteomics 5:3506-19. 2005
    ..The HPPP-organized, multi-laboratory effort, as described herein, resulted in much synergy and was essential to the success of this project...
  28. ncbi request reprint Bioinformatics code must enforce citation
    David J States
    Nature 417:588. 2002
  29. pmc Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications
    Xiuxia Du
    Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Proteome Res 7:2195-203. 2008
    ..The Phosphopeptide FDR Estimator software is freely available for download at http://ncrr.pnl.gov/software/...

Research Grants2

  1. Training Program in Bioinformatics
    David States; Fiscal Year: 2007
    ..The establishment of an NIH multidisciplinary Bioinformatics Training Program will enhance faculty productivity and facilitate progress toward attaining the goals of the National Institutes of Health. ..