Leroy E Hood

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. ncbi request reprint Printing your own inkjet microarrays
    Christopher G Lausted
    Institute for Systems Biology, Seattle, Washington, USA
    Methods Enzymol 410:168-89. 2006
  2. doi request reprint Every life has equal value
    Leroy E Hood
    Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA Electronic address
    Cell 154:1178-9. 2013
  3. doi request reprint Interview with Leroy Hood
    Leroy Hood
    Institute for Systems Biology, Seattle, WA 98105, USA
    Bioanalysis 5:1475-8. 2013
  4. doi request reprint A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory
    Leroy Hood
    Institute for Systems Biology, 401N Terry Ave, Seattle, WA 98121, USA
    N Biotechnol 29:613-24. 2012
  5. pmc Systems medicine and integrated care to combat chronic noncommunicable diseases
    Jean Bousquet
    Department of Respiratory Diseases, Arnaud de Villeneuve Hospital, CHU Montpellier, INSERM CESP U1018, Villejuif, France
    Genome Med 3:43. 2011
  6. pmc Predictive, preventive, personalized and participatory medicine: back to the future
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 rue Guy Moquet, BP8, 94801 Villejuif Cedex, France
    Genome Med 2:57. 2010
  7. pmc POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer
    Christopher Lausted
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Genome Biol 5:R58. 2004
  8. pmc Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    Frank Desiere
    Nestle Research Center, 1000 Lausanne 26, Switzerland
    Genome Biol 6:R9. 2005
  9. pmc The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    Richard Bonneau
    New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
    Genome Biol 7:R36. 2006
  10. pmc Low-pass sequencing for microbial comparative genomics
    Young Ah Goo
    Institute for Systems Biology, Seattle, Washington 98103, USA
    BMC Genomics 5:3. 2004

Research Grants

Detail Information

Publications82

  1. ncbi request reprint Printing your own inkjet microarrays
    Christopher G Lausted
    Institute for Systems Biology, Seattle, Washington, USA
    Methods Enzymol 410:168-89. 2006
    ..A benchtop inkjet arrayer-nicknamed POSAM-can be built by most skilled molecular biology laboratories. Inkjet arrays can fulfill the changing needs of those studying the complex network of relationships in systems biology...
  2. doi request reprint Every life has equal value
    Leroy E Hood
    Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA Electronic address
    Cell 154:1178-9. 2013
    ....
  3. doi request reprint Interview with Leroy Hood
    Leroy Hood
    Institute for Systems Biology, Seattle, WA 98105, USA
    Bioanalysis 5:1475-8. 2013
    ..He is currently focused on taking a systems approach to disease. Here he talks to Lisa Parks, Assistant Commissioning Editor of Bioanalysis. ..
  4. doi request reprint A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory
    Leroy Hood
    Institute for Systems Biology, 401N Terry Ave, Seattle, WA 98121, USA
    N Biotechnol 29:613-24. 2012
    ..Managing the societal problems will pose the most significant challenges. Strategic partnerships of a variety of types will be necessary to bring P4 medicine to patients...
  5. pmc Systems medicine and integrated care to combat chronic noncommunicable diseases
    Jean Bousquet
    Department of Respiratory Diseases, Arnaud de Villeneuve Hospital, CHU Montpellier, INSERM CESP U1018, Villejuif, France
    Genome Med 3:43. 2011
    ..This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and specificities of local economies and health systems...
  6. pmc Predictive, preventive, personalized and participatory medicine: back to the future
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 rue Guy Moquet, BP8, 94801 Villejuif Cedex, France
    Genome Med 2:57. 2010
    ....
  7. pmc POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer
    Christopher Lausted
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Genome Biol 5:R58. 2004
    ..We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays...
  8. pmc Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    Frank Desiere
    Nestle Research Center, 1000 Lausanne 26, Switzerland
    Genome Biol 6:R9. 2005
    ..This resource could serve as an expandable repository for MS-derived proteome information...
  9. pmc The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    Richard Bonneau
    New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
    Genome Biol 7:R36. 2006
    ..Several specific regulatory predictions were experimentally tested and verified...
  10. pmc Low-pass sequencing for microbial comparative genomics
    Young Ah Goo
    Institute for Systems Biology, Seattle, Washington 98103, USA
    BMC Genomics 5:3. 2004
    ..NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe...
  11. pmc The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis
    Xuefeng Fang
    Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
    BMC Genomics 12:11. 2011
    ..SOX2 appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed response program of SOX2 in GBM has not yet been defined...
  12. pmc An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution
    Gustavo Glusman
    Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
    BMC Evol Biol 4:43. 2004
    ..Three runt domain genes have been described in each vertebrate genome (the RUNX gene family), but only one in other chordates. Therefore, the common ancestor of vertebrates has been thought to have had a single runt domain gene...
  13. pmc WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis
    Fan Mo
    Zhejiang California Nanosystems Institute, Zhejiang University, Hangzhou, China
    BMC Bioinformatics 11:219. 2010
    ..However, limitations of these filtering approaches often result in inaccurate peptide quantification. Here we present the WaveletQuant program, based on wavelet theory, for better or alternative MS-based proteomic quantification...
  14. pmc Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
    Richard Bonneau
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Genome Biol 5:R52. 2004
    ..The work reported here demonstrates that de novo structure prediction is now a viable option for providing general function information for many proteins of unknown function...
  15. ncbi request reprint The impact of systems approaches on biological problems in drug discovery
    Leroy Hood
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Nat Biotechnol 22:1215-7. 2004
  16. ncbi request reprint Wu and Kabat 1970: a transforming view of antibody diversity
    Leroy E Hood
    Institute of Systems Biology, Seattle, WA 98105, USA
    J Immunol 180:7055-6. 2008
  17. ncbi request reprint Systems biology and new technologies enable predictive and preventative medicine
    Leroy Hood
    Institute for Systems Biology, Seattle, WA, USA
    Science 306:640-3. 2004
    ..Such concepts are transforming current diagnostic and therapeutic approaches to medicine and, together with new technologies, will enable a predictive and preventive medicine that will lead to personalized medicine...
  18. doi request reprint Predictive, personalized, preventive, participatory (P4) cancer medicine
    Leroy Hood
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Nat Rev Clin Oncol 8:184-7. 2011
    ....
  19. doi request reprint A personal journey of discovery: developing technology and changing biology
    Lee Hood
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Annu Rev Anal Chem (Palo Alto Calif) 1:1-43. 2008
    ..Finally, I discuss the origins, the philosophy, some accomplishments, and the future trajectories of the Institute for Systems Biology...
  20. pmc Gene regulatory networks and embryonic specification
    Leroy Hood
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 105:5951-2. 2008
  21. ncbi request reprint The digital code of DNA
    Leroy Hood
    Institute for Systems Biology, 4225 Roosevelt Way NE, Seattle, Washington 98105, USA
    Nature 421:444-8. 2003
    ..DNA has two types of digital information--the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes...
  22. ncbi request reprint Systems biology: integrating technology, biology, and computation
    Leroy Hood
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mech Ageing Dev 124:9-16. 2003
    ..These two themes will dominate 21st century biology and medicine. I will discuss these changes and indicate how they may interface with with the process of aging...
  23. ncbi request reprint Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine
    Andrea D Weston
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    J Proteome Res 3:179-96. 2004
    ..In this review, we define systems biology, discuss the current capabilities of proteomics and highlight some of the necessary milestones for moving systems biology and proteomics into mainstream health care...
  24. pmc Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes
    Laura E Pascal
    Department of Urology, University of Washington, Seattle, WA 98195, USA
    BMC Cancer 9:452. 2009
    ..This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure...
  25. pmc Sequence analysis of mouse vomeronasal receptor gene clusters reveals common promoter motifs and a history of recent expansion
    Robert P Lane
    Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 99:291-6. 2002
    ..Orthologous V1R genes appear to have been lost during primate evolution. Exceptional noncoding homology is observed across four V1R subfamilies at one cluster and thus may be important for locus-specific transcriptional regulation...
  26. doi request reprint New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences
    Leroy E Hood
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 12:2773-83. 2012
    ..Opportunities are identified for a coordinated R&D effort to achieve major technology-based goals and address societal challenges in health, agriculture, nutrition, energy, environment, national security, and economic development...
  27. pmc RNASEQR--a streamlined and accurate RNA-seq sequence analysis program
    Leslie Y Chen
    Institute for Systems Biology, Seattle, WA 98109, USA
    Nucleic Acids Res 40:e42. 2012
    ..RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers...
  28. pmc General transcription factor specified global gene regulation in archaea
    Marc T Facciotti
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98121, USA
    Proc Natl Acad Sci U S A 104:4630-5. 2007
    ....
  29. pmc Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells
    Jared C Roach
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 104:16245-50. 2007
    ..A broad range of activation kinetics was observed; thus, combinatorial regulation by small subsets of transcription factors would permit almost any timing input to cis-regulatory elements controlling gene transcription...
  30. pmc Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
    Nils Gehlenborg
    Institute for Systems Biology, Seattle, USA
    Bioinformatics 25:682-3. 2009
    ....
  31. ncbi request reprint KLK31P is a novel androgen regulated and transcribed pseudogene of kallikreins that is expressed at lower levels in prostate cancer cells than in normal prostate cells
    Wei Lu
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Prostate 66:936-44. 2006
    ..KLK expression is associated with various human diseases including cancers. Noncoding RNAs such as PCA3/DD3 and PCGEM1 have been identified in prostate cancer cells...
  32. pmc The evolution of vertebrate Toll-like receptors
    Jared C Roach
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:9577-82. 2005
    ..In addition, we have produced >70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt...
  33. ncbi request reprint Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease
    Biaoyang Lin
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Cancer Res 65:3081-91. 2005
    ..Our efforts represent a significant step toward a systems approach to understanding prostate cancer progression...
  34. pmc A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations
    Xiaowei Yan
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 108:1591-6. 2011
    ..Our systematic analysis provides molecular and genetic support for the stem cell-like nature of CD133(+) cells and an objective means for evaluating cancer aggressiveness...
  35. ncbi request reprint Bridging the BMP and Wnt pathways by PI3 kinase/Akt and 14-3-3zeta
    Qiang Tian
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Cell Cycle 4:215-6. 2005
    ....
  36. doi request reprint Label-free detection with surface plasmon resonance imaging
    Christopher Lausted
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 723:321-33. 2011
    ..In this example, antibody microarrays are used to efficiently profile the secretion of proteins from a cell line exposed to varying concentrations of a toxic compound...
  37. pmc Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden
    Jared C Roach
    Institute for Systems Biology, Seattle, WA 98103, USA
    Am J Hum Genet 79:614-27. 2006
    ..0%-31.0%) suggests that variation within ITPR3 reflects an important contribution to T1D in Sweden. Two-locus regression analysis supports an influence of ITPR3 variation on T1D that is distinct from that of any MHC class II gene...
  38. doi request reprint Quantitative serum proteomics from surface plasmon resonance imaging
    Christopher Lausted
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 7:2464-74. 2008
    ..alpha-Fetoprotein, a known liver cancer marker, was observed to increase. These results demonstrate the feasibility of this high throughput approach for both absolute and relative protein expression profiling...
  39. pmc Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1
    Nitin S Baliga
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 14:1025-35. 2004
    ....
  40. pmc Systems biology and the discovery of diagnostic biomarkers
    Kai Wang
    Institute for Systems Biology, WA, USA
    Dis Markers 28:199-207. 2010
    ..This general approach, including diagnostics and therapeutics, is becoming known as systems medicine...
  41. ncbi request reprint SPR imaging for high throughput, label-free interaction analysis
    Christopher Lausted
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Comb Chem High Throughput Screen 12:741-51. 2009
    ..DNA, RNA, antibodies, enzymes, and a range of other proteins have been arrayed and quantitatively analyzed...
  42. pmc A third approach to gene prediction suggests thousands of additional human transcribed regions
    Gustavo Glusman
    Institute for Systems Biology, Seattle, Washington, USA
    PLoS Comput Biol 2:e18. 2006
    ..They therefore complement existing gene prediction methods and will help identify functional transcripts within many apparent "genomic deserts."..
  43. ncbi request reprint Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen
    Lee Rowen
    Institute for Systems Biology, Seattle, Washington, USA
    Mol Biol Evol 22:1712-20. 2005
    ..These residues could be involved in interactions with inhibitors...
  44. pmc Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach
    Nitin S Baliga
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    Proc Natl Acad Sci U S A 99:14913-8. 2002
    ..phototrophy and arginine fermentation, are inversely regulated, presumably to achieve a balance in ATP production under anaerobic conditions...
  45. pmc Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea
    Nitin S Baliga
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 14:2221-34. 2004
    ..Finally, as expected from the larger genome, H. marismortui encodes many more functions and seems to have fewer nutritional requirements for survival than does Halobacterium sp. NRC-1...
  46. ncbi request reprint ACGT-a comparative genomics tool
    Tao Xie
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Bioinformatics 19:1039-40. 2003
    ..It is written in Java and can be run on Unix, Linux and Windows platforms...
  47. pmc Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt
    Qiang Tian
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 101:15370-5. 2004
    ..We propose that Akt phosphorylates beta-catenin, which results in 14-3-3zeta binding and stabilization of beta-catenin, and these interactions may be involved in stem cell development...
  48. ncbi request reprint Lineage relationship between LNCaP and LNCaP-derived prostate cancer cell lines
    Alvin Y Liu
    Department of Urology, University of Washington, Seattle, 98195, USA
    Prostate 60:98-108. 2004
    ..Unlike LNCaP, the other cell lines show features of progressed disease such as metastatic capability and hormone independence. Analyses were done to determine if C4-2 or CL1 cells were selected from pre-existent subpopulations in LNCaP...
  49. ncbi request reprint Integrated genomic and proteomic analyses of gene expression in Mammalian cells
    Qiang Tian
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mol Cell Proteomics 3:960-9. 2004
    ....
  50. pmc A systems approach to prion disease
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 5:252. 2009
    ..Our systems analysis provides a comprehensive basis for developing models for prion replication and disease, and suggests some possible therapeutic approaches...
  51. doi request reprint Systems biology at the Institute for Systems Biology
    Leroy Hood
    Institute for Systems Biology, Seattle, WA 98103, USA
    Brief Funct Genomic Proteomic 7:239-48. 2008
    ..The Institute for Systems Biology has aspired to pioneer and seamlessly integrate each of these concepts...
  52. pmc Long-range multilocus haplotype phasing of the MHC
    Zhen Guo
    Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 103:6964-9. 2006
    ..Availability of an efficient method for MHC haplotype phase determination will facilitate the mapping of causative MHC-resident genes in many human diseases and has the potential to be broadened to other polymorphic gene complexes...
  53. pmc Analysis of genetic inheritance in a family quartet by whole-genome sequencing
    Jared C Roach
    Institute for Systems Biology, Seattle, WA 98103, USA
    Science 328:636-9. 2010
    ..Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the value of complete genome sequencing in families...
  54. pmc Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse
    Tao Xie
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 13:2621-36. 2003
    ..4) Conserved noncoding sequences are found primarily in or near the 5'-UTR or the first intron of genes, and seldom in the intergenic regions. Many of these conserved blocks are likely to be cis-regulatory elements...
  55. ncbi request reprint Predicting demographic group structures based on DNA sequence data
    Jon P Anderson
    Department of Molecular Biotechnology, Health Sciences Center, University of Washington, Seattle, USA
    Mol Biol Evol 20:1168-80. 2003
    ..Such predictions of demographic epidemiology based on sequence information may become valuable in assigning different treatment regimens to infected individuals...
  56. ncbi request reprint A personal view of molecular technology and how it has changed biology
    Leroy Hood
    President and Director, Institute for Systems Biology, Seattle, Washington 98103, USA
    J Proteome Res 1:399-409. 2002
  57. ncbi request reprint Human prostate epithelial cell-type cDNA libraries and prostate expression patterns
    Alvin Y Liu
    Department of Urology, University of Washington, Seattle, Washington 98195, USA
    Prostate 50:92-103. 2002
    ..Transcriptome analysis is a powerful approach to uncovering genes responsible for diseases such as prostate cancer. Ideally, one would like to compare the transcriptomes of a cancer cell and its normal counterpart for differences...
  58. ncbi request reprint Molecular profiling of stem cells
    Li Ma
    Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, United States
    Clin Chim Acta 378:24-32. 2007
    ....
  59. pmc Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas
    Nathan D Price
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 104:3414-9. 2007
    ..We expect that the use of simple marker pairs that exhibit these traits will be of significant clinical use in a variety of contexts...
  60. ncbi request reprint Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels
    Jennifer J Stewart
    The Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 5:433-43. 2006
    ..Several proteins may be involved in modulating response to cisplatin and have potential as markers of treatment response or treatment targets...
  61. pmc Circulating microRNAs, potential biomarkers for drug-induced liver injury
    Kai Wang
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 106:4402-7. 2009
    ..These findings suggest the potential of using specific circulating microRNAs as sensitive and informative biomarkers for drug-induced liver injury...
  62. ncbi request reprint Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity
    Lee Rowen
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Genomics 79:587-97. 2002
    ..The sequences of these genes provide insight into the mechanisms used to generate the diversity of neurexin protein isoforms and raise several interesting questions regarding the expression mechanism of large genes...
  63. pmc The program of androgen-responsive genes in neoplastic prostate epithelium
    Peter S Nelson
    Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Proc Natl Acad Sci U S A 99:11890-5. 2002
    ....
  64. pmc A molecular correlate to the Gleason grading system for prostate adenocarcinoma
    Lawrence True
    Department of Pathology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 103:10991-6. 2006
    ..Furthermore, in identifying a profile of 86 genes that distinguish high- from low-grade carcinomas, we have generated a set of potential targets for modulating the development and progression of the lethal prostate cancer phenotype...
  65. pmc A data integration methodology for systems biology: experimental verification
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:17302-7. 2005
    ..The methodology described here, addresses a critical need across all domains of molecular and cell biology, to effectively integrate large and disparate data sets...
  66. ncbi request reprint Genomic scan of 254 hereditary prostate cancer families
    Marta Janer
    Institute for Systems Biology, Seattle, Washington, USA
    Prostate 57:309-19. 2003
    ..These analyses support the existence of multiple HPC loci, whose presence may be best identified by analyses of large, including pooled, datasets which consider locus heterogeneity...
  67. ncbi request reprint Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells
    Lan Chun Tu
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 6:575-88. 2007
    ....
  68. doi request reprint Direct multiplexed measurement of gene expression with color-coded probe pairs
    Gary K Geiss
    NanoString Technologies Inc, 201 Elliott Ave West, Suite 300, Seattle, Washington 98119, USA
    Nat Biotechnol 26:317-25. 2008
    ..Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels...
  69. pmc Identification of a prostate cancer susceptibility locus on chromosome 7q11-21 in Jewish families
    Danielle M Friedrichsen
    Divisions of Clinical Research and Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 101:1939-44. 2004
    ..12 (P = 0.00007). These studies highlight the utility of analyzing defined sets of families with a common origin for reducing locus heterogeneity problems associated with studying complex traits...
  70. pmc MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Bioinformatics 24:2641-2. 2008
    ....
  71. ncbi request reprint Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1
    Young Ah Goo
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Cell Proteomics 2:506-24. 2003
    ....
  72. pmc Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor
    Biaoyang Lin
    Department of Urology, University of Washington, Seattle, WA, USA
    PLoS ONE 4:e6589. 2009
    ..The AR can act either as a promoter or a tumor suppressor depending on cell types. The AR proliferative response program has been well studied, but its prohibitive response program has not yet been thoroughly studied...
  73. ncbi request reprint Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae
    Timothy J Griffin
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 1:323-33. 2002
    ....
  74. ncbi request reprint Isolation and characterization of human and mouse WDR19,a novel WD-repeat protein exhibiting androgen-regulated expression in prostate epithelium
    Biaoyang Lin
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA, 98103, USA
    Genomics 82:331-42. 2003
    ..WDR19 transcripts exhibit alternative splicing in which two isoforms appear to be prostate restricted, a property that could be exploited for designing diagnostic or therapeutic strategies for prostate carcinoma...
  75. pmc A data integration methodology for systems biology
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:17296-301. 2005
    ..In an accompanying companion paper, we demonstrate the applicability of our approach to biological data. We have integrated our methodology into a free open source software package named POINTILLIST...
  76. doi request reprint Quantitative proteomics analysis integrated with microarray data reveals that extracellular matrix proteins, catenins, and p53 binding protein 1 are important for chemotherapy response in ovarian cancers
    Sheng Pan
    Department of Pathology, University of Washington, Seattle, Washington, USA
    OMICS 13:345-54. 2009
    ..Our results suggest that chemotherapy response may be determined by multiple and complex system properties involving extracellular-matrix, cell adhesion and junction proteins...
  77. ncbi request reprint Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics
    Bingyun Sun
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 6:141-9. 2007
    ..4) The approach is demonstrated here on the analysis of N-linked glycopeptides; however, it can be applied equally well to O-glycoprotein analysis...
  78. ncbi request reprint Proteomic analysis of human prostasomes
    Angelita G Utleg
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Prostate 56:150-61. 2003
    ..Other than a microscopic description of these secretory particles and an incomplete two-dimensional gel electrophoresis (2DE) study, little is known about the composition of proteins in prostasomes...
  79. pmc A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17
    Heon Park
    Department of Immunology, University of Washington, Seattle, Washington 98195, USA
    Nat Immunol 6:1133-41. 2005
    ..Thus, IL-17 expression characterizes a unique T helper lineage that regulates tissue inflammation...
  80. ncbi request reprint Systems biology and cancer stem cells
    Nathan D Price
    Institute for Systems Biology, Seattle, WA 98103, USA
    J Cell Mol Med 12:97-110. 2008
    ..These approaches also hold significant promise for identifying distinctive properties of the cancer stem cells, and progress is already being made...
  81. pmc Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci
    Robert P Lane
    Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195, USA
    Genome Res 12:81-7. 2002
    ..g., to recombine ORs into a transcriptionally active locus. We searched the mouse sequence for OR-flanking RSS motifs, but did not find evidence to suggest that these OR genes use TCR-like recombination target sequences...
  82. pmc Gene expression dynamics in the macrophage exhibit criticality
    Matti Nykter
    Institute of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland
    Proc Natl Acad Sci U S A 105:1897-900. 2008
    ....

Research Grants3

  1. Intelligent Information Systems for Systems Biology
    Leroy Hood; Fiscal Year: 2003
    ..Finally, we propose some novel educational programs designed to put graduate students together into interdisciplinary teams for problem solving. ..