Leroy Hood, MD, PhD

President and Co-founder

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Dr. Hood’s outstanding contributions have had a resounding effect on the advancement of science since the 1960s. Throughout his career, he has adhered to the advice of his mentor, Dr. William J. Dreyer: “If you want to practice biology, do it on the leading edge, and if you want to be on the leading edge, invent new tools for deciphering biological information.”

Hood was involved in the development of five instruments critical for contemporary biology—namely, automated DNA sequencers, DNA synthesizers, protein sequencers, peptide synthesizers, and an ink jet printer for constructing DNA arrays. These instruments opened the door to high-throughput biological data and the era of big data in biology and medicine.  He helped pioneer the human genome program—making it possible with the automated DNA sequencer. Under Hood’s direction, the Human Genome Center sequenced portions of human chromosomes 14 and 15.

In 1992, Hood created the first cross-disciplinary biology department, Molecular Biotechnology, at the University of Washington. In 2000, he left the UW to co-found Institute for Systems Biology, the first of its kind. He has pioneered systems medicine the years since ISB’s founding. Hood has made many seminal discoveries in the fields of immunology, neurobiology and biotechnology and, most recently, has been a leader in the development of systems biology, its applications to cancer, neurodegenerative disease, and the linkage of systems biology to personalized medicine.

Hood is now pioneering new approaches to P4 medicine—predictive, preventive, personalized and participatory, and most recently, has embarked on creating a P4 pilot project on 100,000 well individuals, that is transforming healthcare.

In addition to his ground-breaking research, Hood has published 750 papers, received 36 patents, 17 honorary degrees and more than 100 awards and honors. He is one of only 15 individuals elected to all three National Academies—the National Academy of Science, the National Academy of Engineering, and the Institute of Medicine. Hood has founded or co-founded 15 different biotechnology companies including Amgen, Applied Biosystems, Rosetta, Darwin, Integrated Diagnostics, Indi Molecular and Arivale.

2015      The Johns Hopkins University Alumni Association Global Achievement Award
2014      Institute of Electrical and Electronics Engineers Medal for Innovations in Healthcare Technology
2014      Geoffrey Beene Builders of Science award presented by Research!America
2013      Alvin J. Thompson Award for Leadership in K-12 education and science (awarded by NW Assoc. for Biomed Research)
2013     Future in Review, CEO of the year
2012     Elected as a Fellow to the American Association for Cancer Research
2011     National Medal of Science
2011     Fritz and Dolores Russ Prize, National Academy of Engineering
2007     Elected Member, National Academy of Engineering
2007     Elected Member, Inventors Hall of Fame for the automated DNA sequencer
2006     Heinz Award for pioneering work in Systems Biology
2005     AACR-Irving Weinstein Foundation Distinguished Lecturer Award
2003     Elected Member, Institute of Medicine of the National Academy of Science
2003     Lemelson-MIT Prize for Innovation and Invention
2002     Kyoto Prize in Advanced Technology
2000     Elected Member, American Philosophical Society
1993     Scientist of the Year, Research and Development Magazine
1987     Albert Lasker Basic Medical Research Award
1982     Elected Member, National Academy of Science
1982     Elected Fellow, National Academy of Arts and Sciences

2000-present
President and Co-Founder of the Institute for Systems Biology in Seattle, WA
1992-2000
Chairman and Founder of the Department of Molecular Biotechnology at the UW
1970-1992
Caltech Faculty Member — Chair of Biology for 10 years
1967-1970
Senior Investigator, National Cancer Institute, National Institutes of Health
1967 PhD
Caltech
1964 MD
The Johns Hopkins School of Medicine
1960 BS
Caltech

Download Hood_CV_June 2015

2015

Keller A, Bader S.L, Shteynberg D, Hood L, Moritz RL.  2015.  Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data Independent Acquisition MS using SWATHProphet. Molecular & cellular proteomics : MCP.

Zhu X, Yuan R., Hood L, Ao P.  2015.  Endogenous molecular-cellular hierarchical modeling of prostate carcinogenesis uncovers robust structure. Progress in biophysics and molecular biology. 117:30-42.

He Y, Zeng K., Zhang X., Chen Q., Wu J, Li H, Zhou Y, Glusman G, Roach J,Etheridge A et al..  2015.  A Gain-of-Function Mutation in TRPV3 Causes Focal Palmoplantar Keratoderma in a Chinese Family. The Journal of investigative dermatology. 135:907-9.

Lin B, Lee H, Yoon JG, Madan A, Wayner E., Tonning S., Hothi P., Schroeder B.,Ulasov I., Foltz G et al..  2015.  Global analysis of H3K4me3 and H3K27me3 profiles in glioblastoma stem cells and identification of SLC17A7 as a bivalent tumor suppressor gene.Oncotarget.

Glusman G, Severson A., Dhankani V., Robinson M, Farrah T, Mauldin DE,Stittrich A.B, Ament SA, Roach JC, Brunkow M.E et al..  2015.  Identification of copy number variants in whole-genome data using Reference Coverage Profiles. Frontiers in genetics. 6:45.

Hood L, Lovejoy J.C, Price ND.  2015.  Integrating big data and actionable health coaching to optimize wellness. BMC medicine. 13:4.

Ament SA, Szelinger S., Glusman G, Ashworth J, Hou L., Akula N., Shekhtman T., Badner J.A, Brunkow M.E, Mauldin DE et al..  2015.  Rare variants in neuronal excitability genes influence risk for bipolar disorder. Proceedings of the National Academy of Sciences of the United States of America. 112:3576-81.

2014

Hood L, Price ND.  2014.  Demystifying disease, democratizing health care. Science translational medicine. 6:225ed5.

Cho JH, Lee I, Hammamieh R., Wang K, Baxter D, Scherler K., Etheridge A,Kulchenko A., Gautam A., Muhie S. et al..  2014.  Molecular evidence of stress-induced acute heart injury in a mouse model simulating posttraumatic stress disorder.Proceedings of the National Academy of Sciences of the United States of America. 111:3188-93.

Hu Z, Lausted C, Yoo H, Yan X, Brightman A, Chen J, Wang W, Bu X., Hood L.  2014.  Quantitative liver-specific protein fingerprint in blood: a signature for hepatotoxicity.Theranostics. 4:215-28.

Li H, Glusman G, Hu H, , Caballero J, Hubley R, Witherspoon D., Guthery S.L,Mauldin DE, Jorde LB et al..  2014.  Relationship estimation from whole-genome sequence data. PLoS genetics. 10:e1004144.

Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K.  2014.  Systems approach to neurodegenerative disease biomarker discovery. Annual review of pharmacology and toxicology. 54:457-81.

Lopes M., Kutlu B, Miani M., Bang-Berthelsen C.H, Storling J., Pociot F.,Goodman N, Hood L, Welsh N, Bontempi G. et al..  2014.  Temporal profiling of cytokine-induced genes in pancreatic beta-cells by meta-analysis and network inference.Genomics.

Hu H, Roach JC, Coon H., Guthery S.L, Voelkerding K.V, Margraf R.L, Durtschi J.D, Tavtigian SV, , Wu W. et al..  2014.  A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nature biotechnology.

2013

Ko Y., Ament SA, Eddy JA, Caballero J, Earls J.C, Hood L, Price ND.  2013.  Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. 110:3095-100.

Hood LE, Lazowska E.D.  2013.  Every life has equal value. Cell. 154:1178-9.

Sun B, Utleg AG, Hu Z, Qin S, Keller A, Lorang C, Gray L, Brightman A, Lee D,Alexander V et al..  2013.  Glycocapture-Assisted Global Quantitative Proteomics (gagQP) Reveals Multiorgan Responses in Serum Toxicoproteome. Journal of proteome research.

Hood L, Rowen L.  2013.  The human genome project: big science transforms biology and medicine. Genome Med. 5:79.

Hood L.  2013.  Interview with Leroy Hood. Bioanalysis. 5:1475-8.

Sung J, Kim P.J, Ma S, Funk C.C, Magis AT, Wang Y, Hood L, Geman D, Price ND.  2013.  Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures. PLoS Comput Biol. 9:e1003148.

Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L,Tian Q, Hood L.  2013.  N-glycoproteome of e14.tg2a mouse embryonic stem cells.PloS one. 8:e55722.

Hood L, Auffray C.  2013.  Participatory medicine: a driving force for revolutionizing healthcare. Genome medicine. 5:110.

Goverman J, Woods A., Larson L., Weiner L.P, Hood L, Zaller D.M.  2013.  Pillars article: Transgenic mice that express a myelin basic protein-specific T cell receptor develop spontaneous autoimmunity. Cell. 1993. 72: 551-560. J Immunol. 190:3018-27.

Gomes C.P, Cho JH, Hood L, Franco O.L, Pereira R.W, Wang K.  2013.  A Review of Computational Tools in microRNA Discovery. Front Genet. 4:81.

Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K.  2013.  Systems Approach to Neurodegenerative Disease Biomarker Discovery. Annu Rev Pharmacol Toxicol.

2012

Hood LE, Omenn GS, Moritz RL, Aebersold R, K YR, Amos M, Hunter-Cevera J,Locascio L.  2012.  New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences.Proteomics.

Hood L, Balling R, Auffray C.  2012.  Revolutionizing medicine in the 21(st) century through systems approaches. Biotechnology journal.

Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.  2012.  RNASEQR–a streamlined and accurate RNA-seq sequence analysis program. Nucleic acids research. 40:e42.

Shi Q, Qin L, Wei W, Geng F, Fan R, Shin YS, Guo D, Hood L, Mischel PS, Heath JR.  2012.  Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. Proceedings of the National Academy of Sciences of the United States of America. 109:419-24.

Qin S, Zhou Y, Lok AS, Tsodikov A, Yan X, Gray L, Yuan M, Moritz RL, Galas D,Omenn GS et al..  2012.  SRM targeted proteomics in search for biomarkers of HCV-induced progression of fibrosis to cirrhosis in HALT-C patients. Proteomics. 12:1244-52.

Hood L.  2012.  Tackling the microbiome. Science. 336:1209.

2011

Ideker T, Dutkowski J, Hood L.  2011.  Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power. Cell. 144:860-3.

Yan X, Ma L, Yi D, Yoon JG, Diercks A, Foltz G, Price ND, Hood LE, Tian Q.  2011.  A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A. 108:1591-6.

Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE,Srivastava D, Garg V, Pollard KS, Galas DJ et al..  2011.  Chromosomal Haplotypes by Genetic Phasing of Human Families. American journal of human genetics.

Westaway D, Genovesi S, Daude N, Brown R, Lau A, Lee I, Mays CE,Coomaraswamy J, Canine B, Pitstick R et al..  2011.  Down-regulation of Shadoo in prion infections traces a pre-clinical event inversely related to PrP(Sc) accumulation. PLoS pathogens. 7:e1002391.

Etheridge A, Lee I, Hood L, Galas D, Wang K.  2011.  Extracellular microRNA: A new source of biomarkers. Mutat Res.

Thiel KJ, Engelhardt B, Hood LE, Peartree NA, Neisewander JL.  2011.  The interactive effects of environmental enrichment and extinction interventions in attenuating cue-elicited cocaine-seeking behavior in rats. Pharmacol Biochem Behav. 97:595-602.

Glusman G, Caballero J, Mauldin D, Hood L, Roach J.  2011.  KAVIAR: an accessible system for testing SNV novelty. Bioinformatics.

Lausted C, Hu Z, Hood L.  2011.  Label-free detection with surface plasmon resonance imaging. Methods Mol Biol. 723:321-33.

Fang X, Yoon JG, Li L, Tsai YS, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B.  2011.  Landscape of the SOX2 protein-protein interactome. Proteomics.

Hood L.  2011.  Lee Hood. Nat Biotechnol. 29:191.

Moussay E, Wang K, Cho JH, van Moer K, Pierson S, Paggetti J, Nazarov PV,Palissot V, Hood LE, Berchem G et al..  2011.  MicroRNA as biomarkers and regulators in B-cell chronic lymphocytic leukemia. Proc Natl Acad Sci U S A. 108:6573-8.

Hood L, Friend SH.  2011.  Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat Rev Clin Oncol. 8:184-7.

Kim Y, Kim TK, Yoo J, You S, Lee I, Carlson G, Hood L, Choi S, Hwang D.  2011.  Principal network analysis: identification of subnetworks representing major dynamics using gene expression data. Bioinformatics. 27:391-8.

Fang X, Yoon JG, Li L, Yu W, Shao J, Hua D, Zheng S, Hood L, Goodlett DR,Foltz G et al..  2011.  The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis. BMC Genomics. 12:11.

Tian Q, Price ND, Hood L.  2011.  Systems Cancer Medicine: Towards Realization of Predictive, Preventive, Personalized, and Participatory (P4) Medicine. Journal of internal medicine.

Bousquet J, Anto JM, Sterk PJ, Adcock IM, Chung KF, Roca J, Agusti A,Brightling C, Cambon-Thomsen A, Cesario A et al..  2011.  Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome medicine. 3:43.

2010

Cheng L, Lu W, Kulkarni B, Pejovic T, Yan X, Chiang JH, Hood L, Odunsi K, Lin B.  2010.  Analysis of chemotherapy response programs in ovarian cancers by the next-generation sequencing technologies. Gynecol Oncol. 117:159-69.

Roach J, Glusman G, Smit A, Huff CD, Hubley R, Shannon P, Rowen L, Pant KP,Goodman N, Bamshad M et al..  2010.  Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 328:636-9.

Panchalingam KM, Paramchuk WJ, Chiang CY, Shah N, Madan A, Hood L, Foltz G, Behie LA.  2010.  Bioprocessing of human glioblastoma brain cancer tissue. Tissue Eng Part A. 16:1169-77.

del Sol A, Balling R, Hood L, Galas DJ.  2010.  Diseases as network perturbations.Curr Opin Biotechnol. 21:566-71.

Foltz G, Yoon JG, Lee H, Ma L, Tian Q, Hood L, Madan A.  2010.  Epigenetic Regulation of Wnt Pathway Antagonists in Human Glioblastoma Multiforme. Genes & Cancer. 1:81.

Auffray C, Ideker T, Galas DJ, Hood L.  2010.  The hallmarks of cancer revisited through systems biology and network modeling. Cancer Systems Biology, Bioinformatics and Medicine: Research and Clinical Applications.

Eddy JA, Hood L, Price ND, Geman D.  2010.  Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol. 6:e1000792.

Lin B, Madan A, Yoon JG, Fang X, Yan X, Kim TK, Hwang D, Hood L, Foltz G.  2010.  Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma. PLoS OnePLoS ONE. 5:e10210.

Ouellet E, Lausted C, Lin T, Yang CW, Hood L, Lagally ET.  2010.  Parallel microfluidic surface plasmon resonance imaging arrays. Lab Chip. 10:581-8.

Wang K, Lee I, Carlson G, Hood L, Galas DJ.  2010.  Systems biology and the discovery of diagnostic biomarkers. Dis Markers. 28:199-207.

Ao P, Galas DJ, Hood L, Yin L, Zhu XM.  2010.  Towards predictive stochastic dynamical modeling of cancer genesis and progression. Interdiscip Sci. 2:140-4.

Mo F, Mo Q, Chen Y, Goodlett DR, Hood L, Omenn GS, Li S, Lin B.  2010.  WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. BMC Bioinformatics. 11:219.

2009

Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ.  2009.  Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci U S A. 106:4402-7.

Lin B, White JT, Wu J, Lele S, Old LJ, Hood L, Odunsi K.  2009.  Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl. 3:853-861.

Stanford JL, Fitzgerald LM, McDonnell SK, Carlson EE, McIntosh LM, Deutsch K,Hood L, Ostrander EA, Schaid DJ.  2009.  Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage. Hum Mol Genet. 18:1839-48.

Kutlu B, Burdick D, Baxter D, Rasschaert J, Flamez D, Eizirik DL, Welsh N,Goodman N, Hood L.  2009.  Detailed transcriptome atlas of the pancreatic beta cell.BMC Med Genomics. 2:3.

Foltz G, Yoon JG, Lee H, Ryken TC, Sibenaller Z, Ehrich M, Hood L, Madan A.  2009.  DNA methyltransferase-mediated transcriptional silencing in malignant glioma: a combined whole-genome microarray and promoter array analysis. Oncogene. 28:2667-77.

Majeti R, Becker MW, Tian Q, Lee TL, Yan X, Liu R, Chiang JH, Hood L, Clarke MF, Weissman IL.  2009.  Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A. 106:3396-401.

Yu B, Yang X, Xu Y, Yao G, Shu H, Lin B, Hood L, Wang H, Yang S, Gu J et al..  2009.  Elevated expression of DKK1 is associated with cytoplasmic/nuclear beta-catenin accumulation and poor prognosis in hepatocellular carcinomas. J Hepatol. 50:948-57.

Pascal LE, Vencio RZ, Page LS, Liebeskind ES, Shadle CP, Troisch P, Marzolf B,True LD, Hood LE, Liu AY.  2009.  Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes. BMC Cancer. 9:452.

Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X,Schones DE et al..  2009.  Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS OnePLoS ONE. 4:e6589.

Kutlu B, Kayali AG, Jung S, Parnaud G, Baxter D, Glusman G, Goodman N,Behie LA, Hayek A, Hood L.  2009.  Meta-analysis of gene expression in human pancreatic islets after in vitro expansion. Physiol Genomics. 39:72-81.

Heath JR, Davis ME, Hood L.  2009.  Nanomedicine targets cancer. Sci Am. 300:44-51.

Gehlenborg N, Yan W, Lee I, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L.  2009.  Prequips–an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics. 25:682-3.

Gehlenborg N, Hwang D, Lee I, Yoo H, Baxter D, Petritis B, Pitstick R, Marzolf B,Dearmond SJ, Carlson GA et al..  2009.  The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases.Database : the journal of biological databases and curation. 2009:bap011.

Pan S, Cheng L, White JT, Lu W, Utleg AG, Yan X, Urban ND, Drescher CW,Hood L, Lin B.  2009.  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. OMICS. 13:345-54.

Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J et al..  2009.  Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 3:9-17.

Lausted C, Hu Z, Hood L, Campbell CT.  2009.  SPR imaging for high throughput, label-free interaction analysis. Comb Chem High Throughput Screen. 12:741-51.

Hwang D, Lee I, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R,Young R, Spicer D et al..  2009.  A systems approach to prion disease. Molecular systems biology. 5:252.

Galas DJ, Hood L.  2009.  Systems biology and emerging technologies will catalyze the transition from reactive medicine to predictive, personalized, preventive and participatory (P4) medicine. Interdisciplinary Bio Central. 1:0006.

Price ND, Edelman LB, Lee I, Yoo H, Hwang D, Carlson G, Galas DJ, Heath JR,Hood L.  2009.  Systems biology and the emergence of systems medicine. Genomic and Personalized Medicine: From Principles to Practice.

Auffray C, Chen Z, Hood L.  2009.  Systems medicine: the future of medical genomics and healthcare. Genome Med. 1:2.

Tu LC, Foltz G, Lin E, Hood L, Tian Q.  2009.  Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther. 4:147-53.

2008

Ao P, Galas DJ, Hood L, Zhu X.  2008.  Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution. Med Hypotheses. 70:678-84.

Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, Fell HP,Ferree S, George RD, Grogan T et al..  2008.  Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol. 26:317-25.

Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O,Shmulevich I.  2008.  Gene expression dynamics in the macrophage exhibit criticality.Proc Natl Acad Sci U S A. 105:1897-900.

Hood L.  2008.  Gene regulatory networks and embryonic specification. Proc Natl Acad Sci U S A. 105:5951-2.

Tischkowitz MD, Yilmaz A, Chen LQ, Karyadi DM, Novak D, Kirchhoff T, Hamel N, Tavtigian SV, Kolb S, Bismar TA et al..  2008.  Identification and characterization of novel SNPs in CHEK2 in Ashkenazi Jewish men with prostate cancer. Cancer Lett. 270:173-80.

Fan R, Vermesh O, Srivastava A, Yen BK, Qin L, Ahmad H, Kwong GA, Liu CC,Gould J, Hood L et al..  2008.  Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood. Nat Biotechnol. 26:1373-8.

Hwang D, Zhang N, Lee H, Yi E, Zhang H, Lee I, Hood L, Aebersold R.  2008.  MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. Bioinformatics. 24:2641-2.

Hood L.  2008.  A personal journey of discovery: developing technology and changing biology. Annu Rev Anal Chem (Palo Alto Calif). 1:1-43.

Li R, Guo Y, Han BM, Yan X, Utleg AG, Li W, Tu LC, Wang J, Hood L, Xia S et al..  2008.  Proteomics cataloging analysis of human expressed prostatic secretions reveals rich source of biomarker candidates. Proteomics Clin Appl. 2:543-555.

Lausted C, Hu Z, Hood L.  2008.  Quantitative serum proteomics from surface plasmon resonance imaging. Mol Cell Proteomics. 7:2464-74.

Price ND, Foltz G, Madan A, Hood L, Tian Q.  2008.  Systems biology and cancer stem cells. J Cell Mol Med. 12:97-110.

Hood L, Rowen L, Galas DJ, Aitchison JD.  2008.  Systems biology at the Institute for Systems Biology. Brief Funct Genomic Proteomic. 7:239-48.

Lin B, Utleg AG, Gravdal K, White JT, Halvorsen OJ, Lu W, True LD, Vessella R,Lange PH, Nelson PS et al..  2008.  WDR19 expression is increased in prostate cancer compared with normal cells, but low-intensity expression in cancers is associated with shorter time to biochemical failures and local recurrence. Clin Cancer Res. 14:1397-406.

Hood LE.  2008.  Wu and Kabat 1970: a transforming view of antibody diversity. J Immunol. 180:7055-6.

2007

Zhu X-M, Yin L, Hood L, Galas DJ, Ao P.  2007.  Efficiency, Robustness, and Stochasticity of Gene Regulatory Networks in Systems Biology: λ Switch as a Working Example. Introduction to Systems Biology. :336-371.

Rostad K, Mannelqvist M, Halvorsen OJ, Oyan AM, Bo TH, Stordrange L, Olsen S, Haukaas SA, Lin B, Hood L et al..  2007.  ERG upregulation and related ETS transcription factors in prostate cancer. Int J Oncol. 30:19-32.

Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P,Srivastava A, Donohoe SM, Hood LE et al..  2007.  General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 104:4630-5.

Schaid DJ, Stanford JL, McDonnell SK, Suuriniemi M, McIntosh L, Karyadi DM,Carlson EE, Deutsch K, Janer M, Hood L et al..  2007.  Genome-wide linkage scan of prostate cancer Gleason score and confirmation of chromosome 19q. Hum Genet. 121:729-35.

Pierce BL, Friedrichsen-Karyadi DM, McIntosh L, Deutsch K, Hood L, Ostrander EA, Austin MA, Stanford JL.  2007.  Genomic scan of 12 hereditary prostate cancer families having an occurrence of pancreas cancer. Prostate. 67:410-5.

Price ND, Trent J, El-Naggar AK, Cogdell D, Taylor E, Hunt KK, Pollock RE, Hood L, Shmulevich I, Zhang W.  2007.  Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A. 104:3414-9.

2007

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B et al..  2007.  Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2:2366-82.

Ma L, Sun B, Hood L, Tian Q.  2007.  Molecular profiling of stem cells. Clin Chim Acta. 378:24-32.

Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V,Shannon P, Johnson MH, Bare JC et al..  2007.  A predictive model for transcriptional control of physiology in a free living cell. Cell. 131:1354-65.

Tu LC, Yan X, Hood L, Lin B.  2007.  Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells. Mol Cell Proteomics. 6:575-88.

He XC, Yin T, Grindley JC, Tian Q, Sato T, Tao WA, Dirisina R, Porter-Westpfahl KS, Hembree M, Johnson T et al..  2007.  PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nat Genet. 39:189-98.

Hu Z, Hood L, Tian Q.  2007.  Quantitative proteomic approaches for biomarker discovery. Proteomics Clin Appl. 1:1036-41.

Sun B, Ranish J, Utleg AG, White JT, Yan X, Lin B, Hood L.  2007.  Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol Cell Proteomics. 6:141-9.

Johanneson B, Deutsch K, McIntosh L, Friedrichsen-Karyadi DM, Janer M, Kwon EM, Iwasaki L, Hood L, Ostrander EA, Stanford JL.  2007.  Suggestive genetic linkage to chromosome 11p11.2-q12.2 in hereditary prostate cancer families with primary kidney cancer. Prostate. 67:732-42.

Roach J, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE et al..  2007.  Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proc Natl Acad Sci U S A. 104:16245-50.

2006

Burrage K, Hood L, Ragan MA.  2006.  Advanced computing for systems biology.Brief Bioinform. 7:390-8.

Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O’Neill K, Whittaker CA,Kamal M, Chang JL, Cuomo CA et al..  2006.  Analysis of the DNA sequence and duplication history of human chromosome 15. Nature. 440:671-5.

Purcell MK, Smith KD, Hood L, Winton JR, Roach J.  2006.  Conservation of Toll-Like Receptor Signaling Pathways in Teleost Fish. Comp Biochem Physiol Part D Genomics Proteomics. 1:77-88.

Roach J, Deutsch K, Li S, Siegel AF, Bekris LM, Einhaus DC, Sheridan CM,Glusman G, Hood L, Lernmark A et al..  2006.  Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. Am J Hum Genet. 79:614-27.

Foltz G, Ryu GY, Yoon JG, Nelson T, Fahey J, Frakes A, Lee H, Field L, Zander K,Sibenaller Z et al..  2006.  Genome-wide analysis of epigenetic silencing identifies BEX1 and BEX2 as candidate tumor suppressor genes in malignant glioma. Cancer Res. 66:6665-74.

Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V.  2006.  The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 7:R36.

Lu W, Zhou D, Glusman G, Utleg AG, White JT, Nelson PS, Vasicek TJ, Hood L,Lin B.  2006.  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. Prostate. 66:936-44.

Guo Z, Hood L, Malkki M, Petersdorf EW.  2006.  Long-range multilocus haplotype phasing of the MHC. Proc Natl Acad Sci U S A. 103:6964-9.

True L, Coleman I, Hawley S, Huang CY, Gifford D, Coleman R, Beer TM,Gelmann E, Datta M, Mostaghel E et al..  2006.  A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A. 103:10991-6.

Schaid DJ, McDonnell SK, Zarfas KE, Cunningham JM, Hebbring S, Thibodeau SN, Eeles RA, Easton DF, Foulkes WD, Simard J et al..  2006.  Pooled genome linkage scan of aggressive prostate cancer: results from the International Consortium for Prostate Cancer Genetics. Hum Genet. 120:471-85.

Lausted C, Warren CB, Hood LE, Lasky SR.  2006.  Printing your own inkjet microarrays. Methods Enzymol. 410:168-89.

Stanford JL, McDonnell SK, Friedrichsen DM, Carlson EE, Kolb S, Deutsch K,Janer M, Hood L, Ostrander EA, Schaid DJ.  2006.  Prostate cancer and genetic susceptibility: a genome scan incorporating disease aggressiveness. Prostate. 66:317-25.

Stewart JJ, White JT, Yan X, Collins S, Drescher CW, Urban ND, Hood L, Lin B.  2006.  Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels. Mol Cell Proteomics. 5:433-43.

Glusman G, Qin S, El-Gewely MR, Siegel AF, Roach J, Hood L, Smit A.  2006.  A third approach to gene prediction suggests thousands of additional human transcribed regions. PLoS Comput Biol. 2:e18.

Cameron RA, Rowen L, Nesbitt R, Bloom S, Rast JP, Berney K, Arenas-Mena C,Martinez P, Lucas S, Richardson PM et al..  2006.  Unusual gene order and organization of the sea urchin hox cluster. J Exp Zool B Mol Dev Evol. 306:45-58.

2005

Tian Q, He XC, Hood L, Li L.  2005.  Bridging the BMP and Wnt pathways by PI3 kinase/Akt and 14-3-3zeta. Cell Cycle. 4:215-6.

Xu J, Dimitrov L, Chang BL, Adams TS, Turner AR, Meyers DA, Eeles RA, Easton DF, Foulkes WD, Simard J et al..  2005.  A combined genomewide linkage scan of 1,233 families for prostate cancer-susceptibility genes conducted by the international consortium for prostate cancer genetics. Am J Hum Genet. 77:219-29.

Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P,Aitchison JD, Hood L, Siegel AF et al..  2005.  A data integration methodology for systems biology. Proc Natl Acad Sci U S A. 102:17296-301.

Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P,Siegel AF, Bolouri H, Aitchison JD et al..  2005.  A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A. 102:17302-7.

Park H, Li Z, Yang XO, Chang SH, Nurieva R, Wang YH, Wang Y, Hood L, Zhu Z,Tian Q et al..  2005.  A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol. 6:1133-41.

Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova I,Lange PH et al..  2005.  Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease.Cancer Res. 65:3081-91.

Roach J, Glusman G, Rowen L, Kaur A, Purcell MK, Smith KD, Hood LE, Aderem A.  2005.  The evolution of vertebrate Toll-like receptors. Proc Natl Acad Sci U S A. 102:9577-82.

Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A,Boyle R, Brunner E, Donohoe S et al..  2005.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6:R9.

Rowen L, Williams E, Glusman G, Linardopoulou E, Friedman C, Ahearn ME,Seto J, Boysen C, Qin S, Wang K et al..  2005.  Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen. Mol Biol Evol. 22:1712-20.

Tao WA, Wollscheid B, O’Brien R, Eng JK, Li XJ, Bodenmiller B, Watts J, Hood L,Aebersold R.  2005.  Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods. 2:591-8.

Thorsson V, Hornquist M, Siegel AF, Hood L.  2005.  Reverse engineering galactose regulation in yeast through model selection. Stat Appl Genet Mol Biol. 4:Article28.

2004

Hood L.  2004.  Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins.:Foreword.

Hood L.  2004.  Biotechnology Annual Review. :Preface.

Zhu XM, Yin L, Hood L, Ao P.  2004.  Calculating biological behaviors of epigenetic states in the phage lambda life cycle. Funct Integr Genomics. 4:188-95.

Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L.  2004.  Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol. 5:R52.

Bunimovich YL, Ge G, Beverly KC, Ries RS, Hood L, Heath JR.  2004.  Electrochemically programmed, spatially selective biofunctionalization of silicon wires. Langmuir. 20:10630-8.

Glusman G, Kaur A, Hood L, Rowen L.  2004.  An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution. BMC Evol Biol. 4:43.

Moises H, Zoega T, Li L, Hood L.  2004.  Genes and Neurodevelopment in Schizophrenia. Behavior Genetics Principles: Perspectives in Development, Personality, and Psycophathology. :145-157.

Hartwell L, Hood L, Goldberg ML, Reynolds AE, Silver LM, Veres RC.  2004.  Genetics: from genes to genomes.

Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR et al..  2004.  Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14:2221-34.

Friedrichsen DM, Stanford JL, Isaacs SD, Janer M, Chang BL, Deutsch K,Gillanders E, Kolb S, Wiley KE, Badzioch MD et al..  2004.  Identification of a prostate cancer susceptibility locus on chromosome 7q11-21 in Jewish families. Proc Natl Acad Sci U S A. 101:1939-44.

Hood L, Perlmutter RM.  2004.  The impact of systems approaches on biological problems in drug discovery. Nat Biotechnol. 22:1215-7.

Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H,Thorsson V, Eng J et al..  2004.  Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics. 3:960-9.

Liu AY, Brubaker KD, Goo YA, Quinn JE, Kral S, Sorensen CM, Vessella RL,Belldegrun AS, Hood LE.  2004.  Lineage relationship between LNCaP and LNCaP-derived prostate cancer cell lines. Prostate. 60:98-108.

Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S,DasSarma S, Ng WV, Hood L.  2004.  Low-pass sequencing for microbial comparative genomics. BMC Genomics. 5:3.

Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison JD, Hood L, Lasky SR.  2004.  POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol. 5:R58.

Tian Q, Feetham MC, Tao WA, He XC, Li L, Aebersold R, Hood L.  2004.  Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proc Natl Acad Sci U S A. 101:15370-5.

Zhu XM, Yin L, Hood L, Ao P.  2004.  Robustness, stability and efficiency of phage lambda genetic switch: dynamical structure analysis. J Bioinform Comput Biol. 2:785-817.

Hood L, Heath JR, Phelps ME, Lin B.  2004.  Systems biology and new technologies enable predictive and preventative medicine. Science. 306:640-3.

Facciotti MT, Bonneau R, Hood L, Baliga NS.  2004.  Systems Biology Experimental Design – Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems. Current Genomics. 5:527-544(18).

Weston AD, Hood L.  2004.  Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res. 3:179-96.

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L,DiRuggiero J.  2004.  Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14:1025-35.

2003

Xie T, Hood L.  2003.  ACGT-a comparative genomics tool. Bioinformatics. 19:1039-40.

Xie T, Rowen L, Aguado B, Ahearn ME, Madan A, Qin S, Campbell RD, Hood L.  2003.  Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res. 13:2621-36.

Hood L, Galas DJ.  2003.  The digital code of DNA. Nature. 421:444-8.

McBride CM, Pollak KI, Garst J, Keefe F, Lyna P, Fish L, Hood L.  2003.  Distress and motivation for smoking cessation among lung cancer patients’ relatives who smoke. J Cancer Educ. 18:150-6.

Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M,Barbe V, de Berardinis V, Ureta-Vidal A et al..  2003.  The DNA sequence and analysis of human chromosome 14. Nature. 421:601-7.

Auffray C, Chen Z, Hood L, Soares B, Sugano S.  2003.  Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C R Biol. 326:867-75.

Auffray C, Imbeaud S, Roux-Rouquie M, Hood L.  2003.  From functional genomics to systems biology: concepts and practices. C R Biol. 326:879-92.

Janer M, Friedrichsen DM, Stanford JL, Badzioch MD, Kolb S, Deutsch K, Peters MA, Goode EL, Welti R, DeFrance HB et al..  2003.  Genomic scan of 254 hereditary prostate cancer families. Prostate. 57:309-19.

Lin F, Cordes K, Li L, Hood L, Couser WG, Shankland SJ, Igarashi P.  2003.  Hematopoietic stem cells contribute to the regeneration of renal tubules after renal ischemia-reperfusion injury in mice. J Am Soc Nephrol. 14:1188-99.

Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E et al..  2003.  Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol. 185:4593-602.

Lin B, White JT, Utleg AG, Wang S, Ferguson C, True LD, Vessella R, Hood L,Nelson PS.  2003.  Isolation and characterization of human and mouse WDR19,a novel WD-repeat protein exhibiting androgen-regulated expression in prostate epithelium.Genomics. 82:331-42.

Hood L.  2003.  Leroy Hood expounds the principles, practice and future of systems biology. Drug Discov Today. 8:436-8.

Heath JR, Phelps ME, Hood L.  2003.  NanoSystems biology. Mol Imaging Biol. 5:312-25.

Conlon EM, Goode EL, Gibbs M, Stanford JL, Badzioch M, Janer M, Kolb S, Hood L, Ostrander EA, Jarvik GP et al..  2003.  Oligogenic segregation analysis of hereditary prostate cancer pedigrees: evidence for multiple loci affecting age at onset. Int J Cancer. 105:630-5.

Anderson JP, Learn GH, Rodrigo AG, He X, Wang Y, Weinstock H, Kalish ML,Robbins KE, Hood L, Mullins JI.  2003.  Predicting demographic group structures based on DNA sequence data. Mol Biol Evol. 20:1168-80.

Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV.  2003.  Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics. 2:506-24.

Utleg AG, Yi EC, Xie T, Shannon P, White JT, Goodlett DR, Hood L, Lin B.  2003.  Proteomic analysis of human prostasomes. Prostate. 56:150-61.

Davidson EH, McClay DR, Hood L.  2003.  Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A. 100:1475-80.

Auffray C, Imbeaud S, Roux-Rouquie M, Hood L.  2003.  Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-time. Philos Transact A Math Phys Eng Sci. 361:1125-39.

Weston AD, Baliga NS, Bonneau R, Hood L.  2003.  Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harb Symp Quant Biol. 68:345-57.

Hood L.  2003.  Systems biology: integrating technology, biology, and computation.Mech Ageing Dev. 124:9-16.

2002

Leong KG, Hu X, Li L, Noseda M, Larrivee B, Hull C, Hood L, Wong F, Karsan A.  2002.  Activated Notch4 inhibits angiogenesis: role of beta 1-integrin activation. Mol Cell Biol. 22:2830-41.

Futter, E., Wade N, Varmus H, Green E, Venter C, Hood L, Bazell R, Haseltine W, Levine A, Kreek MJ et al..  2002.  After the Genome: Where Should We Go? The Genomic Revolution: Unveiling the Unity of Life. :64-73.

Gjertsen BT, Oyan AM, Marzolf B, Hovland R, Gausdal G, Doskeland SO,Dimitrov K, Golden A, Kalland KH, Hood L et al..  2002.  Analysis of acute myelogenous leukemia: preparation of samples for genomic and proteomic analyses. J Hematother Stem Cell Res. 11:469-81.

Rowen L, Young J, Birditt B, Kaur A, Madan A, Philipps DL, Qin S, Minx P, Wilson RK, Hood L et al..  2002.  Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics. 79:587-97.

Foltz G, Madan A, Hood L.  2002.  Cancer Proteomics: Methodologies for the Selection of Immunotherapy Targets. Principles and Practice of Biologic Therapy of Cancer Updates, Third Edition.

Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R.  2002.  Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics. 1:323-33.

Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P,Aebersold R, Ng WV, Hood L.  2002.  Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A. 99:14913-8.

Park IK, He Y, Lin F, Laerum OD, Tian Q, Bumgarner R, Klug CA, Li K, Kuhr C,Doyle MJ et al..  2002.  Differential gene expression profiling of adult murine hematopoietic stem cells. Blood. 99:488-98.

Graham J, Hagopian WA, Kockum I, Li LS, Sanjeevi CB, Lowe RM, Schaefer JB,Zarghami M, Day HL, Landin-Olsson M et al..  2002.  Genetic effects on age-dependent onset and islet cell autoantibody markers in type 1 diabetes. Diabetes. 51:1346-55.

Lane RP, Roach JC, Lee I, Boysen C, Smit A, Trask BJ, Hood L.  2002.  Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci. Genome research. 12:81-7.

Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T,Amore G, Hinman V, Arenas-Mena C et al..  2002.  A genomic regulatory network for development. Science. 295:1669-78.

Liu AY, Nelson PS, van den Engh G, Hood L.  2002.  Human prostate epithelial cell-type cDNA libraries and prostate expression patterns. Prostate. 50:92-103.

Hood L.  2002.  The InTouch interview with biotech man Leroy Hood, MD, PhD. Interview by Peter Tarr. InTouch. 4:28-32.

Guo Z, Gatterman MS, Hood L, Hansen JA, Petersdorf EW.  2002.  Oligonucleotide arrays for high-throughput SNPs detection in the MHC class I genes: HLA-B as a model system. Genome Res. 12:447-57.

Hood L.  2002.  A personal view of molecular technology and how it has changed biology.J Proteome Res. 1:399-409.

Nelson PS, Clegg N, Arnold H, Ferguson C, Bonham M, White J, Hood L, Lin B.  2002.  The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A. 99:11890-5.

Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T,Amore G, Hinman V, Arenas-Mena C et al..  2002.  A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol. 246:162-90.

Kumanovics A, Madan A, Qin S, Rowen L, Hood L, Fischer Lindahl K.  2002.  QUOD ERAT FACIENDUM: sequence analysis of the H2-D and H2-Q regions of 129/SvJ mice. Immunogenetics. 54:479-89.

Lane RP, Cutforth T, Axel R, Hood L, Trask BJ.  2002.  Sequence analysis of mouse vomeronasal receptor gene clusters reveals common promoter motifs and a history of recent expansion. Proc Natl Acad Sci U S A. 99:291-6.

Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A,Rash S, Hoon S, Smit A et al..  2002.  Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:1301-10.

2001

Peck RF, Echavarri-Erasun C, Johnson EA, Ng WV, Kennedy SP, Hood L,DasSarma S, Krebs MP.  2001.  brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum. J Biol Chem. 276:5739-44.

Wang K, Gan L, Kunisada T, Lee I, Yamagishi H, Hood L.  2001.  Characterization of the Japanese pufferfish (Takifugu rubripes) T-cell receptor alpha locus reveals a unique genomic organization. Immunogenetics. 53:31-42.

Goode EL, Stanford JL, Peters MA, Janer M, Gibbs M, Kolb S, Badzioch MD, Hood L, Ostrander EA, Jarvik GP.  2001.  Clinical characteristics of prostate cancer in an analysis of linkage to four putative susceptibility loci. Clin Cancer Res. 7:2739-49.

2001

Glusman G, Rowen L, Lee I, Boysen C, Roach J, Smit A, Wang K, Koop BF, Hood L.  2001.  Comparative genomics of the human and mouse T cell receptor loci.Immunity. 15:337-49.

Hood L.  2001.  Computing life: the challenge ahead. IEEE Eng Med Biol Mag. 20:20.

Hood L.  2001.  Deciphering Heredity. The Alfred Deakin Lectures: Ideas for the Future of a Civil Society. :164-176.

Chen F, Rowen L, Hood L, Rothenberg EV.  2001.  Differential transcriptional regulation of individual TCR V beta segments before gene rearrangement. J Immunol. 166:1771-80.

Moore RC, Mastrangelo P, Bouzamondo E, Heinrich C, Legname G, Prusiner SB,Hood L, Westaway D, Dearmond SJ, Tremblay P.  2001.  Doppel-induced cerebellar degeneration in transgenic mice. Proc Natl Acad Sci U S A. 98:15288-93.

Terskikh AV, Easterday MC, Li L, Hood L, Kornblum HI, Geschwind DH,Weissman IL.  2001.  From hematopoiesis to neuropoiesis: evidence of overlapping genetic programs. Proc Natl Acad Sci U S A. 98:7934-9.

Peters MA, Jarvik GP, Janer M, Chakrabarti L, Kolb S, Goode EL, Gibbs M,DuBois CC, Schuster EF, Hood L et al..  2001.  Genetic linkage analysis of prostate cancer families to Xq27-28. Hum Hered. 51:107-13.

Lane RP, Cutforth T, Young J, Athanasiou M, Friedman C, Rowen L, Evans G,Axel R, Hood L, Trask BJ.  2001.  Genomic analysis of orthologous mouse and human olfactory receptor loci. Proc Natl Acad Sci U S A. 98:7390-5.

Baliga NS, Kennedy SP, Ng WV, Hood L, DasSarma S.  2001.  Genomic and genetic dissection of an archaeal regulon. Proc Natl Acad Sci U S A. 98:2521-5..

DasSarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L.  2001.  Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth Res. 70:3-17.

Aderem A, Hood L.  2001.  Immunology in the post-genomic era. Nat Immunol. 2:373-5.

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K,Dewar K, Doyle M, FitzHugh W et al..  2001.  Initial sequencing and analysis of the human genome. Nature. 409:860-921.

Ideker T, Thorsson V, Ranish J, Christmas R, Buhler J, Eng JK, Bumgarner R,Goodlett DR, Aebersold R, Hood L.  2001.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:929-34.

Hood L.  2001.  Melanoma techniques and protocols: molecular diagnosis, treatment, and monitoring. Methods in Molecular Medicine. 61:ForwardbyHood,L.

Park IK, Klug CA, Li K, Jerabek L, Li L, Nanamori M, Neubig RR, Hood L,Weissman IL, Clarke MF.  2001.  Molecular cloning and characterization of a novel regulator of G-protein signaling from mouse hematopoietic stem cells. J Biol Chem. 276:915-23.

Ideker T, Galitski T, Hood L.  2001.  A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2:343-72.

Bruls T, Gyapay G, Petit JL, Artiguenave F, Vico V, Qin S, Tin-Wollam AM, Da Silva C, Muselet D, Mavel D et al..  2001.  A physical map of human chromosome 14.Nature. 409:947-8.

McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK et al..  2001.  A physical map of the human genome. Nature. 409:934-41.

Lin B, White JT, Ferguson C, Wang S, Vessella R, Bumgarner R, True LD, Hood L, Nelson PS.  2001.  Prostate short-chain dehydrogenase reductase 1 (PSDR1): a new member of the short-chain steroid dehydrogenase/reductase family highly expressed in normal and neoplastic prostate epithelium. Cancer Res. 61:1611-8.

Meyer AL, Benson J, Song F, Javed N, Gienapp IE, Goverman J, Brabb TA, Hood L, Whitacre CC.  2001.  Rapid depletion of peripheral antigen-specific T cells in TCR-transgenic mice after oral administration of myelin basic protein. J Immunol. 166:5773-81.

Anderson JP, Rodrigo AG, Learn GH, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI.  2001.  Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region. J Mol Evol. 53:55-62.

Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S.  2001.  Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res. 11:1641-50.

2000

Chaudhary PM, Eby MT, Jasmin A, Kumar A, Liu L, Hood L.  2000.  Activation of the NF-kappaB pathway by caspase 8 and its homologs. Oncogene. 19:4451-60.

Allen EE, Hood L.  2000.  Biotechnology, inquiry, and public education. Trends Biotechnol. 18:329-30.

Deng Y, Madan A, Banta AB, Friedman C, Trask BJ, Hood L, Li L.  2000.  Characterization, chromosomal localization, and the complete 30-kb DNA sequence of the human Jagged2 (JAG2) gene. Genomics. 63:133-8.

Rampazzo A, Pivotto F, Occhi G, Tiso N, Bortoluzzi S, Rowen L, Hood L, Nava A,Danieli GA.  2000.  Characterization of C14orf4, a novel intronless human gene containing a polyglutamine repeat, mapped to the ARVD1 critical region. Biochem Biophys Res Commun. 278:766-74.

Nelson PS, Han D, Rochon Y, Corthals GL, Lin B, Monson A, Nguyen V, Franza BR, Plymate SR, Aebersold R et al..  2000.  Comprehensive analyses of prostate gene expression: convergence of expressed sequence tag databases, transcript profiling and proteomics. Electrophoresis. 21:1823-31.

Brewster JL, Martin SL, Toms J, Goss D, Wang K, Zachrone K, Davis A, Carlson G, Hood L, Coffin JD.  2000.  Deletion of Dad1 in mice induces an apoptosis-associated embryonic death. Genesis. 26:271-8.

Aebersold R, Hood LE, Watts J.  2000.  Equipping scientists for the new biology. Nat Biotechnol. 18:359.

Baliga NS, Goo YA, Ng WV, Hood L, Daniels CJ, DasSarma S.  2000.  Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol. 36:1184-5.

Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR,Baliga NS, Thorsson V, Sbrogna J et al..  2000.  Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A. 97:12176-81.

Gibbs M, Stanford JL, Jarvik GP, Janer M, Badzioch M, Peters MA, Goode EL,Kolb S, Chakrabarti L, Shook M et al..  2000.  A genomic scan of families with prostate cancer identifies multiple regions of interest. Am J Hum Genet. 67:100-9.

Hood L.  2000.  The human genome project–launch pad for human genetic engineering.Engineering the Human Germline (1st Edition). :17-24.

Rowen L, Wong GK, Lane RP, Hood L.  2000.  Intellectual property. Publication rights in the era of open data release policies. Science. 289:1881.

Goode EL, Stanford JL, Chakrabarti L, Gibbs M, Kolb S, McIndoe RA, Buckley VA,Schuster EF, Neal CL, Miller EL et al..  2000.  Linkage analysis of 150 high-risk prostate cancer families at 1q24-25. Genet Epidemiol. 18:251-75.

Siegel AF, van den Engh G, Hood L, Trask B, Roach J.  2000.  Modeling the feasibility of whole genome shotgun sequencing using a pairwise end strategy. Genomics. 68:237-46.

Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W, Lange P, Hood L, Nelson PS.  2000.  PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12. Cancer Res. 60:858-63.

Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L.  2000.  The prostate expression database (PEDB): status and enhancements in 2000.Nucleic Acids Res. 28:212-3.

Cameron RA, Mahairas G, Rast JP, Martinez P, Biondi TR, Swartzell S, Wallace JC, Poustka AJ, Livingston BT, Wray GA et al..  2000.  A sea urchin genome project: sequence scan, virtual map, and additional resources. Proc Natl Acad Sci U S A. 97:9514-8.

Ideker T, Thorsson V, Siegel AF, Hood LE.  2000.  Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J Comput Biol. 7:805-17.

Anderson JP, Rodrigo AG, Learn GH, Madan A, Delahunty C, Coon M, Girard M,Osmanov S, Hood L, Mullins JI.  2000.  Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E. J Virol. 74:10752-65.