Publications

Found 233 results
Filters: Author is Hood, L.  [Clear All Filters]
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.
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.
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.

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