Publications

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

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