Publications

Found 1264 results
2012
Holmes KM, Annala M, Chua CY, Dunlap SM, Liu Y, Hugen N, Moore LM, Cogdell D, Hu L, Nykter M et al..  2012.  Insulin-like growth factor-binding protein 2-driven glioma progression is prevented by blocking a clinically significant integrin, integrin-linked kinase, and NF-kappaB network. Proceedings of the National Academy of Sciences of the United States of America. 109:3475-80.
Liu Y, Sun Y, Broaddus R, Liu J, Sood AK, Shmulevich I, Zhang W.  2012.  Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma. PloS one. 7:e36383.
Luo J, Fishburn J, Hahn S, Ranish J.  2012.  An Integrated Chemical Cross-linking and Mass Spectrometry Approach to Study Protein Complex Architecture and Function. Molecular & cellular proteomics : MCP. 11:M111008318.
Whitmore TE, Peterson A, Holzman T, Eastham A, Amon L, McIntosh M, Ozinsky A, Nelson PS, Martin DB.  2012.  Integrative Analysis of N-Linked Human Glycoproteomic Data Sets Reveals PTPRF Ectodomain as a Novel Plasma Biomarker Candidate for Prostate Cancer. Journal of proteome research. 11:2653-65.
Killcoyne S, Handcock J, Robinson T, Deutsch EW, Boyle J.  2012.  Interfaces to PeptideAtlas: a case study of standard data access systems. Briefings in bioinformatics. 13:615-26.
Austin RJ, Chang DK, Holstein CA, Lee LW, Risler J, Wang JH, Adams L, Krusberski NB, Martin DB.  2012.  IQcat: Multiplexed protein quantification by isoelectric QconCAT. Proteomics. 12:2078-83.
Buchner DA, Geisinger JM, Glazebrook PA, Morgan MG, Spiezio SH, Kaiyala KJ, Schwartz MW, Sakurai T, Furley AJ, Kunze DL et al..  2012.  The juxtaparanodal proteins CNTNAP2 and TAG1 regulate diet-induced obesity. Mammalian genome : official journal of the International Mammalian Genome Society. 23:431-42.
Dougherty ER, Shmulevich I.  2012.  On the Limitations of Biological Knowledge. Current Genomics. 13:574-587.
Simcha D., Price ND, Geman D.  2012.  The limits of de novo DNA motif discovery. PloS one. 7:e47836.
Glusman G, Cariaso M, R J.  2012.  Low budget analysis of Direct-To-Consumer genomic testing familial data. F1000Research. 1:38.
Brogaard K, Xi L, Wang JP, Widom J.  2012.  A map of nucleosome positions in yeast at base-pair resolution. Nature. 486:496-501.
Sangar V, Eddy JA, Simeonidis E, Price ND.  2012.  Mechanistic modeling of aberrant energy metabolism in human disease. Frontiers in physiology. 3:404.
Huang S, Holzel M., Knijnenburg T, Schlicker A., Roepman P., McDermott U., Garnett M., Grernrum W., Sun C., Prahallad A. et al..  2012.  MED12 controls the response to multiple cancer drugs through regulation of TGF-beta receptor signaling. Cell. 151:937-50.
Boyle J, Kreisberg R, Bressler R, Killcoyne S.  2012.  Methods for visual mining of genomic and proteomic data atlases. BMC bioinformatics. 13:58.
Killcoyne S, Deutsch EW, Boyle J.  2012.  Mining PeptideAtlas for Biomarkers and Therapeutics in Human Disease. Current pharmaceutical design.
Plaisier CL, Pan M, Baliga NS.  2012.  A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome research.
Huang S.  2012.  The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology? BioEssays : news and reviews in molecular, cellular and developmental biology. 34:149-57.
Sung J, Wang Y, Chandrasekaran S, Witten DM, Price ND.  2012.  Molecular signatures from omics data: From chaos to consensus. Biotechnology journal.
Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard S, Selley J, Searle B, Shofstahl J, Seymour S et al..  2012.  The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & cellular proteomics : MCP.
Bebek G, Koyuturk M, Price ND, Chance MR.  2012.  Network biology methods integrating biological data for translational science. Briefings in bioinformatics.
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.
DeGracia DJ, Huang Z-F, Huang S.  2012.  A nonlinear dynamical theory of cell injury.. J Cereb Blood Flow Metab. 32(6):1000-13.
Dubois KN, Alsford S, Holden JM, Buisson J, Swiderski M, Bart JM, Ratushny AV, Wan Y, Bastin P, Barry JD et al..  2012.  NUP-1 Is a Large Coiled-Coil Nucleoskeletal Protein in Trypanosomes with Lamin-Like Functions. PLoS biology. 10:e1001287.
Jagger BW, Wise HM, Kash JC, Walters KA, Wills NM, Xiao YL, Dunfee RL, Schwartzman LM, Ozinsky A, Bell GL et al..  2012.  An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response. Science.
Ho HJ, Lin TI, Chang HH, Haase SB, Huang S, Pyne S.  2012.  Parametric modeling of cellular state transitions as measured with flow cytometry.. BMC Bioinformatics. 13 Suppl 5:S5.
Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Huttenhain R, Schiess R et al..  2012.  PASSEL: The PeptideAtlas SRM Experiment Library. Proteomics.
Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA et al..  2012.  Peroxiredoxins are conserved markers of circadian rhythms.. Nature. 485(7399):459-64.
Hood L, Flores M.  2012.  A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory.. N Biotechnol. 29(6):613-24.
London N, Ceto S, Ranish J, Biggins S.  2012.  Phosphoregulation of Spc105 by Mps1 and PP1 regulates Bub1 localization to kinetochores.. Curr Biol. 22(10):900-6.
Kloet SL, Whiting JL, Gafken P, Ranish J, Wang EH.  2012.  Phosphorylation-Dependent Regulation of Cyclin D1 and Cyclin A Gene Transcription by TFIID Subunits TAF1 and TAF7. Molecular and cellular biology. 32:3358-69.
Sakhanenko NA, Galas DJ.  2012.  Probabilistic logic methods and some applications to biology and medicine. Journal of computational biology : a journal of computational molecular cell biology. 19:316-36.
Austin RJ, Smidansky HM, Holstein CA, Chang DK, Epp A, Josephson NC, Martin DB.  2012.  Proteomic analysis of the androgen receptor via MS-compatible purification of biotinylated protein on streptavidin resin. Proteomics. 12:43-53.
Thompson EG, Galitski T.  2012.  Quantifying and analyzing the network basis of genetic complexity. PLoS computational biology. 8:e1002583.
Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Rontved CM, Aebersold R, Moritz RL, Bendixen E.  2012.  Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus uberis. Journal of proteome research. 11:1832-43.
Zhou JX, Aliyu MD, Aurell E, Huang S.  2012.  Quasi-potential landscape in complex multi-stable systems. Journal of the Royal Society, Interface / the Royal Society.
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B et al..  2012.  Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). Journal of proteome research. 11:1412-1419.
Wang Y, Eddy JA, Price ND.  2012.  Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC systems biology. 6:153.
Huttenhain R, Soste M, Selevsek N, Rost H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL et al..  2012.  Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Science translational medicine. 4:142ra94.
Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, Magis AT, Funk C, Price ND, Ekker SC et al..  2012.  Research resource: whole transcriptome RNA sequencing detects multiple 1alpha,25-dihydroxyvitamin d3-sensitive metabolic pathways in developing zebrafish. Molecular endocrinology. 26:1630-42.
Hood L, Balling R, Auffray C.  2012.  Revolutionizing medicine in the 21st century through systems approaches.. Biotechnol J. 7(8):992-1001.
Hood L, Balling R, Auffray C.  2012.  Revolutionizing medicine in the 21(st) century through systems approaches. Biotechnology journal.
Orellana MV, Hansell DA.  2012.  Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO): A long-lived protein inthe deep ocean. Limnology & Oceanography. 57:826-834.
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.
Halley JD, Smith-Miles K, Winkler DA, Kalkan T, Huang S, Smith A.  2012.  Self-organizing circuitry and emergent computation in mouse embryonic stem cells.. Stem Cell Res. 8(2):324-33.
Han X, Fang X, Lou X, Hua D, Ding W, Foltz G, Hood L, Yuan Y, Lin B.  2012.  Silencing SOX2 induced mesenchymal-epithelial transition and its expression predicts liver and lymph node metastasis of CRC patients.. PLoS One. 7(8):e41335.
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.
Kastenmüller W, Torabi-Parizi P, Subramanian N, Lämmermann T, Germain RN.  2012.  A spatially-organized multicellular innate immune response in lymph nodes limits systemic pathogen spread.. Cell. 150(6):1235-48.
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.
Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL.  2012.  The State of the Human Proteome in 2012 as Viewed through PeptideAtlas. Journal of proteome research.
You S, Cho C-S, Lee I, Hood L, Hwang D, Kim W-U.  2012.  A systems approach to rheumatoid arthritis.. PLoS One. 7(12):e51508.
Hood L, Tian Q.  2012.  Systems approaches to biology and disease enable translational systems medicine.. Genomics Proteomics Bioinformatics. 10(4):181-5.
Lee MJ, Cho JH, Galas DJ, Wang K.  2012.  The systems biology of neurofibromatosis type 1--critical roles for microRNA. Experimental neurology. 235:464-8.
Hood L.  2012.  Tackling the microbiome. Science. 336:1209.
Magis AT, Price ND.  2012.  The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules. BMC bioinformatics. 13:227.
Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K et al..  2012.  TraML--A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists. Molecular & cellular proteomics : MCP. 11:R111015040.
Moore LM, Kivinen V, Liu Y, Annala M, Cogdell D, Liu X, Liu CG, Sawaya R, Yli-Harja O, Shmulevich I et al..  2012.  Transcriptome and Small RNA Deep Sequencing Reveals Deregulation of miRNA Biogenesis in Human Glioma. The Journal of pathology.
Deus HF, Prud'hommeaux E, Miller M, Zhao J, Malone J, Adamusiak T, McCusker J, Das S, Rocca Serra P, Fox R et al..  2012.  Translating standards into practice - One Semantic Web API for Gene Expression. Journal of biomedical informatics. 45:782-94.
Huang S.  2012.  Tumor progression: Chance and necessity in Darwinian and Lamarckian somatic (mutationless) evolution. Progress in biophysics and molecular biology.
Kolodkin A, Simeonidis E, Balling R, Westerhoff HV.  2012.  Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence.. Front Physiol. 3:291.
Aitchison JD, Rout MP.  2012.  The yeast nuclear pore complex and transport through it. Genetics. 190:855-83.
2011
Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, Krijgsveld J, Lane WS, Lilley KS, MacCoss MJ, Moritz RL et al..  2011.  The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics. 11:1371-81.
Yang D, Khan S, Sun Y, Hess K, Shmulevich I, Sood AK, Zhang W.  2011.  Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer. JAMA : the journal of the American Medical Association. 306:1557-65.
Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J et al..  2011.  ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinformatics. 12:78.
Chandrasekaran S, Ament SA, Eddy JA, Rodriguez-Zas SL, Schatz BR, Price ND, Robinson GE.  2011.  Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states. Proceedings of the National Academy of Sciences of the United States of America. 108:18020-5.
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.
Lenz D, May P, Walther D.  2011.  Comparative analysis of miRNAs and their targets across four plant species.. BMC Res Notes. 4:483.
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al..  2011.  Comparative and demographic analysis of orang-utan genomes. Nature. 469:529-33.
Tian Q, Hanlon Newell AE, Wang Y, Olson SB, Fedorov LM.  2011.  Complex cytogenetic analysis of early lethality mouse embryos. Chromosome Res.
Yazbek SN, Buchner DA, Geisinger JM, Burrage LC, Spiezio SH, Zentner GE, Hsieh CW, Scacheri PC, Croniger CM, Nadeau JH.  2011.  Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis. Genome Res.
Lightfield KL, Persson J, Trinidad NJ, Brubaker SW, Kofoed EM, Sauer JD, Dunipace EA, Warren SE, Miao EA, Vance RE.  2011.  Differential requirements for NAIP5 in activation of the NLRC4 inflammasome. Infect Immun. 79:1606-14.
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.
Chung TW, Moss CL, Zimnicka M, Johnson RS, Moritz RL, Turecek F.  2011.  Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics. J Am Soc Mass Spectrom. 22:13-30.
Vencio EF, Pascal LE, Page LS, Denyer G, Wang AJ, Ruohola-Baker H, Zhang S, Wang K, Galas DJ, Liu AY.  2011.  Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells. J Cell Physiol. 226:1479-88.
Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD.  2011.  Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol Syst Biol. 7:455.
Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I.  2011.  EPEPT: A web service for enhanced P-value estimation in permutation tests. BMC bioinformatics. 12:411.
Etheridge A, Lee I, Hood L, Galas D, Wang K.  2011.  Extracellular microRNA: A new source of biomarkers. Mutat Res.
Baumgardner LA, Shanmugam AK, Lam H, Eng JK, Martin DB.  2011.  Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration. J Proteome Res.
Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR.  2011.  Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem. 83:2250-7.
Warren SE, Duong H, Mao DP, Armstrong A, Rajan J, Miao EA, Aderem A.  2011.  Generation of a Listeria vaccine strain by enhanced Caspase-1 activation. Eur J Immunol.
Kim P.J, Price ND.  2011.  Genetic co-occurrence network across sequenced microbes. PLoS computational biology. 7:e1002340.
Nadeau JH, Dudley AM.  2011.  Genetics. Systems genetics. Science. 331:1015-6.
Magis AT, Earls J.C, Ko Y.H, Eddy JA, Price ND.  2011.  Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics. 27:872-3.
Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmstrom J, Ossola R et al..  2011.  A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular & cellular proteomics : MCP.
Falconnet D, Niemisto A, Taylor RJ, Ricicova M, Galitski T, Shmulevich I, Hansen CL.  2011.  High-throughput tracking of single yeast cells in a microfluidic imaging matrix. Lab Chip. 11:466-73.
Chan QW, Parker R, Sun Z, Deutsch EW, Foster LJ.  2011.  A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues. BMC genomics. 12:290.
Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers C, Corthals GL, Costello CE et al..  2011.  The human proteome project: Current state and future direction. Mol Cell Proteomics.
Buchner DA, Yazbek SN, Solinas P, Burrage LC, Morgan MG, Hoppel CL, Nadeau JH.  2011.  Increased mitochondrial oxidative phosphorylation in the liver is associated with obesity and insulin resistance. Obesity (Silver Spring). 19:917-24.
Yan W, Luo J, Robinson M, Eng J, Aebersold R, Ranish J.  2011.  Index-ion Triggered MS2 Ion Quantification: A Novel Proteomics Approach for Reproducible Detection and Quantification of Targeted Proteins in Complex Mixtures. Mol Cell Proteomics. 10:M110005611.
Cho JH, Wang K, Galas DJ.  2011.  An integrative approach to inferring biologically meaningful gene modules. BMC systems biology. 5:117.
Bebek G, Koyuturk M, Chance MR, Price ND.  2011.  INTEGRATIVE -OMICS FOR TRANSLATIONAL SCIENCE - Session Introduction. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. :1-3.
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.
Pedroza M, Schneider DJ, Karmouty-Quintana H, Coote J, Shaw S, Corrigan R, Molina JG, Alcorn JL, Galas D, Gelinas R et al..  2011.  Interleukin-6 contributes to inflammation and remodeling in a model of adenosine mediated lung injury. PloS one. 6:e22667.
Groves M, van Duijn E, Anderson K, Craufurd D, Edmondson MC, Goodman N, van Kammen DP, Goodman L.  2011.  An International Survey-based Algorithm for the Pharmacologic Treatment of Irritability in Huntington's Disease. PLoS currents. 3:RRN1259.
Burgunder JM, Guttman M, Perlman S, Goodman N, van Kammen DP, Goodman L.  2011.  An International Survey-based Algorithm for the Pharmacologic Treatment of Chorea in Huntington's Disease. PLoS currents. 3:RRN1260.
Anderson K, Craufurd D, Edmondson MC, Goodman N, Groves M, van Duijn E, van Kammen DP, Goodman L.  2011.  An International Survey-based Algorithm for the Pharmacologic Treatment of Obsessive-Compulsive Behaviors in Huntington's Disease. PLoS currents. 3:RRN1261.
Huang S.  2011.  On the intrinsic inevitability of cancer: from foetal to fatal attraction. Semin Cancer Biol. 21:183-99.
Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.  2011.  iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular & cellular proteomics : MCP.
Najm FJ, Chenoweth JG, Anderson PD, Nadeau JH, Redline RW, McKay RD, Tesar PJ.  2011.  Isolation of epiblast stem cells from preimplantation mouse embryos. Cell Stem Cell. 8:318-25.

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