Publications

Found 1315 results
2012
Bare JC, Baliga NS.  2012.  Architecture for interoperable software in biology. Briefings in bioinformatics.
Brusniak MY, Chu CS, Kusebauch U, Sartain MJ, Watts JD, Moritz RL.  2012.  An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology. Proteomics. 12:1176-84.
Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD.  2012.  Asymmetric positive feedback loops reliably control biological responses. Molecular systems biology. 8:577.
Gold ES, Ramsey SA, Sartain MJ, Selinummi J, Podolsky I, Rodriguez DJ, Moritz RL, Aderem A.  2012.  ATF3 protects against atherosclerosis by suppressing 25-hydroxycholesterol-induced lipid body formation. The Journal of experimental medicine. 209:807-17.
Longabaugh WJ.  2012.  BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks. Methods in molecular biology. 786:359-94.
Cruz-Ramirez A, Diaz-Trivino S, Blilou I, Grieneisen VA, Sozzani R, Zamioudis C, Miskolczi P, Nieuwland J, Benjamins R, Dhonukshe P et al..  2012.  A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division. Cell. 150:1002-15.
Bislev SL, Deutsch EW, Sun Z, Farrah T, Aebersold R, Moritz RL, Bendixen E, Codrea MC.  2012.  A Bovine PeptideAtlas of milk and mammary gland proteomes. Proteomics.
Skupin A, Thurley K.  2012.  Calcium signaling: from single channels to pathways.. Adv Exp Med Biol. 740:531-51.
Lee G-S, Subramanian N, Kim AI, Aksentijevich I, Goldbach-Mansky R, Sacks DB, Germain RN, Kastner DL, Chae JJin.  2012.  The calcium-sensing receptor regulates the NLRP3 inflammasome through Ca2+ and cAMP.. Nature. 492(7427):123-7.
Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F et al..  2012.  The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature biotechnology. 30:221-3.
Ombrello MJ, Remmers EF, Sun G, Freeman AF, Datta S, Torabi-Parizi P, Subramanian N, Bunney TD, Baxendale RW, Martins MS et al..  2012.  Cold urticaria, immunodeficiency, and autoimmunity related to PLCG2 deletions.. N Engl J Med. 366(4):330-8.
Wang K, Yuan Y, Cho JH, McClarty S, Baxter D, Galas DJ.  2012.  Comparing the MicroRNA Spectrum between Serum and Plasma. PloS one. 7:e41561.
Wang K, Li H, Yuan Y, Etheridge A, Zhou Y, Huang D, Wilmes P, Galas D.  2012.  The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PloS one. 7:e51009.
Cancer Genome Atlas Network.  2012.  Comprehensive molecular characterization of human colon and rectal cancer.. Nature. 487(7407):330-7.
Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, Fulton LL, Dooling DJ, Ding L, Mardis ER et al..  2012.  Comprehensive molecular portraits of human breast tumours. Nature.
Torres-Sosa C, Huang S, Aldana M.  2012.  Criticality is an emergent property of genetic networks that exhibit evolvability.. PLoS Comput Biol. 8(9):e1002669.
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J et al..  2012.  A cross-platform toolkit for mass spectrometry and proteomics. Nature biotechnology. 30:918-20.
Hoopmann MR, Moritz RL.  2012.  Current algorithmic solutions for peptide-based proteomics data generation and identification. Current opinion in biotechnology.
Liu G, Yang D, Sun Y, Shmulevich I, Xue F, Sood AK, Zhang W.  2012.  Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer. Pharmacogenomics. 13:1523-35.
Rasmussen AL, Tchitchek N, Susnow NJ, Krasnoselsky AL, Diamond DL, Yeh MM, Proll SC, Korth MJ, Walters KA, Lederer S et al..  2012.  Early transcriptional programming links progression to hepatitis C virus-induced severe liver disease in transplant patients.. Hepatology. 56(1):17-27.
Auffray C, Hood L.  2012.  Editorial: Systems biology and personalized medicine - the future is now.. Biotechnol J. 7(8):938-9.
Panigrahy D, Edin ML, Lee CR, Huang S, Bielenberg DR, Butterfield CE, Barnés CM, Mammoto A, Mammoto T, Luria A et al..  2012.  Epoxyeicosanoids stimulate multiorgan metastasis and tumor dormancy escape in mice.. J Clin Invest. 122(1):178-91.
Bressler R, Lin J, Eakin A, Robinson T, Kreisberg R, Rovira H, Knijnenburg T, Boyle J, Shmulevich I.  2012.  Fastbreak: a tool for analysis and visualization of structural variations in genomic data. EURASIP journal on bioinformatics & systems biology. 2012:15.
Deutsch EW.  2012.  File formats commonly used in mass spectrometry proteomics. Molecular & cellular proteomics : MCP.
Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A.  2012.  A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses. Nature.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolome S, Vizcaino JA, Hermjakob H.  2012.  From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland. Proteomics. 12:351-5.
Thurley K, Skupin A, Thul R, Falcke M.  2012.  Fundamental properties of Ca2+ signals.. Biochim Biophys Acta. 1820(8):1185-94.
Ezzie ME, Crawford M, Cho JH, Orellana R, Zhang S, Gelinas R, Batte K, Yu L, Nuovo G, Galas D et al..  2012.  Gene expression networks in COPD: microRNA and mRNA regulation. Thorax. 67:122-31.
Muller EE, Pinel N, Gillece JD, Schupp JM, Price LB, Engelthaler DM, Levantesi C, Tandoi V, Luong K, Baliga NS et al..  2012.  Genome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant. Journal of bacteriology. 194:6670-1.
Benedict MN, Gonnerman MC, Metcalf WW, Price ND.  2012.  Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A. Journal of bacteriology. 194:855-65.
Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR.  2012.  Global analysis of mRNA stability in Mycobacterium tuberculosis. Nucleic acids research.
Plaisier CL, Baliga NS.  2012.  Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies. Pigment cell & melanoma research. 25:406-8.
Swearingen KE, Moritz RL.  2012.  High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics. Expert review of proteomics. 9:505-17.
Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, Sechi S, Apweiler R, Bader J, Barnes S et al..  2012.  The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clinical proteomics. 9:6.
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.  2012.  Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC bioinformatics. 13:324.
Hoopmann MR, MacCoss MJ, Moritz RL.  2012.  Identification of Peptide features in precursor spectra using hardklor and kronik. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 13:Unit1318.
Bernard B, Thorsson V, Rovira H, Shmulevich I.  2012.  Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-level Homology. PloS one. 7:e42779.
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, Jimenez R, Swan D, Greshake B, Bhak J, Logan DW, Corpas M.  2012.  Low budget analysis of Direct-To-Consumer genomic testing familial data.. F1000Res. 1:3.
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.
Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson B-J, McDermott JE, Yeh MM, Dzib JFelipe Gol, Susnow N, Strom S et al..  2012.  Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation.. Hepatology. 56(1):28-38.
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.

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