Publications

Found 1186 results
2011
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.
Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L.  2011.  jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions. Journal of proteome research.
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.
Li Q., Singh C.R, Ma S, Price ND, Jagannath C..  2011.  Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages. Journal of proteome research. 10:2425-39.
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.
Robinson CK, Webb K, Kaur A, Jaruga P, Dizdaroglu M, Baliga NS, Place A, DiRuggiero J.  2011.  A Major Role for Nonenzymatic Antioxidant Processes in the Radioresistance of Halobacterium salinarum. J Bacteriol. 193:1653-62.
Orellana MV, Matrai PA, Leck C, Rauschenberg CD, Lee AM, Coz E.  2011.  Marine microgels as a source of cloud condensation nuclei in the high Arctic. Proceedings of the National Academy of Sciences of the United States of America. 108:13612-7.
Ratushny AV, Ramsey SA, Aitchison JD.  2011.  Mathematical modeling of biomolecular network dynamics. Methods in molecular biology. 781:415-33.
Milne C.B, Eddy JA, Raju R., Ardekani S., Kim P.J, Senger R.S, Jin Y.S, Blaschek H.P, Price ND.  2011.  Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC systems biology. 5:130.
Tautenhahn R, Patti GJ, Kalisiak E, Miyamoto T, Schmidt M, Lo FY, McBee J, Baliga NS, Siuzdak G.  2011.  metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem. 83:696-700.
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.
Plaisier CL, Bare JC, Baliga NS.  2011.  miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Res.
Reiter L, Rinner O, Picotti P, Huttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R.  2011.  mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods.
Heldring N, Isaacs GD, Diehl AG, Sun M, Cheung E, Ranish J, Kraus WL.  2011.  Multiple Sequence-Specific DNA-Binding Proteins Mediate Estrogen Receptor Signaling through a Tethering Pathway. Mol Endocrinol.
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Rompp A, Neumann S, Pizarro AD et al..  2011.  mzML--a community standard for mass spectrometry data. Mol Cell Proteomics. 10:R110000133.
Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL.  2011.  Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Molecular & cellular proteomics : MCP.
Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS.  2011.  Niche adaptation by expansion and reprogramming of general transcription factors. Molecular systems biology. 7:554.
Rajan JV, Rodriguez D, Miao EA, Aderem A.  2011.  The NLRP3 inflammasome detects EMCV and VSV infection. J Virol.
Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL et al..  2011.  Parallel evolution of transcriptome architecture during genome reorganization. Genome research. 21:1892-904.
Subramaniam S, Nadeau JH.  2011.  Pathways, networks, and systems medicine-the meeting place of the Aegean and the mind. Wiley Interdiscip Rev Syst Biol Med. 3:253-4.
Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA.  2011.  The Peroxin Pex34p Functions with the Pex11 Family of Peroxisomal Divisional Proteins to Regulate the Peroxisome Population in Yeast. Mol Biol Cell.
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.
Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R.  2011.  The Protein Information and Property Explorer 2: Gaggle-like exploration of biological proteomic data within one webpage. Proteomics. 11:154-8.
Austin RJ, Smidansky HM, Holstein CA, Chang DK, Epp A, Josephson NC, Martin DB.  2011.  Proteomic analysis of the androgen receptor via MS-compatible purification of biotinylated protein on streptavidin resin. Proteomics.
Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.  2011.  A regression model approach to enable cell morphology correction in high-throughput flow cytometry. Molecular systems biology. 7:531.
Cook MS, Munger SC, Nadeau JH, Capel B.  2011.  Regulation of male germ cell cycle arrest and differentiation by DND1 is modulated by genetic background. Development. 138:23-32.
Kastenmüller W, Gasteiger G, Subramanian N, Sparwasser T, Busch DH, Belkaid Y, Drexler I, Germain RN.  2011.  Regulatory T cells selectively control CD8+ T cell effector pool size via IL-2 restriction.. J Immunol. 187(6):3186-97.
Ashworth J, Wurtmann EJ, Baliga NS.  2011.  Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Current opinion in biotechnology.
Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD.  2011.  Role of the nuclear envelope in genome organization and gene expression. Wiley Interdiscip Rev Syst Biol Med. 3:147-66.
Robinson T, Killcoyne S, Bressler R, Boyle J.  2011.  SAMQA: error classification and validation of high-throughput sequenced read data. BMC genomics. 12:419.
Austin RJ, Kuestner RE, Chang DK, Madden KR, Martin DB.  2011.  SILAC Compatible Strain of Pichia pastoris for Expression of Isotopically Labeled Protein Standards and Quantitative Proteomics. Journal of proteome research.
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.
Turewicz M, Deutsch EW.  2011.  Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output. Methods Mol Biol. 696:179-203.
Zechel JL, Maclennan GT, Heaney JD, Nadeau JH.  2011.  Spontaneous metastasis in mouse models of testicular germ-cell tumours. International journal of andrology.
Smith JJ, Saleem RA, Aitchison JD.  2011.  Statistical analysis of dynamic transcriptional regulatory network structure. Methods in molecular biology. 781:337-52.
Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C et al..  2011.  A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. MBio. 2
Cho JH, Gelinas R, Wang K, Etheridge A, Piper MG, Batte K, Dakhallah D, Price J, Bornman D, Zhang S et al..  2011.  Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes. BMC Med Genomics. 4:8.
Cho JH, Gelinas R, Wang K, Etheridge A, Piper MG, Batte K, Dakhallah D, Price J, Bornman D, Zhang S et al..  2011.  Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes. BMC medical genomics. 4:8.
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.
Subramaniam S, Nadeau JH.  2011.  Systems physiology--the heart of the matter or a bone of contention? Wiley Interdiscip Rev Syst Biol Med. 3:127-8.
Mathias RA, Chen YS, Goode RJ, Kapp EA, Mathivanan S, Moritz RL, Zhu HJ, Simpson RJ.  2011.  Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: towards developing an MDCK protein database. Proteomics. 11:1238-53.
Deutsch EW.  2011.  Tandem mass spectrometry spectral libraries and library searching. Methods Mol Biol. 696:225-32.
Ratushny AV, Shmulevich I, Aitchison JD.  2011.  Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues. PLoS computational biology. 7:e1002091.
Farrah T, Deutsch EW, Aebersold R.  2011.  Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins. Methods Mol Biol. 728:349-74.
2010
Ezeji T., Milne C., Price ND, Blaschek H.P.  2010.  Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms. Applied microbiology and biotechnology. 85:1697-712.
Rajan JV, Warren SE, Miao EA, Aderem A.  2010.  Activation of the NLRP3 inflammasome by intracellular poly I:C. FEBS Lett.
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.
Lam H, Deutsch EW, Aebersold R.  2010.  Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. J Proteome Res. 9:605-10.
Maziarz M, Janer M, Roach J, Hagopian W, Palmer JP, Deutsch K, Sanjeevi CB, Kockum I, Breslow N, Lernmark A.  2010.  The association between the PTPN22 1858C>T variant and type 1 diabetes depends on HLA risk and GAD65 autoantibodies. Genes Immun. 11:406-15.
Yin X, Wolford CC, Chang YS, McConoughey SJ, Ramsey SA, Aderem A, Hai T.  2010.  ATF3, an adaptive-response gene, enhances TGF{beta} signaling and cancer-initiating cell features in breast cancer cells. J Cell Sci. 123:3558-65.
Glusman G, Marzolf B, Wang K, Cho J-H, Kutlu B, Tian Q.  2010.  Bioinformatics strategies for understanding gene expression in human pluripotent cells. Human Stem Cell Technology and Biology: A Research Guide and Laboratory Manual.
Galas DJ, Nykter M, Carter GW, Price ND, Shmulevich I.  2010.  Biological Information as Set-Based Complexity. IEEE transactions on information theory. 56:667-677.
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.
Miao EA, Leaf IA, Treuting PM, Mao DP, Dors M, Sarkar A, Warren SE, Wewers MD, Aderem A.  2010.  Caspase-1-induced pyroptosis is an innate immune effector mechanism against intracellular bacteria. Nat Immunol. 11:1136-42.
Mirzaei H, Rogers RS, Grimes B, Eng J, Aderem A, Aebersold R.  2010.  Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry. Mol Biosyst. 6:2004-14.
Sigmon I, Lee LW, Chang DK, Krusberski N, Cohen D, Eng JK, Martin DB.  2010.  ChromEval: a software application for the rapid evaluation of HPLC system performance in proteomic applications. Anal Chem. 82:5060-8.
Beck C, Morbach H, Beer M, Stenzel M, Tappe D, Gattenlohner S, Hofmann U, Raab P, Girschick HJ.  2010.  Chronic nonbacterial osteomyelitis in childhood: prospective follow-up during the first year of anti-inflammatory treatment. Arthritis Res Ther. 12:R74.
Holstein Sherwood CA, Gafken PR, Martin DB.  2010.  Collision Energy Optimization of b- and y-Ions for Multiple Reaction Monitoring Mass Spectrometry. J Proteome Res.
Berrington WR, Macdonald M, Khadge S, Sapkota BR, Janer M, Hagge DA, Kaplan G, Hawn TR.  2010.  Common polymorphisms in the NOD2 gene region are associated with leprosy and its reactive states. J Infect Dis. 201:1422-35.
Lee LW, Zhang S, Etheridge A, Ma L, Martin D, Galas DJ, Wang K.  2010.  Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA. 16:2170-80.
Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS.  2010.  Coordination of frontline defense mechanisms under severe oxidative stress. Mol Syst Biol. 6:393.
Warren SE, Armstrong A, Hamilton MK, Mao DP, Leaf IA, Miao EA, Aderem A.  2010.  Cutting edge: Cytosolic bacterial DNA activates the inflammasome via Aim2. J Immunol. 185:818-21.
Gizzatkulov NM, Goryanin II, Metelkin EA, Mogilevskaya EA, Peskov KV, Demin OV.  2010.  DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. BMC Syst Biol. 4:109.
Lee HJ, Suk JE, Patrick C, Bae EJ, Cho JH, Rho S, Hwang D, Masliah E, Lee SJ.  2010.  Direct transfer of alpha-synuclein from neuron to astroglia causes inflammatory responses in synucleinopathies. J Biol Chem. 285:9262-72.
del Sol A, Balling R, Hood L, Galas DJ.  2010.  Diseases as network perturbations. Curr Opin Biotechnol. 21:566-71.
Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD.  2010.  Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem. 285:6739-49.
Price ND, Lee S.Y.  2010.  Editorial: Systems biology for biotech applications. Biotechnology journal. 5:636-7.
Diercks AK, Schwab A, Rittgen W, Kruspel A, Heuss E, Schenkel J.  2010.  Environmental influences on the production of pre-implantation embryos. Theriogenology. 73:1238-43.
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.

Pages