Publications

Found 1248 results
2014
Wang Y, Janssen H, Milne CB, Magis AT, Jin Y-S, Price ND, Blaschek HP.  2014.  136. Understanding Fundamental Aspects of Butanol Production by Clostridium beijerinckii. 2014 Genomic Science Contractor-Grantee Meeting XII. :234.
Li H, Glusman G, Huff C., Caballero J, Roach JC.  2014.  Accurate and robust prediction of genetic relationship from whole-genome sequences. PloS one. 9:e85437.
Laczny C.C, Pinel N, Vlassis N., Wilmes P.  2014.  Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction. Scientific reports. 4:4516.
Vialas V., Sun Z, Y. Loureiro PCV, Carrascal M., Abian J., Monteoliva L., Deutsch EW, Aebersold R, Moritz RL, Gil C..  2014.  A Candida albicans PeptideAtlas. Journal of proteomics. 97:62-8.
Kemp CJ, Moore J.M, Moser R., Bernard B, Teater M., Smith L.E, Rabaia N.A, Gurley K.E, Guinney J., Busch S.E et al..  2014.  CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer. Cell reports.
Hood L, Price ND.  2014.  Demystifying disease, democratizing health care. Science translational medicine. 6:225ed5.
Craig TA, Zhang Y, Magis AT, Funk CC, Price ND, Ekker SC, Kumar, iv R.  2014.  Detection of 1,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing.. Zebrafish.
Shaw S, Bourne T., Meier C., Carrington B., Gelinas R, Henry A., Popplewell A., Adams R., Baker T., Rapecki S. et al..  2014.  Discovery and characterization of olokizumab: A humanized antibody targeting interleukin-6 and neutralizing gp130-signaling. mAbs. 6:773-81.
Powell S., Forslund K., Szklarczyk D., Trachana K., Roth A., Huerta-Cepas J., Gabaldon T., Rattei T., Creevey C., Kuhn M. et al..  2014.  eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic acids research. 42:D231-9.
Labhsetwar P, Cole J, Price N, Luthey-Schulten Z.  2014.  Elucidating Metabolic Variability in Isogenic Microbial Populations Arising due to Noise in Protein Expression. Biophysical Journal. 106:644a.
Lindner SE, Sartain MJ, Hayes K, Harupa A, Moritz RL, Kappe SHI, Vaughan AM.  2014.  Enzymes involved in plastid-targeted phosphatidic acid synthesis are essential for Plasmodium yoelii liver-stage development.. Mol Microbiol. 91(4):679-93.
Chiang J-H, Cheng W-S, Hood L, Tian Q.  2014.  An Epigenetic Biomarker Panel for Glioblastoma Multiforme Personalized Medicine through DNA Methylation Analysis of Human Embryonic Stem Cell-like Signature. Omics: a journal of integrative biology.
Bundgaard L, Jacobsen S, Sørensen MAamand, Sun Z, Deutsch EW, Moritz RL, Bendixen E.  2014.  The Equine PeptideAtlas–a resource for developing proteomics‐based veterinary research. Proteomics.
Wurtmann EJ, Ratushny AV, Pan M, Beer K.D, Aitchison JD, Baliga NS.  2014.  An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular microbiology. 92:369-82.
Mast FD, Barlow L.D, Rachubinski RA, Dacks J.B.  2014.  Evolutionary mechanisms for establishing eukaryotic cellular complexity. Trends in cell biology.
Stolyar S, Liu Z, Thiel V, Tomsho LP, Pinel N, Nelson WC, Lindemann SR, Romine MF, Haruta S, Schuster SC et al..  2014.  Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.. Genome Announc. 2(1)
Cary G.A, Yoon SH, C. Torres G, Wang K, Hays M., Ludlow C., Goodlett DR, Dudley AM.  2014.  Identification and characterization of a drug-sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae. Yeast. 31:167-78.
Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M.  2014.  Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network.. Nucleic Acids Res. 42(3):1474-96.
Ekici S, Turkarslan S, Pawlik G, Dancis A, Baliga NS, Koch H-G, Daldal F.  2014.  Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production. mBio. 5:e01055-13.
Chevillet J.R, Lee I, Briggs H.A, He Y, Wang K.  2014.  Issues and prospects of microRNA-based biomarkers in blood and other body fluids. Molecules. 19:6080-105.
Benedict MN, Henriksen J.R, Metcalf WW, Whitaker R.J, Price ND.  2014.  ITEP: An integrated toolkit for exploration of microbial pan-genomes. BMC genomics. 15:8.
Christian N., Skupin A., Morante S., Jansen K., Rossi G., Ebenhoh O..  2014.  Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. Journal of theoretical biology. 343:102-12.
Randhawa M., Sangar V, Tucker-Samaras S., Southall M..  2014.  Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway. PLoS ONE. 9:e90367.
Liu G, Sun Y, Ji P, Li X, Cogdell D, Yang D, Kerrigan BCParker, Shmulevich I, Chen K, Sood AK et al..  2014.  MiR-506 Suppresses Proliferation and Induces Senescence by Directly Targeting the CDK4/6-FOXM1 Axis in Ovarian Cancer.. J Pathol.
Beer K.D, Wurtmann EJ, Pinel N, Baliga NS.  2014.  Model organisms have memory of complex ecologically-relevant environmental variation. Applied and environmental microbiology.
Ghaffarizadeh A., Podgorski G.J, Flann N.S.  2014.  Modeling and visualizing cell type switching. Computational and mathematical methods in medicine. 2014:293980.
Cho JH, Lee I, Hammamieh R., Wang K, Baxter D, Scherler K., Etheridge A, Kulchenko A., Gautam A., Muhie S. et al..  2014.  Molecular evidence of stress-induced acute heart injury in a mouse model simulating posttraumatic stress disorder. Proceedings of the National Academy of Sciences of the United States of America. 111:3188-93.
Danziger S.A, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH et al..  2014.  Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic acids research. 42:1442-60.
Ptak C, Aitchison JD, Wozniak RW.  2014.  The multifunctional nuclear pore complex: a platform for controlling gene expression. Current opinion in cell biology. 28C:46-53.
Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.  2014.  Multiscale representation of genomic signals. Nature methods.
Kusebauch U, Ortega C., Ollodart A., Rogers RS, Sherman DR, Moritz RL, Grundner C..  2014.  Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proceedings of the National Academy of Sciences of the United States of America.
Turkarslan S, Wurtmann EJ, Wu W.J, Jiang N., Bare JC, Foley K, Reiss DJ, Novichkov P., Baliga NS.  2014.  Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Res. 42:D184-90.
Holden JM, Koreny L., Obado S., Ratushny AV, Chen WM, Chiang JH, Kelly S., Chait BT, Aitchison JD, Rout MP et al..  2014.  Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity. Molecular biology of the cell. 25:1421-36.
Schoggins J.W, Macduff D.A, Imanaka N., Gainey M.D, Shrestha B., Eitson J.L, Mar K.B, Richardson R.B, Ratushny AV, Litvak V et al..  2014.  Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature. 505:691-5.
Wu X., Hasan M.A, Chen J.Y.  2014.  Pathway and network analysis in proteomics. Journal of theoretical biology.
Omenn GS.  2014.  Plasma proteomics, the human proteome project, and cancer-associated alternative splice variant proteins. Biochimica et biophysica acta. 1844:866-73.
Guo F, Kerrigan BCParker, Yang D, Hu L, Shmulevich I, Sood AK, Xue F, Zhang W.  2014.  Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions.. J Hematol Oncol. 7:19.
Silva R.R, Jourdan F., Salvanha D.M, Letisse F., Jamin E.L, Guidetti-Gonzalez S., Labate C.A, Vencio RZ.  2014.  ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. Bioinformatics.
Kauffman SA.  2014.  Prolegomenon to patterns in evolution. Bio Systems.
Sun B, Hood L.  2014.  Protein-Centric N-Glycoproteomics Analysis of Membrane and Plasma Membrane Proteins.. J Proteome Res.
Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D., Dianes J.A, Sun Z, Farrah T, Bandeira N. et al..  2014.  ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature biotechnology. 32:223-6.
Ruusuvuori P, Lin J, Scott A.C, Tan Z., Sorsa S., Kallio A., Nykter M, Yli-Harja O, Shmulevich I, Dudley AM.  2014.  Quantitative analysis of colony morphology in yeast. BioTechniques. 56:18-27.
Hu Z, Lausted C, Yoo H, Yan X, Brightman A, Chen J, Wang W, Bu X., Hood L.  2014.  Quantitative liver-specific protein fingerprint in blood: a signature for hepatotoxicity. Theranostics. 4:215-28.
Carpp L.N, Rogers RS, Moritz RL, Aitchison JD.  2014.  Quantitative proteomic analysis of host-virus interactions reveals a role for GBF1 in dengue infection. Molecular & cellular proteomics : MCP.
Daugherty M.D, Young J.M, Kerns J.A, Malik H.S.  2014.  Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts. PLoS genetics. 10:e1004403.
Caballero J, Smit AF, Hood L, Glusman G.  2014.  Realistic artificial DNA sequences as negative controls for computational genomics. Nucleic acids research.
Li H, Glusman G, Hu H, , Caballero J, Hubley R, Witherspoon D., Guthery S.L, Mauldin DE, Jorde LB et al..  2014.  Relationship estimation from whole-genome sequence data. PLoS genetics. 10:e1004144.
Thyme S.B, Boissel S.J, S. Quadri A, Nolan T., Baker D.A, Park R.U, Kusak L., Ashworth J, Baker D..  2014.  Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic acids research. 42:2564-76.
Goldberg R., Kauffman S, Topol E.J.  2014.  Study design and the drug development process. JAMA : the journal of the American Medical Association. 311:2023.
Hao D., Wang G., Yin Z, Li C., Cui Y., Zhou M.  2014.  Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. European journal of human genetics : EJHG.
Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K.  2014.  Systems approach to neurodegenerative disease biomarker discovery. Annual review of pharmacology and toxicology. 54:457-81.
Bai JPF, Fontana RJ, Price ND, Sangar V.  2014.  Systems pharmacology modeling: an approach to improving drug safety. Biopharmaceutics & drug disposition. 35:1-14.
Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, uumlttenhain R, Koomen JM.  2014.  Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach. Molecular & Cellular Proteomics. :mcp.M113.036095.
Lopes M., Kutlu B, Miani M., Bang-Berthelsen C.H, Storling J., Pociot F., Goodman N, Hood L, Welsh N, Bontempi G. et al..  2014.  Temporal profiling of cytokine-induced genes in pancreatic beta-cells by meta-analysis and network inference. Genomics.
Liu X, Chen X, Zhong B., Wang A., Wang X, Chu F, Nurieva RI, Yan X, Chen P., van der Flier L.G et al..  2014.  Transcription factor achaete-scute homologue 2 initiates follicular T-helper-cell development. Nature. 507:513-8.
Kash JC, Xiao Y., Davis A.S, Walters KA, Chertow D.S, Easterbrook J.D, Dunfee RL, Sandouk A., Jagger BW, Schwartzman LM et al..  2014.  Treatment with the reactive oxygen species scavenger EUK-207 reduces lung damage and increases survival during 1918 influenza virus infection in mice. Free radical biology & medicine. 67:235-47.
Li X, Liu Y, Granberg K.J, Wang Q, Moore LM, Ji P, Gumin J., Sulman E.P, Calin G.A, Haapasalo H. et al..  2014.  Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma. Oncogene.
Garmendia-Torres C, Skupin A., Michael S.A, Ruusuvuori P, Kuwada N.J, Falconnet D, Cary G.A, Hansen C., Wiggins P.A, Dudley AM.  2014.  Unidirectional P-Body Transport during the Yeast Cell Cycle. PLoS ONE. 9:e99428.
Hu H, Roach JC, Coon H., Guthery S.L, Voelkerding K.V, Margraf R.L, Durtschi J.D, Tavtigian SV, , Wu W. et al..  2014.  A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nature biotechnology.
Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL.  2014.  Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. 46:13251-132528.
Huang S.  2014.  When correlation and causation coincide.. Bioessays. 36(1):1-2.
2013
Subramanian N, Natarajan K, Clatworthy MR, Wang Z, Germain RN.  2013.  The adaptor MAVS promotes NLRP3 mitochondrial localization and inflammasome activation.. Cell. 153(2):348-61.
Tan Z., Hays M., Cromie G.A, Jeffery E.W, Scott A.C, Ahyong V., Sirr A., Skupin A., Dudley AM.  2013.  Aneuploidy underlies a multicellular phenotypic switch. Proc Natl Acad Sci U S A. 110:12367-72.
Tjernström M, Leck C, Birch CE, Bottenheim JW, Brooks BJ, Brooks IM, Bäcklin L, Chang RY-W, Granath E, Graus M et al..  2013.  The Arctic Summer Cloud-Ocean Study (ASCOS): 1 Overview and experimental design. Atmospheric Chemsitry and Physics. 13
Earls J.C, Eddy JA, Funk C.C, Ko Y., Magis AT, Price ND.  2013.  AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. BMC bioinformatics. 14:78.
Zheng H, Wang W, Li X, Wang Z, Hood L, Lausted C, Hu Z.  2013.  An automated Teflon microfluidic peptide synthesizer.. Lab Chip. 13(17):3347-50.
Omenn GS.  2013.  On best practices: The Institute of Medicine scheme for developing, validating, and demonstrating clinical utility of omics-based diagnostic and predictive tests. Proteomics Clin Appl. 7:748-55.
Zhou Y, Qin S, Wang K.  2013.  Biomarkers of drug-induced liver injury.. Current Biomarker Findings. 2013:1-9.
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.
Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C et al..  2013.  A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. Journal of proteome research. 12:45-57.
Glusman G.  2013.  Clinical applications of sequencing take center stage. Genome Biol. 14:303.
Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.  2013.  Combining results of multiple search engines in proteomics. Mol Cell Proteomics. 12:2383-93.
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD et al..  2013.  A community-driven global reconstruction of human metabolism. Nature biotechnology.
Picotti P, Clement-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Rost H, Sun Z, Rinner O, Reiter L et al..  2013.  A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaino JA, Hermjakob H, Oveillero D, Julian R et al..  2013.  Controlled Vocabularies and Ontologies in Proteomics: Overview, Principles and Practice. Biochimica et biophysica acta.
Hoopmann MR, Moritz RL.  2013.  Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol. 24:31-8.
Wang Y, Li X, Milne CB, Janssen H, Lin W, Phan G, Hu H, Jin Y-S, Price ND, Blaschek HP.  2013.  Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii.. Appl Environ Microbiol. 79(19):5853-63.
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.  2013.  Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic acids research. 41:D70-82.
Xu D, Caballero J, Glusman G, Tian Q.  2013.  Diagnostic Perspectives in the Epoch of Next-Generation Sequencing.. Next-Generation Sequencing & Molecular Diagnostics. .
Costa KC, Yoon SH, Pan M, Burn JA, Baliga NS, Leigh JA.  2013.  Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. Journal of bacteriology.
Panigrahy D, Kalish BT, Huang S, Bielenberg DR, Le HD, Yang J, Edin ML, Lee CR, Benny O, Mudge DK et al..  2013.  Epoxyeicosanoids promote organ and tissue regeneration.. Proc Natl Acad Sci U S A. 110(33):13528-33.
Hood LE, Lazowska E.D.  2013.  Every life has equal value. Cell. 154:1178-9.
Melnicki M.R, Pinchuk G.E, Hill E.A, Kucek L.A, Stolyar S.M, Fredrickson J.K, Konopka A.E, Beliaev A.S.  2013.  Feedback-controlled LED photobioreactor for photophysiological studies of cyanobacteria. Bioresour Technol. 134:127-33.
Walters KA, Olsufka R., Kuestner RE, Cho JH, Li H, Zornetzer G.A, Wang K, Skerrett SJ, Ozinsky A.  2013.  Francisella tularensis subsp. tularensis induces a unique pulmonary inflammatory response: role of bacterial gene expression in temporal regulation of host defense responses. PLoS One. 8:e62412.
Heinäniemi M, Nykter M, Kramer R, Wienecke-Baldacchino A, Sinkkonen L, Zhou JXu, Kreisberg R, Kauffman SA, Huang S, Shmulevich I.  2013.  Gene-pair expression signatures reveal lineage control.. Nat Methods. 10(6):577-83.
Huang S.  2013.  Genetic and non-genetic instability in tumor progression: link between the fitness landscape and the epigenetic landscape of cancer cells. Cancer Metastasis Rev. 32:423-48.
Cromie G.A, Hyma K.E, Ludlow C.L, Garmendia-Torres C, Gilbert T.L, May P., Huang A.A, Dudley AM, Fay J.C.  2013.  Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq. G3 (Bethesda). 3:2163-71.
Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.  2013.  Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnology journal.
Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD.  2013.  Global analysis of condition-specific subcellular protein distribution and abundance. Mol Cell Proteomics. 12:1421-35.
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.
Simeonidis E, Chandrasekaran S, Price ND.  2013.  A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism). Methods Mol Biol. 985:103-12.
Martinez-Bartolome S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A., Canals F., Bech-Serra J.J, Carrascal M. et al..  2013.  Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. J Proteomics.
Dong Y, Kumar CGupta, Chia N, Kim P-J, Miller PA, Price ND, Cann IKO, Flynn TM, Sanford RA, Krapac IG et al..  2013.  Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.. Environ Microbiol.
Labhsetwar P, Cole JAndrew, Roberts E, Price ND, Luthey-Schulten ZA.  2013.  Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population.. Proc Natl Acad Sci U S A. 110(34):14006-11.
Ludlow C.L, Scott A.C, Cromie G.A, Jeffery E.W, Sirr A., May P., Lin J, Gilbert T.L, Hays M., Dudley AM.  2013.  High-throughput tetrad analysis. Nat Methods. 10:671-5.
Huang S, Kauffman S.  2013.  How to escape the cancer attractor: rationale and limitations of multi-target drugs. Semin Cancer Biol. 23:270-8.
Hood L, Rowen L.  2013.  The human genome project: big science transforms biology and medicine. Genome Med. 5:79.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M., Levander F, Shofstahl J et al..  2013.  The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford). 2013:bat009.
Huang S.  2013.  Hybrid T-helper cells: stabilizing the moderate center in a polarized system. PLoS Biol. 11:e1001632.
Sadot A., Sarbu S., Kesseli J., Amir-Kroll H., Zhang W, Nykter M, Shmulevich I.  2013.  Information-theoretic analysis of the dynamics of an executable biological model. PLoS One. 8:e59303.

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