Publications

Found 1195 results
2014
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.
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.
Hood L, Price ND.  2014.  Demystifying disease, democratizing health care. Science translational medicine. 6:225ed5.
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.
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.
Beer K.D, Wurtmann EJ, Pinel N, Baliga NS.  2014.  Model organisms have memory of complex ecologically-relevant environmental variation. Applied and environmental microbiology.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Shao J, Zhang J, Zhang Z., Jiang H, Lou X., Huang B., Foltz G, Lan Q., Huang Q., Lin B.  2013.  Alternative polyadenylation in glioblastoma multiforme and changes in predicted RNA binding protein profiles. OMICS. 17:136-49.
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.
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.
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.
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(3-4):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.
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.
Huang S, Kauffman S.  2013.  How to escape the cancer attractor: rationale and limitations of multi-target drugs.. Semin Cancer Biol. 23(4):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.
Huang S.  2013.  Hybrid T-helper cells: stabilizing the moderate center in a polarized system.. PLoS Biol. 11(8):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.
Yang D, Sun Y, Hu L, Zheng H, Ji P, Pecot CV, Zhao Y, Reynolds S, Cheng H, Rupaimoole R et al..  2013.  Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer. Cancer cell. 23:186-99.
Hood L.  2013.  Interview with Leroy Hood. Bioanalysis. 5:1475-8.
Moruz L., Hoopmann MR, Rosenlund M., Granholm V., Moritz RL, Kall L..  2013.  Mass fingerprinting of complex mixtures: protein inference from high-resolution Peptide masses and predicted retention times. J Proteome Res. 12:5730-41.
Christian N., Skupin A., Morante S., Jansen K., Rossi G., Ebenhoh O..  2013.  Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. J Theor Biol. 343C:102-112.
Chandrasekaran S, Price ND.  2013.  Metabolic constraint-based refinement of transcriptional regulatory networks. PLoS Comput Biol. 9:e1003370.
Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS.  2013.  Metallochaperones regulate intracellular copper levels. PLoS computational biology. 9:e1002880.
Beer K.D, Orellana MV, Baliga NS.  2013.  Modeling the evolution of C4 photosynthesis. Cell. 153:1427-9.
Danziger S.A, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH et al..  2013.  Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic Acids Res.
Akiyoshi B, Nelson CR, Duggan N., Ceto S., Ranish J, Biggins S.  2013.  The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein. PLoS Genet. 9:e1003216.
Kay P., Choudhury R., Nel M., Orellana M.V., .M.Durand P.  2013.  Multicolour flow cytometry analyses and autofluorescence in chlorophytes: lessons from programmed cell death studies in Chlamydomonas reinhardtii. Journal of Applied Phycology. 25:1473-1482.
Sung J, Kim P.J, Ma S, Funk C.C, Magis AT, Wang Y, Hood L, Geman D, Price ND.  2013.  Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures. PLoS Comput Biol. 9:e1003148.
Walzer M., Qi D., Mayer G, Uszkoreit J., Eisenacher M, Sachsenberg T., Gonzalez-Galarza F.F, Fan J, Bessant C., Deutsch EW et al..  2013.  The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics.
H. S, Orellana M.V., Howald W.N..  2013.  A NAD(P) reductase like protein is the salicylic acid receptor in the appendix of the Sauromatum guttatum inflorescence. Landes Bioscience. 1
Huttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J et al..  2013.  N-Glycoprotein SRMAtlas: a resource of mass-spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Molecular & cellular proteomics : MCP.
Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L, Tian Q, Hood L.  2013.  N-glycoproteome of e14.tg2a mouse embryonic stem cells. PloS one. 8:e55722.
Pisco AOliveira, Brock A, Zhou J, Moor A, Mojtahedi M, Jackson D, Huang S.  2013.  Non-Darwinian dynamics in therapy-induced cancer drug resistance.. Nat Commun. 4:2467.
Pisco A.O, Brock A., Zhou J., Moor A., Mojtahedi M., Jackson D., Huang S..  2013.  Non-Darwinian dynamics in therapy-induced cancer drug resistance. Nat Commun. 4:2467.
Tauro B.J, Mathias RA, Greening D.W, Gopal S.K, Ji H, Kapp EA, Coleman B.M, Hill A.F, Kusebauch U, Hallows JL et al..  2013.  Oncogenic H-Ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition. Mol Cell Proteomics.
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..  2013.  Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature.
Hood L, Auffray C.  2013.  Participatory medicine: a driving force for revolutionizing healthcare. Genome medicine. 5:110.
Smith JJ, Aitchison JD.  2013.  Peroxisomes take shape. Nat Rev Mol Cell Biol. 14:803-17.
Chen WM, Danziger S.A, Chiang JH, Aitchison JD.  2013.  PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. Bioinformatics. 29:2435-44.
Goverman J, Woods A., Larson L., Weiner L.P, Hood L, Zaller D.M.  2013.  Pillars article: Transgenic mice that express a myelin basic protein-specific T cell receptor develop spontaneous autoimmunity. Cell. 1993. 72: 551-560. J Immunol. 190:3018-27.
Kadoch C., Hargreaves D.C, Hodges C., Elias L., Ho L, Ranish J, Crabtree GR.  2013.  Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nat Genet.
Sims A.C, Tilton S.C, Menachery V.D, Gralinski L.E, Schafer A., Matzke M.M, Webb-Robertson B.J, Chang J., Luna M.L, Long C.E et al..  2013.  Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. J Virol. 87:3885-902.
Thyme S.B, Boissel S.J, S. Quadri A, Nolan T., Baker D.A, Park R.U, Kusak L., Ashworth J, Baker D..  2013.  Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res.
Gomes C.P, Cho JH, Hood L, Franco O.L, Pereira R.W, Wang K.  2013.  A Review of Computational Tools in microRNA Discovery. Front Genet. 4:81.
Mandin P., Toledo-Arana A., A. d'Hérouel F, Repoila F..  2013.  RNA-mediated Control of Bacterial Gene Expression: Role of Regulatory non-Coding RNAs. Encyclopedia of Molecular Cell Biology and Molecular Medicine. :1–36.
Orellana MV, Pang WL, Durand P.M, Whitehead K, Baliga NS.  2013.  A role for programmed cell death in the microbial loop. PLoS One. 8:e62595.
Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW.  2013.  A role for the nucleoporin nup170p in chromatin structure and gene silencing. Cell. 152:969-83.
Wang K, Yuan Y, Li H, Cho JH, Huang D, Gray L, Qin S, Galas D.J.  2013.  The spectrum of circulating RNA: a window into systems toxicology. Toxicol Sci. 132:478-92.
Jensen H.A, Styskal L.E, Tasseff R., Bunaciu R.P, Congleton J., Varner J.D, Yen A..  2013.  The Src-family kinase inhibitor PP2 rescues inducible differentiation events in emergent retinoic acid-resistant myeloblastic leukemia cells. PLoS One. 8:e58621.
Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL.  2013.  The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res. 12:162-71.
Larjo A, Shmulevich I, Lahdesmaki H.  2013.  Structure learning for bayesian networks as models of biological networks. Methods in molecular biology. 939:35-45.
Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD et al..  2013.  Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proceedings of the National Academy of Sciences of the United States of America. 110:3645-50.
Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K.  2013.  Systems Approach to Neurodegenerative Disease Biomarker Discovery. Annu Rev Pharmacol Toxicol.
Hood L.  2013.  Systems biology and p4 medicine: past, present, and future.. Rambam Maimonides Med J. 4(2):e0012.
Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie T.J, Slagel J, Moritz RL, Hackett M et al..  2013.  A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res. 23:1839-51.
Boyle J.  2013.  There and back again. Nat Biotechnol. 31:13-5.
Lindner SE, Swearingen KE, Harupa A, Vaughan AM, Sinnis P, Moritz RL, Kappe SH.  2013.  Total and putative surface proteomics of malaria parasite salivary gland sporozoites. Molecular & cellular proteomics : MCP.

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