Publications

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.

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.

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.

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.

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. Molecular & cellular proteomics : MCP.

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 in molecular biology. 985:103-12.

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.

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.

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.

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.  2013.  The spectrum of circulating RNA, a window into systems toxicology. Toxicological sciences : an official journal of the Society of Toxicology.

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.

Klose C.S, Kiss E.A, Schwierzeck V., Ebert K., Hoyler T., d'Hargues Y., Goppert N., Croxford A.L, Waisman A., Tanriver Y. et al..  2013.  A T-bet gradient controls the fate and function of CCR6-RORgammat+ innate lymphoid cells. Nature. 494:261-5.

Boyle J.  2013.  There and back again. Nature biotechnology. 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.

Argyropoulos C, Wang K, McClarty S, Huang D, Bernardo J, Ellis D, Orchard T, Galas D, Johnson J.  2013.  Urinary MicroRNA Profiling in the Nephropathy of Type 1 Diabetes. PloS one. 8:e54662.

Huang S.  2013.  When peers are not peers and don't know it: The Dunning-Kruger effect and self-fulfilling prophecy in peer-review. BioEssays : news and reviews in molecular, cellular and developmental biology.

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.

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.

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.

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.

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.

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.

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.

G G, et al..  2012.  Low budget analysis of Direct-To-Consumer genomic testing familial data. F1000Research. 1

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.

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.

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.

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.

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 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.

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.

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.

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.