Resources

2015

Chandrasekaran S, Rittschof C.C, Djukovic D., Gu H., Raftery D., Price ND,Robinson GE.  2015.  Aggression is associated with aerobic glycolysis in the honey bee brain. Genes, brain, and behavior.

Viollet L, Glusman G, Murphy KJ, Newcomb TM, Reyna SP, Sweney M, Nelson B,Andermann F, Andermann E, Acsadi G et al..  2015.  Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry.. PLoS One. 10(5):e0127045.

He Y, Yang J, Kong D, Lin J, Xu C, Ren H, Ouyang P, Ding Y, Wang K.  2015.  Association of miR-146a rs2910164 polymorphism with cardio-cerebrovascular diseases: A systematic review and meta-analysis.. Gene. 565(2):171-9.

Liu G, Yang D, Rupaimoole R, Pecot CV, Sun Y, Mangala LS, Li X, Ji P, Cogdell D,Hu L et al..  2015.  Augmentation of Response to Chemotherapy by microRNA-506 Through Regulation of RAD51 in Serous Ovarian Cancers.. J Natl Cancer Inst. 107(7)

Keller A, Bader S.L, Shteynberg D, Hood L, Moritz RL.  2015.  Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data Independent Acquisition MS using SWATHProphet. Molecular & cellular proteomics : MCP.

von Karstedt S, Conti A, Nobis M, Montinaro A, Hartwig T, Lemke J, Legler K,Annewanter F, Campbell AD, Taraborrelli L et al..  2015.  Cancer cell-autonomous TRAIL-R signaling promotes KRAS-driven cancer progression, invasion, and metastasis..Cancer Cell. 27(4):561-73.

Reiss DJ, Plaisier CL, Wu W-J, Baliga NS.  2015.  cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.. Nucleic Acids Res.

Turkarslan S, Peterson EJR, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S,Price ND, Sherman DR, Baliga NS.  2015.  A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.. Sci Data. 2:150010.

Hu T, Li X, Zhang Q, Huang K, Jia Y, Yang R, Tang F, Tian Q, Ma D, Li S.  2015.  Could the extent of lymphadenectomy be modified by neoadjuvant chemotherapy in cervical cancer? A large-scale retrospective study. PLoS One. 10(4):e0123539.

Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND.  2015.  Data-driven integration of genome-scale regulatory and metabolic network models.. Front Microbiol. 6:409.

Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS,Orchard S, Vizcaino JA, Hermjakob H.  2015.  Development of data representation standards by the human proteome organization proteomics standards initiative. Journal of the American Medical Informatics Association : JAMIA.

Minch KJ, Rustad TR, Peterson EJR, Winkler J, Reiss DJ, Ma S, Hickey M,Brabant W, Morrison B, Turkarslan S et al..  2015.  The DNA-binding network of Mycobacterium tuberculosis.. Nat Commun. 6:5829.

He Y, Chevillet JR, Liu G, Kim TK, Wang K.  2015.  The effects of microRNA on the absorption, distribution, metabolism and excretion of drugs.. Br J Pharmacol. 172(11):2733-47.

Zhu X, Yuan R., Hood L, Ao P.  2015.  Endogenous molecular-cellular hierarchical modeling of prostate carcinogenesis uncovers robust structure. Progress in biophysics and molecular biology. 117:30-42.

Eddy JA, Funk CC, Price ND.  2015.  Fostering synergy between cell biology and systems biology.. Trends Cell Biol.

He Y, Zeng K., Zhang X., Chen Q., Wu J, Li H, Zhou Y, Glusman G, Roach J,Etheridge A et al..  2015.  A Gain-of-Function Mutation in TRPV3 Causes Focal Palmoplantar Keratoderma in a Chinese Family. The Journal of investigative dermatology. 135:907-9.

Simeonidis E, Price ND.  2015.  Genome-scale modeling for metabolic engineering.Journal of industrial microbiology & biotechnology. 42:327-38.

Turner K.M, Sun Y, Ji P, Granberg K.J, Bernard B, Hu L, Cogdell D.E, Zhou X.,Yli-Harja O, Nykter M et al..  2015.  Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression. Proceedings of the National Academy of Sciences of the United States of America. 112:3421-6.

Lee HJ, Kim J.M, Kim K.H, Heo J.I, Kwak S.J, Han J.A.  2015.  Genotoxic stress/p53-induced DNAJB9 inhibits the pro-apoptotic function of p53. Cell death and differentiation. 22:86-95.

Lin B, Lee H, Yoon JG, Madan A, Wayner E., Tonning S., Hothi P., Schroeder B.,Ulasov I., Foltz G et al..  2015.  Global analysis of H3K4me3 and H3K27me3 profiles in glioblastoma stem cells and identification of SLC17A7 as a bivalent tumor suppressor gene.Oncotarget.

Glusman G, Severson A., Dhankani V., Robinson M, Farrah T, Mauldin DE,Stittrich A.B, Ament SA, Roach JC, Brunkow M.E et al..  2015.  Identification of copy number variants in whole-genome data using Reference Coverage Profiles. Frontiers in genetics. 6:45.

Chakrabarty P., Li A., Ceballos-Diaz C., Eddy JA, Funk C.C, Moore B., DiNunno N., Rosario A.M, Cruz P.E, Verbeeck C. et al..  2015.  IL-10 Alters Immunoproteostasis in APP Mice, Increasing Plaque Burden and Worsening Cognitive Behavior. Neuron. 85:519-33.

Hood L, Lovejoy J.C, Price ND.  2015.  Integrating big data and actionable health coaching to optimize wellness. BMC medicine. 13:4.

Basler G., Simeonidis E.  2015.  Integrating food webs with metabolic networks: modeling contaminant degradation in marine ecosystems. Frontiers in genetics. 6:20.

Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.  2015.  Kojak: Efficient analysis of chemically cross-linked protein complexes.. J Proteome Res.

Wang W, Zhang D., Wei Z., Wang Z, Bu X., Yang S, Fang Q., Hu Z.  2015.  Label-free detection microarray for novel peptide ligands screening base on MS-SPRi combination. Talanta. 134:705-11.

Gillespie MA, Gold ES, Ramsey SA, Podolsky I, Aderem A, Ranish J.  2015.  An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux. The EMBO journal.

Ichiyama K, Chen T, Wang X, Yan X, Kim B-S, Tanaka S, Ndiaye-Lobry D, Deng Y, Zou Y, Zheng P et al..  2015.  The methylcytosine dioxygenase Tet2 promotes DNA demethylation and activation of cytokine gene expression in T cells.. Immunity. 42(4):613-26.

Elbelt U., Trovato A., Kloth M., Gentz E., Finke R., Spranger J., Galas D, Weber S., Wolf C., Konig K. et al..  2015.  Molecular and clinical evidence for an ARMC5 tumor syndrome: concurrent inactivating germline and somatic mutations are associated with both primary macronodular adrenal hyperplasia and meningioma. The Journal of clinical endocrinology and metabolism. 100:E119-28.

Lee M-J, Chen Y-F, Fan P-C, Wang K-C, Wang K, Wang J, Kuo M-F.  2015.  Mutation genotypes of RNF213 gene from moyamoya patients in Taiwan.. J Neurol Sci. 353(1-2):161-5.

Subramanian N., Torabi-Parizi P., Gottschalk R.A, Germain R.N, Dutta B..  2015.  Network representations of immune system complexity. Wiley interdisciplinary reviews. Systems biology and medicine. 7:13-38.

Pisco AO, Huang S.  2015.  Non-genetic cancer cell plasticity and therapy-induced stemness in tumour relapse: ‘What does not kill me strengthens me’.. Br J Cancer. 112(11):1725-32.

Cheng Z, Wang Z, Gillespie DE, Lausted C, Zheng Z, Yang M, Zhu J.  2015.  Plain silver surface plasmon resonance for microarray application.. Anal Chem. 87(3):1466-9.

Winget JM, Watts JD, Hoopmann MR, DiColandrea T, Robinson MK, Huggins T,Bascom CC, Isfort RJ, Moritz RL.  2015.  Quantitative proteogenomic profiling of epidermal barrier formation in vitro.. J Dermatol Sci. 78(3):173-80.

Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S,Dilworth DJ, Molloy KR, Sherman V, Aitchison JD et al..  2015.  Rapid, optimized interactomic screening.. Nat Methods. 12(6):553-60.

Ament SA, Szelinger S., Glusman G, Ashworth J, Hou L., Akula N., Shekhtman T., Badner J.A, Brunkow M.E, Mauldin DE et al..  2015.  Rare variants in neuronal excitability genes influence risk for bipolar disorder. Proceedings of the National Academy of Sciences of the United States of America. 112:3576-81.

Hardies K, May P, Djémié T, Tarta-Arsene O, Deconinck T, Craiu D, Helbig I,Suls A, Balling R, Weckhuysen S et al..  2015.  Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly.. Hum Mol Genet. 24(8):2218-27.

Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J,Bartholomew B, Shen X.  2015.  Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex.. Genes Dev. 29(6):591-602.

Mast FD, Rachubinski RA, Aitchison JD.  2015.  Signaling dynamics and peroxisomes.. Curr Opin Cell Biol. 35:131-136.

Han B, Park D, Li R, Xie M, Owonikoko TK, Zhang G, Sica GL, Ding C, Zhou J,Magis AT et al..  2015.  Small-Molecule Bcl2 BH4 Antagonist for Lung Cancer Therapy..Cancer Cell. 27(6):852-63.

Papadakis A.I, Sun C., Knijnenburg TA, Xue Y., Grernrum W., Holzel M.,Nijkamp W., Wessels LF, Beijersbergen R.L, Bernards R. et al..  2015.  SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer. Cell research.

Grosse-Wilde A, d’Hérouël AFouquier, McIntosh E, Ertaylan G, Skupin A,Kuestner RE, Del Sol A, Walters KA, Huang S.  2015.  Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival..PLoS One. 10(5):e0126522.

He Y, Lin J, Ding Y, Liu G, Luo Y, Huang M, Xu C, Kim T-K, Etheridge A, Lin M et al..  2015.  A systematic study on dysregulated microRNAs in cervical cancer development.. Int J Cancer.

Heavner B.D, Price ND.  2015.  Transparency in metabolic network reconstruction enables scalable biological discovery. Current opinion in biotechnology. 34C:105-109.

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.  2015.  Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics. Clinical applications.

Yoon H, Knight SAB, Pandey A, Pain J, Turkarslan S, Pain D, Dancis A.  2015.  Turning Saccharomyces cerevisiae into a Frataxin-Independent Organism.. PLoS Genet. 11(5):e1005135.

Li X, Liu Y, Granberg KJ, Wang Q, Moore LM, Ji P, Gumin J, Sulman EP, Calin GA, Haapasalo H et al..  2015.  Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma.. Oncogene. 34(13):1619-28.

Rosenbloom K.R, Armstrong J., Barber G.P, Casper J., Clawson H., Diekhans M,Dreszer T.R, Fujita P.A, Guruvadoo L., Haeussler M. et al..  2015.  The UCSC Genome Browser database: 2015 update. Nucleic acids research. 43:D670-81.

Raman A.V, Baliga NS.  2015.  The universe under a microscope. Environmental microbiology reports. 7:11-2.

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.

Ma H, Ning J, Jin X, Mao C, Bu X, Wang M, Liu H, Wang K, Lausted C, Hood L et al.. 2014. Betaine homocysteine methyltransferase (BHMT) as a specific and sensitive blood marker for acute liver injury.. Biomarkers. 19(7):578-84.

Kang S, Kahan S, McDermott J, Flann N, Shmulevich I. 2014. Biocellion: accelerating computer simulation of multicellular biological system models.. Bioinformatics.

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.

Liu Y, Patel L, Mills GB, Lu KH, Sood AK, Ding L, Kucherlapati R, Mardis ER, Levine DA, Shmulevich I et al.. 2014. Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma.. J Natl Cancer Inst. 106(9)

Muller EEL, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA, Roume H, Lin J, May P, Hicks ND et al.. 2014. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.. Nat Commun. 5:5603.

Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D et al.. 2014. Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells.. Front Microbiol. 5:392.

Cancer Genome Atlas Research Network. 2014. Comprehensive molecular characterization of gastric adenocarcinoma.. Nature. 513(7517):202-9.

Qi L, Pujanauski LM, A Davis S, Schwartzman LM, Chertow DS, Baxter D, Scherler K, Hartshorn KL, Slemons RD, Walters KA et al.. 2014. Contemporary avian influenza A virus subtype H1, H6, H7, H10, and H15 hemagglutinin genes encode a mammalian virulence factor similar to the 1918 pandemic virus H1 hemagglutinin.. MBio. 5(6):e02116.

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.

Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran J-M. 2014. Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.. Yeast.

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.

Lehman A, Stittrich A-B, Glusman G, Zong Z, Li H, Eydoux P, Senger C, Lyons C, Roach JC, Patel M. 2014. Diffuse angiopathy in Adams-Oliver syndrome associated with truncating DOCK6 mutations.. Am J Med Genet A. 164A(10):2656-62.

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.

Hillesland K.L, Lim S, Flowers J.J, Turkarslan S, Pinel N, Zane G.M, Elliott N., Qin Y., Wu L., Baliga NS et al.. 2014. Erosion of functional independence early in the evolution of a microbial mutualism. Proceedings of the National Academy of Sciences of the United States of America.

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.

He Y, Zeng K, Zhang X, Chen Q, Wu J, Li H, Zhou Y, Glusman G, Roach J, Etheridge A et al.. 2014. A Gain-of-Function Mutation in TRPV3 Causes Focal Palmoplantar Keratoderma in a Chinese Family.. J Invest Dermatol.

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)

Peterson EJR, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJR, Sherman DR, Baliga NS. 2014. A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.. Nucleic Acids Res.

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.

Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN et al.. 2014. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.. Genome Biol. 15(3):R53.

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.

Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR, MacCoss MJ, Moritz RL et al.. 2014. Kinetochore Biorientation in Saccharomyces cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex.. Genetics.

Zhu L, Wang K, Cui J, Liu H, Bu X, Ma H, Wang W, Gong H, Lausted C, Hood L et al.. 2014. Label-free quantitative detection of tumor-derived exosomes through surface plasmon resonance imaging.. Anal Chem. 86(17):8857-64.

Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A. 2014. Macromolecular networks and intelligence in microorganisms.. Front Microbiol. 5:379.

Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS et al.. 2014. Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.. Genome Biol. 15(11):502.

Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND. 2014. MediaDB: a database of microbial growth conditions in defined media.. PLoS One. 9(8):e103548.

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 B.CParker, 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. The Journal of pathology. 233:308-18.

Sperber H, Beem A, Shannon S, Jones R, Banik P, Chen Y, Ku S, Varani G, Yao S, Ruohola-Baker H. 2014. miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure.. RNA. 20(5):621-31.

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 AFA, Wessels LFA, Laird PW, Aderem A, Shmulevich I. 2014. Multiscale representation of genomic signals.. Nature Methods. 11(6):689-94.

Stittrich A-B, Lehman A, Bodian DL, Ashworth J, Zong Z, Li H, Lam P, Khromykh A, Iyer RK, Vockley JG et al.. 2014. Mutations in NOTCH1 cause Adams-Oliver syndrome.. Am J Hum Genet. 95(3):275-84.

Schubert J, Siekierska A, Langlois M, May P, Huneau C, Becker F, Muhle H, Suls A, Lemke JR, de Kovel CGF et al.. 2014. Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes.. Nat Genet. 46(12):1327-32.

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.

Lalli MA, Cox HC, Arcila ML, Cadavid L, Moreno S, Garcia G, Madrigal L, Reiman EM, Arcos-Burgos M, Bedoya G et al.. 2014. Origin of the PSEN1 E280A mutation causing early-onset Alzheimer’s disease.. Alzheimers Dement. 10(5 Suppl):S277-S283.e10.

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(2):215-28.

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.

Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND. 2014. Quantitative Proteomic Analysis Reveals Effects of Epidermal Growth Factor Receptor (EGFR) on Invasion-promoting Proteins Secreted by Glioblastoma Cells.. Mol Cell Proteomics. 13(10):2618-31.

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.

Wang W, Wei Z, Zhang D, Ma H, Wang Z, Bu X, Li M, Geng L, Lausted C, Hood L et al.. 2014. Rapid screening of peptide probes through in situ single-bead sequencing microarray.. Anal Chem. 86(23):11854-9.

Caballero J, Smit AFA, Hood L, Glusman G. 2014. Realistic artificial DNA sequences as negative controls for computational genomics.. Nucleic Acids Res. 42(12):e99.

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