Publications

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.