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Bioinformatics and Systems Biology


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Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes.
Chen YG, Mordes JP, Blankenhorn EP, Kashmiri H, Kaldunski ML, Jia S, Geoffrey R, Wang X, Hessner MJ.
Genes Immun. 2013 Sep ;14(6):387-400.
[Text Abstract on PubMed]

Identification of highly synchronized subnetworks from gene expression data.
Gao S, Wang X.
BMC Bioinformatics. 2013 Jun 28;14 Suppl 9:S5.
[Text Abstract on PubMed]

Mathematical modeling of insulin secretion and the role of glucose-dependent mobilization, docking, priming and fusion of insulin granules.
Stamper IJ, Wang X.
J Theor Biol. 2013 Feb 7;318:210-25.
[Text Abstract on PubMed]

Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.
Okur A, Miller BT, Joo K, Lee J, Brooks BR.
J Chem Theory Comput. 2013 Feb 1;9(2):1115-1124.
[Text Abstract on PubMed]

Syndecan-2 Exerts Anti-Fibrotic Effects by Promoting Caveolin-1 Mediated TβRI Internalization and Inhibiting TGF-β1 Signaling.
Shi Y, Gochuico BR, Yu G, Tang X, Osorio JC, Fernandez IE, Risquez CF, Patel AS, Shi Y, Wathelet MG, Goodwin AJ, Haspel JA, Ryter SW, Billings EM, Kaminski N, Morse D, Rosas IO.
Am J Respir Crit Care Med. 2013 Aug 7.
[Text Abstract on PubMed]

Brefeldin A-inhibited ADP-ribosylation factor activator BIG2 regulates cell migration via integrin ß1 cycling and actin remodeling.
Shen X, Li CC, Aponte AM, Shen RF, Billings EM, Moss J, Vaughan M.
Proc. Natl. Acad. Sci. U.S.A. 2012 Sep 4;109(36):14464-9.
[Text Abstract on PubMed]

Predicting disease-related subnetworks for type 1 diabetes using a new network activity score.
Gao S, Jia S, Hessner MJ, Wang X.
OMICS. 2012 Oct ;16(10):566-78.
[Text Abstract on PubMed]

MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.
Smith DB, Okur A, Brooks B.
Chem Phys Lett. 2012 Aug 30;545:118-124.
[Text Abstract on PubMed]

Cross tissue trait-pathway network reveals the importance of oxidative stress and inflammation pathways in obesity-induced diabetes in mouse.
Gao S, Roberts HK, Wang X.
PLoS One. 2012 01 ;7(9):e44544.
[Text Abstract on PubMed]

Use of transcriptional signatures induced in lymphoid and myeloid cell lines as an inflammatory biomarker in Type 1 diabetes.
Jia S, Kaldunski M, Jailwala P, Geoffrey R, Kramer J, Wang X, Hessner MJ.
Physiol Genomics. 2011 Jun 15;43(11):697-709.
[Text Abstract on PubMed]

Intrinsic optical signal imaging of glucose-stimulated insulin secreting β-cells.
Li YC, Cui WX, Wang XJ, Amthor F, Lu RW, Thompson A, Yao XC.
Opt Express. 2011 Jan 3;19(1):99-106.
[Text Abstract on PubMed]

Improving the description of salt bridge strength and geometry in a Generalized Born model.
Shang Y, Nguyen H, Wickstrom L, Okur A, Simmerling C.
J Mol Graph Model. 2011 Feb ;29(5):676-84.
[Text Abstract on PubMed]

MSCALE: A General Utility for Multiscale Modeling.
Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR.
J Chem Theory Comput. 2011 Apr 12;7(4):1208-1219.
[Text Abstract on PubMed]

Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data.
Gao S, Wang X.
BMC Bioinformatics. 2011 01 ;12:359.
[Text Abstract on PubMed]

Time course analysis of gene expression identifies multiple genes with differential expression in patients with in-stent restenosis.
Ganesh SK, Joo J, Skelding K, Mehta L, Zheng G, O'Neill K, Billings EM, Helgadottir A, Andersen K, Thorgeirsson G, Gudnason T, Geller NL, Simari RD, Holmes DR, O'Neill WW, Nabel EG.
BMC Med Genomics. 2011 01 ;4:20.
[Text Abstract on PubMed]

Identification of a serum-induced transcriptional signature associated with type 1 diabetes in the BioBreeding rat.
Kaldunski M, Jia S, Geoffrey R, Basken J, Prosser S, Kansra S, Mordes JP, Lernmark A, Wang X, Hessner MJ.
Diabetes. 2010 Oct ;59(10):2375-85.
[Text Abstract on PubMed]

Single-nucleotide polymorphisms in the IL2RA gene are associated with age at diagnosis in late-onset Finnish type 1 diabetes subjects.
Klinker MW, Schiller JJ, Magnuson VL, Wang T, Basken J, Veth K, Pearce KI, Kinnunen L, Harjutsalo V, Wang X, Tuomilehto J, Sarti C, Ghosh S.
Immunogenetics. 2010 Feb ;62(2):101-7.
[Text Abstract on PubMed]

The fractal dimension of cell membrane correlates with its capacitance: a new fractal single-shell model.
Wang X, Becker FF, Gascoyne PR.
Chaos. 2010 Dec ;20(4):043133.
[Text Abstract on PubMed]

Kinetics of insulin secretion to acute, repetitive stimulation of islets in vivo in Sprague Dawley rats.
Chen J, Nittala A, Gao S, Ghosh S, Wang X, Patel S.
Islets. 2010 01 ;2(1):10-7.
[Text Abstract on PubMed]

Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling.
Gao S, Hartman JL 4th, Carter JL, Hessner MJ, Wang X.
BMC Syst Biol. 2010 01 ;4:167.
[Text Abstract on PubMed]

Microalterations of inherently unstable genomic regions in rat mammary carcinomas as revealed by long oligonucleotide array-based comparative genomic hybridization.
Adamovic T, McAllister D, Guryev V, Wang X, Andrae JW, Cuppen E, Jacob HJ, Sugg SL.
Cancer Res. 2009 Jun 15;69(12):5159-67.
[Text Abstract on PubMed]

Chemokine-enhanced chemotaxis of lymphangioleiomyomatosis cells with mutations in the tumor suppressor TSC2 gene.
Pacheco-Rodriguez G, Kumaki F, Steagall WK, Zhang Y, Ikeda Y, Lin JP, Billings EM, Moss J.
J. Immunol. 2009 Feb 1;182(3):1270-7.
[Text Abstract on PubMed]

A joint association test for multiple SNPs in genetic case-control studies.
Wang T, Jacob H, Ghosh S, Wang X, Zeng ZB.
Genet Epidemiol. 2009 Feb ;33(2):151-63.
[Text Abstract on PubMed]

Evaluating the performance of the ff99SB force field based on NMR scalar coupling data.
Wickstrom L, Okur A, Simmerling C.
Biophys J. 2009 Aug 5;97(3):853-6.
[Text Abstract on PubMed]

Predicting Type 1 Diabetes Candidate Genes using Human Protein-Protein Interaction Networks.
Gao S, Wang X.
J Comput Sci Syst Biol. 2009 Apr 1;2:133.
[Text Abstract on PubMed]

Increasing incidence of pediatric type 1 diabetes mellitus in Southeastern Wisconsin: relationship with body weight at diagnosis.
Evertsen J, Alemzadeh R, Wang X.
PLoS One. 2009 01 ;4(9):e6873.
[Text Abstract on PubMed]

Apoptosis of CD4+ CD25(high) T cells in type 1 diabetes may be partially mediated by IL-2 deprivation.
Jailwala P, Waukau J, Glisic S, Jana S, Ehlenbach S, Hessner M, Alemzadeh R, Matsuyama S, Laud P, Wang X, Ghosh S.
PLoS One. 2009 01 ;4(8):e6527.
[Text Abstract on PubMed]

Optical spectroscopy in turbid media utilizing an integrating sphere: mitochondrial chromophore analysis during metabolic transitions.
Chess DJ, Billings E, Covian R, Glancy B, French S, Taylor J, Bari HD, Murphy E, Balaban RS.
Anal Biochem..
[Text Abstract on PubMed]