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Biomedical Informatics

Biomedical Informatics

 
  1. Comstock CE, Augello MA, Schiewer MJ, Karch J, Burd CJ, Ertel A, Knudsen ES, Jessen WJ, Aronow BJ, Knudsen KE. Cyclin D1 is a selective modifier of androgen-dependent signaling and androgen receptor function. J Biol Chem. 2011; 286:8117-27.
  2. Deng J, Deng L, Su S, Zhang M, Lin X, Wei L, Minai AA, Hassett DJ, Lu LJ. Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res. 2011; 39:795-807.
  3. Giannini CM, Kim HK, Mortensen J, Marsolo K, Huppert J. Culture of non-genital sites increases the detection of gonorrhea in women. Journal of pediatric and adolescent gynecology. 2010; 23:246-52.
  4. Gordon SM, Deng J, Lu LJ, Davidson WS. Proteomic characterization of human plasma high density lipoprotein fractionated by gel filtration chromatography. J Proteome Res. 2010; 9:5239-49.
  5. Hamada N, Miyata M, Eto H, Ikeda Y, Shirasawa T, Akasaki Y, Miyauchi T, Furusho Y, Nagaki A, Aronow BJ, Tei C. Loss of clusterin limits atherosclerosis in apolipoprotein E-deficient mice via reduced expression of Egr-1 and TNF-alpha. J Atheroscler Thromb. 2011; 18:209-16.
  6. He F, Ren J, Wang W, Ma J. A multiscale investigation of bicoid-dependent transcriptional events in Drosophila embryos. PLoS One. 2011; 6:e19122.
  7. He F, Saunders TE, Wen Y, Cheung D, Jiao R, ten Wolde PR, Howard M, Ma J. Shaping a morphogen gradient for positional precision. Biophys J. 2010; 99:697-707.
  8. He F, Wen Y, Cheung D, Deng J, Lu LJ, Jiao R, Ma J. Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos. BMC Dev Biol. 2010; 10:80.
  9. Huang H, Du G, Chen H, Liang X, Li C, Zhu N, Xue L, Ma J, Jiao R. Drosophila Smt3 negatively regulates JNK signaling through sequestering Hipk in the nucleus. Development. 2011; 138:2477-85.
  10. Huang H, Yu Z, Zhang S, Liang X, Chen J, Li C, Ma J, Jiao R. Drosophila CAF-1 regulates HP1-mediated epigenetic silencing and pericentric heterochromatin stability. J Cell Sci. 2010; 123:2853-61.
  11. Hummel TR, Jessen WJ, Miller SJ, Kluwe L, Mautner VF, Wallace MR, Lazaro C, Page GP, Worley PF, Aronow BJ, Schorry EK, Ratner N. Gene expression analysis identifies potential biomarkers of neurofibromatosis type 1 including adrenomedullin. Clin Cancer Res. 2010; 16:5048-57.
  12. Jegga AG, Schneider L, Ouyang X, Zhang J. Systems biology of the autophagy-lysosomal pathway. Autophagy. 2011; 7:477-89.
  13. Kaimal V, Bardes EE, Tabar SC, Jegga AG, Aronow BJ. ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. Nucleic Acids Res. 2010; 38:W96-102.
  14. Kaimal V, Sardana D, Bardes EE, Gudivada RC, Chen J, Jegga AG. Integrative systems biology approaches to identify and prioritize disease and drug candidate genes. Methods Mol Biol. 2011; 700:241-59.
  15. Kehat I, Accornero F, Aronow BJ, Molkentin JD. Modulation of chromatin position and gene expression by HDAC4 interaction with nucleoporins. J Cell Biol. 2011; 193:21-9.
  16. Lee S, Hong SW, Min BH, Shim YJ, Lee KU, Lee IK, Bendayan M, Aronow BJ, Park IS. Essential role of clusterin in pancreas regeneration. Dev Dyn. 2011; 240:605-15.
  17. Lin SA, Kolle G, Grimmond SM, Zhou Q, Doust E, Little MH, Aronow B, Ricardo SD, Pera MF, Bertram JF, Laslett AL. Subfractionation of differentiating human embryonic stem cell populations allows the isolation of a mesodermal population enriched for intermediate mesoderm and putative renal progenitors. Stem Cells Dev. 2010; 19:1637-48.
  18. Liu J, Ma J. Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos. Nat Cell Biol. 2011; 13:22-9.
  19. Maldonado AR, Klanke C, Jegga AG, Aronow BJ, Mahller YY, Cripe TP, Crombleholme TM. Molecular engineering and validation of an oncolytic herpes simplex virus type 1 transcriptionally targeted to midkine-positive tumors. J Gene Med. 2010; 12:613-23.
  20. Margolis DJ, Hoffstad O, Thom S, Bilker W, Maldonado AR, Cohen RM, Aronow BJ, Crombleholme T. The differential effect of angiotensin-converting enzyme inhibitors and angiotensin receptor blockers with respect to foot ulcer and limb amputation in those with diabetes. Wound Repair Regen. 2010; 18:445-51.
  21. Mason E, Tronc G, Nones K, Matigian N, Kim J, Aronow BJ, Wolfinger RD, Wells C, Gibson G. Maternal influences on the transmission of leukocyte gene expression profiles in population samples from Brisbane, Australia. PLoS One. 2010; 5:e14479.
  22. Perkins C, Yanase N, Smulian G, Gildea L, Orekov T, Potter C, Brombacher F, Aronow B, Wills-Karp M, Finkelman FD. Selective stimulation of IL-4 receptor on smooth muscle induces airway hyperresponsiveness in mice. J Exp Med. 2011; 208:853-67.
  23. Pestian J, Nasrallah H, Matykiewicz P, Bennett A, Leenaars A. Suicide Note Classification Using Natural Language Processing: A Content Analysis. Biomed Inform Insights. 2010; 2010:19-28.
  24. Popkie AP, Zeidner LC, Albrecht AM, D'Ippolito A, Eckardt S, Newsom DE, Groden J, Doble BW, Aronow B, McLaughlin KJ, White P, Phiel CJ. Phosphatidylinositol 3-kinase (PI3K) signaling via glycogen synthase kinase-3 (Gsk-3) regulates DNA methylation of imprinted loci. J Biol Chem. 2010; 285:41337-47.
  25. Rankin SA, Kormish J, Kofron M, Jegga A, Zorn AM. A gene regulatory network controlling hhex transcription in the anterior endoderm of the organizer. Dev Biol. 2011; 351:297-310.
  26. Sardana D, Vasa S, Vepachedu N, Chen J, Gudivada RC, Aronow BJ, Jegga AG. PhenoHM: human-mouse comparative phenome-genome server. Nucleic Acids Res. 2010; 38:W165-74.
  27. Thompson SD, Sudman M, Ramos PS, Marion MC, Ryan M, Tsoras M, Weiler T, Wagner M, Keddache M, Haas JP, Mueller C, Prahalad S, Bohnsack J, Wise CA, Punaro M, Zhang D, Rose CD, Comeau ME, Divers J, Glass DN, Langefeld CD. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. Arthritis Rheum. 2010; 62:3265-76.
  28. Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W, Aronow B, Gozani O, Fischle W, Hung MC, Patel DJ, Barton MC. TRIM24 links a non-canonical histone signature to breast cancer. Nature. 2010; 468:927-32.
  29. Uzuner O, Solti I, Cadag E. Extracting medication information from clinical text. J Am Med Inform Assoc. 2010; 17:514-8.
  30. Uzuner O, Solti I, Xia F, Cadag E. Community annotation experiment for ground truth generation for the i2b2 medication challenge. J Am Med Inform Assoc. 2010; 17:519-23.
  31. van Berlo JH, Elrod JW, van den Hoogenhof MM, York AJ, Aronow BJ, Duncan SA, Molkentin JD. The transcription factor GATA-6 regulates pathological cardiac hypertrophy. Circ Res. 2010; 107:1032-40.
  32. Widdice LE, Bernstein DI, Leonard AC, Marsolo KA, Kahn JA. Adherence to the HPV vaccine dosing intervals and factors associated with completion of 3 doses. Pediatrics. 2011; 127:77-84.
  33. Xu Y, Zhang M, Wang Y, Kadambi P, Dave V, Lu LJ, Whitsett JA. A systems approach to mapping transcriptional networks controlling surfactant homeostasis. BMC Genomics. 2010; 11:451.
  34. Xu YH, Jia L, Quinn B, Zamzow M, Stringer K, Aronow B, Sun Y, Zhang W, Setchell KD, Grabowski GA. Global gene expression profile progression in Gaucher disease mouse models. BMC Genomics. 2011; 12:20.
  35. Yang L, Wang K, Chen J, Jegga AG, Luo H, Shi L, Wan C, Guo X, Qin S, He G, Feng G, He L. Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study. PLoS Comput Biol. 2011; 7:e1002016.
  36. Yang L, Wang KJ, Wang LS, Jegga AG, Qin SY, He G, Chen J, Xiao Y, He L. Chemical-protein interactome and its application in off-target identification. Interdiscip Sci. 2011; 3:22-30.
  37. Zender M, P.Pestian J, Glauser TA. Visual language system for representing medical concepts. Information Design Journal. 2010; 18:184-197.
  38. Zhang M, Deng J, Fang C, Zhang X, Lu LJ. Biomolecular Network Analysis and Applications. Knowledge based bioinformatics : from analysis to interpretation. Chichester, West Sussex, U.K.: John Wiley & Sons; 2010:253-288.
  39. Zhang M, Lu LJ. Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics. 2010; 11:466.
  40. Zhang M, Zhu C, Jacomy A, Lu LJ, Jegga AG. The orphan disease networks. Am J Hum Genet. 2011; 88:755-66.
  41. Zhang X, Wang X, Zhu H, Zhu C, Wang Y, Pu WT, Jegga AG, Fan GC. Synergistic effects of the GATA-4-mediated miR-144/451 cluster in protection against simulated ischemia/reperfusion-induced cardiomyocyte death. J Mol Cell Cardiol. 2010; 49:841-50.
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