Biomedical Informatics

Biomedical Informatics Publications

  1. Biesiada JW, Senthilkumar Sadhasivam MD M, Wagner M, Meller J. From SNP Genotyping to Improved Pediatric Healthcare. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:359-378.
  2. Bonafide CP, Brady PW, Keren R, Conway PH, Marsolo K, Daymont C. Development of heart and respiratory rate percentile curves for hospitalized children. Pediatrics. 2013; 131:e1150-7.
  3. Brown EB, Layne JE, Zhu C, Jegga AG, Rollmann SM. Genome-wide Association Mapping of Natural Variation in Odor-guided Behavior in Drosophila. Genes Brain Behav. 2013; .
  4. Chen Y, Mazlack L, Lu L. (2012) Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference. Philadelphia, ACM. .
  5. Chen Y, Mazlack LJ, Lu LJ. (2012) Fuzzy Information Processing Society (NAFIPS), 2012 Annual Meeting of the North American. Berkley, CA, IEEE. .
  6. Chen Y, Mazlack LJ, Lu LJ. (2012) 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Philadelphia, IEEE. .
  7. Davies JA, Little MH, Aronow B, Armstrong J, Brennan J, Lloyd-MacGilp S, Armit C, Harding S, Piu X, Roochun Y, Haggarty B, Houghton D, Davidson D, Baldock R. Access and use of the GUDMAP database of genitourinary development. Methods Mol Biol. 2012; 886:185-201.
  8. Deleger L, Brodzinski H, Zhai H, Li Q, Lingren T, Kirkendall E, Alessandrini E, Solti I. (2012) 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB). San Diego, CA, IEEE. .
  9. Deleger L, Li Q, Lingren T, Kaiser M, Molnar K, Stoutenborough L, Kouril M, Marsolo K, Solti I. Building gold standard corpora for medical natural language processing tasks. AMIA Annu Symp Proc. 2012; 2012:144-53.
  10. Deleger L, Molnar K, Savova G, Xia F, Lingren T, Li Q, Marsolo K, Jegga A, Kaiser M, Stoutenborough L, Solti I. Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. J Am Med Inform Assoc. 2013; 20:84-94.
  11. Deng J, Su S, Lin X, Hassett DJ, Lu LJ. A Statistical Framework for Improving Genomic Annotations of Prokaryotic Essential Genes. PloS one. 2013; 8:e58178.
  12. Dexheimer JW. Interfaces and Data Transmission Standards. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:27-42.
  13. Dexheimer JW, Johnson LH, Imre Solti M, Dominik Aronsky M, Pestian JP. Informatics and Decision Support. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:193-209.
  14. Dui W, Lu W, Ma J, Jiao R. A systematic phenotypic screen of F-box genes through a tissue-specific RNAi-based approach in Drosophila. J Genet Genomics. 2012; 39:397-413.
  15. Glauser TA, Cnaan A, Shinnar S, Hirtz DG, Dlugos D, Masur D, Clark PO, Adamson PC, Childhood Absence Epilepsy Study T. Ethosuximide, valproic acid, and lamotrigine in childhood absence epilepsy: initial monotherapy outcomes at 12 months. Epilepsia. 2013; 54:141-55.
  16. Godby RC, Van Den Berg YW, Srinivasan R, Sturm R, Hui DY, Konieczny SF, Aronow BJ, Ozhegov E, Ruf W, Versteeg HH, Bogdanov VY. Nonproteolytic properties of murine alternatively spliced tissue factor: implications for integrin-mediated signaling in murine models. Mol Med. 2012; 18:771-9.
  17. He F, Ma J. A Spatial Point Pattern Analysis in Drosophila Blastoderm Embryos Evaluating the Potential Inheritance of Transcriptional States. PLOS ONE. 2013; 8:e60876.
  18. Hutton JJ, Dexheimer P, Grabowski G. Gene Variation and Gene Discovery. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:379-394.
  19. Jessen WJ, Miller SJ, Jousma E, Wu J, Rizvi TA, Brundage ME, Eaves D, Widemann B, Kim MO, Dombi E, Sabo J, Hardiman Dudley A, Niwa-Kawakita M, Page GP, Giovannini M, Aronow BJ, Cripe TP, Ratner N. MEK inhibition exhibits efficacy in human and mouse neurofibromatosis tumors. J Clin Invest. 2013; 123:340-7.
  20. Kouril M. (2012) Computing the van der Waerden number W (3, 4)=293. Integers Electronic J Combinatorial Number Theory. 12:A46.
  21. Kouril M, Hunt N, Wagner M. Data Storage and Access Management. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:43-61.
  22. Li Q, Deleger L, Lingren T, Zhai H, Kaiser M, Stoutenborough L, Jegga AG, Cohen KB, Solti I. Mining FDA drug labels for medical conditions. BMC medical informatics and decision making. 2013; 13:53.
  23. Li Q, Zhai H, Deleger L, Lingren T, Kaiser M, Stoutenborough L, Solti I. (2012) 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology. San Diego, CA, IEEE. .
  24. Lingren T, Deleger L, Molnar K, Zhai H, Meinzen-Derr J, Kaiser M, Stoutenborough L, Li Q, Solti I. (2012) 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology. San Diego, CA, IEEE. .
  25. Liu J, Ma J. Uncovering a dynamic feature of the transcriptional regulatory network for anterior-posterior patterning in the Drosophila embryo. PLoS One. 2013; 8:e62641.
  26. Lu L, Zhang M, Deng J, Tan L, Chen Y. Network Analysis and Applications in Pediatric Diseases. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:265-285.
  27. Lu TX, Lim EJ, Wen T, Plassard AJ, Hogan SP, Martin LJ, Aronow BJ, Rothenberg ME. MiR-375 is downregulated in epithelial cells after IL-13 stimulation and regulates an IL-13-induced epithelial transcriptome. Mucosal Immunol. 2012; 5:388-96.
  28. Lu TX, Lim E-J, Besse JA, Itskovich S, Plassard AJ, Fulkerson PC, Aronow BJ, Rothenberg ME. miR-223 Deficiency Increases Eosinophil Progenitor Proliferation. The Journal of Immunology. 2013; 190:1576-1582.
  29. Lu TX, Lim E-J, Itskovich S, Besse JA, Plassard AJ, Mingler MK, Rothenberg JA, Fulkerson PC, Aronow BJ, Rothenberg ME. Targeted Ablation of miR-21 Decreases Murine Eosinophil Progenitor Cell Growth. PloS one. 2013; 8:e59397.
  30. Lu TX, Sherrill JD, Wen T, Plassard AJ, Besse JA, Abonia JP, Franciosi JP, Putnam PE, Eby M, Martin LJ, Aronow BJ, Rothenberg ME. MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids, and assessment as disease biomarkers. J Allergy Clin Immunol. 2012; 129:1064-75 e9.
  31. Lynch JM, Maillet M, Vanhoutte D, Schloemer A, Sargent MA, Blair NS, Lynch KA, Okada T, Aronow BJ, Osinska H. A thrombospondin-dependent pathway for a protective ER stress response. Cell. 2012; 149:1257-1268.
  32. Marsolo K. Informatics and operations--let's get integrated. J Am Med Inform Assoc. 2013; 20:122-4.
  33. Marsolo K. EHR-Linked Registries for Studies of Populations. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:133-148.
  34. Marsolo K. Informatics Support of Outcome Measures. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:231-241.
  35. Marsolo K. Research Patient Data Warehousing. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:93-108.
  36. Marsolo K. In Search of a Data-in-Once, Electronic Health Record-Linked, Multicenter Registry—How Far We Have Come and How Far We Still Have to Go. eGEMs (Generating Evidence & Methods to improve patient outcomes). 2012; 1:3.
  37. Marsolo K. Approaches to facilitate institutional review board approval of multicenter research studies. Med Care. 2012; 50 Suppl:S77-81.
  38. Marsolo K, Corsmo J, Barnes MG, Pollick C, Chalfin J, Nix J, Smith C, Ganta R. Challenges in creating an opt-in biobank with a registrar-based consent process and a commercial EHR. Journal of the American Medical Informatics Association. 2012; 19:1115-1118.
  39. Matykiewicz P, Pestian J. (2012) Proceedings of the 2012 Workshop on Biomedical Natural Language Processing. Montreal, Quebec, Association for Computational Linguistics. .
  40. Morrow AL, Lagomarcino AJ, Schibler KR, Taft DH, Yu Z, Wang B, Altaye M, Wagner M, Gevers D, Ward DV. Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome. 2013; 1:13.
  41. Myronovych A, Kirby M, Ryan KK, Zhang W, Jha P, Setchell KD, Dexheimer PJ, Aronow B, Seeley RJ, Kohli R. Vertical sleeve gastrectomy reduces hepatic steatosis while increasing serum bile acids in a weight-loss-independent manner. Obesity (Silver Spring). 2013; .
  42. Natter MD, Quan J, Ortiz DM, Bousvaros A, Ilowite NT, Inman CJ, Marsolo K, McMurry AJ, Sandborg CI, Schanberg LE. An i2b2-based, generalizable, open source, self-scaling chronic disease registry. Journal of the American Medical Informatics Association. 2013; 20:172-179.
  43. Noah TK, Lo YH, Price A, Chen G, King E, Washington MK, Aronow BJ, Shroyer NF. SPDEF functions as a colorectal tumor suppressor by inhibiting beta-catenin activity. Gastroenterology. 2013; 144:1012-1023 e6.
  44. Park JK, Martin LJ, Zhang X, Jegga AG, Benson DW. Genetic variants in SCN5A promoter are associated with arrhythmia phenotype severity in patients with heterozygous loss-of-function mutation. Heart Rhythm. 2012; 9:1090-6.
  45. Patel AV, Eaves D, Jessen WJ, Rizvi TA, Ecsedy JA, Qian MG, Aronow BJ, Perentesis JP, Serra E, Cripe TP, Miller SJ, Ratner N. Ras-driven transcriptome analysis identifies aurora kinase A as a potential malignant peripheral nerve sheath tumor therapeutic target. Clin Cancer Res. 2012; 18:5020-30.
  46. Pestian J, Matykiewicz P, Holland‐Bouley K, Standridge S, Spencer M, Glauser T. Selecting anti‐epileptic drugs: a pediatric epileptologist's view, a computer's view. Acta Neurologica Scandinavica. 2012; 127:208-15.
  47. Pestian JP, Deleger L, Savova GK, Dexheimer JW, Imre Solti M. Natural Language Processing–The Basics. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:149-172.
  48. Pestian JP, Matykiewicz P, Linn-Gust M. What’s In a note: construction of a suicide note corpus. Biomedical informatics insights. 2012; 5:1.
  49. Pestian JP, Matykiewicz P, Linn-Gust M, South B, Uzuner O, Wiebe J, Cohen KB, Hurdle J, Brew C. Sentiment analysis of suicide notes: A shared task. Biomedical Informatics Insights. 2012; 5:3.
  50. Powell AE, Wang Y, Li Y, Poulin EJ, Means AL, Washington MK, Higginbotham JN, Juchheim A, Prasad N, Levy SE, Guo Y, Shyr Y, Aronow BJ, Haigis KM, Franklin JL, Coffey RJ. The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell. 2012; 149:146-58.
  51. Savova GK, Deleger L, Imre Solti M, Pestian J, Dexheimer JW. Natural Language Processing: Applications in Pediatric Research. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:173-192.
  52. Spooner SA. Protecting Privacy in the Child’s Electronic Health Record. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:83-91.
  53. Spooner SA. We are still waiting for fully supportive electronic health records in pediatrics. Pediatrics. 2012; 130:e1674-6.
  54. Spooner SA, Kirkendall ES. Pediatric Electronic Health Records and Research. In: Hutton JJ, ed. Pediatric Biomedical Informatics: Computer Applications in Pediatric Research. Dordrecht; New York: Springer; 2012:3-25.
  55. Sun S, Wang W, Latchman Y, Gao D, Aronow B, Reems JA. Expression of plasma membrane receptor genes during megakaryocyte development. Physiol Genomics. 2013; 45:217-27.
  56. Thomas HE, Mercer CA, Carnevalli LS, Park J, Andersen JB, Conner EA, Tanaka K, Matsutani T, Iwanami A, Aronow BJ, Manway L, Maira SM, Thorgeirsson SS, Mischel PS, Thomas G, Kozma SC. mTOR inhibitors synergize on regression, reversal of gene expression, and autophagy in hepatocellular carcinoma. Sci Transl Med. 2012; 4:139ra84.
  57. Thompson SD, Marion MC, Sudman M, Ryan M, Tsoras M, Howard TD, Barnes MG, Ramos PS, Thomson W, Hinks A, Haas JP, Prahalad S, Bohnsack JF, Wise CA, Punaro M, Rose CD, Pajewski NM, Spigarelli M, Keddache M, Wagner M, Langefeld CD, Glass DN. Genome-wide association analysis of juvenile idiopathic arthritis identifies a new susceptibility locus at chromosomal region 3q13. Arthritis Rheum. 2012; 64:2781-91.
  58. Uzuner O, Bodnari A, Shen S, Forbush T, Pestian J, South BR. Evaluating the state of the art in coreference resolution for electronic medical records. Journal of the American Medical Informatics Association. 2012; 19:786-791.
  59. Willson TA, Kuhn BR, Jurickova I, Gerad S, Moon D, Bonkowski E, Carey R, Collins MH, Xu H, Jegga AG, Guthery SL, Denson LA. STAT3 genotypic variation and cellular STAT3 activation and colon leukocyte recruitment in pediatric Crohn disease. J Pediatr Gastroenterol Nutr. 2012; 55:32-43.
  60. Wilson EB, Yamada DH, Elsaesser H, Herskovitz J, Deng J, Cheng G, Aronow BJ, Karp CL, Brooks DG. Blockade of chronic type I interferon signaling to control persistent LCMV infection. Science. 2013; 340:202-7.
  61. Xie H, Sun X, Piao Y, Jegga AG, Handwerger S, Ko MS, Dey SK. Silencing or amplification of endocannabinoid signaling in blastocysts via CB1 compromises trophoblast cell migration. J Biol Chem. 2012; 287:32288-97.
  62. Zhai H, Lingren T, Deleger L, Li Q, Kaiser M, Stoutenborough L, Solti I. Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processing. Journal of medical Internet research. 2013; 15:e73.
  63. Zhai H, Lingren T, Deleger L, Li Q, Kaiser M, Stoutenborough L, Solti I. (2012) 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology. San Diego, CA, IEEE. .
  64. Zhang M, Su S, Bhatnagar RK, Hassett DJ, Lu LJ. Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PLoS One. 2012; 7:e41202.
  65. Zhu C, Kushwaha A, Berman K, Jegga AG. A vertex similarity-based framework to discover and rank orphan disease-related genes. BMC Syst Biol. 2012; 6 Suppl 3:S8.