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Bruce J. Aronow, PhD Co-director, Computational Medicine Center
Co-director, Computational Medicine Center
Professor, UC Department of Pediatrics
Dr. Aronow's research is devoted to unraveling both the role and mechanism by which the functional capabilities of the human genome shape human health and our ability to adapt to stressful challenges. His lab is using a variety of available structural and functional genomic and biological systems descriptive data to form models of how biological systems assemble, adapt and become impaired in disease. The lab's overall hypothesis is that by interconnecting as much experimental and observational information as possible, we can gain new insights into the mechanisms by which different biological systems can achieve health or healthy adaptation, or undergo disease processes. More specific, with the co-leadership of Anil Jegga, DVM, the lab is identifying genetic features that control gene expression including cis-elements, trans factors and microRNAs, which normally work together in extended cell, tissue, organ and systems networks to enable development and homeostasis. Alterations of these features can alter phenotypes and increase or decrease disease. Some of the lab's work includes the identification of conserved, diverged and evolved cis-element clusters that are acted on by transcription and chromatin proteins. The lab has developed a Web-based tool called GenomeTraFaC that at present allows discovery of shared cis-elements in conserved non-coding sequences of mice and humans.
Barnes MG, Grom AA, Thompson SD, Griffin TA, Pavlidis P, Itert L, et al. Subtype-specific peripheral blood gene expression profiles in recent-onset juvenile idiopathic arthritis. Arthritis and rheumatism. 2009 Jul;60(7):2102-12.
Qu XA, Gudivada RC, Jegga AG, Neumann EK, Aronow BJ. Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. BMC Bioinformatics. 2009 May;10 Suppl 5:S4.
Gu Y, Harley IT, Henderson LB, Aronow BJ, Vietor I, Huber LA, et al. Identification of IFRD1 as a modifier gene for cystic fibrosis lung disease. Nature. 2009 Apr 23;458(7241):1039-42.
Nishijo K, Chen QR, Zhang L, McCleish AT, Rodriguez A, Cho MJ, et al. Credentialing a preclinical mouse model of alveolar rhabdomyosarcoma. Cancer Res. 2009 Apr 1;69(7):2902-11.
Chen J, Aronow BJ, Jegga AG. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics. 2009 Feb;10:73.
Shen H, Powers N, Saini N, Comstock CE, Sharma A, Weaver K, et al. The SWI/SNF ATPase Brm is a gatekeeper of proliferative control in prostate cancer. Cancer Res. 2008 Dec 15;68(24):10154-62.
Brunskill EW, Aronow BJ, Georgas K, Rumballe B, Valerius MT, Aronow J, et al. Atlas of gene expression in the developing kidney at microanatomic resolution. Developmental cell. 2008 Nov;15(5):781-91.
Mahller YY, Sakthivel B, Baird WH, Aronow BJ, Hsu YH, Cripe TP, et al. Molecular analysis of human cancer cells infected by an oncolytic HSV-1 reveals multiple upregulated cellular genes and a role for SOCS1 in virus replication. Cancer Gene Ther. 2008 Nov;15(11):733-41.
Kucherlapati MH, Yang K, Fan K, Kuraguchi M, Sonkin D, Rosulek A, et al. Loss of Rb1 in the gastrointestinal tract of Apc1638N mice promotes tumors of the cecum and proximal colon. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15493-8.
Gudivada RC, Qu XA, Chen J, Jegga AG, Neumann EK, Aronow BJ. Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge. J Biomed Inform. 2008 Oct;41(5):717-29.
Anil Goud Jegga, DVM, MRes
Assistant Professor, UC Department of Pediatrics
Anil Jegga, DVM, MRes, is a biological and medically-oriented computational biologist. He has led bioinformatics analysis and database development initiatives and played a critical role in a variety of successful projects and consortia focusing on genetic and genomic biology of developmental systems, human disease and mouse disease models. His work focuses on the elucidation of gene regulatory networks and the interaction between genotype and phenotype using a variety of bioinformatics approaches. He has extensive experience in transcription factor and micro-RNA based gene regulatory mechanisms, gene polymorphism functional analysis, candidate disease gene identification and prioritization. To aid in the diffusion of genomics into biomedical research and education, Dr. Jegga works with Bruce Aronow, PhD, and their research lab has developed several approaches that integrate bioinformatics with clinical informatics. His current interests include elucidating the p53 tumor suppressor network. In collaboration with scientists at National Institute of Environmental Health Sciences, Dr. Jegga is exploring the evolution of p53 targets and recently reported the unexpected finding that rodents lack some of the evolution-based safeguards in p53 function as humans. Collaborating with researchers from National Institute for Cancer Research, Italy, he is exploring the microRNA-based regulatory mechanisms of the p53 master regulatory network and impact of sequence variations on it.
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 Jan 4.
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.
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 Nov;49(5):841-50.
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 Jul;12(7):613-23.
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 Jul;38(Web Server issue):W165-74.
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 Jul;38(Web Server issue):W96-102.
Moyer K, Kaimal V, Pacheco C, Mourya R, Xu H, Shivakumar P, Chakraborty R, Rao M, Magee JC, Bove K, Aronow BJ, Jegga AG, Bezerra JA. Staging of biliary atresia at diagnosis by molecular profiling of the liver. Genome Med. 2010 May 13;2(5):33.
Miller SJ, Jessen WJ, Mehta T, Hardiman A, Sites E, Kaiser S, Jegga AG, Li H, Upadhyaya M, Giovannini M, Muir D, Wallace MR, Lopez E, Serra E, Nielsen GP, Lazaro C, Stemmer-Rachamimov A, Page G, Aronow BJ, Ratner N. Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene. EMBO Mol Med. 2009 Jul;1(4):236-48.
Gowrisankar S, Jegga AG. Regression based predictor for p53 transactivation. BMC Bioinformatics. 2009 Jul 14;10:215.
Chen J, Bardes EE, Aronow BJ, Jegga AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W305-11.
Michal Kouril, PhD Director, Research IT Services
Director, Research IT Services
UC Department of Pediatrics
Long (Jason) Lu, PhD
BS: Biotechnology/Bioengineering, Peking University, Beijing, China, 1998.
PhD: Biochemistry, specialized in Computational Molecular Biology, Washington University School of Medicine, St. Louis, MO, 2003.
Postdoc: Research Associate, Bioinformatics, Yale University, New Haven, CT, 2003-06.
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 Feb;39(3):795-807.
Zhang M, Lu LJ. Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics. 2010 Sep 16;11:466. 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 Oct 1;9(10):5239-49. 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 Jul 26;11:451.
Deng J, Wang W, Lu LJ, Ma J. A two-dimensional simulation model of the bicoid gradient in Drosophila. PLoS One. 2010 Apr;5(4):e10275.
Gordon S, Durairaj A, Lu LJ, Davidson WS. HDL proteomics: identifying new drug targets and biomarkers by understanding functionality. Current Cardiovascular Risk Report. 2010;4:1-8.
He F, Wen Y, Deng J, Lin X, Lu LJ, Jiao R, et al. Probing intrinsic properties of a robust morphogen gradient in Drosophila. Dev Cell. 2008 Oct;15(4):558-67.
Huang YJ, Hang D, Lu LJ, Tong L, Gerstein MB, Montelione GT. Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics. 2008 Oct;7(10):2048-60. Wu L, Hwang SI, Rezaul K, Lu LJ, Mayya V, Gerstein M, et al. Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling. Mol Cell Proteomics. 2007 Aug;6(8):1343-53. Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA, Yip KY, et al. Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci. 2007 Jul;32(7):320-31.
Jun Ma, PhD
investigates fundamental mechanisms of development through a combination of quantitative experimental approaches and theoretical and simulation approaches. One major focus of Ma’s lab concerns the questions of how morphogen gradients are established, and how precise positional information is encoded by these gradients and interpreted by cells in developing tissues.
Molecular mechanisms of gene regulation and embryonic development
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 Jan;13(1):22-9.
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 Aug 4;99(3):697-707.
Deng J, Wang W, Lu LJ, Ma J. A two-dimensional simulation model of the bicoid gradient in Drosophila. PLoS One. 2010 Apr 21;5(4):e10275.
He F, Wen Y, Deng J, Lin X, Lu LJ, Jiao R, Ma J. Probing intrinsic properties of a robust morphogen gradient in Drosophila. Dev Cell. 2008 Oct;15(4):558-67.
Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M. The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. J Mol Biol. 2006 Mar 10;356(5):1137-51.
Fu D, Ma J. Interplay between positive and negative activities that influence the role of Bicoid in transcription. Nucleic Acids Res. 2005 Jul 19;33(13):3985-93. Print 2005.
Chaney BA, Clark-Baldwin K, Dave V, Ma J, Rance M. Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome. Biochemistry. 2005 May 24;44(20):7497-511.
Ma J. Crossing the line between activation and repression. Trends Genet. 2005 Jan;21(1):54-9.
Fu D, Wen Y, Ma J. The co-activator CREB-binding protein participates in enhancer-dependent activities of bicoid. J Biol Chem. 2004 Nov 19;279(47):48725-33.
Ma J. Actively seeking activating sequences. Cell. 2004 Jan 23;116(2 Suppl):S75-6, 2 p following S76.
Keith Marsolo, PhD Director, Software Development and Data Warehouse
leads the development of the i2b2 research data warehouse at Cincinnati Children’s, which incorporates data from the Epic electronic health record and many other database systems used by hospital clinicians and researchers. He is head of the software development group, which focuses on developing systems for electronic data capture and reporting / creating collaborative websites for clients within the research foundation.
Director, Software Development and Data Warehouse
BS: Computer Science and Engineering, The Ohio State University, Columbus, OH, 2002.
MS: Biomedical Engineering, The Ohio State University, Columbus, OH, 2005; Computer and Information Science, The Ohio State University, Columbus, OH, 2006.
PhD: Computer and Information Science, The Ohio State University, Columbus, OH, 2007.
John P. Pestian, PhD, MBA Director, Computational Medicine Center
Director, Computational Medicine Center
Associate Professor, UC Department of Pediatrics
The founding director of the Division of Biomedical Informatics, Dr. Pestian now focuses on directing and developing the Computational Medicine Center (CMC). The CMC was established in 2003 by a $28 million grant from Ohio's Third Frontier Project.
Dr. Pestian's research lab is focused on using the science of natural language understanding in biomedical settings. Along with a growing list of collaborators, lab members focus on developing and implementing neuro-cognitive algorithms that enable computers to understand the concepts and semantic relationships within clinical text
Pestian J. A conversation with Edwin Shneidman. Suicide Life Threat Behav. 2010 Oct;40(5):516-23.
Pestian J, Spencer M, Matykiewicz P, Zhang K, Vinks AA, Glauser T. Personalizing Drug Selection Using Advanced Clinical Decision Support. Biomed Inform Insights. 2009 Jun 23;2:19-29.
Demner-Fushman D, Ananiadou S, Cohen KB, Pestian J, Tsujii J, Webber B. Themes in biomedical natural language processing: BioNLP08. BMC Bioinformatics. 2008 Nov 19;9 Suppl 11:S1.
Pestian JP, Matykiewicz P, Grupp-Phelan J, Lavanier SA, Combs J, Kowatch R. Using natural language processing to classify suicide notes. AMIA Annu Symp Proc. 2008 Nov 6:1091.
Duch W, Matykiewicz P, Pestian J. Neurolinguistic approach to natural language processing with applications to medical text analysis. Neural Netw. 2008 Dec;21(10):1500-10.
Matykiewicz P, Pestian J, Duch W, Johnson N. Unambiguous concept mapping in radiology reports: graphs of consistent concepts. AMIA Annu Symp Proc. 2006:1024.
Wade SL, Wolfe C, Brown TM, Pestian JP. Putting the pieces together: preliminary efficacy of a web-based family intervention for children with traumatic brain injury. J Pediatr Psychol. 2005 Jul-Aug;30(5):437-42.
Wade SL, Wolfe CR, Pestian JP. A web-based family problem-solving intervention for families of children with traumatic brain injury. Behav Res Methods Instrum Comput. 2004 May;36(2):261-9.
Siegel RM, Kiely M, Bien JP, Joseph EC, Davis JB, Mendel SG, Pestian JP, DeWitt TG. Treatment of otitis media with observation and a safety-net antibiotic prescription. Pediatrics. 2003 Sep;112(3 Pt 1):527-31.
Jegga AG, Sherwood SP, Carman JW, Pinski AT, Phillips JL, Pestian JP, Aronow BJ. Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res. 2002 Sep;12(9):1408-17.
Imre Solti MD, PhD
Information extraction from EHR; use of computational linguistics and machine learning in health services research; EHR data mining for medication safety and predictive modeling research; automated clinical trial eligibility screening
MD: Albert Szent-Gyorgyi Medical University, Szeged, Hungary, 1992.
PhD: Health Services Organization and Research, Virginia Commonwealth University, Richmond, VA, 2006.
MA: Computational Linguistics, University of Washington, Seattle, WA, 2011.
Stephen A. Spooner, MD, MS, FAAP Chief Medical Information Officer, Biomedical Informatics
practices general academic pediatrics and serves as the Chief Medical Information Officer for Cincinnati Children’s. He is active in the area of data standards in support of child health, and is currently the co-chair of the HL 7 child health work group. He is also co-chair of the Certification Commission for Health Information Technology inpatient work group.
Chief Medical Information Officer, Biomedical Informatics
Attending Physician, Hospital Medicine
Michael Wagner, PhD Faculty Liaison, Biomedical Informatics Core
Faculty Liaison, Biomedical Informatics Core
Large-scale optimization; applications in bioinformatics
Visit the Wagner Lab.
Dipl. Wi-Ing.: Universitaet Karlsruhe, Germany, 1995.
MS: Operations Research, Cornell University, Ithaca, New York, 1998.
PhD: Operations Research, Cornell University, Ithaca, New York, 2000.
Eric S. Hall, PhD
participates in a number of interdisciplinary teams investigating prematurity and neonatal disease. Along with coordinating data collection and exchange efforts, his work involves the application of knowledge discovery techniques to clinical data sets, as well as the development of software tools to assist in the summarization of clinical data and the modeling of clinical processes.
Eric S. Hall, PhD, participates in a number of interdisciplinary teams investigating prematurity and neonatal disease. Along with coordinating data collection and exchange efforts, his work involves the application of knowledge discovery techniques to clinical data sets as well as the development of software tools to assist in the summarization of clinical data and the modeling of clinical processes.
Hall ES, Poynton MR, Narus SP, Jones SS, Evans RS, Varner MW, Thornton SN. Patient-level analysis of outcomes using structured labor and delivery data. J Biomed Inform. 2009 Aug;42(4):702-9.
Hall ES, Thornton SN. Generating nurse profiles from computerized labor and delivery documentation. AMIA Annu Symp Proc. 2008 Nov 6:268-72.
Hall ES, Thornton SN. Extracting nursing practice patterns from structured labor and delivery data sets. AMIA Annu Symp Proc. 2007 Oct 11:309-13.
Hall ES, Poynton MR, Narus SP, Thornton SN. Modeling the distribution of Nursing Effort using structured Labor and Delivery documentation. J Biomed Inform. 2008 Dec;41(6):1001-8.
Hall ES, Thornton SN. Aiding clinicians through summarization of perinatal data. AMIA Annu Symp Proc. 2005:975.
Hall ES, Vawdrey DK, Knutson CD, Archibald JK. Enabling remote access to personal electronic medical records. IEEE Eng Med Biol Mag. 2003 May-Jun;22(3):133-9.
Johnson KJ, Hall ES, Boekelheide K. Kinesin localizes to the trans-Golgi network regardless of microtubule organization. Eur J Cell Biol. 1996 Mar;69(3):276-87.
Redenbach DM, Hall ES, Boekelheide K. Distribution of Sertoli cell microtubules, microtubule-dependent motors, and the Golgi apparatus before and after tight junction formation in developing rat testis. Microsc Res Tech. 1995 Dec 15;32(6):504-19.
Stivelman JC, Soucie JM, Hall ES, Macon EJ. Dialysis survival in a large inner-city facility: a comparison to national rates. J Am Soc Nephrol. 1995 Oct;6(4):1256-61.
Hall ES, Hall SJ, Boekelheide K. 2,5-Hexanedione exposure alters microtubule motor distribution in adult rat testis. Fundam Appl Toxicol. 1995 Feb;24(2):173-82.
Mario Medvedovic, PhD
Bayesian hierarchical models for unsupervised and semi-supervised learning from diverse data types
Jarek Meller, PhD
Adamczak R, Pillardy J, Vallat BK, Meller J. Fast Geometric Consensus Approach for Protein Model Quality Assessment. J Comput Biol. 2011 Jan 18.
Yi Y, Mikhaylova O, Mamedova A, Bastola P, Biesiada J, Alshaikh E, Levin L, Sheridan RM, Meller J, Czyzyk-Krzeska MF. von Hippel-Lindau-dependent patterns of RNA polymerase II hydroxylation in human renal clear cell carcinomas. Clin Cancer Res. 2010 Nov 1;16(21):5142-52.
Shu D, Zhang H, Petrenko R, Meller J, Guo P. Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters for RNA nanoparticles. ACS Nano. 2010 Nov 23;4(11):6843-53.
Swaminathan K, Adamczak R, Porollo A, Meller J. Enhanced prediction of conformational flexibility and phosphorylation in proteins. Adv Exp Med Biol. 2010;680:307-19.
Porollo A, Meller J. POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W662-6.
Lam YW, Yuan Y, Isaac J, Babu CV, Meller J, Ho SM. Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithelial cells. PLoS One. 2010 Feb 5;5(2):e9075.
Shinde K, Phatak M, Johannes FM, Chen J, Li Q, Vineet JK, Hu Z, Ghosh K, Meller J, Medvedovic M. Genomics Portals: integrative web-platform for mining genomics data. BMC Genomics. 2010 Jan 13;11:27.
Tan M, Xia M, Chen Y, Bu W, Hegde RS, Meller J, Li X, Jiang X. Conservation of carbohydrate binding interfaces: evidence of human HBGA selection in norovirus evolution. PLoS One. 2009;4(4):e5058.
Haffey WD, Mikhaylova O, Meller J, Yi Y, Greis KD, Czyzyk-Krzeska MF. iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylase knockdown in renal carcinoma cells. Adv Enzyme Regul. 2009;49(1):121-32.
Tan M, Xia M, Cao S, Huang P, Farkas T, Meller J, Hegde RS, Li X, Rao Z, Jiang X. Elucidation of strain-specific interaction of a GII-4 norovirus with HBGA receptors by site-directed mutagenesis study. Virology. 2008 Sep 30;379(2):324-34.
Yan Xu, PhD Director, Bioinformatics Microarray Core
focuses on bioinformatics applications and systems biology. Her research interests are the identification of gene signatures, regulatory networks and biological pathways controlling 1) surfactant homeostasis, 2) lung maturation, 3) lung cell type specific signaling and 4) asthma associated pathology. The goal is to gain better understanding of molecular mechanisms underlying lung development and pathogenesis.
Director, Bioinformatics Microarray Core
Bioinformatics; systems biology application in pulmonary research; lung cell type specific signaling; asthma associated pathology
BS: Pharmacology, Shanghai Medical University, China, 1986.
MS: Pathology, Shanghai Medical University, China, 1989.
PhD: Molecular and Cellular Pharmacology, University of South Alabama, Mobile, Alabama, 1997.
Transcriptional Control of Respiratory Epithelial Progenitor Cells. Co-investigator. National Heart, Lung and Blood Institute. Sep 2007 - Sep 2011. #5R01HL090156-02.
Role of SFTPC in Pathogenesis of Interstitial Lung Disease. Co-investigator. National Institutes of Health. Dec 2008 - Nov 2013. #1R01HL086492-01A2.
Role of C/EBPa in Cytoprotection and Recovery from Lung Injury. Co-investigator. National Heart, Lung and Blood Institute. Apr 2009 - Mar 2014. #1R01HL095464-01.
Transcriptional Programming of Asthma Related Pathology in Respiratory Epithelial. Co-investigator. National Heart, Lung and Blood Institute. Apr 2009 - Mar 2014. #1R01HL095589-01.
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