2013 Research Annual Report

Biomedical Informatics

Division Details

Division Data Summary

Research and Training Details

Number of Faculty11
Number of Joint Appointment Faculty8
Number of Research Fellows8
Number of Research Students11
Number of Support Personnel116
Direct Annual Grant Support$5,068,027
Direct Annual Industry Support$296,060
Peer Reviewed Publications65

Division Photo

Biomedical Informatics

Row 1: J Meller, M Weirauch, N Salomonis, J Ma

Row 2: E Hall, A Porollo, E Kirkendall, I Solti, J Hutton

Row 3: K Marsolo, M Wagner, A Spooner, M Kouril



Significant Accomplishments

Significant Accomplishments

Enhanced Registry for ImproveCareNow

Our Division recently completed the implementation of an electronic health record (EHR)-linked “enhanced” registry for ImproveCareNow, a 54-center quality improvement and research network of gastroenterologists, researchers, patients and families that focuses on improving outcomes of children with inflammatory bowel disease (IBD). This effort is supported by a 3-year, $12-million grant from the Agency for Healthcare Research and Quality (AHRQ). The registry has allowed ImproveCareNow to create tools and processes to capture data directly from the EHR, which can be then uploaded to the registry to improve the quality of information obtained during the patient encounter, and support quality improvement. The registry helps automate pre-visit planning and population management activities and supports creation of mobile applications to increase patient participation in chronic care. The registry data supports novel research by generating estimates of the comparative treatment effects of biologic agents and allowing simulations. The data also can be used to generate ad hoc queries for cohort identification or for clinical trial feasibility.  The registry, now in its third year, has grown from 6,000 to more than 10,000 individuals and the number of centers in the network more than doubled. At the same time, the overall remission rate of patients in the network increased from 73 percent to 77 percent. Next year, the registry architecture will be extended to include adult patients with IBD.

Finding New Indications for Established Drugs

We continue to focus on design, development and application of network-based approaches to understand human disease and to accelerate drug discovery. Focusing on rare or orphan disorders, we are using the emerging tools of network medicine to explore the molecular complexity of these diseases. Our goal is to identify novel rare disease genes and more potential drug targets using algorithms and developed software systems we designed to help biomedical researchers form novel hypotheses from high-throughput data. One of our current focus areas is to find new indications for existing drugs. Our ultimate goal is to move drug repositioning from a serendipitous event to a systematic, comprehensive and rational search for drug repositioning candidates.

Reconstructing Critical Events of Embryonic Development

Jun Ma, PhD, focuses on the fundamental question of how an embryo develops the initial, elaborate patterns that later lead to the formation of organ structures. His team uses the fruit fly Drosophila as a model organism to study how the mother provides positional cues to the embryo and how cells in the embryo interpret such cues to form the initial spatial patterns. They have developed quantitative tools that allow them to investigate and reconstruct the critical events of early embryonic development at an increasingly fine resolution of both space and time. Their study, which is funded by the National Institutes of Health and the National Science Foundation, will not only advance the fundamental knowledge of how biological systems operate but also will reveal insights critical to our understanding of the molecular basis of human diseases including birth defects and cancer.


Research Highlights

Research IT & Security (Michal Kouril, PhD and Nicholas Hunt)

Research IT has expanded the IT infrastructure to accommodate the increasing demands by investigators for storage of data, hosting of databases and web based applications, and access to servers. Security has been tightened by moving servers into a more secure Research Network Environment. Regular internal and external security scans have been implemented; vulnerabilities that are identified are being promptly addressed. A disaster recovery plan has been formalized and is being implemented over the next year.

In cooperation with hospital Information Services, network connectivity has been increased to 10Gb to prepare for projects such as clinical Exome sequencing, which will generate 10s of TB of data that must be stored and processed in a short time. Additional examples of successful collaborations include research PACS publishing to increase the ability of investigators to access research images and eConsent management with user facing portals which improves the ease with which consent to participate in research studies can be obtained from potential subjects.

Network Approaches to Study Human Diseases (Jason Lu, PhD)

Jason Lu, PhD, focused on developing network-based approaches to study a variety of human diseases. He developed a network-based approach that combines proteomics experiments and computational predictions to discover the subspecies in High Density Lipoprotein (HDL). If the subspecies that are responsible for the cardiovascular protective functions are successfully identified, they may serve as more accurate biomarkers to assess the risk of developing cardiovascular diseases. The expression level of these subspecies can also be elevated to reduce the risk of cardiovascular diseases.

Jason has also predicted the protein interaction networks in bacterial pathogen Pseudomonas aeruginosa, and the human-Pseudomonas interaction networks. These networks are important in enabling network pharmacology where new antibiotic drug targets can be identified to treat Pseudomonas infection. His webserver has been linked by the comprehensive database Pseudomonas.

Data Warehousing & Software Development (Keith Marsolo, PhD)

The data warehousing group completed the implementation of a federated query tool for the Ohio Pediatric Asthma Repository (OPAR), a network made up of all Ohio children’s hospitals that is collecting data on asthma-related hospital admissions and corresponding treatment. This tool allows investigators in the network to run cohort identification and feasibility queries on their own center’s data as well as data from the entire network. In addition, the team continues to support the institutional research biorepository, finalizing functionality that will allow investigators at CCHMC to search for and request available biosamples from within the de-identified i2b2 warehouse.

The software group continues to support the quality improvement networks that are part of the Best Evidence for Advancing Child Health in Ohio Now (BEACON) collaborative, which focuses on improving outcomes in childhood obesity, children’s mental health and preterm births in Ohio. The group is completed development of patient registries for eosinophilic esophagitis and bone marrow transplant and the “drug dashboard” for kidney transplant that pulls together adherence data from electronic pill bottles, clinical data and pharmacogenomics information to support pre-clinic planning. Initial efforts have begun to integrate this dashboard in the EHR and disseminate it to other institutions.


Division Publications

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.

Faculty, Staff, and Trainees

Faculty Members

John Hutton, MD, Professor
Leadership Director, Division Chief
Bruce Aronow, PhD, Professor
Research Interests Gene Expression Analysis, Gene Regulation, Clinical Genomics, Functional Genomics of Development and Disease
Anil Jegga, MS, DVM, Assistant Professor
Research Interests Gene Regulatory Networks, Biomedical Ontologies, Integrative Genomics
Michal Kouril, PhD, Assistant Professor
Research Interests Computational Support, High-performance computing, Parallel Programming, High-end Data Storage
Long Jason Lu, PhD, Assistant Professor
Research Interests Bioinformatics, Machine Learning, Integrative Genomics, Biological Networks, Computational Modeling, Software Development
Jun Ma, PhD, Professor
Research Interests Development, Transcription, Morphogen Gradient, Embryo, Robustness, Quantitative Studies
Keith Marsolo, PhD, Assistant Professor
Research Interests i2b2, Data Integration, Data Warehousing and Data Management
John Pestian, PhD, MBA, Professor
Research Interests Natural Language Processing, Clinical Decision Support, Suicide Research, Pathology Research, Psychiatric Research
S. Andrew Spooner, MD, FAAP, Associate Professor
Leadership Chief Medical Information Officer
Research Interests Decision Support, Pharmacy Information Systems
Imre Solti, MD, PhD, MA, Assistant Professor
Research Interests Computational Linguistics
Michael Wagner, PhD, Associate Professor
Leadership Faculty Liaison
Research Interests Machine Learning, Proteomics, Genome-wide Association, Parallel Computing, Computational Infrastructure, Bioinformatics

Joint Appointment Faculty Members

Judith Dexheimer, PhD, Instructor (Emergency Medicine)
Research Interests Clinical Decision Support, Informatics
Eric Hall, PhD, Assistant Professor (Neonatology & Pulmonary Biology)
Research Interests Clinical Informatics, Knowledge Discovery Tools, Data Mining and Warehousing
Eric Kirkendall, MD, Assistant Professor (Hospital Medicine)
Research Interests General Pediatrics, Clinical Informatics
Kakajan Komurov, PhD, Assistant Professor (Experimental Hematology & Cancer Biology)
Research Interests Bioinformatics, Cancer Biology
Mario Medvedovic, PhD, Associate Professor (UC Environmental Health)
Research Interests Biostatistics
Jarek Meller, PhD, Associate Professor (UC Environmental Health)
Research Interests Protein Modeling
Matthew Weirauch, PhD, Assistant Professor (Rheumatology)
Research Interests Transcriptional Regulation, Bioinformatics, Functional Genomics
Yan Xu, PhD, Associate Professor (Neonatology & Pulmonary Biology)
Research Interests Bioinformatics; Systems Biology

Trainees

  • Jacek Biesiada, PhD, 2000, University of Silesia, Poland
  • Brian Connolly, PhD, 2002, Florida State University, Gainesville, FL, USA
  • Louise Deleger, PhD, 2009, Pierre et Marie Curie University, Paris, France
  • Feng He, PhD, 2009, Fudan University, Shanghai, China
  • Rebekah Karns, PhD, 2012, University of Cincinnati, Cincinnati, OH, USA
  • Hailong Li, PhD, 2013, University of Cincinnati, Cincinnati, OH, USA
  • Qi Li, PhD, 2011, University of Pittsburgh, Pittsburgh, PA, USA
  • Junbo Liu, PhD, 2000, Fudan University, Shanghai, China
  • Yizhao Ni, PhD, 2010, University of Southampton, Southampton, UK
  • Mayur Sarangdhar, PhD, 2011, University of Hull, Hull, UK
  • Haijun Zhai, PhD, 2010, University of Science and Technology of China, Hefei, Anhui Province, China

Division Collaboration

Adherence Psychology » Dr. Ahna Pai
Dr. Marsolo and team completed the development of a registry that captures patient reported outcomes and medication adherence data from patients who have received a bone marrow transplant.
Allergy & Immunology/Gastroenterology, Hepatology & Nutrition; » Dr. Pablo Abonia and Dr. Marc Rothenberg
Dr. Marsolo and team completed the development of a multi-center registry focused on Eosinophilic Esophagitis. This registry allows patients to complete registry forms and patient reported outcome/quality of life surveys from home, saving tame in the initial clinic visit. This study was the first to pilot a new consent management system developed by BMI that enables patients to electronically consent through a web browser.
Behavioral Medicine and Clinical Psychology » Dr. Jennie Noll
Dr. Kouril, as Co-Investigator on an R01 grant studying Internet and media use in the teenage population is leading efforts to develop hardware and software that will allow naturalistic observation of adolescents’ “Internet Footprint”.
Biomedical Informatics » Dr. Bruce Aronow, Dr. Anil Jegga, and Dr. Jason Lu
Dr. Ma collaborates with Drs. Aronow, Jegga, and Lu to investigate the pathological mechanisms of polyglutamine-mediated neurodegenerative disorders through the use of a fruit fly disease model.
Center for Technology Commercialization » Dr. Nicole Robinson
Dr. Pestian collaborates with the CTC looking for novel approaches to disseminate the laboratories innovations.
Clinical Pharmacology » Dr. Sander Vinks
Dr. Marsolo and his team have completed the development of a "Drug Dashboard" that pulls electronic health record data, medication adherence data from electronic pill bottles (MEMS caps) and pharmacokinetic and pharmacogenetic information into a single interface along with care recommendations that can be used by clinicians when conducting pre-visit planning. Dr. Vinks was asked to present this application at an “all Epic” town hall meeting as an example of the type of clinical informatics projects being done at Cincinnati Children’s.
Developmental Biology » Dr. James Lessard and Dr. Steven Potter
Dr. Aronow's group collaborates with Drs. Potter and Lessard along with an international consortium on the use of genomics analyses to gain insight into the normal or abnormal development of the kidney and lower urinary tract.
Emergency Medicine » Dr. Judith Dexheimer
Dr. Solti is collaborating with Dr. Dexheimer in developing an automated eligibility screening system for ED clinical trials.
Emergency Medicine » Dr. Jackie Grupp-Phelan
Dr. Pestian and his team are collaborating with Dr. Grupp-Phelan in the development of decision support tools to measure the likelihood of repeated suicide attempts.
Gastroenterology, Hepatology & Nutrition » Dr. Jorge Bezerra
Dr. Jegga collaborates with Bezerra Lab to understand the molecular basis of biliary atresia, a rare condition in newborn infants which if unrecognized could lead to liver failure. He provides bioinformatic support that includes data analysis, data-mining and hypothesis generation using systems biology-based approaches.
Gastroenterology, Hepatology & Nutrition » Dr. Jorge Bezerra
Dr. Aronow serves as the Bioinformatics Core Director on the Digestive Health Center: Bench to Bedside Research in Pediatric Digestive Disease grant project. His role is to aid or supervise in strategic planning, experimental designs, data analysis, and to generate a data portal for the genomics data and sample characterizations.
Heart Institute » Dr. Stephanie Ware
Dr. Marsolo and his team completed the first phase of an application to automate the processing and analysis of samples used in genetic and viral testing by the Heart Institute Diagnostic Lab (HIDL). This application has significantly streamlined the lab's workflow and more easily allows queries to be run on previous test results, enabling both quality assurance and future research.
Hematology/Oncology » Dr. John Perentesis
Dr. Pestian and his team are collaborating with clinicians and scientists to develop methods to identify the clinical needs of end-of-life patients. Drs. Pestian and Solti are collaborating with Dr. Perentesis in detecting Adverse Drug Reactions in the electronic health record notes of patients enrolled in clinical studies. Drs. Solti and Perentesis are collaborating to automate the clinical trial eligibility screening of cancer patients along the aims of Dr. Solti's NIH Grant.
Hematology/Oncology » Dr. John Perentesis and Dr. Jordan Wright
Dr. Solti collaborates with Dr. Perentesis and Dr. Wright on the clinical trial announcement grant. Their collaboration efforts focus on extracting eligibility criteria for oncology patients.
Human Genetics » Dr. William Nichols
Dr. Marsolo and his team are creating an i2b2-based web portal that will allow external users to browse phenotypic and genotypic information on patients with pulmonary arterial hypertension (PAH). Once a cohort has been identified, users will be able to send a request for data and samples to the PAH biorepository, which will then service the request.
Human Genetics » Dr. Daniel Prows
Dr. Aronow is a leading expert in the design and analysis of DNA microarrays, including Incyte and Affymetrix technologies. His collaboration efforts with Dr. Prows include microarray design, oversight in all aspects of microarray analysis, including data sorting and data analysis. Additionally, Dr. Aronow oversees the in-depth in silico analyses and generates appropriate figures, tables and the related text for manuscript preparation.
James M. Anderson Center of Excellence; Emergency Medicine » Dr. Evaline Alessandrini
Dr. Marsolo and the i2b2 team have worked with colleagues in Emergency Medicine to identify and extract data from the electronic health record so that it can be uploaded into the expanded version of the Pediatric Emergency Care Applied Research Network (PECARN) registry. The i2b2 team has successfully transmitted a full month’s worth of emergency department data to the coordinating center and is working to pilot test a de-identification process for a larger extract.
James M. Anderson Center of Excellence; Emergency Medicine » Dr. Evaline Alessandrini, Dr. Holly Brodzinski, and Dr. Judith Dexheimer
Dr. Solti collaborates with the members of the Anderson Center and Emergency Medicine in the appendicitis risk stratification project. The divisions are developing an automated system to determine the risk of appendicitis in abdominal pain patients.
James M. Anderson Center of Excellence » Yiscah Bracha
Dr. Marsolo and the i2b2 team completed an initial pilot with colleagues in the Anderson Center in their efforts to operationalize Epic-based outcome measures, including some that were part of the institution’s Care Coordination and Outcomes (CCO) project. These data are used to populate dashboards and control charts displayed using the institution’s Performance Measurement and Reporting System (PMRS).
James M. Anderson Center of Excellence » Dr. Eric Kirkendall, Dr. Stephen Muething, and Dr. Uma Kotagal
Dr. Solti is collaborating with Drs. Kirkendall, Muething, and Kotagal in developing and EHR-based patient safety and predictive modeling research agenda.
James M. Anderson Center of Excellence » Dr. Carole Lannon
Dr. Marsolo and his team are developing the second phase of an infrastructure for data collection, reporting and analysis that is being used by quality improvement networks that are part of the State of Ohio's BEACON initiative (Best Evidence for Advancing Childhealth in Ohio Now), including the Ohio Perinatal Quality Collaborative, where Dr. Lannon is co-PI.
James M. Anderson Center of Excellence » Dr. Stephen Muething
Dr. Marsolo and his team have completed the development of a data collection and reporting infrastructure that is being used by the newly expanded Solutions for Patient Safety collaborative, a network that is focused on reducing serious safety events.
James M. Anderson Center of Excellence; Gastroenterology, Hepatology & Nutrition » Dr. Peter Margolis and Dr. Shehzad Saeed
Dr. Marsolo and his team deployed an i2b2-based registry to support the quality improvement and research efforts of the ImproveCareNow Network, which focuses on improving the outcomes of children with Inflammatory Bowel Disease (IBD). This registry supports two methods of data collection: 1) manual data into an i2b2-based web form, or 2) direct entry into the electronic health record, after which it can be transferred to the registry via file upload. Also included are automated pre-visit planning, population management and monthly quality reports. These reports can be generated on demand and allow investigators to see data on patients from their own site as well as aggregate numbers from the collaborative as a whole.
James M. Anderson Center of Excellence; Pulmonary Medicine » Dr. Peter Margolis and Dr. Michael Seid
Dr. Marsolo serves as a consultant to Drs. Margolis and Seid on the design of the technical infrastructure needed to support their growing C3N (Clinical Collaborative Care Network). This infrastructure includes personal health records, the ability to visualize and display patient-specific health and outcomes data, the ability to conduct N of 1 trials, and social networking and data sharing functionality.
Neonatology and Pulmonary Biology; Hospital Medicine » Dr. Kristin Melton and Dr. Eric Kirkendall
Dr. Solti works in collaboration with Drs. Melton and Kirkendall to automate adverse event detection in the Neonatal Intensive Care Unit by using electronic health record data and natural language processing techniques to find harm that is not usually identified by other means. The project is funded by an NIH R21 (PI Solti) grant.
Neonatology and Pulmonary Biology; Biostatistics and Epidemiology » Dr. Laurel Bookman and Dr. Jareen Meinzen-Derr
Dr. Solti and his team have worked in collaboration with Dr. Bookman (Neonatology) and Dr. Meinzen-Derr (Biostatistics and Epidemiology) to develop a classification algorithm for Tongue-Based Airway Obstruction risk.
Neonatology and Pulmonary Biology » Dr. Yan Xu
Dr. Lu and his team work closely with Dr. Xu in developing statistical models to analyze gene expression during the development of mouse models with the goal of understanding the role of SREBP network in surfactant lipid homeostasis and lung maturation.
Nephrology » Dr. Prasad Devarajan
Drs. Aronow and Wagner serve as Co-Investigators on Dr. Prasad Devarajan’s Pediatric Center Excellence in Nephrology grant entitled “Critical Translational Studies in Pediatric Nephrology”, where the goal is to support basic, translational, and clinical research on critical pediatric kidney diseases that have major unmet needs. The overarching theme of the Cincinnati Children’s PCEN is to conduct innovative and high-impact bench-to-bedside studies on three critical but underserved pediatric kidney diseases. The three areas of focus at Cincinnati Children’s include acute kidney injury, focal segmental glomerulosclerosis, and lupus nephritis. Dr. Aronow serves as the Bioinformatics Core lead and Dr. Wagner is part of the proteomics core led by Dr. Ken Greis.
Neurology » Dr. Anna Weber Byars
Dr. Pestian and his team are collaborating with Dr. Byars on innovations in neuropsychology research
Neurology » Dr. Tracy Glauser, Dr. Hansel Greiner, Dr. Katherine Holland-Bouley, and Dr. Shannon Standridge
Dr. Pestian and his team are collaborating with the Neurology team for the on-going development of CHRISTINE, a clinical decision support system for identifying optimal drug therapy for patients with epilepsy, and ADHD.
Neuroimaging Research; Neurology » Dr. Scott Holland and Dr. Jennifer VanNest
Dr. Wagner, in his role of informatics lead on an NICHD contract ("Cincinnati MRI Imaging Neuronal Development", Dr. Holland, PI), collaborates with the PI and Dr. VanNest (Division. of Neurology) to build and disseminate a database of fMRI images of normally developing brains.
Psychiatry » Dr. Michael Sorter
Dr. Pestian and his team are collaborating with Dr. Sorter in the development of decision support tools to measure the likelihood of repeated suicide attempts.
Pulmonary Medicine » Dr. John Clancy
Dr. Lu serves as a Co-Investigator on Dr. Clancy’s R01 grant entitled “MR Predictors of Infection, Inflammation and Structural Lung Damage in CF”, where the goal is to develop new tools needed to monitor early lung disease, and to bring new therapies to infants and toddlers with Cystic Fibrosis. On this grant project, the team uses new imaging and blood-based technologies to improve our ability to monitor lung status in young children with CF.
Reproductive Sciences » Sudhansu Dey
Dr. Jegga collaborates with the Dey Lab in their mission to understand the signaling networks that influence uterine biology in the context of embryo-uterine interactions during pregnancy and delivery. He is specifically focusing on the miRNA-based regulation of labor and pre-term birth.
Rheumatology; Center for Autoimmune Genomics and Etiology (CAGE) » Dr. Susan Thompson and Dr. John Harley
Dr. Wagner, as Director of the Informatics Core of the NIAMS-sponsored Cincinnati Core Center for Rheumatic Diseases (Dr. Thompson, PI),collaborates closely with Investigators Drs. Thompson and Harley on genome-wide analyses of variants contributing to juvenile rheumatic disease.
Rheumatology » Dr. Susan Thompson and Dr. Michael Barnes
Dr. Marsolo provides consultation and advice to the Biomedical Informatics staff that supports the institutional biorepository software used by the Cincinnati Children's biobank and other investigators. Included in this effort has been the development of tools to support the Better Outcomes for Children (BOfC) project, which collects residual clinical samples for research purposes from patients who have provided consent. Dr. Marsolo and his team created an application that allows biobank staff to scan a clinical sample and determine whether it can be retained for research purposes. This functionality was added to allow investigators to search for and request samples using the institution’s de-identified i2b2 warehouse.
Center for Autoimmune Genomics and Etiology (CAGE) » Dr. John Harley
Drs. Hutton, Marsolo, Solti, and Wagner are providing informatics support for Cincinnati Children’s participation in the electronic MEdical Records and GEnomics (eMERGE) Network. Cincinnati Children's Hospital Medical Center, in collaboration with colleagues from Boston Children's, is looking at correlations between EMR-derived phenotypes and genotypes. Dr. Marsolo and his team have been working to establish a federated SHRINE network between Cincinnati Children’s and Boston Children’s, allowing de-identified queries to be executed between the two institutions.

Grants, Contracts, and Industry Agreements

Biomedical Informatics Grants

Grant and Contract AwardsAnnual Direct

Aronow, B

A GenitoUrinary Development Molecular Anatomy Project - Database and Website
U01 DK 09298309/15/11-08/31/16$110,607
Generating Molecular Markers that Subjectively Label Urothelial Sub-Populations
U01 DK 09453009/30/11-08/31/16$8,000
NHLBI Progenitor Cell Biology Consortium Administrative Coordinating Center
U01 HL 09999705/01/13-04/30/16$149,157
Digestive Health Center: Bench to Bedside Research in Pediatric Digestive Disease - Bioinformatics Core
P30 DK 07839206/01/12-05/31/17$99,872

Aronow, B / Potter, S

NextGen Dissection of the Genomic Basis of Kidney Development
RC4 DK 09089109/30/10-09/29/13$106,946

Hutton, J

Building Modular Pediatric Chronic Disease Registries for QI and CE Research
R01 HS 02002409/30/2010-09/29/2013$2,938,991
Cincinnati Center for Clinical and Translational Sciences and Training - Informatics Core
UL1 RR 02631404/03/09-03/31/14$96,491

Lu, L

A Network-Based Approach to Associate HDL Subspeciation with Function
R01 HL 11182908/01/12-06/30/17$430,563

Ma, J

Regulation and Scaling of a Morphogen Gradient
R01 GM10137308/15/12-06/30/17$190,000

Marsolo, K

Implementation of the BEACON Quality Improvement Data Infrastructure - Federal
G-1213-07-034309/23/11-06/30/14$136,965
Implementation of the BEACON Quality Improvement Data Infrastructure - State
FAM-32320-03b07/01/12-06/30/13$55,400
Test a Practical User Interface to Grid Logistic Regression Across Clinic Sites
U13 HS 1956408/15/12-04/15/13$10,000

Pestian, J

Multi-Institutional Pediatric Epilepsy Decision Support
R01 LM 01112407/22/11-06/30/14$256,736

Solti, I

EHR-Based Patient Safety: Automated Error Detection in Neonatal Intensive Care
R21 HD 07288308/01/12-07/31/14$100,000
Increasing Clinical Trial Enrollment: A Semi-Automated Patient Centered Approach
R00 LM 01022710/02/10-09/29/13$156,172

Wagner, M

Gene Expression in Pediatric Arthritis - Core B
P01 AR 04892909/01/11-08/31/16$172,696
Cincinnati Rheumatic Disease Core - Core 4
P30 AR 04746408/25/11-06/30/16$49,431
Current Year Direct$5,068,027
Industry Contracts

Marsolo, K

$296,060
Current Year Direct Receipts$296,060
Service Collaborations

Marsolo, K

$20,000
Current Year Direct$20,000
Funded Collaborative Efforts

Aronow, B

Immunobiology of IFRD1, a Gene Modifying CF Lung Disease
Karp, C08/01/09-07/31/135%
Global Gene Expression Atlas of Craniofacial Development
Potter, S09/21/09-04/30/145%
Genetic Analysis of Murine Chronic Hypoxia-Induced Pulmonary Hypertension
Nichols, W04/01/10-03/31/145%
Risk Stratification and Identification of Immunogenetic and Microbial Markers of Complicated Disease Course in Pediatric Crohn's Disease
Denson, L07/01/09-12/31/125%
Critical Translational Studies in Pediatric Nephrology
Devarajan, P09/21/12-08/31/174%
Transflammation: Its Role in Direct Reprogramming
Lutzko, C03/01/13-02/28/145%
Genotype-Phenotype Associations in Pediatric Cardiomyopathy
Ware, S04/01/13-03/31/165%

Jegga, A

Cincinnati Cell Characterization Core
Malik, P05/1/11-04/30/165%
Biological Basis of Phenotypes and Clinical Outcomes in Biliary Atresia
Bezerra, J09/1/09-08/31/145%
Digestive Health Center: Bench to Bedside Research in Pediatric Digestive Diseases - Biomedical Informatics Core
Bezerra, J07/1/07-05/31/1710%
NextGen Dissection of the Genomic Basis of Kidney Development
Potter, S09/30/10-09/29/1315%
NHLBI Progenitor Cell Biology Consortium Systems Biology Bioinformatics Core
Aronow, B05/01/13-04/30/1620%

Kouril, M

Cincinnati Center for Clinical and Translational Sciences and Training
Heubi, J04/03/09-03/31/1415%
Abused and Non-abused Females' High-risk Online Behaviors: Impact on Development
Noll, J07/01/12-06/30/1725%

Lu, L

Role of SREBP Network in Surfactant Lipid Homeostasis and Lung Maturation
Xu, Y07/01/11-06/30/1610%
MR Predictors of Infection, Inflammation and Structural Lung Damage in CF
Clancy, J09/26/12-06/30/1620%

Marsolo, K

Cincinnati Center for Clinical & Translational Sciences & Training
Heubi, J04/03/09-03/31/1415%
Building Modular Pediatric Chronic Disease Registries of QI and CE Research
Hutton, J09/30/10-09/29/1350%
Open Source Science: Transforming Chronic Illness Care
Margolis, P09/30/09-08/31/143%
National Biological Sample and Data Repository for Pulmonary Arterial Hypertension
Nichols, W03/03/12-02/28/175%
Better Outcomes for Children: GWAS and PheWAS in eMERGEII
Harley, J05/01/12-04/30/1510%

Pestian, J

Impact of Initial Therapy and Response on Long Term Outcome in Children with CAE
Glauser, T09/01/10-08/31/1420%

Solti, I

Better Outcomes for Children: GWAS and PheWAS in eMERGEII
Harley, J05/01/12-04/30/1510%

Wagner, M

Cincinnati Center for Clinical and Translational Sciences and Training
Heubi, J04/03/09-03/31/1415%
Pediatric Functional Neuroimaging Research Network
Holland, S09/28/09-09/27/1420%
The Genetic Linkage in Lupus
Harley, J09/07/10-02/28/1510%
Better Outcomes for Children: GWAS and PheWAS in eMERGEII
Harley, J05/01/12-04/30/1510%
Critical Translational Studies in Pediatric Nephrology
Devarajan, P09/21/12-08/31/175%
Total$5,384,087