Biomedical Informatics

  • Research Faculty

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    Faculty

    A photo of Bruce Aronow.

    Bruce J. Aronow, PhD Co-director, Computational Medicine Center

    focuses his research on unraveling the role and mechanism by which the functional capabilities of the human genome shape human health and the body’s ability to adapt to stressful challenges. With the co-leadership of Anil Jegga, DVM, his lab is using a variety of available data on structural and functional genomics and biological systems to form models of how biological systems assemble, adapt and become impaired in disease.
    Visit the Aronow/Jegga Lab.

    513-636-0263
    bruce.aronow@cchmc.org

    Bruce J. Aronow, PhD

    Co-director, Computational Medicine Center

    Academic Information

    Professor, UC Department of Pediatrics

    Phone: 513-636-0263

    Fax: 513-636-2056

    Email: bruce.aronow@cchmc.org

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    Specialties

    Biography

    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.

    Education and Training

    BS: Chemistry, Stanford University, Stanford, CA, 1976.

    PhD: Biochemistry, University of Kentucky, Lexington, KY, 1986.

    Research Fellowship: Division of Basic Science Research, Cincinnati Children's Research Foundation, Cincinnati, OH, 1986-1989.

    Publications

    View PubMed Publications

    Grants

    CTSA - Enabling Tehnologies: Center for Translational & Molecular Disease. National Institutes of Health. Apr 2009 - Mar 2014.
    A photo of Anil Jegga.

    Anil Goud Jegga, DVM, MRes

    is a medically oriented computational biologist. His work with Bruce Aronow, PhD, uses a variety of bioinformatics approaches to explore gene regulatory networks and the interaction between genotype and phenotype. He has extensive experience in transcription factor and micro-RNA based gene regulatory mechanisms, gene polymorphism functional analysis, candidate disease gene identification and prioritization.
    Visit the Aronow/Jegga Lab.

    513-636-0261
    anil.jegga@cchmc.org

    Anil Goud Jegga, DVM, MRes

    Academic Information

    Associate Professor, UC Department of Pediatrics

    Phone: 513-636-0261

    Fax: 513-636-2056

    Email: anil.jegga@cchmc.org

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    Specialties

    Biography

    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.

    Education and Training

    Master of Research: University of York, England, UK.

    Master of Veterinary Science: College of Veterinary Science, Hyderabad, India.

    Bachelor of Veterinary Science & Animal Husbandry: College of Veterinary Science, Hyderabad, India.

    Publications

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    A photo of Michal Kouril.

    Michal Kouril, PhD Director, Research IT Services

    leads the team that provides IT resources and support to the research community at Cincinnati Children’s. He also specializes in high performance computing applications in biomedical informatics and combinatorics.

    513-636-1302
    michal.kouril@cchmc.org

    Michal Kouril, PhD

    Director, Research IT Services

    Academic Information

    Assistant Professor, UC Department of Pediatrics

    Phone: 513-636-1302

    Fax: 513-636-2056

    Email: michal.kouril@cchmc.org

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    Education and Training

    PhD: Computer Science, University of Cincinnati, Cincinnati, OH, 2006.
    A photo of Jason Lu.

    Long (Jason) Lu, PhD

    works in bioinformatics and systems biology. He focuses on using quantitative approaches from disciplines such as computer science and applied mathematics to address fundamental questions in molecular biology. In particular, he is interested in deciphering the human genetic blueprint, modeling complex biological systems (such as biomolecular networks and pathways), and facilitating drug discovery and development.
    Visit the Lu Lab. 

    513-636-8720
    long.lu@cchmc.org

    Long (Jason) Lu, PhD

    Academic Information

    Associate Professor, UC Department of Pediatrics

    Phone: 513-636-8720

    Fax: 513-636-2056

    Email: long.lu@cchmc.org

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    Specialties

    Education and Training

    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.

    Publications

    View PubMed Publications
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    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.

    513-636-7977
    jun.ma@cchmc.org

    Jun Ma, PhD

    Academic Information

    Professor, UC Department of Pediatrics

    Phone: 513-636-7977

    Fax: 513-636-4317

    Email: jun.ma@cchmc.org

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    Specialties

    Molecular mechanisms of gene regulation and embryonic development

    Education and Training

    PhD: Harvard University, Cambridge, MA, 1983-1988 (degree awarded 1990).

    BS: Peking University, 1978-1982.

    Publications

    View PubMed Publications

    Grants

    Probing the Robustness of a Developmental System. National Science Foundation.  May 2009 - Apr 2013.  #IOS-0843424.
    No photo available

    Keith Marsolo, PhD

    leads the team that supports Cincinnati Children's i2b2 research data warehouse. His team participates in a number of large clinical data sharing networks, and also has a focus on developing tools to support multi-center quality improvement and research networks.

    513-803-0333
    keith.marsolo@cchmc.org

    Keith Marsolo, PhD

    Academic Information

    Associate Professor, UC Department of Pediatrics

    Phone: 513-803-0333

    Fax: 513-636-2056

    Email: keith.marsolo@cchmc.org

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    Biography

    Dr. Keith Marsolo is an associate professor in the Division of Biomedical Informatics. He led the implementation of Cincinnati Children's research data warehouse, which utilizes a custom version of the open-source i2b2 framework. The software allows users to perform de-identified cohort queries, request datasets or biosamples for research purposes, and in select cases, perform de-identified chart review. Dr. Marsolo and his team have developed several other stand-alone applications that interface with the EHR, including a tool that supports Cincinnati Children's research biobank. At the time of registration, patients are asked whether they would allow their residual clinical samples to be kept for research purposes. The tool allows biobank personnel to query a sample and then determine, based on the patient’s consent decision and several other factors, whether it can be kept for research.

    Dr. Marsolo is also heavily involved in the creation of data collection and reporting systems to support multi-center quality improvement and research networks, as well as query tools for a number of other federated data sharing networks. Most recently, led the design and development of an EHR-linked "enhanced" registry for ImproveCareNow, a multi-center collaborative focused on improving care and outcomes for children with inflammatory bowel disease. The registry allows users to collect data directly in the EHR, where it can then be uploaded to the registry and used in a number of different automated reports. Much of his most recent work involves projects to support the development and implementation of the PCORI National Patient-Center Clinical Research Network. Dr. Marsolo earned a bachelor’s in computer science and engineering, a master’s in biomedical engineering and in computer and information science, and a PhD in computer and information science from The Ohio State University.

    Education and Training

    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.

    Publications

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    John P. Pestian, PhD, MBA Director, Computational Medicine Center

    advances the science of natural language processing and understanding in biomedical settings. Along with a growing list of collaborators, his lab has developed neuro-cognitive algorithms that enable computers to understand concepts and semantic relationships within clinical text. Pestian also directs the Computational Medicine Center, established in 2003 by a $28 million grant from Ohio's Third Frontier Project.
    Visit the Pestian Lab.

    513-636-1627
    john.pestian@cchmc.org

    John P. Pestian, PhD, MBA

    Director, Computational Medicine Center

    Academic Information

    Professor, UC Department of Pediatrics

    Phone: 513-636-1627

    Fax: 513-636-2056

    Email: john.pestian@cchmc.org

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    Specialties

    Biography

    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

    Education and Training

    BS: St. Francis College, Loreto, PA, 1981.

    MA: University of Steubenville, Steubenville, OH, 1987.

    PhD: Virginia Commonwealth University, Richmond, VA, 1994.

    Publications

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    A photo of Nathan Salomonis.

    Nathan Salomonis, PhD

    is a genomics and bioinformatics research scientist focusing on understanding human development and genetic networks underlying disease. His lab develops computational approaches to evaluate distinct modes of gene regulation and define molecular networks that govern mammalian progenitor cell specification and human disease pathology (e.g., Sudden Infant Death Syndrome) from genome-wide experimental datasets.

    650-576-1646
    nathan.salomonis@cchmc.org

    Nathan Salomonis, PhD

    Academic Information

    Assistant Professor, UC Department of Pediatrics

    Phone: 650-576-1646

    Email: nathan.salomonis@cchmc.org

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    Specialties

    Research

    Bioinformatics; genomics; alternative splicing; microRNA biology; pathway analysis; pathway visualization; pathway curation; SIDS; stem cell biology; cardiac specification; renal graft dysfunction


    Biography

    Our understanding of human health and ability to treat disease is being radically transformed by new technologies to read genomes and transcriptomes at an unprecedented resolution. To capitalize on these technologies it is essential that we develop holistic models of gene biology that will best inform clinicians of disease risk. Dr. Salomonis uses computational approaches to examine the interplay between diverse modes of gene regulation, including transcription, alternative splicing and microRNA regulation that underlie important cellular interaction networks.

    By applying such techniques to human disease and cellular dysfunction paradigms, we strive to shed new light on existing problems. To achieve these goals, we develop community available tools, such AltAnalyze and GO-Elite, to analyze and interpret genome-level data that is accessible by both untrained and skilled computational biologists alike. To identify global trends from complex data sets, we take advantage of pathway-driven approaches, such as WikiPathways models and aggregate large amounts of publically available data from a broad range of developmental and disease datasets available in the public domain. With these tools in hand, we strive to validate predicted functional effects in the laboratory with a diverse team of collaborative scientists.

    Education and Training

    PhD: University of California, San Francisco, CA, 2008.

    Publications

    View Pub Med Publications

    Grants

    Bioinformatics Core for the Progenitor Cell Biology Consortium.  Co-Principle Investigator. National Institutes of Health, Heart, Lung and Blood Institute. May 2013 - April 2016. U01HL099997.

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    Imre Solti MD, PhD

    specializes in clinical informatics and health services research informatics.  The mission of his research lab is to develop informatics algorithms and tools to extract all relevant information from the Electronic Health Record, including information buried in narrative text, and to utilize the extracted information in computerized clinical care, patient safety and outcome improvement systems. 
    Visit the Solti Lab..

    513-636-2477
    imre.solti@cchmc.org

    Imre Solti MD, PhD

    Academic Information

    Assistant Professor, UC Department of Pediatrics

    Phone: 513-636-2477

    Email: imre.solti@cchmc.org

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    Specialties

    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

    Education and Training

    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.

    Publications

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    Grants

    Increasing Clinical Trial Enrollment: A Semi-Automated Patient Centered Approach. Principal Investigator. National Institutes of Health. Sep 2010 - Sep 2013.
    A photo of Stephen A. Spooner

    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. 

    513-636-2290
    andrew.spooner@cchmc.org

    Stephen A. Spooner, MD, MS, FAAP

    Chief Medical Information Officer, Biomedical Informatics

    Attending Physician, Division of Hospital Medicine

    Academic Information

    Associate Professor, UC Department of Pediatrics

    Phone: 513-636-2290

    Email: andrew.spooner@cchmc.org

    A photo of Michael Wagner.

    Michael Wagner, PhD Faculty Liaison, Biomedical Informatics Core

    works on applications of machine learning techniques to bioinformatics problems such as protein structure prediction, disease classification and protein identification. His lab is investigating machine-learning-based scoring algorithms for peptide mass fingerprinting to better understand how to optimally mine mass spectrometry data and make high-confidence predictions of protein identities.
    Visit the Wagner Lab. 

    513-636-2935
    michael.wagner@cchmc.org

    Michael Wagner, PhD

    Faculty Liaison, Biomedical Informatics Core

    Academic Information

    Associate Professor, UC Department of Pediatrics

    Phone: 513-636-2935

    Fax: 513-636-2056

    Email: michael.wagner@cchmc.org

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    Specialties

    Large-scale optimization; applications in bioinformatics

    Visit the Wagner Lab.

    Biography

    Michael Wagner, PhD, works on applications of machine learning techniques to bioinformatics problems such as protein structure prediction, disease classification and protein identification. His research lab currently is investigating machine-learning based scoring algorithms for peptide mass fingerprinting to better understand how to optimally mine mass spectrometry data to make high-confidence predictions of protein identities. The underlying computational engine for many of these problems is a massively parallel implementation of a linear programming solver (PCx), which can solve large-scale support vector regression, support vector machine and linear feasibility problems. 

    Dr. Wagner also is involved in collaborations to perform genome-wide association studies, where his work has concentrated on developing an adequate, rapid data flow infrastructure that includes parallelized genotype calling algorithms.

    Education and Training

    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.

    Publications

    View PubMed Publications
    A photo of Peter White.

    Peter S. White, PhD Director, Division of Biomedical Informatics

    has an active laboratory that is developing genomic analysis, natural language processing, data integration, and knowledge representation methods to help determine the molecular etiologies of particular pediatric diseases, including childhood cancer, ADHD, mitochondrial disorders, and congenital cardiac defects.

    513-803-4172
    peter.white@cchmc.org

    Peter S. White, PhD

    Director, Division of Biomedical Informatics

    Academic Information

    N/A

    Professor, UC Department of Biomedical Informatics

    Phone: 513-803-4172

    Email: peter.white@cchmc.org

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    Specialties

    Clinical

    Bioinformatics; biomedical informatics; genome informatics

    Biography

    Peter White, PhD, is the chair of the Division of Biomedical Informatics at the University of Cincinnati College of Medicine and Cincinnati Children's. In this role, he oversees informatics research and resources at both institutions, including academic, educational, data services, software development, and Research IT missions. Prior to 2014, Dr. White was research associate professor of pediatrics and section chief of Clinical Informatics at the University of Pennsylvania, and the recipient of the David Lawrence Altschuler Endowed Chair in Genomics and Computational Biology at The Children’s Hospital of Philadelphia (CHOP), where he served as director of the Center for Biomedical Informatics, faculty advisor of CHOP's Bioinformatics Core Facility, co-director of CHOP's Division of Genome Diagnostics, and co-director of the Bioinformatics in Translation section of the Penn/CHOP Clinical and Translational Science Award.

    In his research career, Dr. White has explored the development and application of novel approaches for disease gene discovery, including identifying causative genes for neuroblastoma, ADHD, autism, and congenital heart defects. He has also developed innovative approaches for integrating and disseminating clinical, phenotypic, and molecular data to researchers for promoting discovery and hypothesis validation. Dr. White has recently played a lead informatics role on a number of national data projects, including the NICHD Newborn Screening Translational Research Network, the NHLBI Bench to Bassinet Program, the NHGRI Clinical Sequencing and Exploratory Research and IGNITE Consortia, and the NIDCD Audiology and Genetics Database.

    Education and Training

    PhD: Washington University, St. Louis, MO, 1993.

    Publications

    View PubMed Publications

    Grants

    NHLBI Pediatric Translational Consortium Administrative Coordinating Center. Co-investigator. National Heart, Lung, and Blood Institute (NHLBI)/ National Institutes of Health (NIH). Mar 2011-Aug 2015.

    Cincinnati Center for Clinical and Translational Sciences and Training. Co-investigator. National Center for Advancing Translational Sciences (NCATS) / National Institutes of Health (NIH). Apr 2009-Mar 2015.

    Joint Appointment Faculty

    A photo of Eric Hall.

    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.

    513-803-2083
    eric.hall@cchmc.org

    Eric S. Hall, PhD

    Academic Information

    Assistant Professor, UC Department of Pediatrics

    Phone: 513-803-2083

    Fax: 513-803-0968

    Email: eric.hall@cchmc.org

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    Specialties

    Clinical informatics; process modeling; knowledge discovery in databases; data summarization

    Biography

    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.

    Education and Training

    PhD: University of Utah, Salt Lake City, UT, 2008.

    MS: Brigham Young University, Provo, UT, 2003.

    BS: Brigham Young University, Provo, UT, 2001.

    Publications

    View PubMed Publications
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    Jarek Meller, PhD

    researches the development and application of computational methods for learning from biological data, including applications to protein structure prediction, mapping protein interactions, functional annotation and genotype-phenotype associations. State-of-the-art modeling and annotation tools developed by his group are publicly available.
    Visit the Meller Lab.

    513-636-0270
    jmeller@cchmc.org

    Jarek Meller, PhD

    Academic Information

    Associate Professor, UC Department of Pediatrics

    Phone: 513-636-0270

    Fax: 513-636-2056

    Email: jmeller@cchmc.org

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    Specialties

    Publications

    View PubMed Publications
    A photo of Yan Xu.

    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.

    513-636-8921
    yan.xu@cchmc.org

    Yan Xu, PhD

    Director, Bioinformatics Microarray Core

    Academic Information

    Associate Professor, UC Department of Pediatrics

    Phone: 513-636-8921

    Fax: 513-636-7868

    Email: yan.xu@cchmc.org

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    Specialties

    Bioinformatics; systems biology application in pulmonary research; lung cell type specific signaling; asthma associated pathology

    Biography

    Yan Xu, PhD, is an associate professor in the Department of Pediatrics, Divisions of Pulmonary Biology and Biomedical Informatics. Her main research interests are bioinformatics applications and systems biology.  She is currently focusing on the identification of gene signatures, regulatory networks and biological pathways controlling 1) surfactant homeostasis, 2) lung maturation and 3) lung cell type specific signaling. Her research goal is to integrate the data and information from new computational methods and experimental approaches in a synergistic way to gain better understanding of molecular mechanisms underlying lung development and pathogenesis.

    Education and Training

    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.

    Publications

    View PubMed Publications

    Grants

    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.