People
CCDU People
The CCDU is comprised two cores: the Bioinformatics Analysis Core and the IT Computing Core.
Contact us ccmb-core@ctools.umich.edu
Bioinformatics Analysis Core
James Cavalcoli, Ph.D. (cavalcol@umich.edu)
Dr. Cavalcoli received his Ph.D. in Molecular Virology from Louisiana State University in 1993. A second post-doctoral opportunity in 1997 brought Dr. Cavalcoli from the lab bench to the bioinformatics field at Parke-Davis. Over the next 8 years Dr. Cavalcoli helped develop the bioinformatics infrastructure and applications groups at Parke-Davis and Pfizer. He is currently the Project Manager for the National Center for Integrative Biomedical informatics and Director of the Bioinformatics Core Unit, part of the Center for Computational Medicine and Biology (CCMB) at the University of Michigan Medical School and adjunct assistant professor of medicinal chemistry at the College of Pharmacy. Dr. Cavalcoli has always been at the juncture of molecular biology, bioinformatics and computational technology and his most recent work has been in helping to establish the analysis core for next-generation sequencing and related technology.
Yongsheng Bai, Ph.D. (ybai@umich.edu)
Dr. Bai’s current research interests focuses on bioinformatics analysis of clinical data, including but not limited to: identification of novel transcription factor binding sites and motifs; identification of pathways; mapping genes onto pathways; uncovering disease genes and variants; the novel next-generation sequencing technologies; and networks and gene association studies.
Alla Karnovsky, Ph.D. (akarnovs@umich.edu)
Dr. Karnovsky’s background includes a Ph.D. in cell and developmental biology (Russian Academy of Sciences, 1992), postdoctoral work at the University of Colorado at Boulder, and nine years of bioinformatics work in Pharmaceutical industry at Pharmacia and at Pfizer. She has broad experience in identification and validation of therapeutic targets in variety of disease areas including antibacterials and CNS and dermatology. Dr. Karnovsky’s current research interests involve the analysis of high throughout “omics” data, focusing primarily on metabolomics and the development of computational methods and tools for the analysis and integration of metabolomics data with other types of genomic data. She is also interested in structural aspects of drug/target interactions and the integration of chemical and genomic domains.
Maureen Sartor , Ph.D. (sartorma@umich.edu)
The advent of tiling arrays and next-generation sequencing has created many new biases and issues surrounding the question of biological significance and functionality. Dr. Sartor’s main research interests involve exploring these issues with empirical and hierarchical Bayesian models, and other statistical modeling, applied to the analysis of high-throughput genomic data. These statistical models allow her to understand and assess the biological significance of results and molecular pathways involved.
Jeffrey de Wet, Ph.D. (jrdewet@umich.edu)
Dr. de Wet received a Ph.D. in Biology from the University of California, San Diego. He headed a molecular biology lab at Pfizer Inc in Groton, CT that initially worked on cloning and expressing mammalian genes and later specialized in central nervous system molecular biology. In 1998, Dr. de Wet moved to the bioinformatics group at Pfizer and worked on projects to identify genes from genome and EST sequence data. In 2003, he moved to the University of Michigan, Ann Arbor where he currently designs and teaches bioinformatics courses. Dr. de Wet is interested in the analysis of next generation sequencing data, especially in ChIP-Seq and RNA-Seq projects.
IT Computing Core
Aaron V. Bookvich
Mr. Bookvich started work at the University of Michigan on the Visible Human project and Michigan Center for Biological Information (MCBI) in 2001, working with web enabled content management systems (CMS) and web development. He later worked on the DARPA Virtual Soldier Project performing image processing and assembling Edgewarp 3D Browser models derived from CT scans. Mr. Bookvich currently works for the National Center for Integrative Biomedical Informatics (NCBI) and the CCMB as a web designer and administrator as well as developing web based user interfaces for online tools and conducting usability evaluations.
LihShwu Ke, MS, MBA
Ms. Ke has an MBA and MS in Computer Science and is a certified database professional in the design, development, administration, and tuning of databases. LihShwu currently manages Oracle and MS SQL Server databases for NCIBI. Prior to working at CCMB, she was a computer system and database specialist for a variety of companies such as Ford Credit, UM Hospital and Pfizer. She has designed and implemented the enterprise's data access architecture and database administration practices for both transaction processing systems and data warehouses. She has been involved with all aspects of computer Systems Validation under FDA guidelines and regulations including HIPAA, GLP, GCP and 21 CFR Part 11 concerning data security and digital signatures. She had provided assistance to companies for the development, implementation and tuning of their business-critical database applications in Oracle Clinical, Applied Clinical Informatics, LIMS and Chemical & Biological Information Systems.
Jerome Kinlaw
Mr. Kinlaw has fourteen years of experience working as a System Administrator and Software Developer for the University of Michigan. He has worked in various departments of the university over the years including MCIT, MCBI and worked on such projects as Visible Human and Virtual Soldier. Mr. Kinlaw currently works as the Senior System Administrator for the Center for Computational Medicine and Bioinformatics (CCMB) and the National Center for Integrative Biomedical Informatics (NCIBI); he builds and manages the computing infrastructure for researchers and developers across the University relating to CCMB and NCIBI.
Zach Wright, MSI
Mr. Wright received a Master of Science in Information from the University of Michigan School of Information in 2002, specializing in Human Computer Interaction (HCI). As a graduate student researcher, he helped conduct studies on computer mediated communication in the Collaboratory for Research on Electronic Work (CREW). In 2003, Mr. Wright went to work for the Michigan Center for Biological Information (MCBI) and later the DARPA Virtual Soldier Project developing bioinformatics web applications, databases, and managing collaborative tools. Mr. Wright currently works for the National Center for Integrated Biomedical Informatics (NCIBI) developing web applications, conducting usability evaluations, designing and prototyping interfaces based on user-centered criteria, and developing data and database infrastructure.
