University of Michigan Medical School

Bioinformatics

734-998-8564 phone
734-998-8571 fax
ccmb-core@ctools.umich.edu

Address
North Campus Research Complex (NCRC)
Building 22, 2800 Plymouth Road
Ann Arbor, MI 48109-2800

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James Cavalcoli, Ph.D., Director
cavalcol@umich.edu
734-998-8528

Yongsheng Bai, Ph.D. Senior Research Area Specialist
ybai@umich.edu
734-615-5510

Ashwini Bhasi, Research Computer Specialist
abhasi@umich.edu
734-647-3005

Alla Karnovsky, Ph.D. Research Investigator
akarnovs@umich.edu
734-615-9314

Richard McEachin, Ph.D. Research Investigator
mceachin@umich.edu
248-756-8522

Ana Rodrigues, Ph.D., Senior Bioinformatics Analyst
anapcr@umich.edu

Maureen Sartor, Ph.D. Research Assistant Professor
sartorma@umich.edu
734-763-8013

Jeffrey de Wet, Ph.D. Instructional Designer
jrdewet@umich.edu
734-647-4573

Alex Ade, Lead Programmer
asade@umich.edu

Aaron V. Bookvich Web Designer
vittala@umich.edu
734-998-6305

Tim Hull, Application Programmer
thully@umich.edu

Lih Shwu Ke, MS, MBA
lke@umich.edu

Vasudeva Mahavisno, Information Technology Strategist
vmahavis@gmail.com

V. Glenn Tarcea, Research Computer Specialist
gtarcea@umich.edu

Terry Weymouth, Ph.D., Associate Research Scientist
weymouth@umich.edu

Zach Wright, MSI, Research Computer Specialist
zwright@umich.edu
734-615-5916

Marci Brandenburg, MLS, Bioinformationist
mbradenb@umich.edu
734-615-1643

	James Cavalcoli, Ph.D., Director 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. Yongsheng Bai received his Ph.D. in Quantitative Biology from The University of Texas at Arlington in 2007 after obtaining his M.Sc. degree in Poultry Science from the University of Arkansas and his M.Sc. degree in Computer Science from The University of Texas at Arlington, respectively. He has worked as an independent senior bioinformatics research scientist for the Human Genome Sequencing Center at Baylor College of Medicine before he joined the University of Michigan in 2008. He is currently in the Center for Computational Medicine and Bioinformatics, University of Michigan, where he was responsible for analyzing next-generation sequence data (genome resequenceing, exome sequencing, RNA-Seq, and Chip-Seq) generated from high performance computing platforms. Dr. Bai’s current research interests focus on bioinformatics analysis of clinical data, including but not limited to: uncovering disease genes and variants; developing efficient algorithms/software tools and databases for analyzing the genome and next-generation sequence data; computational analysis of cis-regulation and comparative motif finding, large-scale genome annotation and comparative genomics; identification of pathways; mapping genes onto pathways; and networks and gene association studies.
	Ashwini Bhasi Ashwini Bhasi has several years of experience leading the bioinformatics team of a start-up company and is experienced in generating and validating new product ideas, developing new bioinformatics software and managing software project teams. Ashwini enjoys building innovative solutions to resolve hurdles in data access and data analysis and has developed tools like AspAlt, RoBuST, EuSplice and ExDom, which integrate diverse genomic datasets and have intuitive user-interfaces. Her current research interest is in developing efficient data analysis pipelines for Next Generation Sequencing and in creating customized bioinformatics solutions to meet the specific data analysis needs of individual researchers.
	Alla Karnovsky, Ph.D. 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.
	Richard McEachin, Ph.D. Dr. McEachin's education includes a Ph.D. in Human Genetics, an M.S. in Biostatistics (both from the University of Michigan), and post-doctoral work focusing on understanding the genetics of complex diseases. His current work emphasizes the development and use of computational resources to mine the massive data sources emerging from high-throughput genomics experiments, including microarray and next generation sequencing applications, then putting results into context using a statistically rigorous systems biology approach.
	Ana Rodrigues, Ph.D. Dr. Rodrigues has a Ph.D. and Masters in the Bioinformatics area (both from the University of York, UK) and over 7 years of Bioinformatics work experience in diverse settings, including the Bioinformatics department at deCode Genetics, Inc (Iceland), the Godzik laboratory at the Sanford-Burnham Institute (La Jolla, CA) and the Bioinformatics Core at the Salk Institute (La Jolla, CA). Areas of expertise include comparative genomics (transcription, promoter and network analysis), protein structure comparison (evolution and dynamics), and high-throughput data analysis (microarrays, functional profiling and statistical analysis). Ana has a passion for enabling genome scale approaches to understanding, diagnosing, and treating human disease, with a particular focus on aging associated diseases.
	Maureen Sartor , Ph.D. 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. 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.
	Alex Ade Mr. Ade has a Master of Science in Biology from the University of Michigan (UM). He is currently a lead software developer for the National Center for Integrative Biomedical Informatics (NCIBI) at UM specializing in natural language processing, biomedical ontologies, data management, and data integration. Prior to working at NCIBI, Mr. Ade was lead software developer on the DARPA sponsored UM “Virtual Soldier” project, a multi-disciplinary, multi-institutional research effort to improve battlefield triage and treatment. He was also lead programmer for UM’s Visible Human/Next Generation Internet project to develop medical education software deployed at UM and Stanford University. Mr. Ade also worked at the Environmental Research Institute of Michigan in their Advanced Information Systems Group and Signal Information Processing Group.
	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.
	Tim Hull Mr. Hull received his Master of Science in Information degree from the University of Michigan's School of Information in May 2010, specializing in Human-Computer Interaction. Previously, he had received a B.S. in Computer Science and History from U-M in 2008. During his time as a student, Tim worked in an internship position with the U.S. Environmental Protection Agency, working on development of the MOtor Vehicle Emissions Simulator (MOVES) project. As part of the National Center for Integrated Biomedical Informatics (NCIBI), Tim has contributed to Cytoscape plugin development, including the latest version of the MetScape metabolomics plugin, the MiMI (Michigan Molecular Interactions) plugin, and other plugins designed to interface with NCIBI data. Tim's particular areas of interest include usability design and data visualization.
	Lih Shwu 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. Lih Shwu 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.
	Vasudeva Mahavisno Mr. Mahavisno has eight years of experience working as a Software Developer for the University of Michigan. He has worked in various departments of the university over the years including Pathology, MICHR and worked on projects such as Pathview, Oncomine, Molecular Concept Maps. Mr. Mahavisno currently works for the National Center for Integrated Biomedical Informatics (NCIBI) developing web applications, designing and prototyping interfaces, developing data and database infrastructure. His current projects include ConceptGen, MiMI NetBrowser and BioSearch2D.
	V. Glenn Tarcea Mr. Tarcea received his MBA from the Ross School of Business at the University of Michigan in 2009. He has worked in the computer industry since 1988. He has worked for small startups and large corporations in the storage industry, defense and academia. He has designed, implemented and lead the development of large scale storage systems including database backups, and robotic tape library management systems. At the University of Michigan he has worked on integration and loading of biological data including protein interactions, pathways, and metabolomics data. Glenn is also a sometimes contributor to open source projects.
	Terry Weymouth, Ph.D. Dr. Terry E Weymouth received his dissertation in Computer Vision, in 1986, at the University of Massachusetts, Amherst. For 6 years after that, he continued to work in Knowledge-Based Image Understanding in medical image domains. During that time he also did research in Knowledge-Based Sensor-Guided Robot Navigation. The work in robot navigation contributed heavily to the winning effort of the University of Michigan team at the 93-AAAI (first annual) Robot Navigation Contest. The work in medical image understanding resulted and in robot in navigation, resulting in numerous publications and dissertations. Over the next 10 years, he was involved in work in the development of Collaboration Technology for the support of Medical Diagnosis and for the support of Distributed Remote Scientific Experimentation. During that period, he was lead programmer and technical manager on the development and research team for the Upper Atmospheric Research Collaboratory (funded by NSF) in which he guided the development of a large-scale system for remote sharing of data and distributed problem solving for science research. He then applied these skills as lead programmer and supervisor as part of distributed science team in Earthquake Engineering as part of the Department of Energy's NESS project. For the last five years, he has been the senior software architect and manager of the software development team for the NIH funded NCIBI project. Dr. Weymouth will bring these skills to lead the Bioinformatics Core Application Developers group.
	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.
	Marci Brandenburg Ms. Brandenburg received a Master of Science in Information from the University of Michigan’s School of Information in 2002, specializing in Library and Information Services, and a Master of Science in Biology from Ohio University in 2004. She is the Bioinformationist for the University of Michigan, a joint position between the Taubman Health Sciences Library, the Department of Computational Medicine and Bioinformatics, and the Bioinformatics Core. She supports Bioinformatics research by providing outreach, resource training, software licensing administration, web content management, and more. Prior to her current position, she worked as the Biosciences Informationist at the National Cancer Institute-Frederick’s Scientific Library, a Laboratory Technician in the University of Michigan Medical School, and a Biological Sciences Technician (Wildlife) for the USDA Wildlife Services.

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