This is a proposal to renew and grow the University of Michigan (UM) Bioinformatics Training Program (BTP), which currently funds 6 trainee slots/year for 2-3 years of pre-doctoral training, within our University of Michigan-wide Center for Computational Medicine and Bioinformatics (CCMB). The BTP is an interdisciplinary graduate training program in bioinformatics and computational biology, drawing faculty from the School of Medicine, College of Engineering, Literature, Sciences and the Arts (LS&A;Including the Departments of Mathematics, Statistics, Chemistry, and Physics), the School of Public Health, the College of Pharmacy, and the School of Information. The goal of the BTP is to train students in bioinformatics and applied computational biology by engaging them in a rigorous curriculum and pre-doctoral training experience, all the while engaging in cutting-edge collaborative research featuring a strong "driving biological problem" (DBP) application, often leading BTP trainees to have a strong T1 Translational Research orientation. The BTP dissertation training utilizes a "dual-mentor" approach, which combines quantitative/computational and DBP application elements. The UM-based NIH National Center for Integrative Biomedical Informatics (NCIBI), cancer bioinformatics, proteome informatics activities, and CTSA Biomedical Informatics Program have all achieved national recognition, and are a natural magnet for our trainees and faculty. Since its inception in 2001, the BGP has now grown to 38 Ph.D. students and 6 MS, with 17 Ph.D. and 14 MS degrees conferred. Now in its fifth year, the BTP has now contributed to the support of 13 of these students, with the its first 3 graduates expected this academic year. Renewing the UM BTP will enable us to sustain our ability to train promising students in this highly specialized domain who will develop the skills and knowledge necessary to launch successful and independent careers in basic and applied research in academia, industry, and government. The CCMB, BGP, and the BTP are all very actively building a robust minority recruitment pipeline in partnership with the Research Centers for Minority Institutions (RCMI) program institutions across the nation. Institutional support for bioinformatics and computational biology at the U-M is very strong, forming a stable base for the BTP to thrive in this proposed 5-year period and beyond into the foreseeable future.
Bioinformatics and Computational Medicine, which focuses on the basic and translational aspects of bioinformatics as it is applied to meaningful biological and clinical problems, is a rapidly growing field. There is a growing need for rigorously-trained doctoral students with expertise in analyzing, integrating, and organizing digital datasets from next-generation sequencing, gene expression, proteomics and metabolomic platforms within these application context(s).
|Moyers, Bryan A; Zhang, Jianzhi (2016) Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution. Mol Biol Evol 33:1245-56|
|Cavalcante, Raymond G; Patil, Snehal; Weymouth, Terry E et al. (2016) ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. Bioinformatics 32:1536-43|
|Nemzek, Jean A; Hodges, Andrew P; He, Yongqun (2015) Bayesian network analysis of multi-compartmentalized immune responses in a murine model of sepsis and direct lung injury. BMC Res Notes 8:516|
|Rolland, Delphine; Basrur, Venkatesha; Conlon, Kevin et al. (2014) Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas. Am J Pathol 184:1331-42|
|Holmen, Oddgeir L; Zhang, He; Zhou, Wei et al. (2014) No large-effect low-frequency coding variation found for myocardial infarction. Hum Mol Genet 23:4721-8|
|Holmen, Oddgeir L; Zhang, He; Fan, Yanbo et al. (2014) Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk. Nat Genet 46:345-51|
|McDonnell, Scott R P; Hwang, Steven R; Rolland, Delphine et al. (2013) Integrated phosphoproteomic and metabolomic profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma. Blood 122:958-68|
|Khazanov, Nickolay A; Carlson, Heather A (2013) Exploring the composition of protein-ligand binding sites on a large scale. PLoS Comput Biol 9:e1003321|
|Billi, Allison C; Freeberg, Mallory A; Day, Amanda M et al. (2013) A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genet 9:e1003392|
|Jacobsen, Douglas M; Bao, Zhao-Qin; O'Brien, Patrick et al. (2012) Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase. J Am Chem Soc 134:15357-70|
Showing the most recent 10 out of 26 publications