This proposal is a resubmission of an application for a training grant for the Duke University Program in Computational Biology and Bioinformatics (CBB). CBB is a graduate program. It admits its own students and grants the PhD. Its mission is to educate the next generation of scientists who will work at the interface between the life sciences and the quantitative sciences. CBB supports students for their first two years, after which they move onto support from the faculty. The program aims to admit around ten new students each year. This proposal requests ten slots, which would support half the students. The program typically takes five years to complete, and it embodies a wide range of academic activities, including three core courses and three research rotations, all taken in the first year, a required seminar series, careful RCR training, and interdisciplinary mentoring and supervision. The program is supported by an unusually broad, but well integrated group of faculty. Research areas of the faculty are quite broad, and are grouped into six areas: Systems Biology, Genome Analysis, Computational Structural Biology, Genomic Medicine, Evolutionary Genomics and Mathematical and Statistical Modeling of Biological Systems. Students emerge well prepared to work in collaborative research groups where biologists and computational scientists make joint intellectual contributions to solving real biological problems. CBB is completing its fifth year of initial funding from the NIH. These five years have seen significant growth of computational biology at Duke University, the program now includes 57 faculty (24 in quantitative departments and 33 in biological ones) from 15 departments in three schools and one Institute. Excellent students have bee recruited into the Program and retention is excellent with 43 of the 49 students that have been admitted since the program began having finished their PhD or making good progress towards their degree. Graduates have done extremely well, 6 have taken postdoctoral positions at prestigious institutions and 4 have taken strong industrial positions.

Public Health Relevance

The mission of the Duke University Program in Computational Biology and Bioinformatics (CBB) is to educate the next generation of scientists who will work at the interface between the life sciences and the quantitative sciences. The program accomplishes this mission through a wide range of academic activities and is supported by an unusually broad, but well integrated group of faculty who prepare students to work in collaborative research groups to solve real biological problems. Founded in 2001, CBB has become the primary mechanism for training computational biology students and Duke and is a model for similar programs nationwide.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Institutional National Research Service Award (T32)
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National Institute of General Medical Sciences Initial Review Group (BRT)
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Marcus, Stephen
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Duke University
Biostatistics & Other Math Sci
Schools of Arts and Sciences
United States
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Leete, Jessica; Gurley, Susan; Layton, Anita (2018) Modeling Sex Differences in the Renin Angiotensin System and the Efficacy of Antihypertensive Therapies. Comput Chem Eng 112:253-264
McDowell, Ian C; Barrera, Alejandro; D'Ippolito, Anthony M et al. (2018) Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. Genome Res 28:1272-1284
McDowell, Ian C; Manandhar, Dinesh; Vockley, Christopher M et al. (2018) Clustering gene expression time series data using an infinite Gaussian process mixture model. PLoS Comput Biol 14:e1005896
Reese, Aspen T; Cho, Eugenia H; Klitzman, Bruce et al. (2018) Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. Elife 7:
Ojewole, Adegoke A; Jou, Jonathan D; Fowler, Vance G et al. (2018) BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. J Comput Biol 25:726-739
Midani, Firas S; Weil, Ana A; Chowdhury, Fahima et al. (2018) Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection. J Infect Dis 218:645-653
Gussow, Ayal B; Copeland, Brett R; Dhindsa, Ryan S et al. (2017) Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics. PLoS One 12:e0181604
Ojewole, Adegoke; Lowegard, Anna; Gainza, Pablo et al. (2017) OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design. Methods Mol Biol 1529:291-306
Majoros, William H; Campbell, Michael S; Holt, Carson et al. (2017) High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics 33:1437-1446
Hivert, Marie-France; Scholtens, Denise M; Allard, Catherine et al. (2017) Genetic determinants of adiponectin regulation revealed by pregnancy. Obesity (Silver Spring) 25:935-944

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