This proposal for a Penn Computational Genomic Training Program is a renewal application of a training grant to support graduate and post-doctoral students in computational biology and genomics. Current problems in computational genomics, such as trying to understand gene regulatory mechanisms or the genetic basis of disease, require .combining disparate sources of knowledge and comparisons across multiple organisms. Such research requires deep understanding of the biology of the organism or phenomenon being studied, and of the experimental techniques and statistical and algorithmic methods available. The purpose of this grant is to train students with these skills and to produce researchers who will be able to address current and future research needs in computational biology. Over the last 15 years, the University of Pennsylvania has built a strong program for training students in genomics, bioinformatics and computational biology. The graduate training support from this grant is increasingly focused on students in Penn's (relatively new) graduate group in Genomics and Computational Biology (GCB), within the Biomedical Graduate Studies (BGS) program in the School of Medicine (SOM), which now has 27 PhD students with 5 students matriculating in 2008. We also continue to support PhD students and post docs in the Biology and the Computer and Information Science (CIS) departments, as well as in other parts of the School of Medicine. The training program of this grant occurs in the context of a strong collaborative research effort spanning the many disciplines involved in computational biology. Trainees benefit from the Penn Genome Frontiers Institute (PGFI), which provides a wide variety of computational and experimental resources including microarry facilities, proteomics facilities, hardware and software for bioinformatics, and training and consulting, and the Penn Center for Bioinformatics (PCBI), which houses and supports a variety of researchers in computationally biology, including GCB students (and hence many training grant students) until they join research laboratories. BGS has a full time staff member in charge of minority recruitment programs. He has aided us in student recruitment, running many events, including minority recruitment weekend. I have attached a detailed description of the BGS minority recruiting efforts. We currently have nine students (both pre- and post-doctoral) supported by the training grant. Of these, two are URMs (African American) and another five are women. PUBLIC HEALTH REVELANCE Training computational biologists is critical to the continued progress of medical research in the U.S. Increasingly, progress in a wide array of medical fields is based on use of computer models to understand how genes and environment affect health. Skilled researchers are needed to use computational biology to develop treatments or cures from diseases ranging from AIDS to cancer.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Institutional National Research Service Award (T32)
Project #
Application #
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Program Officer
Gatlin, Christine L
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Pennsylvania
Schools of Medicine
United States
Zip Code
Meisel, Jacquelyn S; Hannigan, Geoffrey D; Tyldsley, Amanda S et al. (2016) Skin Microbiome Surveys Are Strongly Influenced by Experimental Design. J Invest Dermatol 136:947-56
Rupp, Levi J; Chen, Liang; Krangel, Michael S et al. (2016) Molecular Analysis of Mouse T Cell Receptor α and β Gene Rearrangements. Methods Mol Biol 1323:179-202
Kraya, Adam A; Piao, Shengfu; Xu, Xiaowei et al. (2015) Identification of secreted proteins that reflect autophagy dynamics within tumor cells. Autophagy 11:60-74
Ocwieja, Karen E; Sherrill-Mix, Scott; Liu, Changchun et al. (2015) A reverse transcription loop-mediated isothermal amplification assay optimized to detect multiple HIV subtypes. PLoS One 10:e0117852
Jiang, Yuchao; Oldridge, Derek A; Diskin, Sharon J et al. (2015) CODEX: a normalization and copy number variation detection method for whole exome sequencing. Nucleic Acids Res 43:e39
Stein, Paula; Rozhkov, Nikolay V; Li, Fan et al. (2015) Essential Role for endogenous siRNAs during meiosis in mouse oocytes. PLoS Genet 11:e1005013
Hannigan, Geoffrey D; Meisel, Jacquelyn S; Tyldsley, Amanda S et al. (2015) The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio 6:e01578-15
Russell, Mike R; Penikis, Annalise; Oldridge, Derek A et al. (2015) CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus. Cancer Res 75:3155-66
Oldridge, Derek A; Wood, Andrew C; Weichert-Leahey, Nina et al. (2015) Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Nature 528:418-21
Mirarab, Siavash; Nguyen, Nam; Guo, Sheng et al. (2015) PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J Comput Biol 22:377-86

Showing the most recent 10 out of 68 publications