This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project implements a bioinformatics core facility, which provides hardware, software, educational/training capabilities, and staffing that enable biomedical researchers to analyze and model biological data. This core is funded by COBRE in conjunction with other sources such as the Idaho BRIN and INBRE Programs (P20RR16454). In the last year, with COBRE funds, we have increased the available disk storage, in order to accommodate exponentially increasing databases. Using other funds, we have also built a new high performance (64-bit, 16 node Xserve) cluster computer, as a test platform for exploring future cluster architectures, and added a third (more powerful) Sun V880 server On the software side, we have upgraded our core bioinformatics software for both research and training, and have augmented our mathematical and molecular modeling capabilities. We have also expanded our MS/PhD program in Bioinformatics and Computational Biology (BCB) to 17 doctoral students and 3 MS students. Most students are working on research projects with COBRE faculty. We also offered formal courses, participated in the third annual BRIN Bioinformatics Workshop, and hosted a COBRE poster session in September. Staff in this core now include: James A. Foster, Director; Ken Blair, Systems Administrator; Celeste Brown, Bioinformatics Coordinator; four student assistant systems administrators; and two student programmers. Our plans for this year are: to improve the production cluster computer to improve availability and reliability, to recruit a second, full-time systems administrator for cluster computing, and to renew software licenses. We are also assisting with the NIH Lariat project, a BRIN supplement to enhance telecommunications in support of collaborative biomedical research among IDEA states in our region.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Exploratory Grants (P20)
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Special Emphasis Panel (ZRR1-RI-A (02))
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University of Idaho
Schools of Arts and Sciences
United States
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Ruffley, Megan; Smith, Megan L; Espíndola, Anahí et al. (2018) Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Mol Ecol 27:1012-1024
Chernikova, Diana A; Madan, Juliette C; Housman, Molly L et al. (2018) The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth. Pediatr Res 84:71-79
Smith, Stephanie A; Benardini 3rd, James N; Anderl, David et al. (2017) Identification and Characterization of Early Mission Phase Microorganisms Residing on the Mars Science Laboratory and Assessment of Their Potential to Survive Mars-like Conditions. Astrobiology 17:253-265
Marx, Hannah E; Dentant, Cédric; Renaud, Julien et al. (2017) Riders in the sky (islands): using a mega-phylogenetic approach to understand plant species distribution and coexistence at the altitudinal limits of angiosperm plant life. J Biogeogr 44:2618-2630
Yano, Hirokazu; Wegrzyn, Katarznya; Loftie-Eaton, Wesley et al. (2016) Evolved plasmid-host interactions reduce plasmid interference cost. Mol Microbiol 101:743-56
Sarver, Brice A J; Demboski, John R; Good, Jeffrey M et al. (2016) Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (TAMIAS). Genome Biol Evol :
Stockmann, Chris; Ampofo, Krow; Pavia, Andrew T et al. (2016) Clinical and Epidemiological Evidence of the Red Queen Hypothesis in Pneumococcal Serotype Dynamics. Clin Infect Dis 63:619-626
Loftie-Eaton, Wesley; Yano, Hirokazu; Burleigh, Stephen et al. (2016) Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance. Mol Biol Evol 33:885-97
Uribe-Convers, Simon; Settles, Matthew L; Tank, David C (2016) A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One 11:e0148203
Chernikova, Diana A; Koestler, Devin C; Hoen, Anne Gatewood et al. (2016) Fetal exposures and perinatal influences on the stool microbiota of premature infants. J Matern Fetal Neonatal Med 29:99-105

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