This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The UK Bioinformatics Core provides bioinformatics and statistical consulting on multiple genomics projects. The facility supports the BLAST server, Computational Proteomics Analysis System (CPAS) proteomics suite and other custom bioinformatics applications. Facility personnel are actively engaged in statistical consulting and program development and all are members of the Center for Biomedical Informatics of the UK Center for Clinical and Translational Sciences. The INBRE bioinformatics core, particularly Dr. Stromberg, continues to serve as the primary statistical consultant on transcription microarray analyses at UK, serving approximately 30 investigators per year and analyzing data from approximately 1000 expression arrays. Dr. Stromberg is a co-PI on numerous grants and participates in writing the statistical parts of proposals. Of particular note, Dr. Stromberg is a Co-PI, with Dr. Randal Voss as the PI, on a recently awarded $2,000,000 grant from the Department of Defense. Dr. Voss and the Salamander Genome Project had been supported in part by this core for eight years, but was discontinued this year due to the great success he has had in obtaining extramural support for his work. The core also provides informatics support of proteomics and protein expression analyses. Dr. Viele is developing statistical methods to handle mass spectroscopic protein quantification. Dr. Bert Lynn, the director of the University of Kentucky Mass Spectrometry Facility (UKMSF), helps direct the efforts of Mr. William Nelson in the proteomics area. They recently designed and implemented Massively Parallel Peptide Discovery methods that they have submitted for publication and which form the basis of an NIH RO1 grant application. UK is a participant in the national LabKey software development consortium and offers support that can be deployed statewide. This year Mr. Nelson provided training for the Labkey Computational Proteomics Analysis System (CPAS) at the University of Louisville for ten members of the CREAM grant and installed CPAS at the CREAM facility. Their CPAS install is integrated with the SEQUEST cluster at the UKMSF. A publication from this effort should be submitted soon. Mr. Nelson also provided a prototype and training on the Labkey Server Study Module for twelve researchers from the Markey Cancer Center and the Kentucky Cancer Registry (KCR). The Study module provides data management and statistical analysis tools for Clinical Translational Studies. As a result, the Study module is being adopted by the KCR to support the Markey Cancer Center's SPORE grant. The KCR is hiring a permanent administrator to support the Labkey server. Also, Dr. Andre Baron's group has adopted the Labkey for their cancer biomarker research. His project has been implemented at the UKMSF's Labkey installation. Dr. Sujin Kim is developing tools to segment pathology images to facilitate computer identification and standardization of pathology data. She has submitted several grants and publications as well as supervised multiple master's-level students in projects to develop web-based information systems. Dr. Jinze Liu has established multiple bioinformatics collaborations across campus, including developing robust methods for analyzing RNA-seq data for an equine gene annotation project (with Dr. James Macleod) and a plant annotation project (with Dr. Chris Schardl). She recently received an NSF ARRA grant to develop methods to discover alternative splicing patterns from RNA-seq data. Dr. Dave Fardo, a biostatistician who studies genome-wide association studies, has established collaborations on campus, with colleagues at U of L and internationally. Dr. Bert Lynn has recently agreed to mentor and collaborate with Dr. Darrin Smith from the EKU department of chemistry. Dr. Peter Mirabito organized and supervised the KBRIN-supported students working at UK over the summer.
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