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. The primary functions of the Bioinformatics Core are to provide expert consultation and analysis in state-of-the-art sequence analysis and annotation, to develop informatics strategy for analysis of complex data sets for RI-INBRE-supported investigators, and to educate the faculty regarding Bioinformatics approaches which may be relevant to their research. The responsibilities of the Core also include other activities such as website management, data collection and storage for the RI-INBRE Program, and coordination of the monthly RI-INBRE seminar series. Until May 2009, Dr. Daniel Udwary served as the Bioinformatics Core Coordinator on a part-time basis, with Dr. Clinton Chichester as the Co-Coordinator for information services. A full-time Bioinformatics Core Coordinator, Dr. Joanna Fueyo, joined the RI-INBRE Program in June. An opportunity to extend her appointment was provided through an administrative supplement awarded from stimulus funds. Her qualifications include a Ph.D. in Pharmacology from the University of Pennsylvania School of Medicine with a concentration in Bioinformatics. Her expertise includes several years of private industry experience in informatics system and algorithm design, with a focus on the integration and query of genomic, medical imaging, and clinical data sets. In addition, she has experience teaching graduate courses on the Basic Local Alignment Search Tool (BLAST) algorithm and its application to both sequence annotation and therapeutic target discovery. She was formerly employed by IBM Healthcare and Life Sciences where she served on multi-national consulting projects for over six years as a subject matter expert in Pharmacogenomics and Medicine and as team leader in Medical Imaging. During two of her former employments at SmithKline Beecham and the University of Pennsylvania, she successfully applied the algorithm and its derivatives to the discovery of novel anti-microbial sequences. She also has applied BLAST on a large scale for genome and proteome comparison in microbial sequence data in the company she co-founded, Infoceutics Inc. Bioinformatics Software: The GCG package is no longer offered in the Bioinformatics Core since Accelrys has stopped supporting this software. The main software provided by the Core at the primarily undergraduate institutions (PUIs) and at URI is Sequencher. Also available at URI is a suite of molecular modeling software (Discovery Studio from Accelrys), for which we purchased a new protein-protein docking module during the past year. A more detailed list of the software available in this Core Facility is described in the bioinformatics section of Shared Facilities. The Core is currently evaluating other Bioinformatics software needs as well. A number of algorithms, databases, and some software that is freely available online were utilized for data analysis. For instance, many of the consultation requests rely heavily on sequence data located in world-wide curated databases. The algorithms that analyze these sequence repositories are typically web-based, as are the datasets that are relevant to these sequences, such as literature or curated literature resources. Most everything accessed in a consultation request is via the internet since the data is numerically 'linked'in cyberspace. Therefore, over time it is anticipated that there will be a decreased dependence on commercially available software packages and a move towards freely available, internet-based state-of-the-art tools that are linked to the most recent sequence and data repositories worldwide. Bioinformatics Instruction and Consultation: The Bioinformatics Core provides instruction and consultation for the RI-INBRE-supported faculty and their pre- and post-doctoral researchers on the recommended approach. Since joining the RI-INBRE Program, Dr. Fueyo has visited all of the RI-INBRE investigators at URI and at the PUIs to learn more about their research and in order to identify potential areas for consultation or collaboration in Bioinformatics. These visits have resulted in several consultation requests, the first of which was completed last summer, and others which were recently received and are planned for initiation in 2010. One of the current project requests involves determining what state-of-the-art web-based tools exist for the analysis of transcription factor binding sites in sequence, followed by use of these tools and training of others in the use of these tools, including mapping out a workflow and strategy for their correct utilization. The investigators requesting this work hope that the consultation can lead to publication of the results including the Bioinformatics analysis. A number of poster presentations by RI-INBRE-supported scientists at regional conferences have already acknowledged use of the RI-INBRE Bioinformatics Core Facility. To encourage continued outreach and awareness of the consultation services the Core can provide, the Bioinformatics Core is creating a list of key bioinformatics consultative skills and strategic approaches that are relevant to RI-INBRE investigators. These materials will be put on the RI-INBRE website as projects are completed and as new approaches become available. Bioinformatics Core Involvement in Teaching: The Bioinformatics Core personnel provided didactic course instruction in Bioinformatics. Dr. Udwary was a co-instructor in a cross-disciplinary graduate-level course in spring 2009. In this class, each student was required to design and implement an innovative, original Bioinformatics research project in collaboration with a URI faculty member. Students completed 7 high-quality projects, many of which are now being applied in the research laboratories and may lead to publications. In fall 2009 Dr. Fueyo lectured in a graduate-level techniques course and taught the theoretical basis of sequence alignment including multiple sequence alignment (MSA), how BLAST and its derivatives are applied to functional assignment of sequence data (annotation), and how therapeutic targets can be identified in microbial genomes, using BLAST. She also taught Genome Orientation skills that enabled the students to figure out where they are within a genome, and what the spatial placement of a gene in a genome means biologically. She may have the opportunity to continue her participation in the formal teaching activities next year. Workshop and Seminar Development: As of January 2010, Dr. Fueyo, in conjunction with the RI-INBRE Program Director, is now organizing the monthly RI-INBRE seminar series. An increased focus on Bioinformatics in the seminar series during the next fiscal year is planned. In fall 2009, she invited Dr. Martha Shenton of Harvard Medical School to give a seminar entitled, """"""""Magnetic Resonance (MR) and Diffusion Tensor Imaging (DTI) Findings in Schizophrenia and Related Disorders"""""""". The Bioinformatics Core will be evaluating the needs of the RI-INBRE faculty and developing a progressive program to meet those needs. One result of this will be a series of workshops in Bioinformatics to increase the understanding of the capabilities of computational methods to enhance their research. Data Collection and Management, and Website Management: The present RI-INBRE records are being scanned and stored for digital archival and retrieval. In the future, reports, surveys, and most other data will be collected electronically in order to facilitate data warehousing and searches. Our present web site was developed a few years ago by the Core personnel. Updating and maintenance functions of the website that are currently performed by the Administrative Core personnel will revert back to the Bioinformatics Core. Video Conferencing: We are increasing the use of video conferencing equipment. The provision of this equipment at each of the participating institutions has led to increased participation in such activities as RI-INBRE seminars, Steering Committee meetings, and meetings of the Northeast Cyberinfrastructure Network (NECC). Enhancement of Cyberinfrastructure: NECC was formed in 2006 to assess the cyberinfrastructure needs and find ways to improve broad bandwidth connectivity, and thereby data sharing, between the various research institutions in Rhode Island, Maine, New Hampshire, Vermont and Delaware. The NECC projects were funded in each state by both NSF and NIH through EPSCoR and INBRE programs, respectively. The administrative supplement, besides providing financial support for extending the appointment of the full-time Bioinformatist, also provides for high speed fiber installation between URI and the existing broadband network in the northern part of the state. At present, this project is in its planning stage. Dr. Chichester serves on the NECC technical committee which will meet in Burlington ,VT in March, 2010 to coordinate the various statewide projects. Meeting Attendance and Presentations: The Bioinformatics Core has had a number of presentations and others are forthcoming. Dr. Fueyo presented a poster based on an RI-INBRE consultation at the Summer Undergraduate Research Fellows Conference in August 2009. She also gave an invited talk at the Northeast Regional IDeA Symposium in New Hampshire in August 2009, where she spoke about """"""""Cyber-Enabled Research Collaborations in INBRE and Beyond"""""""". In addition, she attended an invite-only High Performance Computing event at Brown University, in Fall 2009. She has also been invited to present a talk on """"""""Complex Brain Network Analysis in Schizophrenia"""""""", an area of her own research interest, at the University of Vermont in April 2010.
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