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- Info
Archived News
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Second half of PhD students rotation talks. Jon McCafferty will discuss "Systematic analysis of indels in highly homologous protein structures". His rotation Supervisor was Dr. Jun-tao Guo. Following Jon, Minli Xu will present. Minli will present "A survey of hydrogen bind network conservation within homologous proteins". Minli's rotation supervisor was Dr. Dennis Livesay. Following Minli will be Charles David. Charles, supervised by Dr. Don Jacobs, will present "Investigating flexibility in proteins using Framework Rigidity Optimized Dynamics Algorithm". Pizza lunch will be sponsored by VWR prior seminar at 1:30.
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The New Department of Bioinformatics and Genomics (as of October 2008) invites you to the first ever Bioinformatics & Genomics Retreat, DECEMBER 10, 2008 (Reading Day) at 2pm in Grigg Hall on the CRI Research and Technology Campus.
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PhD students will talk 20 minutes about their rotation talks. Deeptak Verma wil discuss "Predicting mutant stability with a combined experimental/theoretical approach". His rotation Supervisor was Dr. Don Jacobs. Following Deeptak, Shan Li will present her rotation project with Dr. Xintao Wuo. Following Shan will be Cristina Baciu. Cristina will present "Direct Comparison Between mDCM Model and an Associated Gò-like Model". Cristina's rotation supervisor was Dr. Dennis Livesay.
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The Bioinformatics Seminars are generally every Friday at 2pm in Cameron Research Center Room 101. They are open to the public. The seminars are sponsored by the Bioinformatics Research Center and Charlotte Research Center.
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November 21, 2pm -- Dr. Joe Jones (University of South Carolina, Columbia) states that the field of biology has been significantly altered by new technology in the field of DNA sequencing. From the first DNA sequences in 1977 to the com- pleted human genome in 2003, the overwhelming majority of DNA sequence data was obtained using the identical chemistry (i.e., di-deoxy termination). Staring in 2005, a novel means of sequencing DNA via emulsion PCR (emPCR) and pyrosequencing was introduced that allowed a quantum leap in the ability to sequence genomes and survey genetic variation. This talk will cover the methodologies and principles behind emPCR, pyrosequencing, and how the combination of these two techniques can be applied to a variety of biological topics.
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November 14, 3pm -- Dr. Gary Stormo, Distinguished Bioinformatics Lecturer will discuss one of the challenges of genomics research which is to understand the regulation of gene expression. Much of the regulation is controlled through DNA-protein interactions and we have been developing tools, both computational and experimental, to study those interactions for many years. This talk will outline some of the approaches we have been using and how they inform us about the regulatory network that governs the cell's behavior. Post-transcriptional regulation also plays a role in controlling gene expression, and some of our work on that topic will also be described.
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November 7, 2pm -- Dr. Rosina Georgiadis (Chemistry Department, Boston University) will review the fundamentals of SPR as well as describe techniques developed in my laboratory such as two-color SPR and angle-scanning SPR imaging. She will discuss what we have learned about DNA/DNA hybridization kinetics at interfaces from careful measurements as a function of probe density, secondary structure and composition (mismatch) as well as comparative kinetic measurements in solution (obtained by UV-vis absorption spectroscopy). She will also present more recent work on protein/protein interactions and future directions.
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Jean-Luc Mougeot, Ph.D.
Senior Scientist
Carolinas Medical Center
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The 7th Annual Charlotte Biotechnology Conference will provide insight from some of the most recognized biotechnology, business and research professionals from around the globe in addition to highlighting regional opportunities and investment trends within the local biotechnology sector.
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Dr. Sudhir Kumar, Director: Center for Evolutionary Functional Genomics and Professor of Life Sciences, Arizona State University
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Guojun Li, PhD
Senior Research Scientist
Computational System Biology Laboratory
Department of Biochemistry and Molecular Biology
Endowed Professor of Mathematics and System Sciences
University of Georgia
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Debra T. Burhans, PhD, Associate Professor, Computer Science, Department Co-Chair of CS, Director of Bioinformatics, Canisius College
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Jacquelyn S. Fetrow, PhD Wake Forest University, Reynolds Professor of Computational Biophysics, Director, Graduate Track in Structural and Computational Biophysics, Departments of Computer Science and Physics
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Dr. Gabriel del Rio - National Autonomous University of Mexico
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Saurabh Sinha, PhD, Assistant Professor, Computer Science, Affiliated Faculty, Institute for Genomic Biology, University of Illinois at Urbana-Champaign
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NICHOLAS J. PROVART, Ph.D., Department of Cell and Systems Biology, University of Toronto, Toronto, ON. CANADA
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Bioinformatics Orientation: All Bioinformatics students are required to attend. Everyone involved with BRC is encouraged to attend.
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Biomarker detection is dependent upon the dynamic range of the sample of interest. The dynamic range of a typical clinical sample, usually tissue or blood, varies from six to twelve orders of magnitude. Our research has been applied to the optimization of methodologies, including protein preparation, separation, and data analysis, utilized in the identification of early stage disease biomarkers. Proteomics represents the combination of three disciplines: Biology, Mass Spectrometry, and Bioinformatics. Due to the complexity and volume of data generated by proteomics applications, the demands for bioinformatics approaches to data analysis are ever increasing. Using these experimental strategies and bioinformatics tools we have been able to elucidate the global proteome profile for the Jurkat T cell line, determine the feasibility of direct protein sequencing from minute tissue section samples, and establish depletion strategies for removal of the highly abundant proteins found in serum/plasma. Our future goals include improving and streamlining the bioinformatics aspects associated with proteomic research and biomarker discovery.
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Abstract: Uniparentally inherited genetic loci, such as mitochondrial DNA and the Y-chromosome, are inherited as a single genetic locus; mtDNA from the maternal line and the Y chromosome from the parental line. These markers are a valuable aspect of forensic DNA typing, and offer the analyst information not easily discerned from the current set of autosomal STRs. Because of their status as single genetic loci, the statistical power of these markers in forming weight assessments is greatly reduced, and hence these markers must be treated differently in this respect than commonly used autosomal markers. The tool of phylogenetic analysis can assist in the proper interpretation of uniparentally inherited markers and is therefore an important tool of the modern forensic laboratory.
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Abstract: Manatees have been found as far west as Texas and as far North as Rhode Island during the summer months however, the vast majority are found in southern Florida year round. Florida Fish and Wildlife calculates the number of mature manatees at only 2,181 and were until recently listed as an endangered species. During the winter manatees seek warm water refuges such as natural springs and power plant discharges. However, they must leave these warm environments to forage for food in the colder water, causing significant stress and potentially death to the animal. Symptoms of a cold stressed manatee can include but are not limited to white skin around the face, flippers and tail and/or deep grooves on the underside from the animal using significant amounts of their fat stores in order to keep warm. Rapid human population growth in Florida and associated water demand has resulted in the destruction natural spring flows in which the manatees rely on for warmth during the winter. Manatees are reliant on the microbial communities in their digest tract not only for nutrients but also buoyancy and warmth. We examined the microbial population of a healthy manatee and contrasted it with the microbial community associated with a cold stressed manatee sampling from the proximal intestine, distal intestine, and mid large intestine of both animals. Significant and important microbial shifts were seen in all three locations, including the emergence of opportunistic pathogens in the cold stressed manatee. This new insight on manatee health is being used by the Florida Fish and Wildlife in an effort to restore cold stressed manatees to health.
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This talk will discuss three applications of machine learning to mass spectrometry data. It will begin with the task of building diagnostic models from mass spec proteomics data for organisms whose proteomes are not known (whose genomes have not been sequenced). It will use the example of studying prion infection in a hamster model. Second, the talk will examine the task of identifying the isotopic distributions in a spectrum; this task has applications to both mass spec proteomics and metabolomics. It will then apply this approach to the third task, that of quantifying the amounts of various proteins in a sample based on isotopic labeling, in this particular case, metabolic labeling.
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Abstract: Identifying motifs and motif modules is critical to understand gene regulation. Available methods can not be readily applied to high eukaryotes because they either cannot identify motifs and motif modules in non-promoter regions, or they can not identify divergent motifs and motif modules. We have thus developed novel methods to identify motifs and motif modules in high eukaryotes. Besides, we have designed unique ways to assess the reliability of the identified motifs and motif modules. Without necessity of doing multiple alignment, our methods can not only identify motifs and motif modules on the whole genome scale, but also can detect motifs and motif modules across very distant species. Compared with existing motif and motif module identification methods, our methods show much better performance.
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