News
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Bioinformatics Courses Offered in Spring 2010: Undergraduate and Graduate LevelThe Department of Bioinformatics and Genomics is offering several Bioinformatics courses for Spring 2010, which are open to Bioinformatics students as well as undergraduate/graduate students from Biology, Computer Science, Kinesiology, Chemistry, Physics, Math and Statistics. All Bioinformatics courses will be held in the new Bioinformatics Building. Any interested students please inform your adviser and the course's respective professor to register. |
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Academic Common Market may Allow Some Out-of-State Students to Pay In-State Tuition for UNC Charlotte's PSM in BioinformaticsAcademic Common Market has approved UNC Charlotte's Professional Science Master's in Bioinformatics. Students from Alabama, Arkansas, Delaware, Kentucky, Louisiana, Maryland, Mississippi, North Carolina, Oklahoma, Tennessee and West Virginia are encouraged to pursue and utilize the ACM. |
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The BRC welcomes New Faculty Member Dr. Xiuxia DuAugust 2008: Dr. Xiuxia Du joins the Bioinformatics group at North Carolina Research Campus in Kannapolis. Dr. Du received the Ph.D. in Systems Science and Mathematics from Washington University in St. Louis in 2005. She subsequently did a postdoc in Dr. Richard D. Smith’s lab at the Pacific Northwest National Laboratory. |
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Dr. Susan Sell presents "Studies of the Genomics of Obesity-associated Disorders using Three Complementary Genetic Approaches" December 17, 2008Please join us on Wednesday, December 17, 2008 for the following presentation: Studies of the Genomics of Obesity-associated Disorders using Three Complementary Genetic Approaches. The talk will be given by Dr. Susan Sell. Time: 12 noon to 1 Location: Cameron Applied Research Center (CARC) Room 101. |
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WFAE Report on Bioinformatics Research Center - May 6, 2009WFAE's Lisa Miller reported a story on the Bioinformatics Research Center that was aired during WFAE’s morning report on May 6, 2009. The link to the story/recording is below. |
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BiG Welcome to Professor Dr. Susan Sell!The Department of Bioinformatics and Genomics is pleased to announce that Dr. Susan Sell is now a Professor in the Department of Bioinformatics and Genomics. Please welcome her to the Department. |
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PhD and PSM Student Presentations: April 24, 2009The BiG Department PhD and PSM students will showcase the final presentations Friday, April 24, 2009 at 2pm in Cameron Applied Research Center Room 101. Wei Song, adviser Dr. Don Jacobs, will present: "Characterizing the Image Charge Method for Electrostatic Interactions in Molecular Dynamics Simulation." |
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The Department of Bioinformatics and Genomics Microarray Core Lab's New Collaborative Research Project with BioCyticsThe College of Computing and Informatics’ Department of Bioinformatics and Genomics is participating in an exciting new collaborative research project with BioCytics out of Huntersville, North Carolina. |
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BRC Seminar: Dr. Hrishikesh Deshmukh presents “High-resolution, multi-platform genomic analyses of Pilocytic Astrocytomas” May 1, 2009Pilocytic astrocytomas (PAs, WHO grade I) are the most common brain tumors in the pediatric and adolescent population, accounting for approximately one-fifth of central nervous system tumors. Because few consistent molecular alterations have been identified in PAs compared to higher grade gliomas, array comparative genomic hybridization using two independent commercial array platforms was performed. Although whole chromosomal gains and losses were not observed, a 1-Mb amplified region of 7q34 was detected in multiple patient samples using both array platforms. The copy number gain was confirmed in an independent data set by qPCR; this amplification was correlated to both increased mRNA and protein expression of HIPK2, a homeobox-interacting protein kinase associated with malignancy, contained within this locus. This study highlights the need to perform comprehensive genomic analysis and use of high-resolution, multiple platforms to detect small genomic alterations. |
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Dr. ShaoQiang Zhang presents 'Large-scale genome wide de novo prediction of cis-regulatory binding sites in prokaryotes and yeast' April 17, 2009Bioinformatics Seminar: Dr. ShaoQiang Zhang presents 'Large-scale genome wide de novo prediction of cis-regulatory binding sites in prokaryotes and yeast' April 17, 2009 at 2pm in CARC 101. ShaoQiang is Dr. ZhengChang Su's postdoctoral research fellow. |
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Progress of UNC Charlotte's Bioinformatics BuildingBioinformatics Building Photo update: The Bioinformatics Building is months away from the August 19, 2009 opening. See the transformation! |
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Biannual Bioinformatics Lab Rotation Presentations- Spring 2009PhD student lab rotation presentations will occur this Spring semester: March 20th, March 27th, and April 24th. Students Saeed Khoshnevis, Cristina Baciu, Aurora Cain, Wei Song, and Meng Niu will present their rotations. Dr. Jennifer Weller supervised both Saeed and Cristina's rotations. Dr. Robert Kosara supervised Aurora's rotation. Wei's rotation was supervised by Dr. Donald Jacobs. Dr. ZhengChang Su supervised Meng's rotation. |
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First Bioinformatics and Genomics Retreat a SuccessOutside the glass encased hallway, it was cold and rainy in Charlotte, but inside the energy levels were high and enthusiasm hot as more than 200 scientists from industry and academia met at UNC-Charlotte's Center for Bioinformatics and Genomic's first Bioinformatics and Genomics retreat this afternoon. |
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Bioinformatics Seminar -- Professor George Makhatadze presents "Proteins Stabilized to Order" April 10, 2009April 10, 2009 at 2pm in Cameron 101, the BRC and CRI will host Prof. George Makhatadze, Professor of Biology, Rensselaer Polytechnic Institute. "Proteins Stabilized to Order" will be presented. |
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Terry Kenakin presents: 7 Transmembrane Receptor Allostery: Putting Numbers to Shapeshifting Proteins. Bioinformatics Seminar, January 23 1pm.As the technology of discovery advances to the point where various behaviors of 7TM receptors can individually be observed, it is clear that receptors are much more 'micro-processors' of information than 'on-off' switches. This has introduced a phenomenon referred to as 'functional; selectivity' into the field and opened new horizons for drug discovery. In addition, the increased emphasis of functional screening has introduced a great many more allosteric ligands into new chemical entity space. The need to quantify drug effect on these complex systems to guide medicinal chemistry requires new models and approaches; these will be discussed as well as the impact of energy landscape molecular dynamics on 7TM drug discovery. Finally, advances in allosteric HIV entry inhibitors will be presented as an example of where allostery can offer unique therapeutic applications. |
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Distinguished Bioinformatics Lecturer: Professor Steven L. Salzberg presents "Assembling Genomes from Next-Generation Sequencers" February 20, 2009February 20, 2009 -- UNC Charlotte's Bioinformatics Research Center and College of Computing and Informatics will host Distinguished Bioinformatics Lecturer, Prof. Steven L. Salzberg, University of Maryland. Dr. Salzberg will be presenting in Woodward 106 from 3-4 pm. |
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Dr. Morgan Giddings presents "Proteogenomic mapping for the human genome: technologies and challenges for identifying protein-coding sequences" April 4, 2008For complex eukaryotes, it is a significant challenge to determine which parts of the genome are transcribed then translated into proteins and when. Determining how protein expression is regulated from a large population of gene transcripts may play a key role in gaining mechanistic understanding of disease progression. Proteogenomic mapping uses mass-spectrometry to analyze and identify proteins from biological samples in order to determine which genes and their exons are translated in a given biological sample. However, there are significant technical challenges in applying it to large genomes with complex multi-exon genes, including the accuracy of protein/peptide identification, large computation times, and effectively managing and visualizing the resulting data. We have developed several new approaches to improve the accuracy and feasibility of large-scale proteogenomic mapping for complex eukaryotes. We implemented a hidden Markov model based scoring system for matching MS/MS peptide spectra to genomic sequence with significant accuracy improvements, we developed a method for matching peptide ion peak intensity to peptide sequence properties to further improve proteogenomic mapping accuracy, and we are developing highly flexible heterogeneous data management system that uses a relational database system to represents all information from the project as a set of rules within a small cluster of relational tables. In this talk, I discuss both the technical aspects of developing a large scale approach such as this, along with the results of applying these methods to preliminary scans of several large mass spectrometry data sets against both genomes and gene prediction sets. The results indicate that the method is able to find proteomic support for genes where there is no present annotation, in many cases corresponding to other cDNA or gene prediction evidence, but not in all cases. |
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WFAE Report on Bioinformatics Research Center - May 6, 2009WFAE's Lisa Miller reported a story on the Bioinformatics Research Center that was aired during WFAE’s morning report on May 6, 2009. The link to the story/recording is below. |
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UNC Charlotte's Bioinformatics BuildingThe Bioinformatics and Genomics Department is now located in the new Bioinformatics Building! |
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First UNC Charlotte Faculty Member Arrives at N.C. Research CampusUNC Charlotte’s Charlotte Research Institute and Bioinformatics Research Center have announced the arrival of the first research faculty member on the North Carolina Research Campus, the $1.5 billion project being developed by billionaire Dole Food owner David Murdock. Ann Loraine, associate professor of bioinformatics, moved into temporary office space at the campus this week. She is the first of six UNC Charlotte researchers expected on the Kannapolis campus in 2008. |
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Omics Course (Bioinformatics 8203/6203)Welcome to Dr. Cynthia Gibas's Omics Course. Please visit this website for information on syllabus, homework, projects, exams, etc. Contact Dr. Gibas at: cgibas@uncc.edu |
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Dr. Xiaoman Li presents "Discovery of motifs and motif modules in DNA sequences" March 31, 2008Abstract: 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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Dr. Christopher Ellis presents "In Silico: Application of a Novel Software Suite for the Study of Cold Stress Syndrome in Manatees." April 14, 2008Abstract: 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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Dr. Sunil Hwang presents "Biomarker Discovery by Mass Spectrometry and Bioinformatics" April 25, 2008Biomarker 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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Dr. Mark Wilson presents "The role of phylogenetic analysis in forensic DNA typing" April 18, 2008Abstract: 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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Bioinformatics Seminar Series: Fall 2008The 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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Bioinformatics Seminar (PhD Student Rotation Talks)--December 12, 1:30pm, CHHS 155Second 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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First Bioinformatics and Genomics Retreat a SuccessOutside the glass encased hallway, it was cold and rainy in Charlotte, but inside the energy levels were high and enthusiasm hot as more than 200 scientists from industry and academia met at UNC-Charlotte's Center for Bioinformatics and Genomic's first Bioinformatics and Genomics retreat this afternoon. |
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Bioinformatics and Genomics Retreat Day Announcement: December 10, 2008The 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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Bioinformatics Seminar (PhD Student Rotation Talks)--December 5, 2pm, CHHS 155PhD 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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Applications of the Roche/454 FLX Genome SequencerNovember 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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Computational and Experimental Approaches to Modeling Gene RegulationNovember 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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Bioinformatics Seminar -- Nov 7, Surface plasmon resonance spectroscopy measurements of DNA/DNA, DNA/drug and protein/protein bindingNovember 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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Bioinformatics Seminar -- October 31, 2pm, CARC 101Jean-Luc Mougeot, Ph.D. Senior Scientist Carolinas Medical Center |
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2008 Charlotte Biotechnology Conference: October 28, 2008The 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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Bioinformatics Seminar -- October 24, 2pm, CARC 101Dr. Sudhir Kumar, Director: Center for Evolutionary Functional Genomics and Professor of Life Sciences, Arizona State University |
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Bioinformatics Seminar -- October 17, 2pmGuojun 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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Bioinformatics Seminar -- October 10, 2pmDebra T. Burhans, PhD, Associate Professor, Computer Science, Department Co-Chair of CS, Director of Bioinformatics, Canisius College |
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Bioinformatics Seminar -- October 3, 2pmJacquelyn 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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Bioinformatics Seminar -- September 26, 2pmDr. Gabriel del Rio - National Autonomous University of Mexico |
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Bioinformatics Seminar -- September 19, CARC 101 2:00pmSaurabh Sinha, PhD, Assistant Professor, Computer Science, Affiliated Faculty, Institute for Genomic Biology, University of Illinois at Urbana-Champaign |
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Bioinformatics Seminar -- September 12, CARC 101 2:00pmNICHOLAS J. PROVART, Ph.D., Department of Cell and Systems Biology, University of Toronto, Toronto, ON. CANADA |
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Updated* Bioinformatics Orientation -- August 29, 1:30pmBioinformatics Orientation: All Bioinformatics students are required to attend. Everyone involved with BRC is encouraged to attend. |
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Ahead-of-the-Curve CareersU.S. News & World Report Career Guide 2008: Here’s a look at a dozen cutting-edge careers, viable now and poised for future growth. They stem from megatrends like globalization, digitization, and the wave of environmentalism sweeping the world. Ahead-of-the-Curve Overview: Asian Business Development Specialist, Behavioral Geneticist, Computational Biologist, Data Miner, Emergency Planning Manager, Green-Collar Consultant, Health Informatics Specialist, Immigration Specialist, Offshoring Manager, Patient Advocate, Simulation Developer, & Wellness Coach |
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NCRCOn Monday, September 12, 2005, David H. Murdock, owner of Castle & Cooke, Inc. and Dole Food Company, Inc., and Molly Corbett Broad, president of the 16-campus University of North Carolina, unveiled plans for the North Carolina Research Campus, a massive scientific and economic revitalization project that encompasses the former Cannon Mills plant and entire downtown area of Kannapolis, North Carolina. |
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Dr. David Page presents "Machine Learning in the Analysis of Mass Spectrometry Data" April 11, 2008This 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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Accepting applications for UNC Charlotte's Bioinformatics Graduate Programs For Fall 2010Applications are being accepted for Fall 2010 for the IT PhD-Bioinformatics Track and the Professional Science Master's in Bioinformatics degree programs. To apply, please view the Future Students tab for detailed information. |
