Assistant Professor Mike McConnell of the Department of Biochemistry and Molecular Genetics, and affiliate faculty member of the Center, will be working as part of a research team whose aim is to identify the genetic causes of schizophrenia. While some of his collaborators from other institutions will use bulk sequencing, Dr. McConnell will use single-cell genome sequencing to examine samples of donated brains from two groups – people who had schizophrenia and a control group who did not. This research, which was reported in the May 6th issue of UVa Today, is funded with a five-year grant by the National Institute of Mental Health.
Sarah Kucenas, Assistant Professor of Biology, and an affiliate faculty member of the Center, has been recognized with the state’s highest honor given to professors. Nominated by their peers, the awardees are selected by a committee made up of members of the State Council of Higher Education for Virginia, and other business and community leaders. Dr. Kucenas, known internationally for her research, is also dedicated to teaching and service, encouraging her undergraduate students to participate in actual research in her lab, an opportunity that is more often seen for graduate level students.
In a recent article in Nature, a paper by Dr. Wladek Minor, an affiliate faculty member of the Center, was identified as one of the 100 most highly cited papers of all time. Published in 1997, “Processing of X-ray Diffraction Data Collected in Oscillation Mode” is ranked 23rd among papers of all time and is described by Philip Bourne, associate director for data science at the National Institutes of Health, as one of the “bricks and mortar” tools for determining crystal structures. Dr. Minor is a Professor in the Department of Molecular Physiology and Biological Physics.
The Quinlan Lab just published a paper describing the first set of bioinformatics tools to work with nanopore DNA sequencing technologies. Poretools: a toolkit for analyzing nanopore sequence data was published in Bioinformatics online August 20, 2014.
Professor Kimmo Kaski, Dept of Biomedical Engineering & Computational Science - Aalto University, Niina Sandholm, Doctoral of Science (Technology) candidate, Aalto University, and Professor Stephen Rich, University of Virginia
Professor Stephen Rich recently returned from a visit to Aalto University in Helsinki, Finland where he was invited to be the Opponent during the public dissertation defense for doctoral candidate Niina Sandholm. This took place in the customary manner in Finland with the Custos (Chairman) and the Opponent dressed in academic gowns or black tailcoats, carrying their doctoral hats into the hall, while the candidate wears a formal, dark suit to the event. After the Custos opens the proceedings, the doctoral candidate presents the thesis for 20 minutes. This is followed by three to four hours of intensive questioning by the Opponent, and finally the closing formalities. Sandholm’s thesis, Genome-wide associations and computational search for the genetic risk factors for diabetic nephropathy, used a wide range of computational methods to identify risk factors for diabetic nephropathy. Her dissertation work has resulted in the publication of five papers in peer-reviewed journals.
Ryan Layer, PhD, Research Associate in the Quinlan Lab, was selected to give a platform talk at two upcoming conferences this fall. Dr. Layer will discuss new methods for exploring millions of human genomes at the Wellcome Trust Genome Bioinformatics 2014 Conference. This is the premier bioinformatics meeting in the world and will be held September 21-24 in Cambridge, UK. He will also speak at the 64th Annual Meeting of the American Society of Human Genetics. Set to be held October 18-22, 2014 this is the world’s largest human genetics meeting and exposition, with over 6,500 people expected to attend. It provides a forum for presentations and discussion of the latest scientific developments in all areas of human genetics. The program includes 16 invited scientific sessions, 40 platform sessions, as well as thousands of posters on display from submitted abstracts.
In addition, Dr. Layer recently had a paper selected for publication. LUMPY: a probabilistic framework for structural variant discovery was published June 26, 2014 in Genome Biology.
This summer the Center welcomes Aakrosh Ratan, PhD, a new resident faculty member, and Assistant Professor of Public Health Sciences. Dr. Ratan joins the Center from Pennsylvania State University where he worked as a Research Associate with Professor Webb Miller. His primary research interests are comparative genomics, molecular evolution and algorithm design & analysis. Dr. Ratan will be collaborating on projects with CPHG resident and affiliate faculty, including Dr. Tom Loughran and other members of the Cancer Center.
CPHG faculty member, Dr. Aaron Quinlan, gave the plenary session talk at The Biology of Genomes meeting on May 9th. Held annually at Cold Springs Harbor Laboratory in New York, it is considered to be the premier genomics meeting in the world with presentations by many of the top genomic scientists. Dr. Quinlan’s talk described his research which seeks to understand how ovarian cancer genomes evolve subsequent to chemotherapy. He emphasized the importance of this research noting that ovarian cancer has the highest mortality rate among gynecological malignancies, due to the fact that most patients are diagnosed with advanced stage disease, and that the majority develop chemoresistant disease. In order to identify genetic mutations that might give insight into what is driving the acquisition of resistance, the Quinlan Lab sequenced the DNA of patient tumors both before and after chemotherapy. The resulting data yields insight into the common genes and pathways that drive resistance and hint at future personalized therapies.
A study by researchers, including Dr. Aaron Mackey of the Center for Public Health Genomics, was published in a recent edition of BMC Bioinformatics. The study seeks to improve the methods for accurately identifying SNPs and other genomic variants, thus increasing the reliability and usefulness of genomics data in clinical settings. The paper describes BAYSIC (BAYeSian Integrated Caller), a novel algorithm that uses a Bayesian statistical method to combine variant sets produced by different bioinformatic packages into a reliable set of genome variants. Some strengths of BAYSIC highlighted by the authors are that the algorithm integrates data produced from multiple SNP callers, and produces a call set with a posterior probability that is intuitive and can be used for quantitative filtering; BAYSIC is a completely unsupervised method of classification and requires no training on validated data sets; and BAYSIC performance improves along with the sensitivity or specificity gains of the input call sets. BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity can be read in full in the April 12, 2014 issue of BMC Bioinformatics.