The Center for Genomic Sciences is a comprehensive and flexible research facility designed to investigate a broad range of medically and surgically relevant problems using cutting-edge molecular genetics, genomics and bioinformatics techniques. The Center for Genomic Sciences, located at 245 N. 15th Street in Philadelphia, is a self-contained research unit of the College of Medicine's Institute for Molecular Medicine and Infectious Disease.
The Center for Genomic Sciences is broadly focused on understanding the function and evolution of genomes. We use comparative and functional approaches, taking advantage of resources available through the Genomics Core Facility and Center for Advanced Microbial Processing. We are particularly focused on microbial genomes (both prokaryotic and eukaryotic), from the smallest cellular genomes, like Borrelia burgdorferi (the causative agent of Lyme disease) with a single ~1 megabase chromosome, to some of the largest known, like the dinoflagellate Procentrum lima whose genome exceeds 100 gigabases (much larger than the 3 gigabase human genome).
One of our major model systems is the human chronic pathogen Haemophilus influenzae, for which we are obtaining complete sequences of ~1000 clinical strains isolated from both healthy and diseased patients from a variety of body sites and using novel bioinformatics approaches to understanding its population-level genomics. Similar comparative projects are being carried out within other species, including Gardnerella vaginalis, Lactobacillus crispatus, Streptococcus pneumoniae, Moraxella cattarhalis, Burkholderia cenocenocepacia and Acinetobacter baumanii. The goal of this research is to understand the evolution of pathogenesis, particularly in the context of chronic infection, and to isolate virulence determinants by applying phylogenomics and statistical genetics approaches.
Sequencing, Gene Expression and Genotyping Services
The Center for Genomic Sciences provides a collaborative interdisciplinary environment for scientists, engineers and clinicians performing basic, translational, industrial and clinical research programs covering a wide range of programs in both prokaryotic and eukaryotic genomics, including host-pathogen interactions. Center for Genomic Sciences technologies include multiple cutting platforms for whole genome sequencing, genotyping and expression analyses. In addition to standard Illumina sequencing we also have the Pacific Biosciences third generation DNA sequencing technology. Similarly for expression analyses in addition to RNA seq we have other types of nucleic acid counting platforms, including both the nanoString technology and the Bio-Rad droplet digital PCR system.
Bioinformatics is an interdisciplinary science that seamlessly integrates computational methodologies into molecular biology, biological databases and genotypes. It focuses on the molecular biology and physics of the cell and emphasizes the use of advanced mathematics and computation. CGS is not only a consumer of bioinformatic analysis programs, but a major developer as well, particularly in the realm of comparative bacterial genomics where we have played a leadership role for a decade.
News and Announcements
"Omics Studies in Ecological Interactions"
On Wednesday, September 12, Garth Ehrlich, PhD, hosted his postdoctoral researcher, Yves Mone, PhD, at the IMMID research seminar. Dr. Mone joined the Ehrlich Lab after serving as a researcher at the Health Department of the French Institute for Development (IRD).
Dr. Mone’s research focuses on the complexities of Lyme disease.
"Towards Translational Evolutionary Biology Using the Lens of Genomics"
On Wednesday, April 25, Joshua Chang Mell, PhD, hosted Vaughn Cooper, PhD, associate professor of microbiology and molecular genetics at the University of Pittsburgh’s School of Medicine.
Dr. Cooper presented his research, entitled "Towards Translational Evolutionary Biology Using the Lens of Genomics." The primary goal of Dr. Cooper’s lab is to understand how bacterial populations evolve and adapt to colonize hosts and cause disease.
"Discovering the Dark Matter of Microbial Secondary Metabolism"
On Wednesday, February 21, Joris Beld, PhD, hosted Mohammad Seyedsayamdost, PhD, assistant professor of chemistry at Princeton University. Dr. Seyedsayamdost presented his research, entitled "Discovering the dark matter of microbial secondary metabolism." His current research focuses on triggering secondary metabolism in diverse bacteria and natural product discovery.
"The Cholera Bacterium: Human Pathogen and Bacterial Predator"
On Wednesday, February 14, Amy Ma, PhD, hosted Stefan Pukatzki, PhD, professor of immunology and microbiology at the University of Colorado’s School of Medicine.
Dr. Pukatzki presented his research, entitled "The Cholera Bacterium: Human Pathogen and Bacterial Predator." His current research focuses on the molecular mechanisms that drive microbial pathogenesis.
"Gastrointestinal Symptoms in Children with ASD: The Chicken, or the Egg?"
On Wednesday, January 17, Garth Ehrlich, PhD, hosted Steve Walker, PhD, associate professor, Department of Neuroscience, Institute for Regenerative Medicine at Wake Forest University’s School of Medicine.
Dr. Walker presented his research, which focuses on using molecular tools, including whole-genome microarrays, to understand the biological basis for autism spectrum disorder (ASD), in a talk entitled "Gastrointestinal Symptoms in Children with ASD: The Chicken, or the Egg?"
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