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
Kayla Socarras Presents at PA Lyme Resource Network
On Monday, January 28, PhD candidate Kayla Socarras presented her research regarding Lyme disease at the PA Lyme Resource Network of Montgomery County. Kayla met with participants following the meeting to answer additional questions and talk more about her findings.
Kayla Socarras (right) discussing her research with attendees at the PA Lyme Resource Network meeting.
Students Present at Discovery Day
On October 23, 2018, students in the Beld, Ma and Mell Labs, including graduate students Danielle Piazza, Haley Majer, Amanda Platt, Breanna Tyrell, Kristen Buenconsejo, Tucker Collins (mentored by Sandhya Kortagere) and medical student Nga Ying Eng, presented posters at Discovery Day in the Philadelphia Convention Center. Kristen Buenconsejo won a Junior Graduate Student Poster award for her poster, "The Significance of Secondary Metabolism on the Predatory Behavior of Myxococcus fulvus."
Discovery Day is an all-day annual event of intellectual pursuit and discovery, which is organized to celebrate the basic and clinical research accomplishments of the graduate, medical and undergraduate students, clinical research coordinators, postdoctoral fellows, and residents and fellows affiliated with the College of Medicine.
Danielle R. Piazza presenting "Dissecting Mechanisms of Variation of Genome Wide Transportation in Haemophilus influenzae" at Discovery Day
Kristen Buenconsejo with her award-winning poster, "The Significance of Secondary Metabolism on the Predatory Behavior of Myxococcus fulvus" at Discovery Day
Donald Hall Presents at ASM Conference
Donald C. Hall Jr., PhD candidate in the Departments of Microbiology & Immunology and Chemistry, presented his poster entitled "JEKMag Tech: High Throughput Technology to Grow and Assess Bacterial Biofilm Sensitivity to New Drugs" at the 2018 American Society for Microbiology Conference on Biofilms, October 7 – 11, 2018, in Washington, D.C.
The conference provided an interdisciplinary platform to discuss the latest biofilm research. Topics included the molecular basis and regulation of biofilm formation, biofilms in natural and industrial systems, diagnosis and study of clinically-relevant biofilms, and emerging technologies and their application to biofilms.
"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.
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