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
Congratulations on Successful Thesis Defense
On April 23, 2021, Kaytie Innamorati successfully defended her PhD thesis entitled “Comparative genomics of the keystone mucosal pathogens Porphyromonas gingivalis and Gardnerella vaginalis reveal associations between virulence phenotypes and phylogenetic structures.”
On March 31, 2021, Haley Majer successfully defended her PhD thesis entitled “Natural Product Discovery of Thiopeptide Producers and Functional Characterization of Adenylation-Domains in Thiostrepton and Siomycin Biosynthesis.”
August 2020 Karabots Junior Fellows Outreach Initiative
Department of Microbiology and Immunology students and staff have completed another outreach initiative with The College of Physicians of Philadelphia Karabots Junior Fellows. The Junior Fellows are high school students and Philadelphia residents with an interest in health care or medicine, who will be the first in their immediate family to graduate with a higher education degree, and who qualify for free or reduced lunch. The graduate students designed and implemented a three-session program that discussed the need for a cohesive and well-planned national pandemic strategy. The discussions focused on: the role of health care providers and epidemiologists; biostatistics and the creation of databases; the role of biomedical researchers in targeted therapies and vaccine development; and the need for honest and scientifically correct communications between those working to mitigate a pandemic as well as dissemination of information to the public. Participants included Dr. Mary Ann Comunale, Jennifer Conners, Elijah Davis Rachael, Erlich Mohamed Hager, Dr. Ogan Kumova, Teresa LuPone and Kayla Socarras.
Discovery Day 2019
November 7, 2019: Students and professional staff from the Ehrlich, Beld, and Mell Labs, including Jocelyn Hammond, Hayley Majer, Danielle Piazza and Amanda Platt, presented posters at the 2019 Discovery Day at the Philadelphia Convention Center.
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.
- Jocelyn Hammond, MS, a research associate at the Center for Advanced Microbial Processing (CAMP), presented her poster, “Supragenome-wide Association Study in NontypeableHaemophilus influenzae Reveals Role for Polyamine Metabolism and pH Homeostasis in Otitis Media.”
- Haley Majer, a PhD candidate in the lab of Joris Beld, PhD, presented her posted, “Whole Genome Sequencing of Actinomycetes Isolates Reveal Gene Clusters that Encode Potent Antibiotics.”
- Danielle Piazza, a PhD candidate in the lab of Joshua Chang Mell, PhD, presented her poster, “Detecting Genetic Events without Genetics: Direct Visualization of Genome-Wide Recombination in a Pathogenic Bacterium by Optical Mapping.”
- Amanda Platt, a fourth-year PhD candidate in the lab of Joris Beld, PhD, presented her poster, "Understanding protein-protein interactions in natural product biosynthesis using a small synthase."
Amanda Platt at Discovery Day
Hayley Majer at Discovery Day
Dr. Lapides Presents Research on Discrete Classification Mathematics
August 28, 2019: Garth Ehrlich, PhD, hosted Jeffrey Lapides, PhD, at that day’s IMMID research seminar. Dr. Lapides presented his research, “Identifying Predictive Patterns in Microbiome and Genomic Data Using Discrete Classification Mathematics” at that day’s IMMID research seminar. Dr. Lapides, founder and managing director of Lapides Consulting, uses machine learning techniques, predictive analytics and visualization methods to support health care and other organizations seeking to advance how they manage and market.
August 26, 2019: Malaria Invasion, the latest educational mobile game produced by the Institute for Molecular Medicine and Infectious Disease at Drexel University College of Medicine is available for free download from iTunes App Store for iPhone and iPad users, and in the Google Play Store for Android devices. The mobile game is intended to be a supplementary tool to teach university students, in particular graduate students and research trainees in infectious disease, about the molecular mechanisms of disease in malaria. Read more.
August 2019: Lying inside a freezer in Drexel’s College of Medicine are 500 dead, mourned by no one. The deer ticks, dog ticks, lone star ticks and other tiny parasites in the diminutive morgue traveled from nearly every state in the country to reach this resting place. They arrived in baggies or cookie tins or what-have-you, scooped from meadows and forests by helpful volunteers responding to a “call for specimens” on Drexel’s website that was posted by Kayla Socarrás, a doctoral student studying microbiology and immunology. Each tick contains multitudes of smaller organisms — a grab-bag of the pathogenic bacteria that make tick bites so hazardous. Read more.
Malaria Invasion Receives Gold Medal
June 14, 2019: Congratulations to the Department of Microbiology & Immunology and the Institute for Molecular Medicine & Infectious Disease, whose game Malaria Invasion was awarded a gold medal by the 2019 International Serious Play Award program! Dr. Mary Ann Comunale, creative director, and Dr. Sandra Urdaneta-Hartmann, project director, will be traveling to the Serious Play Conference, where they will present game-based learning research and accept the award. John Harvey, a co-op student hired by the Institute and funded in part by the Steinbright Career Development Center, shares in the award as part of the game design team and game developer. John is currently a senior in the Westphal College of Media Arts & Design program.
Kayla Socarras Presents at PA Lyme Resource Network
January 28, 2019: PhD candidate Kayla Socarrás 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.
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