Single Cell Analysis Symposium

March 12, 2014 @ the University of Pennsylvania

Hold the date for this all-day symposium. Speakers include Nancy Allbritton, Helen Blau, Chi Dang, Jim Eberwine, Junhyong Kim, Christopher Murray, Garry Nolan, Arjun Raj and Sherman Weissman.

More details and registration here for this free event.


The next frontier in the genome sciences will be developing technology that captures novel quantitative biological measurements ... more about genomics

PGFI Members

For information on how to become a member click here.
(C) = Core member; Core membership is by invitation to investigators who have or have had roles in PGFI administration, service or programs.


(C) Ted Abel, Ph.D.

Research interest: Research in the Abel lab focuses on the molecular mechanisms of long-term memory storage in the mammalian brain. Transcriptional regulation, including epigenetic modifications such as histone acetylation and DNA methylation, play a critical role in memory storage as well as in the cognitive deficits that accompany many psychiatric and neurological disorders. The Abel lab is using high-throughput sequencing approaches as well as high-throughput qPCR and qChIP to define these transcriptional events in the brain.

(C) Gustavo D. Aguirre, V.M.D., Ph.D.

Medical Genetics and Ophthalmology
Research interest: Dr. Aguirre’s work is directed to identifying the genetic causes of inherited blindness, identifying the mechanisms linking mutation to disease, and developing treatment approaches. Studies are done in the dog models which are affected by a large variety of inherited photoreceptor diseases that are now being characterized at the molecular level. Once the genes and mutations are identified, molecular and proteomic approaches are used to examine the disease mechanism. In parallel, gene based therapies are developed with the goal of restoring function and preventing the degeneration of the mutant photoreceptor cells.

Seena Ajit, Ph.D.

Pharmacology and Physiology
Research interest: Epigenetic modulation in various pain states and the impact of aging induced epigenetic changes in the development and sustenance of chronic pain. I am also pursuing the development of biomarkers that are specifically associated with neuropathic, inflammatory and cancer pain. The three avenues of research being pursued are 1) MicroRNA regulation and its utility as biomarkers in pain 2) Utility of inhibitors targeting enzymes responsible for inducing epigenetic changes such as histone modifications and DNA methylation in pain 3) DNA methylation and histone modifications in DRG and SC using global methylation profiling and ChIP-Seq technology.

Richard Aplenc, M.D.,Ph.D.

Hematologic Malignancies
Research interest: My primary focus is on the treatment and improving of outcome of pediatric myeloid leukemia (AML). I am is currently leading a genome-wide genotyping effort to discover genetic variations that change the risks of relapse, life-threatening infections, and heart complications in children treated for AML in the AAML0531 Phase III trial of the Children’s Oncology Group.

(C) David Artis, Ph.D.


Sophie Astrof, PhD

Thomas Jefferson University Translational Medicine
Research interest: My lab is at the Center for Translational Medicine at Thomas Jefferson University.
The main theme of my lab is understanding molecular and cellular regulation of vertebrate cardiovascular development. Within this framework, we study functions of cell-extracellular interactions during morphogenesis of the heart and the cardiac outflow vasculature.

Alexander A. Bachmanov, D.V.M., Ph.D.

Monell Chemical Senses Center

Research interest: Dr. Bachmanov's primary research interests are the genetics of taste, ingestive behavior and alcohol intake. My research is based on genetic variation among mouse strains and leads to positional cloning of genes involved in taste-related behavior.

Thomas J. Bell, MS, Ph.D.

The National Disease Research Interchange
Research interest: Type 1 Diabetes Microvascular Complications: Defining Phenotypes to Identify Susceptibility Loci in Candidate Genes This project will test for associations between specific genes and the presence or absence of complications in individuals with type 1 diabetes with a major goal of better defining the genetic contribution to complications. The focus of the present experiments is to examine molecular changes that occur in the human retina in response to type 1 diabetes. The current experiment is an initial foray into RNA-Seq. The goal is to define changes in RNA expression, including splicing variants, ncRNA and miRNA that occur in the retina as a result of type 1 diabetes. Human retina tissue will be taken from normal and type 1 diabetic cadervic donors.

Daniel Beiting, Ph.D.

Pathobiology, Veterinary Medicine

Jean Bennett, M.D., Ph.D.

Research interest: Dr. Bennett's research focuses on developing somatic gene delivery for treatment of ocular diseases causing blindness. In preclinical studies, she has demonstrated reversal of blindness in dog and mouse models of a congenital blinding disease called Leber Congenital Amaurosis.

(C) Shelley L. Berger, Ph.D.

Cell and Developmental Biology and Genetics

(C) Wade Berrettini, Ph.D.

Ben E. Black, Ph.D.

Biochemistry and Biophysics
Research Interests: Dr. Black's laboratory is interested in how particular proteins direct accurate chromosome segregation at mitosis. In humans, the chromosomal element—the centromere—that directs this process is not defined by a particular DNA sequence. Rather, the location of the centromere is dictated by an epigenetic mark generated by one or more resident proteins. By taking biophysical, biochemical, genomic, and cell biological approaches, our work is to define the composition and physical characteristics of the protein and protein/DNA complexes that epigenetically mark the location of the centromere on the chromosome.

Ian Blair, Ph.D.

Pharmacology, SOM and Proteomics Core
Research interest: Dr. Blair is interested in Oxidative stress in cancer and cardiovascular disease. Ongoing studies involve an investigation of the role of endogenous DNA- and glutathione-adducts as biomarkers of cancer and cardiovascular disease in vitro, in animal models, and in human populations.

(C) Nancy M. Bonini, Ph.D.

Research Interests: Dr. Bonini uses the model organism Drosophila as a model to study human neurodegenerative disease. In particular, she has focused on Polyglutamine diseases, Parkinson's disease and RNA toxicity. The laboratory uses many techniques, including molecular biology, genetics and cell biology to define disease mechanisms and modifiers, then extend these findings back to the human disease situation.

Dustin Brisson, Ph.D.


Research interest:Brisson laboratory lies at the interface between evolutionary biology, microbial ecology, and molecular genetics. We use molecular techniques, evolutionary theory, and computer modeling to elucidate the evolutionary forces that have shaped the history of populations. Additionally, we use molecular genetics and classic ecology to discover the interactions that govern the current distribution and abundance of populations and genotypically distinct lineages within populations. Our research focuses on interactions between eukaryotes and microbes of interest in public health (Lyme disease bacteria). The approaches used in the Brisson lab can be used to address a wide variety of fundamental issues in evolutionary biology and ecology.

(C) Maja Bucan, Ph.D.

Research interest: Dr. Bucan's laboratory is using classical genetic, genomic and bioinformatic approaches to determine genetic determinants of psychiatric disorders. These studies start with the genetic dissection of a complex psychiatric syndrome into components or endophenotypes, followed by forward genetic screens for corresponding behavioral anomalies in the mouse. Bioinformatic and computational approaches facilitate molecular characterization of behavioral mutants and selection of candidate genes for these mutants, as well as studies of their relevance to human disease.

Jason A. Burdick, Ph.D.

Research interest: Dr. Burdick's research involves the development of biodegradable polymers for a number of tissue regeneration and drug delivery applications. All of the Burdick laboratory projects are focused on translational applications and they hope to motivate all towards clinical problems.

(C) Frederic Bushman, Ph.D.

Research Interest: Dr. Bushman's research focuses on use of genomic methods to study host-pathogen interactions. Systems under study include HIV and the vast population of microbes normally associated with the human body (our "microbiome"). Methods for study focus on deep sequencing and bioinformatics analysis.

Thomas P Cappola, M.D

(C) Christopher S. Chen, M.D., Ph.D.
Research Interests: Regulation of angiogenesis, cancer growth, and stem cell differentiation by adhesive and mechanical cues, Mechanochemical signal transduction, Cadherin and integrin signaling, Rho GTPases and cytoskeletal processes, Cell and tissue engineering.

Jinbo Chen, Ph.D.

Biostatistics and Epidemiology
Research Interests: currently working on statistical genetics methods research and genetic association studies on cardiovascular outcomes.

Youhai H. Chen, M.D., Ph.D.

Pathology and Laboratory Medicine
Research interest: The major goals of Dr. Chen's research program are to understand the molecular mechanisms of autoimmune diseases (such as multiple sclerosis and type 1 diabetes) and to find a cure for these diseases. Dr. Chen's laboratory has recently performed functional genomic studies of autoimmune inflammation in the central nervous system (CNS) in order to explore the spectrum and global patterns of gene expression during autoimmune inflammation. Using models of inflammation, Dr. Chen and colleagues are exploring the physiological and pathological roles of the following genes: the Rel/nuclear factor (NF)-kB family, Bim and TRAIL.

(C) Sara Cherry, Ph.D.

Research interest: Dr. Cherry's laboratory uses high-throughput screening methodologies to identify small molecule inhibitors of viral replication. The identification of such compounds represents the first step in the development of new therapeutics. The viruses they study are important arthropod-borne human pathogens for which there are currently no efficacious drugs including West Nile virus, Dengue virus and Rift Valley Fever virus. Therefore, any inroads that they make will provide a stepping stone to new anti-virals.

Vivian G. Cheung, M.D.

Research interest: Dr. Cheung's research focuses on identifying the genetic determinants of human traits and developing tools that facilitate such studies.

Yongwon Choi, Ph.D.

Noam A. Cohen, M.D., PhD

Yale E. Cohen, Ph.D.

(C) Barry S. Cooperman, Ph.D.

George Coukos, M.D., Ph.D.

Obstetrics and Gynecology
Research interested: The translational understanding of the immune system's response to ovarian cancer. The work focuses on fundamental discovery in the area of tumor vascular and immune biology and the development of novel approaches to immune therapy in the lab and the clinic. My current research interests focus on three areas that evolve around the overarching theme of the tumor microenvironment: 1. Tumor immune surveillance and tolerance. 2. Immune-vascular interactions. 3. Microenvironment editing by tumor cells. I am currently involved in preclinical research focused on the development and optimization of combinatorial biological therapies and am involved in clinical trials testing immune therapies against ovarian cancer. My research is also focusing on various aspects of ovarian cancer genomics, genetics, immunology and biology.

(C) Tom Curran, Ph.D., FRS

Pathology and Laboratory Medicine, Penn
The Children's Hospital of Philadelphia
Research interest: As part of the brain gene expression atlas project (GENSAT), the Curran laboratory is also analyzing gene expression in the brain using high-throughput in situ hybridization. They are taking genomic approaches to identify molecular changes and potential drug targets for several brain tumors including medulloblastoma, atypical teratoid/rhabdoid tumors and choroid plexus carcinomas. They developed a model system with a 100 percent incidence of spontaneous medulloblastoma for use in translational studies. Recently, they found that a small molecule inhibitor of the sonic hedgehog (Shh) pathway eliminated even large tumor masses in vivo. The Curran lab is continuing to analyze the mechanism of action of several anticancer drugs in tumor cells and cancer models.

Fevzi Daldal, Ph.D.

Research Interest: We are interested in the structure-function, regulation and biogenesis of cytochromes and cytochrome complexes in bacteria using combinations of molecular genetic, genomic, proteomic, biochemical and biophysical approaches.

Chi Van Dang, MD, Ph.D.

(C) Susan Davidson, Ph.D.

Research interest: Dr. Davidson's research interests include database systems, data modeling, and bioinformatics. Within bioinformatics she is best known for her work in data integration systems and scientific workflows.

Peter F. Davies, Ph.D.

Institute for Medicine and Engineering
Research interest: Dr. Davies is interested in quantitative aspects of vascular pathophysiology.

(C) Steve DiNardo, Ph.D.

Research interest: Our lab has two areas of focus. First, through genomic-scale analyses, we have identified several genes whose expression is enriched in stem cells or their niche cells, and are studying their function as it relates to fundamental questions of stem and niche cell biology. Our second area of study concerns how developmental signals govern the complex cell biological outputs that guide morphogenesis.

(C) David F. Dinges, Ph.D.

Psychiatry Research Interest: Neurobehavioral consequences of acute and chronic sleep loss in humans, including the physiological and genetic basis of differential human neurocognitive vulnerability to sleep deprivation. In particular, the laboratory seeks ways to establish phenotypic vulnerability to sleep loss and determine the neural mechanisms underlying these phenotypes.

(C) Robert W. Doms, M.D., Ph.D.

Dawei W. Dong, Ph.D.

Animal Biology
Research interest: To uncover the fundamental principles of how the biological systems process information, from the evolutionary perspective of adaptation and natural selection. In particular, we studies systems in two categories: (1) the sensory encoding and representation, and, (2) the gene expression and regulation.

Gideon Dreyfuss, Ph.D.

(C) Marija Drndic, Ph.D.

Physics and Astronomy
Research interest: Dr. Drndic's lab is applying the unique capabilities of their recently developed sub-nanometer precision transmission electron beam ablation lithography (TEBAL) to demonstrate that the precise integration of solid-state nanopores with nanoelectrodes, nanochannels and microfluidics will address key obstacles that must be overcome to achieve nanopore-based low-cost high-speed single molecule analysis of proteins and DNA.

(C) James Eberwine, Ph.D.

Research interest: The Eberwine lab performs fundamental work in elucidating how cells of the central nervous system communicate with one another. In particular, the lab has concentrated their efforts on developing novel methodologies that permit them to detect and quantify in vivo the influence of local subcellular environment on mRNA translation and gene transcription.

(C) Wafik S. El-Deiry, M.D., Ph.D.

(C) Jon Epstein, Ph.D.

Cell and Developmental Biology
Research interest: Dr. Epstein's laboratory studies the genetics and developmental biology of congenital disease and epigenetic modulation of cardiac growth.

(C) Warren Ewens, Ph.D.

Research interest: Dr. Ewens works in three area of statistical genetics, namely evolutionary theory, the use of statistical methods to locate genes involved with diseases, and in bioinformatics. In evolutionary genetics his main interest is in developing statistical methods to detect "signatures of selection": this led to the development of the so-called Ewens sampling formula. In disease genetics he collaborated with Dr. Richard Spielman in developing the widely-used "transmission/disequilibrium" test. In bioinformatics his main interest is in the statistical theory associated with the appearance of various motifs in DNA sequences.

Hua-Ying Fan, Ph.D.

Biochemistry and Biophysics
Research interest: My lab is interested in understanding how chroamtin structure can be regualted by ATP-dependent chroamtin remodelers and how misregulation in chroamtin structure leads to disease. We are also interested in dissecting the mechanism of transcription memory: how cells remember what they are supposed to be through generations.

Rui Feng, Ph.D.

Biostatics and Epidemiology
Research interest: Developing statistical and computational methods for analysis of genetic and genomic data, including methods of linkage and association analysis, in CNV analysis, and in epigenetics.

(C) Garret A. FitzGerald, M.D.

Research interest: Dr. FitzGerald is interested in the role of eicosanoids in inflammatory and cardiovascular disease and in the regulation and function of peripheral clocks.

(C) Steven J. Fluharty, Ph.D.

(C) Arupa Ganguly, Ph.D.

Glen Gaulton, Ph.D.

Executive Vice Dean and Chief Scientific Officer

(C) John D. Gearhart, Ph.D.

Urs Giger, V.M.D, P.D, M.S

Medical Genetics
Research interest: Dr. Giger's laboratory is involved in the discovery and characterization of hereditary disorders in animals as models of human genetic disease. The focus has been on metabolic and blood disorders which we characterize from clinical signs to the molecular defect and also evaluate the safety and efficacy of novel therapies.

Namni Goel, Ph.D.

Research interest: Dr. Goel investigates how physiological, behavioral and environmental factors affect sleep, circadian rhythms and mood. She utilizes multidisciplinary and translational approaches bridging psychiatry, and behavioral neuroscience, clinical and biological psychology to show that environmental, non-drug stimuli substantially alter sleep and mood and modify circadian rhythms in clinical and non clinical populations. Thus, she conducts basic human translational research at the Phase I and II levels. Most recently, she has broadened her interests to include cognitive measures and genetics, and is identifying genes involved in differential vulnerability to partial sleep deprivation in humans.

(C) Yale E. Goldman, M.D., Ph.D.

Ellis Golub, Ph.D.

Research interest: Protein structure function analysis; prediction of protein structure from sequence: protein-protein interaction modeling

(C) Mark Goulian, Ph.D.

Michael Granato, Ph.D.

Department of Cell & Developmental Biology
Research interest: Using the zebrafish as an experimental model system, we study three areas of modern Neuroscience: axonal guidance, injury induced nerve de- and regeneration, and learning behaviors. The zebrafish offers a powerful combination of forward genetics and exquisite cellular analysis: previous and ongoing genetic screens in our lab have identified many mutations that affect specifically axonal guidance or motor behaviors. The transparent, externally developing embryos are accessible to numerous embryological manipulations, and a diverse repertoire of genomics tools, including GFP transgenics and selective gene inactivation allow for an unparalleled molecular and cellular analysis. Using these tools we focus on three research projects: 1) the molecular and cellular mechanisms by which motor axons navigate to and form synaptic contacts with their synaptic muscle targets, 2) the cellular and subcellular and events during and following injury induced peripheral nerve degeneration (Wallerian degeneration) and regeneration, and 3) the cellular and molecular basis of simple learning behaviors.

Dana T. Graves, DDS, DMSc

(C) Doron Greenbaum, Ph.D.

Research interest: Doron's laboratory focuses on developing and exploiting new technologies at the interface between biology and chemistry to study protease function. The lab uses a variety of techniques including the synthesis of small molecule inhibitors, quantitative proteomics, genomics, recombinant protein expression, and molecular genetics in order to better understand proteolytic systems. Although these tools are useful to study any biological system, my laboratory will initially concentrate much of its efforts to validate cysteine and serine proteases as potential therapeutic targets in the parasite P.falciparum, the causative agent of malaria.

Robert M. Greenberg,

(C) Roger A. Greenberg, M.D., Ph.D.

Cancer Biology
Research Interest: Dr. Greenberg’s laboratory investigates basic DNA repair mechanisms that are necessary to maintain genome integrity and prevent the genesis of malignancy. The primary focus centers on BRCA1-dependent DNA double strand break repair and suppression of breast and ovarian cancer. A second area of interest is the complex relationship between chromatin structure and DNA repair. We have recently developed novel systems to investigate interrelationships between chromatin structure and DNA double strand break repair. These systems are being utilized to understand how DNA repair contributes to epigenetic changes in the genome.

(C) Brian D. Gregory, Ph.D

Research interest: Dr. Gregory research is making use of genomic, bioinformatic, and systems biology approaches with molecular genetic and biochemical techniques. His lab is identifying and characterizing additional components required for the metabolism of various classes of small RNAs, as well as proteins involved in the regulation of specific small RNA populations and RNA silencing pathways. More specifically, we make use of high-throughput sequencing technologies to determine how the transcriptome as well as what small RNA populations are affected by these newly identified RNA silencing pathway components.

Elizabeth Grice, Ph.D.

Research interest: Research in Dr. Grice's research focuses on host-microbe interactions, particularly of the skin and of non-healing wounds. We are using deep sequencing approaches to characterize the colonizing microbiota as well as the cutaneous immune response. Furthermore, we are analyzing microbial community dynamics and their response to perturbations, in both animal models and human subjects.

(C) Raquel E. Gur, M.D., Ph.D.

(C) Ruben C. Gur, Ph.D.

Research interest: Dr. Gur's research has been in the study of brain and behavior in healthy people and patients with brain disorders, with a special emphasis on exploiting neuroimaging as experimental probes. His work has documented sex differences, aging effects, and abnormalities in regional brain function associated with schizophrenia, affective disorders, stroke, epilepsy, movement disorders and dementia.

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Based at the University of Pennsylvania, Penn Genome Frontiers Institute (PGFI) is a university-wide institute dedicated to the advancement of the interdisciplinary field of genomics research. PGFI fosters collaborations and scientific exchange across biology, veterinary medicine, pharmacology, medicine, genetics, microbiology, engineering, physics, chemistry and psychology. Our mission...