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

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(C) = Core member; Core membership is by invitation to investigators who have or have had roles in PGFI administration, service or programs.
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Beatrice H. Hahn, M.D.

Medicine and Microbiology
Research interests: My laboratory has had a long-standing interest in elucidating the origins and evolution of infectious diseases including human immunodeficiency virus (HIV) and the malaria parasite, Plasmodium falciparum. Using non-invasive fecal sampling methods to characterize simian immunodeficiency viruses infecting different non-human primate species in sub-Saharan Africa, we have shown that Acquired Immunodeficiency Syndrome (AIDS) – one of the most devastating infectious diseases to have emerged in recent history – was the result of cross-species infections of humans by lentiviruses of primate origin. We have employed similar non-invasive detection methods to elucidate the origin of the human malaria parasite Plasmodium falciparum. As with HIV-1, our work has shown that pandemic P. falciparum had resulted from a single cross-species transmission event.In the future, we will continue to work on emerging infectious diseases and build basic and translational research programs in global health.

(C) Hakon Hakonarson, M.D., Ph.D.

Dan Hammer, Ph.D.

Paula Henthorn, Ph.D.

Clinical Studies
Research interest: Dr. Henthorn's research activities focus on the molecular basis of simple and complex inherited disease, using naturally-occurring disease in dogs as a model system.

(C) John B. Hogenesch, Ph.D.

Research interest: Dr. Hogenesch's research program covers two areas of research, the biology of circadian clocks in the mammal, and the application of functional genomics tools to understanding genome function. By conducting research in two complementary areas of research, I hope to contribute to a better understanding of circadian clocks, as well as to the development of tools that can be broadly applied to other areas of research such as translational medicine. These tools can be employed to construct cell based models of important biological pathways, target identification using cDNA overexpression and RNAi interference, as well as small molecule screen development. Importantly, these approaches can be leveraged along with informatic, proteomic, and RNA dynamics strategies to better inform biology and physiology.

Annamarie Horan,Ph.D

Liquan Huang, Ph.D.

Monell Chemical Senses Center
Research interest: Dr. Huang's primary research interest is in molecular mechanisms underlying taste perception. With the completion of genome sequencing projects for humans, mice and other model organisms, nearly all genes in these genomes are identified, which presents an opportunity and challenge to elucidate genome-wide gene expression patterns for individual cells. I use single cell RT-PCR and other amplification methods, quantitative PCR and DNA arrays to establish global gene expression profiles for various morphological and physiological types of individual taste cells from taste buds. I utilize bioinformatics, molecular and biochemical methods to analyze gene expression patterns and to characterize gene products function in particular cells and to correlate cells "polygenotypes" with their physiological phenotypes. Results from these studies may contribute to uncovering taste cells' intra- and inter-cellular signaling networks and to a more complete understanding of taste perception.

J. Larry Jameson, MD, Ph.D.

Xinjun Ji, Ph.D.

Brad Johnson, M.D., Ph.D.

Pathology and Laboratory Medicine
Research interest: Dr Johnson's lab is investigating the biology of telomeres, including mechanisms underlying their maintenance and how their dysfunction contributes to cellular senescence and tissue dysfunction. A closely related area of investigation is the biological functions of G-quadruplexes, which are non-canonical DNA structures formed by telomeres and other guanine-rich sequences distributed throughout the genome. We are investigating how these structures affect telomeres, gene expression and DNA recombination.

(C) Philip R. Johnson, M.D.

Children's Hospital of Philadelphia

Klaus Kaestner, Ph.D.

Research interest: Dr. Kaestner's research is employing massively parallel sequencing to determine both epigenetic marks and transcription factor binding site across the entire mammalian genome. Applications are the determination of tissue specific gene expression, and the analysis of epigenetic changes that occur in diabetes.

(C) Cherie Kagan, Ph.D.

Electrical and Systems Engineering

Roland Kallen, M.D., Ph.D.

Biochemistry and Biophysics
Research Interest: Dr. Kallen's research deals with ion channel mediated transmembrane signal transduction. What do voltage-gated ion channels look like, how do they work in the presence and absence of modifiers and what regulates the expression of voltage-sensitive sodium channels in normal and pathologic states?

Peter A. Kanetsky, Ph.D., M.P.H.

Biostatistics and Epidemiology

(C) Anna Kashina, Ph.D.

Animal Biology
Research interest: Genomes of higher mammals encode an estimated 40,000 proteins, however the complexity of the functions performed by these proteins in vivo is at least an order of magnitude higher. This complexity is achieved in a large part by posttranslational modifications that modulate structure and functions of proteins after synthesis. Dr. Kashina's research focuses on the biologic role of a poorly understood posttranslational modification - arginylation.

(C) Junhyong Kim, Ph.D.

Research interest: Junhyong Kim is a computational biologist and evolutionary genomicist. His current work involves statistical methods for functional and comparative genomics, laboratory investigations of yeast cell-cycle evolution, data analysis for cancer genomics, and algorithm development for computational phylogenetics.

Thomas Kolon, M.D.

Research interest: Molecular research aimed at the genes associated with the etiology of cryptorchidism and disorders of sex development and the long-term possibility of infertility. Molecular research (microarray of RNA) from the sperm of cryptorchid men to identify novel genes associated with poor seminal parameters.

Ian Krantz, M.D.

Research interest: As a pediatrician and clinical geneticist, my research interests are focused on molecularly characterizing the syndromic and non-syndromic developmental disorders present in the patients that I see and care for clinically. Towards this end my research lab has major projects focused on: 1) understanding the genome-wide implications of alterations in the cohesin complex and its regulation in causing the phenotypic differences seen in Cornelia de Lange Syndrome (CdLS) and other cohesinopathies, 2) Characterizing the effects on genome-wide expression in the Pallister-Killian Syndrome (PKS) and defining a minimal critical region on chromosome 12p, 3) Identification of novel genes for non-syndromic sensorineural hearing loss through linkage, SNP array and exome/genome sequencing analyses and 4) Identifying conserved non-coding element disruptions as a cause of isolated non-syndromic congenital heart defects. Clinically we have been at the forefront of adapting new genomic technologies in the clinical setting and studying how this evolving, complex and often unclear diagnostic information is understood by, and the impact it has on, the clinicians and families involved.

(C) Vijay Kumar, Ph.D.

Mechanical Engineering & Applied Mechanics

(C) Todd Lamitina, Ph.D.

(C) Michael Lampson, Ph.D.

Research interest: Dr. Lampson's research focuses on molecular mechanisms that maintain genome integrity during cell division. In particular, we use high resolution light microscopy, combined with molecular perturbations introduced by RNAi or with small molecule inhibitors, to examine key processes in cell division in real time in the context of living mammalian cells. These processes are critical to prevent aneuploidy, which is strongly associated with human cancer in somatic cells and with infertility and developmental defects in germ cells.

J. Richard Landis, Ph.D.

Biostatistics and Epidemiology
Research interest: Dr. Landis' research is in development and evaluation of methods for the analysis of categorical data, with applications to cardiovascular, ophthalmology, respiratory, psychiatric, renal and urological research.

Mitchell A Lazar, M.D., Ph.D.

Endocrinology, Diabetes & Metabolism
Research interest: The Lazar laboratory is interested in mechanisms of diabetes, obesity, and metabolic diseases, and hopes to make discoveries that can be translated to the clinic.

(C) Virginia M.-Y. Lee, Ph.D., M.B.A.

(C) Mark A. Lemmon

Michael Levine,M.D., FAAP, FACP

(C) Michael Levy, Ph.D.

Biostatistics and Epidemiology
Research interest: I work at the interface of epidemiology, ecology and statistics to understand and control vector-borne and other infectious diseases. My research is focused on the control of urban Chagas disease transmission in Peru. My team conducts epidemiological studies on Chagas disease as well as entomological and ecological research on disease vectors and reservoirs. In addition we develop new Bayesian methods to retrace the history of epidemics, and applying techniques from control theory to optimize interventions against infectious diseases. I work in collaboration with Dustin Brisson in Biology on population genetics of Triatoma infestans the insect vector of Chagas disease. I also work with Dr. Joshua Plotkin on control theory issues related to disease transmission, and Dr. Dylan Small (Wharton) on new statistical techniques to interpret diagnostic tests for Chagas disease.

Mitchell Lewis, D. Phil

(C) Hongzhe Li, Ph.D.

Biostatistics and Epidemiology
Research interest: Development of statistical, probabilistic and computational methods for analysis of high-dimensional genetic and genomic data, including methods linkage and association analysis in the context of the genome-wide association studies, methods for analysis genomic data with a graphical structures and methods for analysis of genetic pathways and networks.

Mingyao Li, Ph.D.

Biostatistics and Epidemiology
Research interest: Developing statistical and computational tools for gene mapping of complex human diseases.

Stephen Liebhaber, M.D

Research interest: Our laboratory has two primary areas of interest : 1.The roles of RNA-protein interactions in mediating critical post-transcriptional controls in mammalian cells. This work focuses on roles the family of triple-KH domain proteins, CPs, in controls over nuclear processing (splicing and polyA site selection) and cytoplasmic control pathways including mRNA stabilization. Extensive use is being made of whole cell transcriptome analyses in a variety of settings to explore how these controls integrate and coordinate multiple control pathways. 2.The mechanisms and pathways of chromatin activation in establishing tissue specific gene expression. The work focuses on the activation of the multigene human Growth Hormone cluster and long-range activation pathways that are utilized by its locus control region. Of particular interest is the multifunctional long-range enhancer, HSI. Current studies address controls over locus positioning within the nucleus, influence of noncoding transcription on LCR functions, differences between epigenetic determinants of initiation vs maintenance of gene expression, and the role(s) played by histone variant H3.3 in these processes.

Falk W. Lohoff, M.D

Department of Psychiatry
Research interest: Genetics and pharmacogenetics of mood and anxiety disorders. Dr. Lohoff has expertise in the identification of molecular genetic targets of complex psychiatric diseases. His focus is on human genetic association studies with translational aspects using in vivo/vitro systems and animal models to verify identified risk alleles.

James B. Lok, Ph.D.

Department of Pathobiology

Research interest: Investigates the cellular and molecular mechanisms governing the host infective process in parasitic nematodes.Currently we are asking whether insulin-like and nuclear hormone receptor-mediated signaling are necessary for normal development of infective larvae during this process.

Kristen W. Lynch, Ph.D.

Biochemistry & Biophysics
Research interest: My research involves alternative pre-mRNA processing. In particular we are working toward defining the networks of alternative splicing that are responsive to signaling pathways in T cells - and then determining the mechanisms of regulation and the functional consequences thereof.

Joel D. Mainland, PhD

Robert F. Margolskee,MD,PhD

Monell Chemical Senses Center
Research interest:Dr. Margolskee’s basic science research focus has been on the molecular mechanisms of taste transduction, utilizing molecular biology, biochemistry, structural biology, electrophysiology and transgenesis to study the mechanisms of signal transduction in mammalian taste cells. The two themes of his current work are: 1. gastrointestinal chemosensation, or how the gut ”tastes“ nutrients and 2. endocrine properties of taste cells, or how gustation contributes to metabolic homeostasis.

Susan S. Margulies, Ph.D.

Research interest:Clinical data, performs animal and cell culture studies, and creates anthropomorphic and computational models to develop functional and structural injury thresholds in the brain and lung, to understand mechanisms of traumatic brain and lung injury.

(C) John M. Maris, M.D.

Nicola Mason, BVetMed, Ph.D., DACVIM

Medicine & Pathobiology
Research interest: Chronic infection with the highly prevalent Epstein-Barr Virus (EBV) is usually asymptomatic, however infection has been associated with lymphoid malignancies in humans. We are exploring the possibility that domestic dogs that are phylogenetically similar to humans and have shared their environment for 15,000 years might be infected with an EBV-like gammaherpesvirus (GHV). We have found evidence of nucleotide sequences with high homology to EBV in malignant canine lymph nodes. We are now studying the association of natural infection with this EBV-like GHV with the development of lymphoma in the Golden Retriever dog that is genetically predisposed to lymphomagenesis. Development of this model of natural viral infection and spontaneous lymphomagenesis will allow us to evaluate genetic factors that influence viral pathogenesis and provide a clinically relevant large animal model that may be employed in the future to evaluate novel therapies for EBV-associated lymphoproliferative disorders in humans.

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

Ralph G. Meyer, PH.D.

Animal Biology
Research interest: In my lab are focused on chromatin remodeling events in male germ cell development. Using mouse models of the environmentally responsive poly(ADP-ribose) metabolism, in combination with genome-wide transcriptional profiling utilizing microarrays and next-generation sequencing, we currently investigate the impact of environmental factors such as diet and toxic agents on the male germ line and characterize epigenetic consequences to the offspring.

Andy Minn, M.D, P.h.D
Radiation Oncology

Nandita Mitra, Ph.D.

Biostatistics and Epidemiology
Research interest: Nandita Mitra, Ph.D. is Assistant Professor of Biostatistics in the Department of Biostatistics and Epidemiology at Penn. Her primary research interest is statistical genetics where she has worked extensively on SNP and haplotype problems in the context of family based and population based association studies. In addition, she has research interests in the theory of causal inference, propensity score methods and health economics. Dr. Mitra has collaborated primarily in the area of cancer research in the areas of breast, ovarian, skin, and prostate cancers. She recently collaborated on the first genome-wide association study of testicular cancer.

Zissimos Mourelatos, M.D

(C) John Murray, Ph.D.

Research interest: How do regulatory factors combine to control animal development? How does contact influence which targets are regulated by a transcription factors? How are these decisions encoded in the genome sequence? The Murray laboratory uses live-cell imaging, genetics, genomics and computational tools to answer these questions. We use the nematode Caenorhabditis elegans because of its ease of manipulation, its invariant development and the powerful experimental tools available for its study.

Katherine L. Nathanson, M.D.

Medical Genetics
Research interest: Dr. Nathanson's primary focus of research is in cancer genetics. Her laboratory has research projects studying both genetic susceptibility to cancer (in high breast cancer and testicular cancer) and the somatic genetics of cancer (in melanoma and renal cancers.) Her research focuses on directly characterizing samples from patients an on translating cancer genetics into clinical care.

(C) Neal Nathanson, M.D.

Associate Dean, Global Health Programs

(C) Allan I. Pack, M.B.Ch.B., Ph.D.

(C) George J. Pappas, Ph.D.

Electrical and Systems Engineering

Warren S. Pear, M.D., Ph.D.

Dipti Pitta, MVSc, Ph.D.

Alice Chen-Plotkin, M.D

Research interest: My lab studies neurodegenerative disease, frequently starting with unbiased genomic-scale screens for lead generation, and then following up those leads mechanistically with molecular and cell biological techniques.

Joshua B. Plotkin, Ph.D.
Biology/Computer Science
Research interest: We use mathematics and computation to study questions in evolutionary biology and ecology. Research in the group is primarily concerned with the origin and maintenance of genetic variation within populations.

R. Scott Poethig, Ph.D.

Mecky Pohlschroder, Ph.D.

Nina Luning Prak, M.D., Ph.D.

Pathology and Laboratory Medicine
Research interest: My lab studies B cell defects in patients and mouse models of autoimmune diseases such as lupus, type 1 diabetes, immune thrombocytopenic purpura and others. We are interested in using high throughput sequencing technology to study the antibody repertoire in different B cell subsets of healthy individuals and in individuals with autoimmune diseases at various times after B cell targeted therapy.

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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...