16 page brochure for Biomedical Graduate Studies program at the University of Pennsylvania

1. Biomedical
g r a d uat e s t u dies

2. graduate group. Consequently, students may enroll in any relevant
graduate level course and may conduct research with virtually any
faculty member within a given field.
Training consists of a multi-faceted program of formal coursework,
informal journal clubs and seminars, interactions with outside senior
scientists, and a formal research experience. During the first year of
study, students take fundamental courses in the areas of biochemistry,
molecular biology, and cell biology and specialized courses in their
chosen field of interest. They also begin structured laboratory rotations
that expose them to hands-on research. The second year is devoted
to focused laboratory work and a limited number of advanced elective
courses and seminars. Beginning in year three, students conduct
dissertation research in the laboratory of their choice; this research
typically takes three to four years.
CONTENTS
1 Program Overview
B iomedical Graduate Studies (BGS) serves as the academic
home within the University of Pennsylvania for over 700 graduate
students pursing a PhD in the basic biomedical sciences. The program is
Students may also participate in several certificate programs that
provide additional training. These include the Graduate Training in
Medical Sciences Certificate Program, which integrates focused
organized into seven interdisciplinary graduate groups: Biochemistry medical education into the doctoral curriculum, affording PhD students
3 Certificate Programs and Molecular Biophysics, Cell and Molecular Biology, an appreciation of medicine and human biology, and the Public Health
Epidemiology and Biostatistics, Genomics and Computational Certificate Program, which provides training in population-based
5 Biochemistry and Molecular Biophysics Biology, Immunology, Neuroscience, and Pharmacological approaches and applications for those with expertise in molecular,
Sciences. The seven BGS graduate groups consist of over 600 scientists cellular, and biochemical sciences.
6 Cell and Molecular Biology and educators representing more than 30 academic departments
The BGS program also provides supplemental training in bioethics and
and seven schools – Medicine, Dental Medicine, Veterinary Medicine,
career development to students at all stages. Most program graduates
7 Epidemiology and Biostatistics Engineering and Applied Science, Wharton, Nursing, and Arts and
accept a prestigious academic postdoctoral fellowship, while other
Sciences – as well as several associated research institutions. BGS faculty
alumni find highly suitable positions in the biomedical industry, in
8 Genomics and Computational Biology cooperate in admitting, funding, advising, teaching, training, and
government agencies, or in professions such as patent law, science
providing career development advice to BGS students. Two affiliated
journalism, or science education.
9 Immunology graduate groups, Biology and Bioengineering, are not administered
by BGS but overlap with BGS groups in faculty membership, course
10 Neuroscience offerings, and other program attributes.
BGS students have ample time and opportunity to explore modern
11 Pharmacological Sciences
biomedical science and develop their true academic interests. The
Graduate groups provide flexible, broad-based, interdisciplinary
training; many courses are cross-listed by two or more graduate
programs, and most faculty members belong to more than one
On the cover: A neurosphere: Primary rat neuroglial
cultures triple stained for MAP-2 (Red), DAPI (blue), and
phospho-pRb (green). (Cagla Akay from lab of Kelly
Jordan-Sciutto)
BIOMEDICAL GRADUATE STUDIES 1

3. a component of the Fox Chase Cancer Center, is another institution
Certificate Programs
closely associated with BGS; its strengths are in the areas of molecular
Students enrolling in BGS doctoral programs have the option of
oncology, virology, and immunology. In addition, researchers at the
applying to certificate programs in medicine and public health.
National Institutes of Health have joined the BGS faculty to participate
The programs offer intensive supplemental training provided by
in training students in the Immunology Graduate Group.
expert practitioners and researchers in these fields. Participants
are expected to complete the certificate program and doctoral
program requirements concurrently.
Combined Degree Opportunities
In recognition of the close relationship between the biomedical Graduate Training in Medical Sciences
disciplines and clinical medicine, Penn offers combined doctoral and The Graduate Training in Medical Sciences (GTMS) program
professional degree programs with the School of Medicine, the School integrates focused medical education into the doctoral curriculum
Research Training Environment of Veterinary Medicine, and the School of Dental Medicine. Students and experience, affording Ph.D. students an appreciation of
Penn is a leader in biomedical research and research training in its in these programs are generally able to earn both degrees in seven medicine and human biology not formerly available. The program
levels of sponsored research and its commitment to interdisciplinary or eight years. Entrance into a combined degree program requires aims to promote clinically relevant research by producing basic
research and training. The university ranks second in the nation in separate application to, and acceptance by, the Combined Degree scientists who not only have a clearer understanding of human
funding from the National Institutes of Health, and the School of Program and professional school. Further information about these biology and pathology, but who can effectively interact with
Medicine is ranked first in NIH training grant funding. programs can be found at www.med.upenn.edu/md_phd. clinical scientists to tackle medically relevant research problems.
Students take fundamental courses in pathophysiology and
Penn’s commitment to interdisciplinary training, embodied in the medicine, “bench to bedside” electives, and clinical clerkships in
structure of graduate groups, is matched by its commitment to addition to their graduate group’s requirements.
interdisciplinary research through campus centers and institutes.
The Genomics Institute and the Penn Center for Bioinformatics foster Public Health Certificate Program
research projects integrating biology, medicine, engineering and The Public Health Certificate Program (PHCP) provides supplemental
computer science. Similarly, the Institute for Medicine and Engineering training to doctoral candidates who are interested in public health.
promotes basic and clinical research at the interface of biomedicine and This program prepares students for careers in academic, industrial,
bioengineering. Other important biomedical centers and institutes and government institutions by providing training in population
on campus include the Institute for Neurological Sciences, the Cancer based approaches and applications for those with expertise in
Center, the Institute for Translational Medicine and Therapeutics, the molecular, cellular, and biochemical sciences. Students take four Application and Financial Aid
Leonard Davis Institute for Health Economics, and the Center for courses in public health in addition to their regular doctoral Students accepted to Biomedical Graduate Studies receive a fully
Bioethics. The integrative nature of research and training at Penn is coursework and participate in either a short-term (six week) public funded fellowship – including tuition, fees, health insurance, and a
made possible by the physical layout of the campus. All of Penn’s health research project or independent study with a member of competitive stipend – regardless of financial need. Application should
schools are located on a single campus, and most classrooms, offices, the MPH faculty for elective credit. It is anticipated that students be initiated in the fall of the academic year preceding the one in which
and laboratories are located within just a few blocks of one another. will explore aspects of public health related to the PhD research the individual proposes to matriculate. Applications are accepted
project during the independent study. online via the BGS website. Applicants considered for admission
Faculty investigators at independent institutions associated with Penn are invited to campus for interviews during the months of January
also play a significant role in graduate student training. Members through March; offers of admissions are made on a rolling basis during
of the Wistar Institute, a research institution in the heart of campus this period.
with outstanding programs in genetics, oncology, immunology, and
virology, are active participants in BGS. The Institute for Cancer Research,
2 w w w.med.upen n .e du/bgs BIOMEDICAL GRADUATE STUDIES 3

4. Biochemistry and Molecular Biophysics
The p53 tumor suppressor protein binds to DNA as a
dimer of dimers to regulate transcription of genes that
mediate responses to cellular stress. Shown is the
structure of a p53 core domain dimer bound to DNA
with the DNA in red, protein subunits in blue and
aqua and bound zinc ions in yellow. (J. Biol. Chem.
281:20494-20502, 2006, Ronen Marmorstein)
Control of gene expression and cellular Chemical and structural biology The central focus of the Graduate Group
programming In the area of chemical and structural
in Biochemistry and Molecular Biophysics
Research focuses on RNA splicing and biology, topics of research include the
disease, transcriptional regulation, histone structural basis of molecular recognition, is the relationship between structure and
acetylation, cell cycle control/cancer, protein design and engineering,
function of molecules involved in biological
chromosome structure and segregation, pathways of protein folding, enzyme
and programming and function of reaction mechanisms, and computational processes. The goal of the program is to
specialized cell types. approaches to molecular biophysics.
provide students with a foundation in the
Cell signaling and intracellular Bioenergetics, metabolism, and
physical, chemical and quantitative methods
trafficking membranes
Research in this area examines mechanisms This area involves radical mechanisms in necessary to explore the molecular basis of
of transmembrane signaling, nuclear metalloenzymes, insulin action/diabetes,
biological events.
import/export of RNA, membranes and electron transfer/redox proteins, integration
ion channels, and intracellular signaling of metabolism, and membrane protein
pathways, apoptosis versus cell survival. structure.
Biomedical imaging and supramolecular
assemblies
Research topics include optical imaging in
tissues/cancer, in vivo Magnetic Resonance
Imaging, spectroscopy, structure and
function of macromolecular motors, and
electron microscopy.
BIOMEDICAL GRADUATE STUDIES 5

5. Cell and Molecular Biology Epidemiology and Biostatistics
The Cell and Molecular Biology Graduate Cell Biology and Physiology Developmental Biology
The Program in Cell Biology and Physiology The Program in Developmental Biology
Group offers programs in six related areas
focuses on basic functions of the cell and offers interdisciplinary training in the
of study: Cell Biology and Physiology, Cancer its links to metabolism and disease, with embryology of animals and plants. The
concentrations in signal transduction, program encompasses research in gameto-
Biology, Developmental Biology, Gene
subcellular protein trafficking, cytoskeleton genesis, fertilization, pattern formation,
Therapy and Vaccines, Genetics and Gene and cell motility, cross-membrane transport, signal transduction, gene regulation, cell
cell cycle regulation and cellular metabolism. cycle control, cell death, cytoskeletal dynam-
Regulation, and Microbiology, Virology and
Much of the research in this program is ics, cell motility, neural connectivity, and
Parasitology, each composed of faculty with directed toward dissecting disease models, adult and embryonic stem cells. Utilizing a
such as diabetes, muscular dystrophy, and diversity of experimental systems, research in
interests focused on similar areas of research.
cancer, in systems ranging from yeast to developmental biology contributes to the
humans. identification of genes and regulatory path-
ways implicated in congenital malformations
Cancer Biology
and human disease.
The Program in Cancer Biology provides the
opportunity to study the basic biological Genetics and Gene Regulation DNA damage associated with
processes that underlie the initiation and The Genetics and Gene Regulation Program pesticide exposure shown using the
progression of cancer. The program stresses provides comprehensive training in the COMET assay. (Linda A. McCauley)
the importance of fundamental genetic fundamentals of modern genetics (including
and molecular pathways regulating cell both model organism and human genetics
proliferation, differentiation, movement, and and genomics) and in the regulation of
Epidemiology Biostatistics The Graduate Group in Epidemiology and
survival. Current research programs include eukaryotic gene expression. Research
oncogenesis, cell migration/metatasis, and areas include developmental, behavioral The Epidemiology program trains students The Biostatistics program is concerned Biostatistics offers graduate training in two
cancer immunology. and cancer genetics, the genetics of human in the study of the distribution and with the development and application of
programs: Epidemiology and Biostatistics.
disease, and transcriptional and post- determinants of health and disease in statistical theory and methods to the health
transcriptional gene regulation. populations, and the basic science underly- sciences. Biostatisticians play a crucial role in Graduate Group faculty are engaged in
ing much of public health and preventive the research process, from inception of the
Gene Therapy and Vaccines multiple active clinical and basic research
medicine. Training in clinical epidemiology research plan through the analysis and pub-
The Gene Therapy and Vaccines Program
extends the principles of epidemiology lication of study results. Every biomedical projects, many of which focus on content-
focuses on using gene transfer for therapeu-
to the critical evaluation of diagnosis and field of study employs biostatistical methods
tic purposes or for vaccination. Although specific areas of interest and include relevant
therapeutic modalities in clinical practice. to some extent. For example, biostatistical
the goals of the research are disease-based
Clinical epidemiologists investigate the tools are used to assess the magnitude, methodologic work.
with an ultimate objective directed to
frequency, outcome, prognosis, etiology, reliability, validity, and precision of associa-
prophylactic and therapeutic applications,
treatment, prevention, diagnosis, costs, and tions (e.g., between exposures and disease)
the research training focuses on basic
policy implications of disease. Specific areas to make inferences about target populations
investigations relevant to understanding the
of interest include: adherence, aging, cancer using sample data, and to derive conclusions
pathobiology of diseases and to developing
epidemiology, cardiovascular epidemiology, about treatment effects from clinical trials.
approaches for achieving efficient and
clinical pharmacogenomic epidemiology, Methodologic interests include: Bayesian
effective gene transfer in humans.
complementary and alternative medicine, modeling, categorical data, causal inference,
Microbiology, Virology, and Parasitology dermatoepidemiology, gastrointestinal clinical trials, clustered data, complex sample
Infectious diseases resulting from viruses, epidemiology, genetic epidemiology, surveys, diagnostic testing, epidemiologic
parasites, prions, and bacteria are a major infectious diseases epidemiology, injury methods, health services research, longitu-
cause of human morbidity and mortality. epidemiology, international health, medical dinal methods, measurement errors, missing
By studying pathogens, it is possible to informatics, molecular epidemiology, data, multivariate analysis, nonparametric
learn much about normal cell biology, nutrition, pharmacoepidemiology, models, patient-oriented research, repeated
molecular biology, and immunology. Major prevention, public health, pulmonary measures, statistical genetics and genomics,
research interests include virology, bacterial epidemiology, renal epidemiology, repro- survival analysis, and time series.
pathogenesis, parasitology, pathogen ductive epidemiology, social epidemiology,
immunology, tumor virology, microbial and women’s health.
Image of the crystal structure glycoprotein B of herpes simplex virus. genomics and evolution, and emerging
(Science 213:217-220, 2006, Roselyn Eisenberg) infectious diseases.
6 w w w.med.upen n .e du/bgs BIOMEDICAL GRADUATE STUDIES 7

6. Genomics and Computational Biology Immunology
Cell, Molecular, and Developmental PENN – NIH Partnership The Immunology Graduate Group provides
Biology of the Immune System A distinguished group of investigators from each trainee with an understanding of the
Studies in this area include molecular the Bethesda, MD campus of the NIH have
immunology, such as signal transduction joined Penn’s faculty in Immunology, conceptual and experimental foundation
and transcriptional control, cell biology of bringing to the Immunology Graduate of modern immunology and imparts
lymphocyte activation, and developmental Group the extraordinary resources and
biology of lymphoid and myeloid subsets. scientific expertise present at the NIH, one of comprehensive knowledge of the immune
the largest and most renowned biomedical system and its regulation while teaching
Immunity to Infections research centers in the world.
Particular foci of research include elucidating the skills necessary for a career in biomedical
A graph of yeast gene interactions estimated
the role of innate immune responses, the Educational opportunities on the NIH cam-
from whole-genome gene expression data. Each pus are offered to all Immunology students. science.
dot represents a gene and each edge represents
CD4+ T cell subsets that secrete inflamma-
tory cytokines and CD8+ cytolytic T cells in The NIH faculty participates fully in all
a significant interaction. The high-lighted and aspects of our teaching programs at Penn’s
colored ellipses represent groups of genes with the defense against microbes and viruses,
both at the site of infection, such as the Philadelphia campus, including service on
known gene function showing that genes with
mucosal surfaces of the gut and lung, and in thesis committees. The partnership also
similar biological function tends to have high
degree of mutual interaction. (Junhyong Kim) peripheral lymphoid organ. allows students to pursue laboratory rota-
tions and a limited number to pursue thesis
Cancer Immunology research in the NIH laboratories.
Cancer immunology research at Penn
encompasses the entire spectrum from basic
Genomics and Computational Biology Evolutionary Genomics methods for genetic association studies
research to clinical trials.
Specific research work includes the and gene-gene interactions, methods for
lies at the center of a rapid convergence of
evolution of the transcriptome in natural systems biology, comparative sequence
Autoimmunity and Tolerance
biomedical research fields. Research in this species and cell lines of different genetic analysis, evolutionary modeling, machine
Using a variety of different approaches and
composition, the evolution of large gene learning in genomics, statistical models for
graduate group focuses on the entire models, several groups of investigators at
families, gene duplication and loss in the analysis of microarray data, and statistical
Penn are focusing their efforts in this area,
genome (as DNA) and the entire material evolution, the evolutionary frequency and methods for mapping genes associated with
with the ultimate goal of developing strate-
significance of horizontal gene transfer, diseases.
determined by genes (as RNA or protein), gies to block deleterious immune responses.
methods for detecting functional non- cod-
and asks about the origins, function, and ing sequences, and the role of retroviral Microbiology
elements in the evolution of new genomic Research programs focus on the investiga-
interactions of the system as a whole. Such
function. tion of the growth and inhibition of
questions and other developments in this medically significant pathogens, replication
Human Genomics of human transposons and consequences
field stimulate experimental laboratory work
In the area of human genomics research for human biology, and retroviral-host
in genomics, as well as computational activi- topics include the analysis of structurally interactions.
variant chromosome regions, the genomic
ties in bioinformatics.
analysis of predisposition to diseases, Computing
genome-wide analysis of gene expression, Studies in this area include computational
the genetics of complex diseases, devel- analysis and modeling of real-time, systems-
opmental genomics, and chromosome level genomics, nanotechnology, com-
organization. putational simulations of the evolutionary
processes of cancer, ,machine learning and
Statistics datamining, and bioinformatics including
Statistics research includes the develop- management, analysis, and visualization of
A dividing, microbe-specific T lymphocyte displaying unequal inheritance
ment of statistical methods for discovery information generated in molecular biology. of signaling proteins to its daughter cells. Asymmetric cell division may be
and clustering of conserved patterns in a mechanism to generate the spectrum of cell fates required for immunity.
DNA sequences, evolution of viral genomes, (Steve Reiner)
8 w w w.med.upen n .e du/bgs BIOMEDICAL GRADUATE STUDIES 9

7. Neuroscience Pharmacological Sciences
The Neuroscience Graduate Group Cell and Molecular Neuroscience Neurological Disease and Dysfunction
Research focuses on the molecular Research programs focus on the cellular
offers training in virtually all areas of
mechanisms of intra- and intercellular signal- and molecular bases of a variety of Progressive microglial
neuroscience research including cellular ing that underlies plasticity in both the neurological and psychiatric diseases, includ- activation in the central
developing and adult nervous system, as ing Alzheimer’s disease, traumatic brain nervous system
and molecular aspects of the brain;
well as changes in signaling underlying injury, autoimmune diseases of the nervous of transgenic tau mice.
development, regeneration, and plasticity; diseases of the nervous system and involves system, diseases of the motor system, and Microglia are progressive-
cutting edge molecular biological, genetic, the neuronal basis of addiction. ly activated with age in
systems neuroscience; behavior and the brains of transgenic
immunological, electrophysiological, and
mice (PS19, 3 months
cognition; the pathology of brain disease; behavioral approaches. Systems Neuroscience
to 9 months) compared
The study of how information is encoded,
and computational neuroscience. Neuronal Development, Regeneration, to normal mice (nTg).
processed in the brain and used to generate
and Plasticity (Virginia Lee)
coordinated movement depends in part on
Current research uses multidisciplinary
the organization of neurons into networks
approaches to address the molecular and
and systems. Approaches here include cel-
cellular processes that lead to the formation
lular-level analyses of small model systems in Cancer Pharmacology cardiovascular disease). Graduates of the Pharmacological Sciences Research employs
of a functioning brain, including how nerve
vitro and larger scale systems studied in vivo. Specific research work includes site-directed program will be prepared for careers in toxi-
cells migrate to their final destination, how a variety of experimental approaches to
All of these studies include realistic neural mutagenesis, structural and functional cology, risk-assessment, environmental and
axons are guided to appropriate targets, and
network. characteristics of GTP-binding regulatory occupational health sciences. identify natural and design synthetic agents
how neurons make and maintain synaptic
connections. proteins, mass spectrometry detection of
Behavioral Neuroscience for both treatment of diseases and experi-
molecular markers of tumor growth and Neuropharmacology
Animal behavior represents the external design of molecular interventions in cancer. The overall focus of neuropharmacology mental interventions in animal and cellular
expression of complex patterned activity in research and training is to provide students
the brain and is continually modulated by in- models. Understanding the action of these
Cardiovascular Pharmacology with an integrated understanding of
ternal and external sensory information and Research programs explore the cellular the interactions of neurotransmitters with agents, both desirable and toxic, is the key
by internal drives and states. Penn has an and molecular basis of atherosclerosis, receptors and the biochemical and
active interdisciplinary program that studies mission of the graduate training program.
thrombosis, hypertension and inflamma- functional effects of these interactions.
the complex relationship between cellular tion using a variety of approaches including The program’s resources allow students to
and molecular events and external patterns knockout and transgenic technologies, gene Pharmacogenetics
of behavior. concentrate on basic science research and to
therapy techniques, recombinant fusion This program focuses on the genetic basis
proteins and modern approaches in chemis- of inter-individual variation in response to participate in translational research where
Cognitive Neuroscience try, biochemistry, molecular biology, and various classes of drugs and therapeutic
Cognitive Neuroscience has a distinctive fundamental discoveries in the laboratory
cell biology. protocols and makes use of this information
goal: the mechanistic understanding of to develop rational “personalized” therapeu- are taken through stages of discovery and
human thought. How do people learn, Cell Signaling tic regimens and to identify genetic
understand language, and plan complex development and culminate in the clinical
Signals of special interest include hormones, susceptibility factors for diseases. It encom-
action? Research programs include those neurotransmitters, sensory stimuli, and passes the study of genetic factors that domain.
focused on understanding visual perception, cell-cell or cell-substratum contacts. Specific influence drug delivery, bio-availability,
learning and memory, and cognition- research works include studies of cellular metabolism and clearance, and toxicity.
emotion interactions. receptors and membrane channels, signal
transduction pathways and nuclear respons- Pharmacological Chemistry
Computational Neuroscience es in diverse models of (patho)physiological Understanding the chemistry of molecular
The objective of Computational processes. recognition between drugs and their targets
A picture of a zebrafish brain. Green is rhombere, Mauthner neuron, and muscle staining. Blue is a pre-synaptic marker. Neuroscience is to uncover basic neuronal (receptors, ion-channels, enzymes, and
Red is a post-synaptic marker. (Yuanquan Song, Paul Scherer, and Rita Balice-Gordon) mechanisms through simulation and Environmental Health Sciences nucleic acids) is a primary focus of research
prediction based on experimental findings. This program explores the mechanisms, and training in Pharmacological Chemistry.
To carry out these studies, collaborations pathogenesis, prevention and treatment Research work includes synthesizing recep-
between experimentalists and of diseases of environmental etiology tor subtype specific ligands and isoform
computational neuroscientists have led to a (e.g., lung and airway disease, cancer, specific enzyme inhibitors and X-ray crystal-
PhD Thesis with co-Advisors. neurodegenerative disease, reproductive lography of membrane bound drug targets.
and developmental disorders, obesity and
10 w w w.med.u pen n .edu/bgs BIOMEDICAL GRADUATE STUDIES 11

9. Biomedical Graduate Studies
University of Pennsylvania
160 BRB II/III
421 Curie Boulevard
Philadelphia, PA 19104-6160
215.898.1030
bgs@mail.med.upenn.edu
www.med.upenn.edu/bgs