Education

Faculty in the Epigenetics Institute participate in several different PhD programs at the University of Pennsylvania. All of the graduate students in Epigenetics labs enter through one of the graduate groups under the aegis of the Biomedical Graduate Studies or the Biology Program at the School of Arts and Sciences.

Graduate Groups

Biochemistry & Molecular Biophysics

Cell & Molecular Biology

Epidemiology & Biostatistics

Genomics & Computational Biology

Immunology

Neuroscience

Pharmacology

Courses

David W. Speicher & Benjamin Garcia

BMB 626 (SPRING): MASS SPECTROMETRY AND PROTEOMICS

This course will provide a detailed introduction to proteomics and mass spectrometry. The role of mass spectrometry in both characterizing proteins for traditional protein structure – function studies and identification of proteins in proteome studies will be emphasized. Targeted and global proteomes, quantitative protein profiling and compositional proteomics, and applications of proteome studies will be discussed. Intended for second year graduate students and others with an interest in proteomics or mass spectrometry.


Matthew Weitzman & Sunny Shin

CAMB 706: (year-long course with sessions in Fall and Spring) 

This is a year-long course for the incoming CAMB-MVP students and others wishing to gain a broad overview of pathogens and their interactions with hosts.  The course will provide students with key fundamental knowledge of Microbiology, Virology, and Parasitology. The course starts with introductory lectures on Concepts of Host-Pathogen Interactions.  The rest of the course is divided into sections on Bacteriology, Virology and Parasitology.  Each week there are three 1 hour class slots that are either lectures on a specific topic or discussions of a relevant paper presented by students.  Classes are led by faculty from across the campus and are highly interactive.  Evaluation is based on mid and final take home essay topics for each of the three sections.  Regular attendance and active participation in the discussions is also part of the evaluation.


Gerd Blobel

BIOM 555 (Fall & Spring) “REGULATION OF THE GENOME”

My lecture is on “Chromatin Regulation In the context of nuclear architecture”.


Doris Wagner

BIOL/CAMB 483 (Fall): Epigenetics

The course aims to introduce students to the field of epigenetics – phenomena that can for example give rise heritable alternate states of gene activity that do not result from an alteration in nucleotide composition (mutations) – through a combination of lectures,  guest research and methods presentations, as well as discussion of recent findings published in this field.


Zhaolan (Joe) Zhou

BIOM555 (Spring): Regulation of the Genome

This is a lecture based survey course covering topics from genome maintenance, gene transcription, chromatin structure, to high-order chromatin regulation, as well as topics of post-transcriptional regulation, of which each topic is lectured by a local leader in that specific field.


Shelley Berger

BIOL / CAMB / GCB493 (Spring): Epigenetics of Human Health and Disease

Epigenetic alterations encompass heritable, non-genetic changes to chromatin (the polymer of DNA plus histone proteins) that influence cellular and organismal processes. This course will examine epigenetic mechanisms in directing development from the earliest stages of growth, and in maintaining normal cellular homeostasis during life. We will also explore how diverse epigenetic processes are at the heart of numerous human disease states. We will review topics ranging from an historical perspective of the discovery of epigenetic mechanisms to the use of modern technology and drug development to target epigenetic mechanisms to increase healthy lifespan and combat human disease. The course will involve a combination of didactic lectures, primary scientific literature and research lectures, and student-led presentations.


Ben Black and James Shorter

BMB650/CAMB702/PHRM650 (Spring): Current Biochemical Topics

This is a discussion-based class in which students study, read, and present the published work of the invited Raiziss Rounds seminar speakers. The goal of the class is to develop the students’ ability to understand the rationale behind the experiments, critically analyze the work, communicate their thoughts to others, and to engage in focused scientific discourse. The Wednesday classes will run in a journal club format with students giving presentations of the papers for that week’s speaker. Thursday will be the noon seminar by the invited speaker, followed by lunch with the speaker.


Arjun Raj

BE/GCB 567: MODELING BIOLOGICAL SYSTEMS (Fall)

This course will cover topics in mathematical models of systems biology at the molecular/cellular scale.  The emphasis will be on quantitative aspects of molecular biology, with possible subjects including probabilistic aspects of DNA replication, transcription, translation, as well as gene regulatory networks and signaling.  The class will involve analyzing and simulating models of biological behavior using MATLAB. The course will be largely based on lectures and group work with occasional discussions of recent literature from the field.  We will cover some aspects of molecular biology, but will focus primarily on a more quantitative viewpoint than a traditional molecular biology course.  We will also cover the development of new experimental methods (including imaging and sequencing) and how researchers are using them to generate a more quantitative picture of molecular biology.


Jennifer E. Phillips-Cremins

ENM375: BIOLOGICAL DATA SCIENCE I – FUNDAMENTALS OF BIOSTATISTICS – SPRING 2019; SPRING 2020

The purpose of this course is to provide students with skills to analyze and interpret small and large biological data set. Fundamentals in statistics will be taught through the use of homework problems, case studies and projects focused on computational analysis of biological data. Topics covered include: populations and samples; random variables; discrete and continuous probability distributions; exploratory data analysis; descriptive statistics (mean, standard deviation, median, variance, quantiles); confidence intervals; expectations; variances; central limit theorem; independence; hypothesis testing; fitting probability models; p-values; goodness-of-fit tests; correlation coefficients; non-parametric tests; ANOVA; linear regression; bootstrapping; and maximum likelihood estimation.

Course Description


Jennifer E. Phillips-Cremins

BE504: BIOLOGICAL DATA SCIENCE II — DATA MINING PRINCIPLES FOR EPIGENOMICS – SPRING 2020; FALL 2020

The purpose of this course is to provide students with skills to analyze and interpret biological data generated by high-throughput sequencing. Fundamentals in biostatistics, computational biology, chromatin biology and epigenetics will be taught through a series of case studies focused on cutting edge biological questions in biomedical research. Example case studies include: measuring gene expression changes during disease progression; analyzing epigenetic marks (histone modifications, DNA methylation) in stem cells and differentiated cells; or investigating changes in transcription factor binding across the genome in response to drug treatment.  Each case study will be covered by 3-4 lectures that (1) provide background on the biology behind the epigenetic modification, (2) describe the molecular biology technique employed to query that particular epigenetic modification, (3) introduce statistical concepts important for analyzing specific types of high-dimensional data. This course will not cover comparative genomics, sequence alignment algorithms, genome assembly or population genetics.

Course Description

 


Ronen Marmorstein

BMB554/CHEM555 (Fall): MACROMOLECULAR CRYSTALLOGRAPHY: METHODS AND APPLICATIONS

This is an introductory course on methods and applications of macromolecular structure determination using X-ray crystallography. The course will be broken up into three parts: 1) Principles of X-ray crystallography involving didactic lectures on the technique with weekly problem sets; 2) Faculty presentations of X-ray crystal structures and their biological implications; 3) Student “journal club” presentations on current high impact publications involving X-ray crystal structure determination.


Irfan Asangani &  Roger Greenberg

CAMB 530:  THE CELL CYCLE, GENOME INTEGRITY, AND CANCER FALL 2019

This seminar course focuses on molecular and biochemical events that regulate cell cycle progression and genome maintenance and explores how these processes influence cancer etiology and treatment.  Specific topics will familiarize students with the key principles and recent developments within these areas.  These topics include CDK-Cyclins and their inhibitors, regulation of G1-S and G2-M phase cell cycle transitions, DNA damage checkpoints and repair, the impact of chromatin regulation on DNA repair, and how each of these processes affects cancer etiology and treatment.  In-depth reading and evaluation of research literature will be primarily used to accomplish these aims, as well as provide instruction on rigorous experimental design and data interpretation.

 


Zhaolan (Joe) Zhou, Elizabeth Heller, & Hao Wu

CAMB / NGG 713 (Fall)
This course intends to bring students up to date concerning our understanding of Neural Epigenetics. It is based on assigned topics and readings covering a variety of experimental systems and concepts in the field of Neuroepigenetics, formal presentations by individual students, critical evaluation of primary data, and in-depth discussion of potential issues and future directions, with goals to 1) review basic concepts of epigenetics in the context of neuroscience; 2) learn to critically evaluate a topic (not a single paper) and set the premise; 3) improve experimental design and enhance rigor and reproducibility; 4) catch up with the most recent development in neuroepigenetics; and finally, develop professional presentation skills – be a story teller.