Physiology, Biophysics & Systems Biology Seminar Series, Quarters Qtrs. l-lV, Annually:
A required course that exposes program students to recent research developments. Outside seminar speakers are invited to discuss their latest research.
Course Director: Dr. Emre Aksay
This course will focus on important aspects of cell physiology that are required for normal cell functioning and disease processes. The contributions of specific organelle and molecular pathways in these processes will be discussed in the context of proper cell function. Topics in theories of biophysics and bioelectricity will also be covered.
The course is divided into 5 modules to address each of the following areas:
- Genes, proteins and membranes
- Biophysics of the cell
- Proteins in the cell
- Signaling in the cell
- The cell as a complex system
Course Director: Dr. Crina Nimigean
Faculty Research Lunches, Quarters I-II:
This course is required for all 1st year PBSB graduate students, but is open to all WGSMS students. Come for lunch and listen to your program faculty describe their research. Make informed decisions about your laboratory rotations!
Course Director: Dr. Emre Aksay
Physical Principles of Medical Imaging, Quarter I-II:
This is a one-semester course covering the basic concepts of major modern diagnostic imaging technologies. Emphasis is placed on magnetic resonance imaging (MRI). Computerized tomography (CT) and ultrasound (US) are also covered. Students will gain fundamental technical knowledge of medical imaging and an overview of current status of medical imaging technologies. See attached SYLLYBUS for details. PREREQUISITE IS CALCULUS BASED PHYSICS.
Course Director: Dr. Yi Wang
Essentials of Human Physiology, Quarters I-III Annually:
This course consists of three parts:
- Assigned independent readings from a textbook of human physiology (Medical Physiology by R.A. Rhodes and G.A. Tanner, 2nd Edition, Lippincott Williams & Wilkins) followed by presentations and discussion of the readings led by an instructor.
- Assignments of Special Topics, Journal Articles, and/or Physiological Problems for student presentation and discussion in class.
- Physiology laboratories, including laboratories with mannequins simulators of physiological functions
Advanced Topics in Cardiac Electrophysiology, Quarter I:
This course will survey current areas of scientific interest in cardiac electrophysiology. Material for this course will include: introduction to cardiac electrophysiology (ion channels, action potentials, basics of cardiac electrophysiology); basic and clinical aspects of cardiac arrhythmia; dynamics, initiation, maintenance, and termination of arrhythmia; atrial and ventricular fibrillation and defibrillation; experimental methods; and mathematical modeling. The course will be comprised of lectures as well as moderated videotaped presentations recorded recently by international experts in the field.
Course Directors: Dr. David Christini and Dr. Trine Krogh-Madsen
Introduction to Bioengineering, Quarters III-IV:
The objective of this one semester course is to prepare graduate students at the Weill Medical College for thesis research in fields that encompass bioengineering. The course will be team taught by Weill and Ithaca faculty using video conferencing facilities. Examples will be chosen from musculoskeletal and cardiovascular fields.
Course Director: Dr. Boskey
Principles of Biomedical Imaging, Quarters III-IV:
This survey course will cover the basic physical, biochemical, computational, and engineering principles underlying current medical imaging techniques, including magnetic resonance imaging, positron emission tomography, radionuclide production and radiochemistry, optical imaging, x-ray computed tomography, and ultrasound. The goal of the course will be to provide students with a broad knowledge of the concepts and implementation strategies of various imaging methods relevant in current research and clinical practice. Practical applications will be used to illustrate the main themes of the course. Tours of the Biomedical Imaging Core Facility and other imaging laboratories will augment the formal course material. At the end of the course students will be able to identify appropriate imaging strategies for clinical research and have a working knowledge of the major techniques available to the investigator.
Course Director: Dr. Douglas Ballon
Scientific Presentation and Critique, Quarters III-IV:
This course is required for all 1st and 2nd year PBSB graduate students, but is open to all WGSMS students. It is designed to train students in scientific presentation and critique. The structure is a formalized, in depth "journal club". Each 1st year student will choose a paper from a list provided by the Course Directors. Each 2nd year student will select a paper in their thesis field, subject to approval of the Course Directors. Each session will consist of a student formally presenting their selected paper to the class, which is expected to serve as a critical audience. The presentation should consist of an introduction of the relevant background literature, an objective presentation of the study, a subjective analysis/critique of the work, and suggestions for future work. Presentations by 2nd year students will be scheduled first, giving the 1st year students the opportunity to learn from their more senior colleagues. Grading will be based on presentation quality and contribution to constructive feedback. [More]
Bioinformatics, Quarters III-IV - OFFERED EVEN YEARS:
This course begins with a discussion of the history, techniques and statistical analyses used in bioinformatics today. Students will begin to analyze how these tools can be used to predict RNA, gene and protein structure. The final two weeks of the course will be focused on systems biology including current techniques used to model of protein-protein interactions, protein networks and cell signaling. [More]
Course Director: Dr. Lucy Skrabanek
Quantitative Physiology, Quarters III-IV:
This course will enable students to be able to formulate, evaluate, and analyze the results of mathematical models important to understanding biological function. Developing the ability to communicate quantitative data and concepts verbally and graphically as well as mathematically is also stressed. This course will emphasize practical as well as theoretical skills; many lectures will be given in a ‘hands-on’ workshop style, and completion of several projects will be required. Topics in algebraic systems, statistical models, differential equations, non-linear dynamics, and numerical methods are introduced to enable quantitative modeling in arenas such as neural function, enzyme kinetics, cardiac dynamics, and signaling pathways.
Course Director: Jason Banfelder
Physiological Genomics of the Cardiovascular System, Quarter IV:
A journal club and discussion seminar approach will be used to study the process of gene regulation of cardiovascular organogenesis and function. The course will focus on fundamental advances in our knowledge in genomics and how genes regulate the structure, organization, and activity of the heart and vasculature. Weekly sessions will address topics that range from molecular to cellular to tissue to organ to organismal events.
Course Director: Dr. Cathy Hatcher
Other Recommended Graduate Program Courses
Fundamental Immunology, Quarters I-IV, Annually:
Quarters I and II of the course provide a comprehensive overview of basic immunology beginning with the innate immune responses, followed by a study of the main aspects of acquired immunity. Specific interactions of target cells and T cells that are regulated by the MHC molecule and peptide antigens on the target cell and the antigen specific T cell receptor are studied. The generation and molecular structure of B and T cell antigen receptors, and signaling through immune receptors are covered in detail. Lastly, the development of antigen specific T and B cells, and specific roles for some cytokines/lymphokines are also important topics.
Quarters III and IV of the course cover in more depth T and B cell mediated immunity and topics of clinical relevance, such as microbial immunity, allergy, autoimmunity, tumor immunology, congenital and acquired immunodeficiencies, transplantation immunology, and immunotherapy. All the topics are studied though lectures and in depth review of selected articles.
Course Director: Dr. Ethel Cesarman.
Introduction to Pharmacological Principles
Principles of Pharmacology (4 Parts):
Quarter I: Chemical Biology
Students should develop an understanding of the chemical reactions used in biological and laboratory synthesis and manipulation of proteins, nucleic acids, lipids, and carbohydrates. Students should also develop an understanding for the chemical principles that underlie enzyme function. By the end of the course, students should be comfortable reading journal articles on chemical biology and will be expected to give an oral presentation and written report on a topic in the field.
Quarter II: Signal Transduction
The goal of the course is to provide students with an understanding of the basic recurring themes in cell signaling mechanisms and to familiarize the students with a majority of the key signal transduction pathways. Additionally, an emphasis is placed on (1) the use of pharmacologic and chemical tools to study problems in signal transduction; and (2) structural insights into signaling mechanisms, based on x-ray, NMR, and computational approaches. By the end of the course, the students should feel comfortable with reading and comprehending journal articles that relate to the latest findings in signal transduction.
Quarter III: Principles and Systems Pharmacology
Systems Pharmacology occupies the third quarter of the yearlong Introduction to Pharmacological Principles. It is a 9-week course arranged into three parts or modules: 5 sessions in the first part covering general pharmacological principles, 9 sessions in the second part focusing on nervous and circulatory systems, and 10 sessions in the third and final module covering the remainder of the circulatory system along with host defense and endocrine systems. An understanding of systems pharmacology is necessary and valuable for all Pharmacology Graduate Students. A recent Senate Committee recommended increased support for research and training in whole systems pharmacology&to define the effects of therapy on disease and the overall function of the human body. Over the past two decades, there has been an emphasis on supporting research and training at the cellular and molecular levels, but diminished support for training and research in systems and integrated biology. The erosion of support in the area of integrated systems threatens to slow the rate at which fundamental discoveries made at the cellular and subcellular levels are translated into useful therapies. These recommendations were recently put into effect at one of our peer institutions with the creation of a new Department of Systems Biology.
Recommended textbook: BG Katzungs Basic and Clinical Pharmacology, 8th edition.
Quarter IV: Cancer Pharmacology
Cancer Pharmacology will focus on the principles and aplications of modern cancer therapeutic approaches. The topics considered range from traditional cytotoxic and anti-mitotic agents, to natural products and their chemistry, to biologic and immunologic therapies, to rationally designed targeted small molecule inhibitors. Basic principles underlying mechanisms of cancer cell death, angiogenesis, and radiobiology and imaging are also covered.
Biochemistry and Structural Biology, Quarters I-II, Annually:
This is a two quarter course in structural biology and contemporary biochemistry. The course covers equilibria, bond formation, protein chemistry and structure, nucleic acid chemistry and structure, ligand binding, chemical and enzyme kinetics, enzyme reaction mechanism, principles of macromolecular analysis, principles of protein purification, and principles of macromolecular recognition and specificity.
Course Directors: Dr. Dimitar Nikolov and Dr. Min Lu (and staff)
From Neuron to the Brain: An Intro to Neuroscience, Quarters I-II, Annually:
Course Director: TBA
Logic and Experimental Design, Quarters I-II, Annually:
This multidisciplinary course combines lectures about the fundamental biochemical, cellular, molecular, immunological, genetic, and bioinformatics approaches that are used in biomedical research with critical discussion of research papers. The course will meet on Tuesday and Thursday afternoons, and each meeting will have provisions for both a lecture and a discussion period. Generally, the discussion period will be used to discuss an original research paper, but occasionally it will be used for a model building laboratory, or a review session. The development of a research proposal is a major component of the course. The course is open to all students and fellows and it is a core course for both neuroscience and pharmacology.
Course Director: Dr. Wagner
Molecular Genetics, Quarters I-II Annually:
This course is organized around the principles of genetic analysis, with examples chosen from organisms that best illustrate those principles. The course is based on lectures, problem sets, and discussion sections. Topics covered include: the nature of the gene; linkage and physical maps; recombination mechanisms; nature of mutations; mutations as tools to dissect gene function; transposition; epigenetics; cancer genetics; genetic analysis of development and cell-cell signaling.
Course Directors: Dr. Scott Keeney (and staff)
Advanced Topics in Immunology (Module I): Advanced Lymphocyte Activation (Quarter II: Jan 9 – Feb 13, 2008)
This module of Advanced Topics in Immunology will provide an opportunity for the participants to discuss and evaluate current concepts in signaling through immune system receptors. Topics will include activation of innate immune system cells as well as activation of antigen specific receptors on T and B lymphocytes. This course integrates our molecular understanding of the immune response with in vivo and in vitro imaging, computational modeling and cytokine-cytokine receptor regulation of the immune response.
The overall areas of study include:
Imaging of immune responses in vivo and in vitro (Morgan Huse); TLR and non-TLR activation of innate and adaptive immunity (Carl Nathan); Tyrosine phosphorylation, tyrosinekinases and tyrosinephosphatases in immunity (Avery August); Computational modeling of lymphocyte activation (Grégoire Altan-Bonnet); Cytokines and activation of JAK-STAT pathways (Lionel Ivashkiv); IL-12 Receptors and activation of Th T Cells (Th1/Th17) (Xiaojing Ma)
Wednesdays from 9am-12 noon at the 16th floor conference room (Rm Z1670), Zuckerman Research
Cell and Developmental Biology, Quarters III-IV, Annually (NOTE: THIS COURSE BEGINS IN JANUARY):
This course explores key aspects of cell and developmental biology at a detailed molecular level. The focus is on the integration of structure/function relationships for proteins and signaling pathways within the cell and in the intact organism. Specific topics include: membrane structure; protein biosynthesis and vesicular trafficking; endocytosis; cell architecture and motility; receptor and oncogene mediated signaling; signaling in a developmentally regulated context; and stem cell biology. The course consists of two lectures per week plus one interactive discussion section involving current research papers.
Dr. Marilyn Resh
Dr. Katherine Hajjar
Dr. Mary Baylies.
Gene Structure and Function, Quarters III-IV, Annually, (NOTE: THIS COURSE BEGINS IN JANUARY):
A two-quarter course that explores the regulatory mechanisms governing the flow of information in cells from DNA to RNA to protein. The first module of the course deals with DNA replication, recombination and repair, and introduces basic principles of DNA topology and protein-DNA interactions as they apply to these and other processes. In the next module, the fundamentals of gene structure and transcription are presented. Topics to be discussed include: structure and function of transcription factors and RNA polymerases; mechanisms of transcriptional activation and repression; the effects of chromatin on transcription; analysis of transcriptional networks by proteomics and functional genomics; and transcriptional control of the cell cycle. The final module covers post-initiation maturation and processing of mRNA, culminating with its translation into protein. Topics include: mRNA capping, splicing and polyadenylation; regulation of mRNA stability; mechanisms and functions of RNA interference (RNAi); and mechanisms and regulation of translation.
Course Directors: Dr. Robert Fisher and Dr. Beate Schwer (and staff)
Ion Channels, Quarters III-IV (NOTE: THIS COURSE BEGINS IN MARCH):
The course will cover all aspects of ion channel and transporter physiology, from the chemistry and physics underlying their function, through to the consequences of their dysfunction at the organismal level. The course comprises three parts. First, we will address the fundamentals of ion channel biophysics, covering the work of early pioneers such as Hodgkin and Huxley (with use of both traditional teaching and computer workshops), and the mechanisms of voltage and ligand gating. Next, we will cover the channel cloning revolution that began in the 1980s and led to a staggering array of ion channel and transporter genes being discovered, work still ongoing today. Lastly, we will describe two of the latest fields that have converged with traditional biophysical research to yield unprecedented advances in our understanding of ion channel and transporter function and physiology: high resolution structural analysis (crystallography, electron microscopy and NMR) and how this has advanced our knowledge of ion selectivity and gating; and molecular genetics and genomics – with the associated discovery of the molecular basis for ion channelopathies (channel-based diseases) in humans and animal models.
The course thus has three modules:
- Basic biophysics
- Cloning and diversity of ion channels
- Ion channel structure and channelopathies
Course Directors: Drs. Geoffrey Abbott and Crina Nimigeam
Neuropharmacology, Quarters III-IV:
Genes, Drug & Behavior, Quarter III:
Neuropeptides and Pain, Quarter IV:
This course consists of modules 3 and 4 of the Genes, Drugs and the Brain (GD&B) course. This course is jointly sponsored by the Neuroscience and Pharmacology Programs. It is designed to present current concepts of the major central nervous system (CNS) neurotransmitters and their functional neuroanatomy. The course will integrate discussions of the mechanisms of neurotransmitter biosynthesis and release, receptor signal transduction and the alterations produced by CNS drugs.
An overview of the diversity of modern biophysical experimental techniques used in the study of biological systems at the cellular and molecular level. Topics covered will include methods that examine both structure and function of biological systems. Topics include light microscopy, fluorescence microscopy, image processing, confocal and multiphoton microscopy, phase contrast, electron microscopy, x-ray diffraction and protein structure determination, multidimensional NMR, spectroscopy, chromophores, calcium measurements, resonance energy transfer, membrane biophysics, electrophysiology, ion channels, action potentials, ligand-gated channels, fluctuation analysis, patch-clamp, molecular biology of ion channels, capacitance measurements, amperometry, optical traps, and molecular force measurements. The course is intended for students who seek an introduction to modern biophysical experimental methods. Due to the interdisciplinary nature of the course, students will have diverse backgrounds. A basic knowledge of and interest in physics and mathematics is expected but strong attempts are made to give an intuitive understanding of the mathematics and physics involved. Some knowledge of physical chemistry, molecular and cell biology, or neurobiology will be helpful. Depending on individual background most students will find certain aspects easy and other aspects demanding.
The course will meet M, W. at 2:45 in Room E-115 of Weill Cornell Medical College (Biochemistry Department) and Fridays at 2 PM in the same room. On Mondays and Wednesdays this course will be taught in a videoconference setting with about half the lectures originating at Cornell-Ithaca. On Fridays, there will be paper discussions and student projects.[Syllabus]
Course Co-Director: Dr. Fred Maxfield
Quantitative Genomics and Genetics (Qtr. III-IV)
(Cornell Ithaca Course# BTRY 4830/6830 )
Class will be taught from Ithaca - to WCMC via video-conference
Days: Mondays and Wednesdays
Time: 8:40 am - 9:55 am
Class begins: January 24, 2011
Location at WCMC: Main Conference Room, Dept. Genetic Medicine (13th Floor, Weill-Greenberg Building)
COURSE DESCRIPTION: A rigorous treatment of analysis techniques used to understand complex genetic systems. This course will cover both the fundamentals and advances in statistical methodology used to identify genetic loci responsible for disease, agriculturally relevant, and evolutionarily important phenotypes. Data focus will be genome-wide data collected for association, inbred, and pedigree experimental designs. Analysis techniques will focus on the central importance of generalized linear models in quantitative genomics with an emphasis on both frequentist and Bayesian computational approaches to inference.
PREREQUISITES: Recommended familiarity with the basics of probability and statistics. We assume no programming experience and will teach R coding from scratch.
Course Director: Jason Mezey, PhD - email@example.com[Flyer]