Required Courses

(These courses are required for all PBSB students, and open to students in all other Programs of the WCGSMS, Rockefeller University, and the Gerstner Sloan Kettering Graduate School.)

All PBSB students are also required to take Responsible Conduct of Research (RCRP.9010.01), preferably in their first year.


Contemporary PBSB: Cells, systems, and quantitative methods, Quarters I-IV:

Students prepare for twenty-first century research in the function, analysis, modeling, and understanding of living systems at each of several scales, from the molecular through the cellular to the organ system and organism. Multiscale and translational examples develop conceptual skills necessary to design meaningful experiments, derive insight from journal reports, work within the group structure now essential for contemporary research, and communicate new developments and related findings to today’s peers and future students. Structural and developmental concepts are covered as they illuminate function. The course is modular, presented in six independent but coordinated modules. All first-year students in the PBSB Program take all six modules. The entire course or individual modules are open to students of other programs with the permission of the course director. NOTE: all students must register separately for each module taken. Each module consists of multiple weeks. Typical weeks for modules 1 through 5 include two in-depth lecture-conferences that combine careful presentation of core material with student participation, and conclude with either a computational analysis and/or model, or a relevant illuminating article from the literature. The final module, CPBSB6, introduces new instructional modalities and perspectives designed to instill skills essential for researchers.

Course Director: Dr. Daniel Gardner


Critical Understanding of Scientific Literature, Quarters III-IV:

Required for all 1st and 2nd year PBSB students, and open to others, this course provides essential training 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.

Course Directors: Dr. Carl Blobel and Dr. Christopher Mason


Faculty Research Lunches, Quarters I-II:

PBSB program faculty unlock their state-of-the-art research via presentations and intensive discussion. Make informed decisions about your laboratory rotations!

Course Director: Dr. Emre Aksay


Physiology, Biophysics & Systems Biology Seminar Series, Quarters I-IV, Annually:

Students develop critical skills through guided exposure to recent research developments, as presented by leading investigators from the global community of biomedical science.

Course Director: Dr. Emre Aksay


Quantitative Understanding in Biology, 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. Both practical and theoretical skills are emphasized and coordinated; 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 web site:http://physiology.med.cornell.edu/people/banfelder/qbio

Course Director: Jason Banfelder


Elective Courses

(These advanced elective courses are offered to PBSB students, and open to students in all other Programs of the WCGSMS, Rockefeller University, and the Gerstner Sloan Kettering Graduate School.)


Bioengineering Topics, Quarters III-IV:

The objective of this one semester course is to prepare students for thesis research in fields that involve concepts of bioengineering including tissue engineering and regenerative medicine. The course will be team taught by Weill Cornell and Ithaca faculty using video conferencing facilities. Examples will be chosen from musculoskeletal and cardiovascular fields.

Course Director: Dr. Adele Boskey


Clinical and Research Genomics, Quarters III-IV:

The rapid advancement of Next-Generation Sequencing (NGS) has opened a wealth of opportunities for research in many fields: cancer biology, epigenetics, tumor evolution, microbiome and infectious disease dynamics, neuro-degeneration, personalized medicine, and improved diagnosis and risk assessment for patients. Moreover, there are emerging, faster NGS technologies that promise comprehensive molecular portraits of disease and actionable clinical results for doctors within a single day. Scientists and physicians will be better equipped to design studies and help patients if they possess an intricate knowledge of these molecular-profiling methods, their biological context, and their applicability to specific cases and diseases. Finally, a rich understanding of the complexity of the human genome is essential for the proper annotation of characterization of any new mutations/modifications found, since large-scale efforts at tumor and normal genome sequencing have dramatically altered our view of the “normal” genome and epigenome.

Thus, in this 10-week course, students will build a strong foundation of knowledge of NGS technologies (both existing and emerging), learn the applications of these technologies for basic and clinical research, and finally learn the essential tools for the analysis, integration, and application of these data relative to other public databases and phenotype repositories. We have a broad range of expertise being contributed from many leaders in the field.

Course Director: Dr. Christopher Mason


Mathematical Structures in Neuroscience, Quarters III-IV - OFFERED 2014-2015:

This course introduces the tools of computational and theoretical neuroscience, with a focus on principles and mathematical foundations. Students should be familiar with complex numbers, matrices, and univariate differential and integral calculus. Many specific topics addressed in the course are tailored to the interests and research focus of students.

For a syllabus of the 2012-2013 Course, see:http://www-users.med.cornell.edu/~jdvicto/mathcourse1213.html

Course Director: Dr. Jonathan D. Victor


Molecular Mechanisms of Membrane transport, Quarters III- IV:

This course focuses on the biophysics, properties, and physiological roles of ion channels and transporter. We discuss the contributions to cell function in physiology and pathology of the principal ion channel and transporter families. We emphasize the mechanistic insights that have emerged from the recent explosion of structural information and how this has drastically changed our understanding of gating and selectivity of these proteins.

Course Directors: Dr. Crina Nimigean and Dr. Alessio Accardi


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


Principles of Magnetic Resonance Imaging, Quarters I-II:

After a brief overview of all major medical modalities: x-ray, CT, MRI, SPECT/PET, and US, this course will focus on the formulations of spatial encoding and image contrasts as exemplified in MRI. The inverse problem between detected signal and image source will be discussed for biomedical applications. The concepts of image resolution, image contrast, SNR, and scan time will be illustrated quantitatively from an engineering point of view.

Students will have hands-on experience to scan phantoms at an MRI facility. Students may also attend field trips to observe imaging in clinical practice. The prerequisite for this course includes calculus based physics and knowledge of Fourier transformation. Lectures of this course are based on the textbook, Principles of Magnetic Resonance Imaging - physics concepts, pulse sequences and biomedical applications by the Course Director http://www.amazon.com/Principles-Magnetic-Resonance-Imaging-Applications/dp/1479350419

Course Director: Dr. Yi Wang


Scientific Computing in Biomedicine, Quarters I-II:

This course will teach students the fundamental skills and knowledge required for scientific computing in the biomedical sciences. Topics include: scripting, working with large datasets, data and software management, and effective use of high-performance computing resources. Students will learn relevant theory as well as develop practical application skills using contemporary tools and technologies including R for data analysis and presentation, SQL databases for structured data management, the Ruby scripting language for practical programming tasks, git for software and data revision control, Sun Grid Engine for batch job management on large clusters, and Maestro from the Schrödinger Suite for molecular modeling and visualization.

Prerequisites: familiarity with basic UNIX/Linux environment and commands (vi/emacs, stdin/stdout/pipe, grep and regular expressions).

Expectations: In addition to two classroom hours per week, students will be expected to spend several hours per week independently learning material. Several lectures will employ a ‘flipped-classroom’ model, in which students will be expected to complete assigned reading and study prior to class time.

This course will require the completion of several projects, which may be tailored to the specific research interests and lab activities of each student. The course will be most practical for those that have the opportunity to integrate learned methods and skills into their current research activities, and be able to demonstrate results of these activities to the class.

Course Director: Jason Banfelder


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.

Course Organizers: Dr. Samie Jaffrey and Dr. Derek Tan

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.

Course Organizers: Dr. Steven Gross and Dr. Samie Jaffrey

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.

Course Organizers: Dr. Roberto Levi and Dr. Lonny Levin

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.

Course Organizers: Dr. David Scheinberg and Dr. Yueming Li


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

Course Directors: Dr. Grégoire Altan-Bonnet; Dr. Bo Dupont and Dr. Xiaojing Ma


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)


Neuropharmacology, Quarters III-IV:

2 Parts:          

Genes, Drug & Behavior, Quarter III:

Course Organizers: Dr. Miklos Toth and Dr. Harriet Baker

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.

Course Organizers: Dr. Charles Inturrisi and Dr. Hazel Szeto


Biophysical Methods, Quarters I-II, Every Other Year:

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 - jgm45@cornell.edu

[Flyer]


See also http://weill.cornell.edu/gradschool/courses/index.html