Molecular Pharmacology and Therapeutics

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Course Director: Nihkil Sharma

This fall-semester course is required for all first-year students and covers basic biochemical and experimental principles, such as protein and nucleic acid structure and chemistry, thermodynamics and enzyme kinetics, and bioinformatics. Also included are biochemical processes common to all cells, such as genome replication and repair, regulation of gene expression, cell-cycle control, and cell membrane and receptor biochemistry. Course Directors: Anna-Lena Steckelberg and Hashim Al-Hashimi.

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Course Director: Nihkil Sharma

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Course Director: Nihkil Sharma

This course provides an in-depth analysis of several organ systems and diseases associated with each organ system. The course has four modules; each module describes the basic physiology, nutritional status and anatomy of the organ system, the genetics, cell and biochemical mechanisms and pathologies associated with the disease, as well as basic pharmacology and therapeutics to treat the disease. Course Directors: Ronald Liem and Steven Spitalnik.

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This spring semester course provides an introduction to the basic statistics commonly used in biomedical research laboratories. Students are provided with a statistical software package for use during the course. Exercises based on relevant experimental data sets use the software to reinforce the lecture material. Topics covered include the role of statistics in biomedical research, principles of statistical analysis, and selecting and applying the appropriate statistical tests. Course Directors: Arthur Palmer.

This spring semester course explores a variety of ethical and policy issues that arise during the conduct of basic and clinical scientific research. Course sessions include lectures, discussion periods, and analyses of case studies. Columbia requires that all graduate students share in the discussions of this course. You will hear from your faculty speaking honestly about problems that you may face. You will find the discussions interesting. Course Directors: Arthur Palmer and Jaime Rubin.

This course provides a detailed analysis of the biophysical and structural properties of ionic channels in biological membranes. In addition, the physiological role of such channels in regulating neuronal excitability is covered. Course Director: Steven Siegelbaum.

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Methods and principles involved in studying the structure and function of proteins, nucleic acids, membranes, and their macro-molecular assemblies. Noncovalent forces and conformational analysis; ultracentrifugation, viscometry, circular dichroism, fluorescence, magnetic resonance; conformational changes in proteins and nucleic acids, topological properties of macromolecules. Course Director: Arthur Palmer.

The Course will comprise general lectures, analyses and discussions of primary literature on stem cell and cell lineage specification biology as well as student presentations. The themes to be presented include basic cell and molecular biological characterization of stem cells, regulation of self-replication versus lineage restriction and differentiation of cells, model systems used in studies of stem cells, and the relevance of tissue formation, regeneration and disease states. Course Directors: Stephen Tsang and Dietrich Egli.

This course provides an in-depth introduction to principles of modern sequencing, key computational algorithms and statistical models, and applications in disease genetics, cancer and fundamental biology. It will cover genome, exome, transcriptome, and epigenome sequencing approaches. Emphasis will be placed on understanding the interplay between experimental design, data acquisition, and data analysis so that students can apply these powerful tools in their own research. Course Directors: Yufeng Shen, Peter Sims, and Chaolin Zhang

Basic Unix, website usage, sequence comparison, database searching, multiple sequence alignment, profile methods, secondary structure prediction, mapping, primer design, genomic analysis, and functional genomics, including micro-array analysis. Course Director: Richard Friedman.

Required for C2B2 students in the spring semester, this course will present computational approaches of reconstruction, analysis, and simulation of cellular networks. Metabolic, signaling, and protein-interaction networks will be covered. The networks will be discussed at several levels of structural organization: overall network, functional and structural modules, network motifs. We will emphasize how specific biophysical and biochemical properties of different networks lead to conceptual simplifications for analysis and simulation. Network evolution and similarities between cellular and nonbiological networks will be discussed. Course Director: Dennis Vitkup.

This fall-semester course is required for all first-year students and covers aspects of molecular biology and genetics, from prokaryotes to mammals, including regulation of gene expression, molecular genetics of bacterial viruses, plasmids, and transposable elements, as well as modern molecular genetic approaches to complex biological phenomena. Format: four to five hours of lecture and discussion per week. Course Director: Jonathan Dworkin.

The course emphasizes the molecular control of vertebrate embryogenesis. Divided into three main areas: early embryogenesis, developmental neurobiology, and the development and differentiation of specialized organs or lineages. Course Director: Andrew Tomlinson.

Advanced treatment of the principles and methods of the molecular biology of eukaryotes, emphasizing the organization, expression, and evolution of eukaryotic genes. Topics include reassociation and hybridization kinetics, gene numbers, genomic organization at the DNA level, mechanisms of recombination, transposable elements, DNA rearrangements, gene amplification, oncogenes, recombinant DNA techniques, transcription and RNA splicing. Students participate in discussions of problems sets on the current literature. Course Director: Tim Bestor.

This course is designed to illustrate how genetic systems have played a fundamental role in our understanding of basic biological problems. Topics include mitosis and meiosis, chromosomal linkage and mapping, consequences of chromosomal rearrangements, mechanisms of recombination and gene conversion, the use of mutants to study gene structure, regulation and the cell cycle, uses of recombinant DNA in genetic analysis, and the genetic analysis of development in Drosophila.

Survey of the major topics in basic immunology with an emphasis on the molecular basis for immune recognition and regulation. Course Director: Steven Reiner.

Course Director: Steven Reiner

Course Director: Anne Moscona

Course Director: Vincent Ferrera

Course Director: (Wesley Grueber)

An integrated and critical review of cancer biology, emphasizing recent research. Topics discussed include: natural history and epidemiology of cancer; morphology and behavior of cancer cells; DNA and RNA tumor viruses; oncogenes; tumor suppressor genes; signal transduction; the genetics of cancer; cancer and cellular differentiation; cancer causation: physical and chemical agents; multistage carcinogenesis; hormones, nutrients, and growth factors in cancer. Readings are largely original research papers and review articles. One 2-hour seminar per week. Course director: Richard Baer.

Course Director: Harmen Bussemaker

The Office of Graduate Affairs (OGA) interacts with trainees in the summer prior to matriculation to facilitate acquisition of Columbia sponsored housing. Off campus housing is available and facilitated by realtors who have long-standing working relations with Columbia housing administration.  The OGA holds a series of orientation events to acclimatize the students to the campus and the city, including an overnight camping and hiking trip, which gives the incoming students a good bonding experience. Following the retreat, you will have a number of lectures/mini-courses on Experimental Design, Research and Data Integrity, Laboratory Safety, Student Conduct, including sexual harassment and sexual violence prevention and response.  There will also be a poster session from current students in the graduate programs to give you a chance to find out more about the research that is being conducted by our students.

At orientation, the program director meets with the students to discuss the basics of the program, including course requirements, laboratory rotations, qualifying examinations, student seminars and any other requirements that they might have during their tenure as graduate students.  The program director is responsible for most of the direct advising of the students during the first year regarding coursework, rotations and any other issues that arise.  The program director also discusses possible mentors for their rotations.  The director meets with the first-year students for formal meetings three times a year, once at the beginning of the year and then at the end of each semester.  The program director is always available for any additional meetings at the student’s request.

Laboratory rotations provide an opportunity for each student to participate actively in ongoing research projects at Columbia, allowing the student to become familiar with techniques, literature and current questions in a variety of research areas.  Rotations also provide the opportunity to identify a mentor with whom to pursue thesis work.  Each graduate student will undertake 3 laboratory rotations (3–4 months in duration) during the first year. In late August/early September students discuss with the Program Director possible lab rotations for approval. The first rotation goes until winter break (third week in December), the second rotation goes from January-March and the third rotation from April-June. 

During the Late Spring/Early Summer semester, second year students take the Qualifying Exam. The student meets with the Director of program to discuss the program requirements and the selection of the faculty serving on the Qualifying Exam Committee. This examination is used as a formal evaluation of the student’s potential as a candidate for the Ph.D. degree. It is designed to assess the student’s ability to develop a sophisticated, in-depth understanding of their thesis project and it also serves as a tool for identifying deficiencies in the students’ background that could be remedied by further coursework or additional reading. The student along with his/her thesis advisor proposes three possible committee members who will serve as examiners.  The program director reviews the proposed committee members and if they approve the committee, will select one of them as chair who has been registered in this graduate program faculty members.  After the students submit their proposal, an oral examination is scheduled.  The exam consists of two parts: a written proposal and an oral defense of that proposal before an Examination Committee. 

Students present a written research proposal on their thesis topic. The proposal is written in the format of an NIH F31 pre-doc fellowship and consists of description of the background and significance of the topic, specific aims and research approaches to address the aims. The student will then deliver a 20 minute “chalk talk” presentation of the written proposal to the Examination Committee with an open panel discussion following. Though questions by the Examination Committee may initially focus on the proposal itself, this is a comprehensive examination where the student is expected to demonstrate an appropriate background in Pharmacology and an understanding of underlying principles.

The Director of the program meets with the student to discuss the selection of the Thesis Committee faculty.  The student, the thesis advisor and program director select a Thesis Research Advisory Committee of at least three members, including the advisor. The function of the Thesis Research Advisory Committee is to follow the student's research progress until its completion. Students usually schedule their first Thesis Committee Meeting during the late Fall or Early Spring of their 3rd year. Thesis Committees meets at least every 9 months. In case that committee meeting cannot be held in 9 months, student and thesis advisor will need to explain reason of the delay and request an approval of the program director. This Committee provides scientific expertise related to the student's projects and monitors thesis research. For the first Committee meeting the student presents a short written report that contains the Specific Aims of their proposal and any progress they have made since the qualifying examination.  The Committee discusses with the student the progress to date and the priorities for the order in which the work will proceed, as well as the chosen design of experiments. It is possible that the Committee may recommend changes to the experimental design or priorities. The Committee also decides when to have the next meeting, which can be in 6-9 months, but no longer than one year. For these subsequent meetings, the student prepares a 1-2 page report outlining their progress on the previous aims and presents their timetable for finishing their thesis work. The Committee can and should recommend improvements to experimental strategies and alternative plans for difficult or risky experiments.

After the thesis committee gives its approval for the student to finish writing the thesis, the defense is scheduled. The final thesis committee consists of the mentor, two existing program faculty members, and two additional examiners (one must be outside of the department and program). If the additional examiner is outside the University, they must be approved by the Program and the Dissertation Office as a competent examiner. The thesis should be submitted to the committee two weeks before the scheduled defense. A public seminar is given immediately before the closed defense. At the time of the closed defense, the student may be asked to make additional revisions that will then need to be approved by the mentor and one other member of the committee (assigned at the time of the defense).  On rare occasions, the student may be required to do additional experimental work, extensive thesis revisions or a second dissertation defense.  Students are expected to publish a first-author paper before their thesis is completed (at least, submit a first-author paper before their defense). 

Students participate in a bi-monthly journal club, where they present and critically analyze a recent paper to the department. This ongoing activity sharpens their presentation skills, enhances their critical thinking, and keeps them updated with the latest advancements in their field.