Biochemistry, Molecular Biophysics, and Structural Biology

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.

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.

Required for all first year-students, this spring-semester course is an introduction to eukaryotic cell biology and covers such topics as membrane trafficking, mitochondria, nuclei, viral biology, and apoptosis, as well as the cytoskeleton and its role in various cellular processes, including mitosis, cell migration, cell polarity, and cell adhesion. Course Directors: Gregg Gundersen and Dritan Agalliu.

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 Director: Arthur Palmer.

This spring-semester course explores a variety of ethical and policy issues that can arise during 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. Course Director: Arthur Palmer.

Course Director: Ai Yamamoto.

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 Directors: Alexander Sobolevsky and 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.

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.

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.

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: Alberto Ciccia.

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

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 Directors: Teresa Palomero and Richard Baer.

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

The Office of Graduate Affairs (OGA) hosts a number of lectures/mini-courses on Experimental Design, Reesrach and Date Integrity, Laboratory Safety, Title IV Training and Student Conduct, including sexual harrassment and sexual violence prevention and responses.  OGA and the Graduate Student Organization (GSO) also hold a series of orientation events to acclimatize first-year students to the CUIMC campus and to NYC.  

The Program Directors and Coordinator interact with trainees in the summer prior to matriculation to help them get acquainted with the program, and to make sure that they have been able to make housing arrangements. The Program Directors meet virtually with incoming students during the summer to discuss possible mentors for their first rotation. Faculty are asked prior to these meetings whether they are willing/able to host a rotation student. At orientation, Program Directors meet with students to discuss the basics of the program, including course requirements, laboratory rotations, qualifying examinations and student seminars, and to answer any questions students may have. The Program Directors are responsible for advising first-year students regarding coursework, rotations and other issues that arise. They meet individually with the first-year students three times a year, once at orientation (in the beginning of the school year) and at the end of each semester. 

To create an equitable and inclusive method for students and potential mentors to meet one another, we created a faculty poster session. This poster session is open to all faculty on campus and is held during orientation week for new PhD students. Faculty are not allowed to send delegates in their place.

The most important information that students must have for rotation selection is the faculty research interests. As noted in Orientation session, there is a Faculty Poster Session during orientation that allows new students to learn more about the research at Columbia VP&S. Each faculty member also has a research description on the program website, but given the large number of faculty and areas of research that students can choose from, individual orientation interviews with the program directors are very important to help guide students to appropriate laboratories. Students are required to do at least two rotations, but they generally complete three rotations during their first year. The first rotation typically begins in September and lasts until winter break (~3rd week in December), the second rotation spans January-March and the third rotation is from April-June. Occasionally it is necessary for a student to do a fourth rotation, although this is not encouraged.   

The Program Coordinator obtains written rotation evaluations from faculty mentors at the end of the rotation period. The Program Directors discuss these reports with trainees during their regularly scheduled meetings at the end of each semester. In the event that trainees are having difficulties with rotations, the Program Directors will meet separately with trainees and rotation mentors to discuss problems that arose and how they can be addressed.

After the third rotation, students should choose a thesis laboratory in consultation with the Program Directors and their chosen mentors.

During the second semester of their second year, students prepare for their qualifying examinations. 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 also to serve as a tool for identifying deficiencies in the student’s background that could be remedied by further coursework and/or additional reading.   

Students present a written research proposal on their thesis topic.  The proposal is written in the format of an NIH F31 fellowship, consisting of a description of the background and significance of the topic, specific aims, and research approach to address the aims. Preliminary data can also be presented if available, but given that the examination occurs shortly after trainees begin their projects, it is not required. Students along with their thesis advisors propose three possible committee members who will serve as examiners. The Program Directors review the proposed committee members and, if they approve, a qualifying examination is scheduled by the student. Proposals are submitted to the committee one week prior to the examination, and a committee chair is chosen by the Program Directors.  At the qualifying examination, students present a ‘chalk talk’ of their proposal and are examined on the proposal, as well as other topics relevant to the project or covered in the students’ coursework.

6-9 months after the qualifying examination, students are expected to have their first thesis committee meeting. The thesis committee composition is typically the same as the qualifying examination committee, although occasionally one or more of the members might be replaced, particularly if a student’s research is going in a different direction. Thesis committees provide scientific expertise related to students’ research projects and monitor their progress. For the first committee meeting, students present 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 students their progress to date and priorities for the order in which work will proceed, as well as the design of experiments. The committee may recommend changes to experimental design or priorities. The committee also decides when to have the next meeting, which can occur 3, 6 or 9 months after the current meeting. For subsequent thesis committee meetings, students should prepare a 1-2 page report outlining their progress and presenting a timetable for experimental progress and thesis completion. The committee can and should recommend improvements to experimental strategies and fallback plans for difficult or risky projects. 

Guidelines for writing your thesis

Here are some guidelines for the order and content of what should be included in your Dissertation

Chapter 1: Introduction – this should be a scholarly synthesis of the background that forms the foundation for the thesis work. It should be comprehensive (30–40 pages) and have original (primary) references – avoid referencing other reviews. The level of detail should be similar to a review in the Annual Reviews series. 

Chapter 2: Materials and Methods – this section should contain all of the methods for the entire thesis. Even if the student has published a paper, they still should compile all the methods into one chapter. 

Chapters 3, 4, etc.: These chapters comprise results that are typically presented in individual manuscripts – each chapter should have a short (1–3 page) introduction, followed by results and figures (thesis format requires figures and legends on separate pages), and concluding with a short discussion. 

Final chapter: Conclusions and future directions. 

Appendices can include computer codes, tables, and any extra random results you want to put in the thesis but don’t belong to any manuscript.

After the thesis committee gives its approval for a student to write their thesis, the defense is scheduled. The final thesis committee consists of the mentor, the three thesis committee members, and one additional outside examiner. If the additional examiner is from outside the university, s/he has to 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 presentation 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 revisions of the thesis, and a second dissertation defense. Students are required to submit a first author paper before their defense. This paper can be submitted to bioRxiv. 

First and second year students participate in the Student Seminar series in both the fall and spring semesters. This series is held every other Tuesday evening and the overall goals of the Seminar course are to: 

• Learn about cellular & molecular biology, broadly defined 
• Learn about research at Columbia/VP&S 
• Learn about scientists as individuals 
• Learn how to give a research presentation to an educated – but non-expert – audience 
• Learn how to give useful feedback 
• Learn how to work as a team to plan and host a seminar series 

Fall Semester: Fall semester is structured as a ~bi-weekly seminar series, planned the prior Spring by rising second-year students in the Program. Second-year students host ~5-6 faculty speakers that are diverse in terms of research topics, personal identities, and career paths. Faculty speakers are asked to speak for ~20 minutes on their research and ~20 minutes on their career trajectory, with ~20 min for open discussion. 

Spring Semester: Spring semester is structured as a ~bi-weekly series where the speakers are first-year students. During each session, two first-year students will give a ~15 minute talk about one of their rotation projects. It is not the intention to overburden students amidst other coursework. In most cases, students will have given at least one presentation in at least one of their rotations, so they will have at least one slide presentation already prepared for use in this exercise. All students in attendance provide feedback on each presentation by submitting a survey form highlighting the strengths and weaknesses of the presentation. Course directors collect the feedback forms and meet with each presenter during the following week to discuss their presentation and provide constructive feedback. 

The program has an annual retreat. Every other year it is a 2-day event, overnight at an off-campus venue. On alternate years, it is a 1-day event held on-campus. Two senior PhD students and two junior faculty are selected to work together to plan the retreat. All presentations are by students.

The goal for this course is to help students navigate the world after the Ph.D.  We will have a series of 11 seminars on careers that our trainees most commonly choose or express interest in. Sessions will feature invited speakers, each with a Ph.D. in biomedical science. Speakers will introduce their experience from their Ph.D. to their current profession followed by questions and discussion.  A reception will follow. The seminar series is open to all PhD students and post-docs in the biomedical sciences.  Students and post-docs can optionally register for the course for credit, or drop in for one or more sessions. The final (optional) session will be a CV workshop for students and postdocs applying for academic positions. Course Directors: Shan Zha, Ron Liem, Becky Haeusler, and Yinghui Mao.