Molecular Biology Academic Year 2022 – 2023 Jump To: General Information Address Lewis Thomas Laboratory Phone 609-258-9455 Website Department of Molecular Biology Program Offerings: Ph.D. M.D./Ph.D. Director of Graduate Studies: Ileana Cristea Graduate Program Administrator: Melissa DiMeglio Overview The graduate program in the Department of Molecular Biology fosters the intellectual development of modern biologists. We welcome students from a variety of educational backgrounds and offer an educational program that goes well beyond traditional biology. The molecular biology department at Princeton is a tightly knit, cohesive group of scientists that includes undergraduate and graduate students, postdoctoral fellows, and faculty with diverse but overlapping interests. Graduate students have a wide choice of advisers, with a broad spectrum of interdisciplinary interests and research objectives. The graduate program offers all entering students the opportunity, with the help of faculty advisers, to design the intellectual program that best meets their unique scientific interests. Each student chooses a series of research rotations with faculty members in molecular biology and associated departments (chemistry, computer science, ecology and evolutionary biology, chemical and biological engineering, physics, and neuroscience). Entering students, with the aid of the graduate committee, select core and elective courses from a large number of offerings in a variety of departments and disciplines. This combination of a cohesive department, one-on-one advising, and individualized programs of course work and research provides an ideal environment for graduate students to flourish as independent scientists. Areas of concentration include biochemistry, biophysics, cancer, cell biology, computation and modeling, development, evolution, genetics, genomics, microbiology and virology, policy, and structural biology. Apply Application deadline December 1, 11:59 p.m. Eastern Standard Time (This deadline is for applications for enrollment beginning in fall 2023) Program length 5 years Fee $75 GRE General Test optional/not required Additional departmental requirements Optional: Applicants may submit a statement with their application, briefly describing how their academic interests, background, or life experiences would advance Princeton’s commitment to diversity within the Graduate School and to training individuals in an increasingly diverse society. Please submit a succinct statement of no more than 500 words. Program Offerings Ph.D. M.D./Ph.D. Courses By the end of the first year, students must have completed four core courses, achieving an average of B or better. Students may take additional elective courses that are closely related to their research topic. By the end of the third year, students must have completed MOL 561 - Scientific Integrity in the Practice of Molecular Biology. Additional pre-generals requirements Rotations Students must complete three laboratory rotations with different advisers as part of their research training during the first year of study (MOL 540, MOL 541 Research Projects); a fourth rotation is optional. Students who complete a full rotation (approximately 8 weeks of research) the summer before entering graduate school are assigned a rotation in September along with other entering students. A student may elect to work with any faculty member or associated faculty member of the program. Students who desire to work with faculty outside the program may do so only with the approval of the director of graduate studies. Faculty/Student Research Talks In the fall of their first year, graduate students attend a series of informal talks given by each faculty mentor. These discussions are designed to introduce first-year students to current research projects that might serve as rotation and thesis topics. Molecular Biology Annual Retreat The molecular biology annual retreat is a two-day symposium of research talks and poster sessions held in the fall and attended by all graduate students, postdoctoral fellows, and faculty in molecular biology and associated departments. Mol Bio Colloquia Graduate students, together with postdoctoral fellows and faculty, attend weekly research seminars given by graduate students and postdoctoral fellows. This colloquium provides both experience in the presentation of research results and a forum for scientific discussion with peers. General exam The general examination is usually administered in the January general examination period of the second year of study, after students have met all formal course requirements. This three-hour oral examination is administered by three faculty members from the graduate program, none of whom may be the student’s thesis adviser. The examination consists of two parts: the thesis proposal and second topic. The thesis proposal probes depth of knowledge in the chosen research field and examines the ability of the student to justify and defend the goals, significance, and the experimental logic and methods of the proposed plan. The second topic, or mini-proposal, is a two-page written document that uses an assigned research paper as the foundation for a research proposal. The student will propose a question and experiments to follow up on the results and/or conclusions in the assigned second topic paper. Qualifying for the M.A. The Master of Arts (M.A.) degree is normally an incidental degree on the way to full Ph.D. candidacy and is earned after successfully passing all parts of the general examination. It may also be awarded to students who, for various reasons, leave the Ph.D. program, provided that the following requirements are met: completion of the formal courses and three laboratory rotations required for Ph.D. students, and demonstration of an appropriate level of research competency. Research experience must include at least one year of independent work in the laboratory, and competency must be demonstrated in writing. A faculty mentor and the graduate committee must approve the master’s paper. Teaching Students are normally required to teach in two undergraduate-level courses. The first assignment is normally a laboratory course, while the second is normally a major undergraduate lecture course. Students may have the opportunity to do additional teaching if they wish to gain more experience. Post-Generals requirements Committee Meetings Each graduate student chooses a thesis committee that consists of the thesis adviser and two other faculty members who are knowledgeable in the student’s area of research. The thesis committee meets formally with the graduate student at least once per year, and sometimes more frequently on an informal basis. The responsibility of this committee is to advise students during the course of their research. Dissertation and FPO When the research is completed, the student writes the dissertation, which is first read by the adviser then by two additional readers chosen by the student. Usually, the second readers are the other members of the student’s thesis committee. Upon acceptance of the dissertation, the student gives a final, public oral presentation of the research to the department. The Ph.D. is awarded after the candidate’s doctoral dissertation has been accepted and the final public oral examination sustained. Program description The Princeton Graduate School has a partnership with the Robert Wood Johnson Medical School (RWJMS) and the Rutgers University (New Brunswick) Graduate School of Biomedical Sciences to serve as a Ph.D. site for students enrolled in the M.D./Ph.D. program of RWJMS. Students admitted to the M.D./Ph.D. program at RWJMS perform laboratory rotations at Princeton during the summer before and the summer after the first year of the pre-clinical portion of the program, prior to their enrollment as doctoral students, and subject to the approval of the faculty member. Following the second rotation, a student will choose a laboratory for Ph.D. research by mutual agreement with a faculty adviser and approval by the Graduate School. Students who are accepted to work with a faculty member in, or an affiliated faculty member of, the Department of Molecular Biology will enter the Ph.D. program and receive that degree from Princeton. These students will fulfill Graduate School and departmental requirements, including the one-year residence requirement, taking and passing the general examination, and sustaining the final public oral examination. (Pre-clinical coursework at RWJMS will typically substitute for the department’s core curriculum.) The Ph.D. portion of the joint program is expected to take three to four years. Extension beyond a fourth year requires approval from the Academic Affairs Committee of the joint degree program. For those students considering the dual degree program, please take time to review the M.D./Ph.D General information page. Courses M.D./Ph.D. students in the Department of Molecular Biology must take two courses, which can be either core or elective courses, from the approved departmental course list. Additional pre-generals requirements Molecular Biology Annual Retreat The molecular biology annual retreat is a two-day symposium of research talks and poster sessions held in the fall and attended by all graduate students, postdoctoral fellows, and faculty in molecular biology and associated departments. Mol Bio Colloquia Graduate students, together with postdoctoral fellows and faculty, attend weekly research seminars given by graduate students and postdoctoral fellows. This colloquium provides both experience in the presentation of research results and a forum for scientific discussion with peers. General exam The general examination is usually administered in the September/October general examination period of the second year of study, after students have met all formal course requirements. This two-hour oral examination is administered by three faculty members from the graduate program, none of whom may be the student’s thesis adviser. The examination consists of a thesis proposal which probes the depth of knowledge in the chosen research field and examines the ability of the student to justify and defend the goals, significance, and the experimental logic and methods of the proposed plan. Qualifying for the M.A. The Master of Arts (M.A.) degree is normally an incidental degree on the way to full Ph.D. candidacy and is earned after successfully passing all parts of the general examination. It may also be awarded to students who, for various reasons, leave the Ph.D. program, provided that the following requirements are met: completion of the formal course requirements and demonstration of an appropriate level of research competency. Research experience must include at least one year of independent work in the laboratory, and competency must be demonstrated in writing. A faculty mentor and the graduate committee must approve the master’s paper. Post-Generals requirements Committee Meetings Each graduate student chooses a thesis committee that consists of the thesis adviser and two other faculty members who are knowledgeable in the student’s area of research. The thesis committee meets formally with the graduate student at least once per year, and sometimes more frequently on an informal basis. The responsibility of this committee is to advise students during the course of their research. Dissertation and FPO When the research is completed, the student writes the dissertation, which is first read by the adviser then by two additional readers chosen by the student. Usually the second readers are the other members of the student’s thesis committee. Upon acceptance of the dissertation, the student gives a final, public oral presentation of the research to the department. The Ph.D. is awarded after the candidate’s doctoral dissertation has been accepted and the final public oral examination sustained. Faculty Chair Bonnie L. Bassler Associate Chair Jean E. Schwarzbauer Director of Graduate Studies Ileana M. Cristea Director of Undergraduate Studies Elizabeth R. Gavis Professor Bonnie L. Bassler Rebecca D. Burdine Ileana M. Cristea Elizabeth R. Gavis Zemer Gitai Frederick M. Hughson Yibin Kang Michael S. Levine Coleen T. Murphy Alexander Ploss Paul D. Schedl Jean E. Schwarzbauer Stanislav Y. Shvartsman Thomas J. Silhavy Jeffry B. Stock Ned S. Wingreen Nieng Yan Associate Professor Mohamed S. Abou Donia Danelle Devenport Martin C. Jonikas Alexei V. Korennykh Sabine Petry Jared E. Toettcher Assistant Professor Brittany Adamson John F. Brooks Michelle M. Chan John Jimah Ai Ing Lim Ricardo Mallarino Cameron A. Myhrvold Eszter Posfai Martin Helmut Wühr AJ te Velthuis Associated Faculty José L. Avalos, Chemical and Biological Eng Clifford P. Brangwynne, Chemical and Biological Eng Mark P. Brynildsen, Chemical and Biological Eng Daniel J. Cohen, Mechanical & Aerospace Eng Thomas Gregor, Physics Ralph E. Kleiner, Chemistry A. James Link, Chemical and Biological Eng Lindy McBride, Ecology & Evolutionary Biology Tom Muir, Chemistry Celeste M. Nelson, Chemical and Biological Eng Joshua D. Rabinowitz, Chemistry Mohammad R. Seyedsayamdost, Chemistry Joshua W. Shaevitz, Physics Stanislav Y. Shvartsman, Chemical and Biological Eng Mona Singh, Computer Science Howard A. Stone, Mechanical & Aerospace Eng John D. Storey, Integrative Genomics Olga G. Troyanskaya, Computer Science Samuel S. Wang, Princeton Neuroscience Inst Bridgett M. vonHoldt, Ecology & Evolutionary Biology Professor Emeritus (teaching) Sarah J. Flint Professor of the Practice Daniel A. Notterman University Lecturer Heather A. Thieringer Senior Lecturer Jodi Schottenfeld-Roames Lecturer Anthar S. Darwish Paola Estrada Gary S. Laevsky Laurel Lorenz Karin R. McDonald Daniel R. Weilandt For a full list of faculty members and fellows please visit the department or program website. Permanent Courses Courses listed below are graduate-level courses that have been approved by the program’s faculty as well as the Curriculum Subcommittee of the Faculty Committee on the Graduate School as permanent course offerings. Permanent courses may be offered by the department or program on an ongoing basis, depending on curricular needs, scheduling requirements, and student interest. Not listed below are undergraduate courses and one-time-only graduate courses, which may be found for a specific term through the Registrar’s website. Also not listed are graduate-level independent reading and research courses, which may be approved by the Graduate School for individual students. CHM 542 - Principles of Macromolecular Structure: Protein Folding, Structure and Design (also MOL 542) Structures and properties of biological macromolecules. The forces and interactions that direct biological polymers to adapt particular 3-dimensional structures are discussed from both a structural and a thermodynamic perspective. Special emphasis is placed on recent experimental work probing the folding and stability of proteins as well as on the design of novel proteins. COS 551 - Introduction to Genomics and Computational Molecular Biology (also MOL 551/QCB 551) Introduction to basic computational and genomic methods for analysis of biological systems. Topics include: sequence similarity and alignment, phylogenic inference, gene recognition, gene expression analysis, transcriptional networks, structure prediction, functional genomics and proteomics. This is primarily a graduate-level course; interested undergraduates will require permission from instructors. COS 557 - Analysis & Visualization of Large-Scale Genomic Data Sets (also MOL 557) Introduces students to computational issues involved in analysis and display of large-scale biological data sets. Algorithms covered will include clustering and machine learning techniques for gene expression and proteomics data analysis, biological networks, joint learning from multiple data sources, and visualization issues for large-scale biological data sets. No prior knowledge of biology or bioinformatics is required; an introduction to bioinformatics and the nature of biological data will be provided. In depth knowledge of computer science is not required, but students should have some understanding of programming and computation. MAT 586 - Computational Methods in Cryo-Electron Microscopy (also APC 511/MOL 511/QCB 513) This course focuses on computational methods in cryo-EM, including three-dimensional ab-initio modelling, structure refinement, resolving structural variability of heterogeneous populations, particle picking, model validation, and resolution determination. Special emphasis is given to methods that play a significant role in many other data science applications. These comprise of key elements of statistical inference, image processing, and linear and non-linear dimensionality reduction. The software packages RELION and ASPIRE are routinely used for class demonstration on both simulated and publicly available experimental datasets. MOL 504 - Cellular Biochemistry Couse focusses on the molecules and molecular assemblies that underlie cellular structure and function. Topics include: protein structure and folding; ligand binding and enzyme catalysis; membranes, ion channels and translocation; intracellular trafficking; signal transduction and cellular communication; and cytoskeleton assembly, regulation, and function. A major goal of the course is to increase students' proficiency in parsing and critically discussing papers from the primary literature. MOL 506 - Cell Biology and Development A continuation of MOL 504, with two modules, Cell Biology II and Development. Cell Biology II concerns how cells assemble into functional tissues, covering the molecular components and fundamental concepts in cell communication, adhesion, shape, division, and differentiation. Development covers the basics of developmental biology, focusing on important concepts and model systems. Primary literature is used to introduce seminal works and classic approaches, modern experimental techniques, and outstanding questions in the field. Students learn the basis of a good paper, to read critically, and to think beyond the reading. MOL 514 - Molecular Biology Advanced-level discussions of selected topics in prokaryotic and eukaryotic molecular biology. Emphasis is placed on original research papers and extensive reading together with critical thinking is required. Topics include the genetic code, mutagenesis, chromosome and chromatin structures, mechanisms of DNA replication, recombination, repair, and transposition, gene structure and function and mechanisms of gene regulation. Examples from bacteriophage, bacteria, lower and higher eukaryotes will be used to illustrate these different areas of molecular biology. MOL 518 - Quantitative Methods in Cell and Molecular Biology Modern biology increasingly relies on quantitative tools to precisely measure cellular states. This course aims to provide an introduction to the experimental techniques and computational methods that enable the quantitative study of biological systems. It focuses on generating and analyzing sequencing data for studying gene networks within/across species, modeling chemical reactions to study the dynamics of gene and protein networks, and extracting information about the spatial organization of biological systems using image processing. It also introduces Python programming, a versatile and powerful platform for scientific computing. MOL 523 - Molecular Basis of Cancer Course explores the molecular events that contribute to the onset and progression of human cancer. Reviews the central elements that make up the cell cycle, then surveys the signal transduction and checkpoint pathways that regulate and coordinate the cell cycle with other cellular events. Oncogenes, tumor suppressor genes and mutator genes will be discussed. Course then explores specific clinical case studies in light of the molecular events underlying different forms of cancer. MOL 540 - Research Projects in Molecular Biology (Laboratory Rotations) Students perform research in the laboratories of two faculty advisers. MOL 541 - Research Projects in Molecular Biology (Laboratory Rotations) Students perform research in the laboratories of two faculty advisers. MOL 558 - Psychopharmacology Medicinal chemistry, mechanisms of action, uses and abuses of drugs and botanical extracts that affect the central nervous system are examined. Relevant issues of mental health are addressed as well as implications for public health. The history and current public policies toward psychotropic drugs and natural products are discussed. Topics include pain management and opiate addiction, schizophrenia hallucinogens and anti-psychotics, anti-depressants and anxiolytics, mechanisms of addiction and withdrawal. MOL 559 - Viruses: Strategy and Tactics Viruses are unique parasites of living cells and may be the most abundant, highest evolved life forms on the planet. The general strategies encoded by all known viral genomes are discussed using selected viruses as examples. The first half of the course covers the molecular biology (the tactics) inherent in these strategies. The second half introduces the biology of engagement of viruses with host defenses, what happens when viral infection leads to disease, vaccines and antiviral drugs, and the evolution of infectious agents and emergence of new viruses. MOL 561 - Scientific Integrity in the Practice of Molecular Biology Through case studies and class discussion, this course will examine the social framework for the public support of basic biomedical research, the rights and responsibilities of students and mentors in the conduct of research, and the significance of intellectual property. Course will also review regulations concerning research with human subjects and animals. The nature of, and response to, personal misconduct will be a principal focus. Course satisfies the mandate of the National Institutes of Health for training molecular biologists in the ethical practice of science. MOL 567 - Electron Microscopy in Structural Biology (Half-Term) (also MSE 542) This course offers a comprehensive introduction to the theory and application of electron microscopy (EM) in biological research. The history for method development, detailed instructions on sample preparation, image acquisition, and data processing are covered. The emphasis of the course is on the use of the single-particle, cryo-EM by biological researchers. Students of other disciplines are welcome. Instruction consists of lectures, demonstrations, and hands-on experience using the electron microscopes in the Imaging and Analysis Center. NEU 501A - Cellular and Circuits Neuroscience (also MOL 501A) A survey of modern neuroscience in lecture format combining theoretical and computational/quantitative approaches. Topics include cellular neurophysiology, neuroanatomy, neural circuits and dynamics, neural development and plasticity, sensory systems, genetic model systems, and molecular neuroscience. This is one-half of a double-credit core course required of all Neuroscience Ph.D. students. NEU 501B - Neuroscience: From Molecules to Systems to Behavior (also MOL 501B) This lab course complements NEU 501A and introduces students to the variety of techniques and concepts used in modern neuroscience, from the point of view of experimental and computational/quantitative approaches. Topics will include synaptic transmission, fluorescent and viral tracers, patch clamp recording in brain slices, optogenetic methods to control neural activity, and computational modeling approaches. In-lab lectures give students the background necessary to understand the scientific content of the labs, but the emphasis is on the labs themselves. Second half of a double-credit core course required of all NEU Ph.D. students. NEU 502A - Systems and Cognitive Neuroscience (also MOL 502A/PSY 502A) A survey of modern neuroscience in lecture format combining theoretical and computational/quantitative approaches. Topics include systems and cognitive neuroscience, perception and attention, learning and behavior, memory, executive function/decision-making, motor control and sequential actions. Diseases of the nervous system are considered. This is one-half of a double-credit core course required of all Neuroscience Ph.D. students. NEU 502B - From Molecules to Systems to Behavior (also MOL 502B) This lab course complements NEU 502A and introduces students to the variety of techniques and concepts used in modern neuroscience, from the point of view of experimental and computational/quantitative approaches. Topics include electrophysiological recording, functional magnetic resonance imaging, psychophysics, and computational modeling. In-lab lectures give students the background necessary to understand the scientific content of the labs, but the emphasis is on the labs themselves. Second half of a double-credit core course required of all Neuroscience Ph.D. students. NEU 503 - Neurogenetics of Behavior (also MOL 503) How do seemingly simple organisms generate complex behaviors? Course will explore our current understanding of the genetic and neural basis for animal behavior, with an emphasis on cutting-edge research and model systems that are amenable to genetic manipulation. Each week students will discuss a new behavior with a focus on the underlying mechanisms; students will also lead discussions of primary literature. The goal of this course is to provide required background knowledge and critical thinking skills to move beyond the published literature to proposing original experiments. This effort will culminate in a final paper from each student. NEU 537 - Computational Neuroscience (also MOL 537/PSY 517) An introduction to the biophysics of nerve cells and synapses, the mathematical description of neural networks, and how neurons represent information. This course surveys computational modeling and data analysis methods for neuroscience and parallels some topics from 549, but from a computational perspective. Topics include representation of visual information, spatial navigation, short-term memory, and decision-making. Two 90 minute lectures, one laboratory. Lectures in common with MOL 437. Graduate students carry out and write up an in-depth semester-long project. Prerequisite: 410, or elementary knowledge of linear algebra. QCB 515 - Method and Logic in Quantitative Biology (also CHM 517/EEB 517/MOL 515/PHY 570) Close reading of published papers illustrating the principles, achievements and difficulties that lie at the interface of theory and experiment in biology. Two important papers, read in advance by all students, will be considered each week; emphasis will be on student discussion, not formal lectures. Topics include: cooperativity, robust adaptation, kinetic proofreading, sequence analysis, clustering, phylogenetics, analysis of fluctuations, maximum likelihood methods.