Molecular, Cellular, and Developmental Biology

Kline Biology Tower, 203.432.3538
http://mcdb.yale.edu
M.S., Ph.D.

Chair
Vivian Irish

Director of Graduate Studies
Farren Isaacs

Professors Ronald Breaker, John Carlson, Lynn Cooley (Genetics), Craig Crews, Stephen Dellaporta, Paul Forscher, Mark Hochstrasser (Molecular Biophysics & Biochemistry), Scott Holley, Vivian Irish, Akiko Iwasaki (Immunobiology), Christine Jacobs-Wagner, Douglas Kankel, Paula Kavathas (Immunobiology), Haig Keshishian, Mark Mooseker, Thomas Pollard, Anna Pyle, Matthew Rodeheffer (Comparative Medicine), Joel Rosenbaum, Alanna Schepartz (Chemistry), Hugh Taylor (Obstetrics, Gynecology, & Reproductive Sciences), Robert Wyman

Associate Professors Murat Acar, Sreeganga Chandra (Neurology), Damon Clark, Thierry Emonet, Valerie Horsley, Farren Isaacs, Kathryn Miller-Jensen (Biomedical Engineering), Weimin Zhong

Assistant Professors Shirin Bahmanyar, David Breslow, Nadya Dimitrova, Joshua Gendron, Stavroula Hatzios, Yannick Jacob, Josien van Wolfswinkel

Fields of Study

Research in genetics and molecular biology encompasses studies of non-coding RNAs, genome engineering, genome organization and regulation, gene dosage, aging, bacterial chemotaxis, and oncogenes. Research topics in cellular and developmental biology include structure and dynamics of the cell cytoskeleton, molecular motors, chemical biology, the nuclear envelope, lncRNAs, regeneration, developmental biomechanics, vertebral column development, neural and epidermal stem cells, and systems developmental biology. Research in neurobiology focuses on growth cone motility, neural differentiation, synaptogenesis, visual perception, olfaction, and the formation of topographic maps. A Special Program in Plant Sciences provides research and training in the molecular genetics of flowering, epigenetics, the physiology of hormone action, pathogen defense systems, sex determination, and the circadian clock. Because of the breadth of the department, students are provided with unique training and research opportunities for interdisciplinary studies.

To enter the Ph.D. program, students apply to the Molecular Cell Biology, Genetics, and Development (MCGD) track; the Biochemistry, Quantitative Biology, Biophysics, and Structural Biology (BQBS) track; or the Plant Molecular Biology (PMB) track within the interdepartmental graduate program in Biological and Biomedical Sciences (BBS), http://bbs.yale.edu.

Special Admissions Requirements

Applicants should have obtained training in the structure, development, and physiology of organisms; the structure, biochemistry, and physiology of cells; genetics; elementary calculus; elementary physics; inorganic and organic chemistry; statistics or advanced mathematics. Lack of some prerequisites can be made up in the first year of graduate study. Students having different science training, such as degrees in chemistry, physics, or engineering, are encouraged to apply. In addition to the GRE General test, a Subject Test is recommended, preferably in Biology, or in Biochemistry, Cell and Molecular Biology.

Integrated Graduate Program in Physical and Engineering Biology (PEB)

Students applying to the MCGD or BQBS track of the Biological and Biomedical Sciences program may simultaneously apply to be part of the PEB program. See the description under Non-Degree-Granting Programs, Councils, and Research Institutes for course requirements, and http://peb.yale.edu for more information about the benefits of this program and application instructions.

Special Requirements for the Ph.D. Degree

Each student is expected to take at least three courses, in addition to MCDB 900/MCDB 901, First-Year Introduction to Research. With the help of a faculty committee, each student will plan a specific program that includes appropriate courses, seminars, laboratory rotations, and independent reading fitted to individual needs and career goals. There is no foreign language requirement. At the beginning of the third term of study, the student meets with a faculty committee to decide on a preliminary topic for dissertation work and to define the research areas in which the student is expected to demonstrate competence. By the end of the fall term of the second year, each student prepares a dissertation prospectus outlining the research proposed for the Ph.D. The student is admitted to candidacy for the Ph.D. when (1) the prospectus is accepted by a dissertation committee of faculty members, (2) the committee is satisfied that the student has demonstrated competence in the areas necessary to conduct the proposed work, and (3) the other requirements indicated above are fulfilled. The student should complete the requirements for admission to candidacy by the end of the fall term of the second year and no later than the end of the second year of study. Following admission to candidacy, students are required to meet with their thesis advisory committee at least once a year. The remaining requirements include completion of the dissertation research, presentation and defense of the dissertation, and submission of acceptable copies of the dissertation to the Graduate School and to the Center for Science and Social Science Information (CSSSI). All students are required to teach in two one-term (TF level 10) courses during their Ph.D. study, but not during the first year of graduate study. Requirements for M.D./Ph.D. students are the same as for Ph.D. students, except that a single term of teaching is required. During their first year of study, students must successfully complete MCDB 901, First-Year Introduction to Research—Ethics: Scientific Integrity in Biomedical Research, to fulfill the responsible conduct and ethics in research requirement. This requirement must be met prior to registering for a second year of study. Further, in the fourth year of study, all students must successfully complete B&BS 503, RCR Refresher for Senior BBS Students.

Honors Requirement

Students must meet the Graduate School’s Honors requirement by the end of the fourth term of full-time study. (See Course and Honors Requirements under Policies and Regulations.)

Master’s Degree

M.S. (en route to the Ph.D.) The minimum requirements for award of the Master of Science degree are (1) two academic years registered and in residence full-time in the graduate program; (2) satisfactory completion of the first two years of study and research leading to the Ph.D.; this requirement may be met either (a) by completing a minimum of five courses with an average grade of High Pass and at least one Honors grade, in addition to satisfactory performance in MCDB 900/MCDB 901, or (b) by (i) successfully completing at least three courses with an average grade of High Pass and at least one Honors grade, (ii) satisfactory performance in MCDB 900/MCDB 901, and (iii) passing the prospectus examination; (3) recommendation by the department for award of the degree, subject to final review and approval by the degree committee. No courses that were taken prior to matriculation in the graduate program, or in Yale College, or in summer programs may be applied toward these requirements.


Prospective applicants are encouraged to visit the BBS website (https://medicine.yale.edu/bbs), MCGD, BQBS, and PMB tracks.

Courses

MCDB 500a / MB&B 500a, BiochemistryRonald Breaker and Donald Engelman

An introduction to the biochemistry of animals, plants, and microorganisms, emphasizing the relations of chemical principles and structure to the evolution and regulation of living systems.
MWF 9:25am-10:15am

MCDB 504b, Responsible Conduct of ResearchStaff

This course meets the NIH requirement that students receive training in the responsible conduct of research at least every four years. Two ninety-minute sessions for MCDB students; additional sessions for fourth-year MCDB students. Attendance is taken, and students who attend both sessions receive a grade of Satisfactory. Graded Satisfactory/Unsatisfactory.
HTBA

MCDB 530a / IBIO 530a / MBIO 530a, Biology of the Immune SystemEric Meffre, David Schatz, Peter Cresswell, Jordan Pober, Joao Pedro Pereira, Ruslan Medzhitov, Craig Roy, Nikhil Joshi, Aaron Ring, Noah Palm, Kevan Herold, Carla Rothlin, and Carrie Lucas

The development of the immune system. Cellular and molecular mechanisms of immune recognition. Effector responses against pathogens. Immunologic memory and vaccines. Human diseases including allergy, autoimmunity, cancer, immunodeficiency, HIV/AIDS.
MWF 9:25am-10:15am

MCDB 550a / C&MP 550a / ENAS 550a / PHAR 550a, Physiological SystemsMark Saltzman and Stuart Campbell

The course develops a foundation in human physiology by examining the homeostasis of vital parameters within the body, and the biophysical properties of cells, tissues, and organs. Basic concepts in cell and membrane physiology are synthesized through exploring the function of skeletal, smooth, and cardiac muscle. The physical basis of blood flow, mechanisms of vascular exchange, cardiac performance, and regulation of overall circulatory function are discussed. Respiratory physiology explores the mechanics of ventilation, gas diffusion, and acid-base balance. Renal physiology examines the formation and composition of urine and the regulation of electrolyte, fluid, and acid-base balance. Organs of the digestive system are discussed from the perspective of substrate metabolism and energy balance. Hormonal regulation is applied to metabolic control and to calcium, water, and electrolyte balance. The biology of nerve cells is addressed with emphasis on synaptic transmission and simple neuronal circuits within the central nervous system. The special senses are considered in the framework of sensory transduction. Weekly discussion sections provide a forum for in-depth exploration of topics. Graduate students evaluate research findings through literature review and weekly meetings with the instructor.
MWF 9:25am-10:15am

MCDB 560b / C&MP 560b / ENAS 570b / PHAR 560b, Cellular and Molecular Physiology: Molecular Machines in Human DiseaseEmile Boulpaep

The course focuses on understanding the processes that transfer molecules across membranes at the cellular, molecular, biophysical, and physiological levels. Students learn about the different classes of molecular machines that mediate membrane transport, generate electrical currents, or perform mechanical displacement. Emphasis is placed on the relationship between the molecular structures of membrane proteins and their individual functions. The interactions among transport proteins in determining the physiological behaviors of cells and tissues are also stressed. Molecular motors are introduced and their mechanical relationship to cell function is explored. Students read papers from the scientific literature that establish the connections between mutations in genes encoding membrane proteins and a wide variety of human genetic diseases.
MWF 9:25am-10:15am

MCDB 561a / CB&B 561a / MB&B 561a / MBIO 561a / PHYS 561a, Introduction to Dynamical Systems in BiologyDamon Clark, Kathryn Miller-Jensen, and Jonathon Howard

Study of the analytic and computational skills needed to model genetic networks and protein signaling pathways. Review of basic biochemical concepts including chemical reactions, ligand binding to receptors, cooperativity, and Michaelis-Menten enzyme kinetics. Deep exploration of biological systems including: kinetics of RNA and protein synthesis and degradation; transcription activators and repressors; lyosogeny/lysis switch of lambda phage and the roles of cooperativity and feedback; network motifs such as feed-forward networks and how they shape response dynamics; cell signaling, MAP kinase networks and cell fate decisions; bacterial chemotaxis; and noise in gene expression and phenotypic variability. Students learn to model using MATLAB in a series of in-class hackathons that illustrate biological examples discussed in lectures.
TTh 2:30pm-3:45pm

MCDB 562b / AMTH 765b / CB&B 562b / INP 562b / MB&B 562b / PHYS 562b, Dynamical Systems in BiologyThierry Emonet and Jonathon Howard

This course covers advanced topics in computational biology. How do cells compute, how do they count and tell time, how do they oscillate and generate spatial patterns? Topics include time-dependent dynamics in regulatory, signal-transduction, and neuronal networks; fluctuations, growth, and form; mechanics of cell shape and motion; spatially heterogeneous processes; diffusion. This year, the course spends roughly half its time on mechanical systems at the cellular and tissue level, and half on models of neurons and neural systems in computational neuroscience. Prerequisite: MCDB 561 or equivalent, or a 200-level biology course, or permission of the instructor.
TTh 2:30pm-3:45pm

MCDB 570b, BiotechnologyCraig Crews, Ronald Breaker, Timothy Nelson, and Joseph Wolenski

The principles and applications of cellular, molecular, and chemical techniques that advance biotechnology. Topics include the most recent tools and strategies used by government agencies, industrial labs, and academic research to adapt biological and chemical compounds as medical treatments, as industrial agents, or for the further study of biological systems.
MW 11:35am-12:50pm

MCDB 585b, Research in MCDB for B.S./M.S. CandidatesDouglas Kankel

A two-credit course taken in the third-to-last term (typically the second term of the junior year). At the start of this course, each student forms a committee composed of the student’s adviser and two faculty members that meets to discuss the research project. At the end of this course, students complete a detailed prospectus describing their thesis project and the work completed thus far. The committee evaluates an oral and written presentation of this prospectus; the evaluation determines whether the student may continue in the combined program. Required of students in the joint B.S./M.S. program with Yale College.  2 Course cr
HTBA

MCDB 591a / ENAS 991a / MB&B 591a / PHYS 991a, Integrated WorkshopCorey O'Hern, Mark Gerstein, Scott Holley, Marcus Bosenberg, Madhusudhan Venkadesan, Michael Murrell, and Nikhil Malvankar

This required course for students in the PEB graduate program involves a series of modules, co-taught by faculty, in which students from different academic backgrounds and research skills collaborate on projects at the interface of physics, engineering, and biology. The modules cover a broad range of PEB research areas and skills. The course starts with an introduction to Matlab, since Matlab is used throughout the course for analysis, simulations, and modeling.  ½ Course cr
MW 9am-10:15am

MCDB 595a, Intensive Research in MCDB for B.S./M.S. CandidatesDouglas Kankel

A four-credit, yearlong course (two credits each term) that is similar to MCDB 495/496 and is taken during the senior year. During this course, students give an oral presentation describing their work. At the end of the course, students are expected to present their work to the department in the form of a poster presentation. In addition, students are expected to give an oral thesis defense, followed by a comprehensive examination of the thesis conducted by the thesis committee. Upon successful completion of this examination, as well as other requirements, the student is awarded the combined B.S./M.S. degree. Required of students in the joint B.S./M.S. program with Yale College.  2 Course cr
HTBA

MCDB 602a / CBIO 602a / MB&B 602a, Molecular Cell BiologyCharles Lusk, Michael Caplan, Nadya Dimitrova, Thomas Pollard, James Rothman, Valerie Horsley, Thomas Melia, Megan King, Martin Schwartz, Christopher Burd, Josephina van Wolfswinkel, and David Breslow

A comprehensive introduction to the molecular and mechanistic aspects of cell biology for graduate students in all programs. Emphasizes fundamental issues of cellular organization, regulation, biogenesis, and function at the molecular level. Prerequisites: none, but some knowledge of basic cell biology and biochemistry is assumed. Students who have not taken courses in these areas can prepare by reading relevant sections in basic molecular cell biology texts. We recommend Pollard et al., Cell Biology (3rd ed., 2016), Alberts et al., Molecular Biology of the Cell (6th ed., 2014), or Lodish et al., Molecular Cell Biology (8th edition, 2016).
MW 1:45pm-3pm

MCDB 603a / CBIO 603a, Seminar in Molecular Cell BiologyCharles Lusk, Michael Caplan, Nadya Dimitrova, Thomas Pollard, James Rothman, Valerie Horsley, Thomas Melia, Megan King, Martin Schwartz, Christopher Burd, and David Breslow

A graduate-level seminar in modern cell biology. The class is devoted to the reading and critical evaluation of classical and current papers. The topics are coordinated with the CBIO 602 lecture schedule. Thus, concurrent enrollment in CBIO 602 is required.
Th 9am-11am

MCDB 625a / GENE 625a / MB&B 625a, Basic Concepts of Genetic AnalysisJun Lu

The universal principles of genetic analysis in eukaryotes are discussed in lectures. Students also read a small selection of primary papers illustrating the very best of genetic analysis and dissect them in detail in the discussion sections. While other Yale graduate molecular genetics courses emphasize molecular biology, this course focuses on the concepts and logic underlying modern genetic analysis.
MW 11:35am-12:50pm

MCDB 630b / MB&B 630b, Biochemical and Biophysical Approaches in Molecular and Cellular BiologyThomas Pollard, Karen Anderson, and Titus Boggon

This course introduces the theory and application of biochemical and biophysical methods to study the structure and function of biological macromolecules. The course considers the basic physical chemistry required in cellular and molecular biology but does not require a previous course in physical chemistry. One class per week is a lecture introducing a topic. The second class is a discussion of one or two research papers utilizing those methods. Does not count for graduate course credit for BQBS graduate students.
TTh 2:30pm-3:45pm

MCDB 650a, EpigeneticsJosephina van Wolfswinkel and Nadya Dimitrova

Study of epigenetic states and the various mechanisms of epigenetic regulation, including histone modification, DNA methylation, nuclear organization, and regulation by noncoding RNAs. Detailed critique of papers from primary literature and discussion of novel technologies, with specific attention to the role of epigenetics in development and its impact on human health. Prerequisite: permission of the instructor.
W 10:15am-11:30am, W 11:35am-12:50pm, F 11:35am-12:50pm

MCDB 670b, Advanced Seminar in Biochemistry and GeneticsRonald Breaker, Stephen Dellaporta, and Josephina van Wolfswinkel

This seminar is designed to expand students’ abilities to critically read and evaluate the primary scientific literature relevant to some of the most active areas of biochemical and genetic research. Special emphasis is placed on topics that deal with recent discoveries in nucleic acids, such as catalytic RNA and DNA, functions of noncoding RNA, gene regulation by RNA, and genomic processing and instability. Students read assigned papers in advance. Discussion focuses on experimental design used by the authors, results of the experiments, and conclusions drawn by the authors.
W 1:30pm-3:20pm

MCDB 677b / GENE 777b, Mechanisms of DevelopmentZhaoxia Sun

An advanced course on mechanisms of animal development focusing on the genetic specification of cell organization and identity during embryogenesis and somatic differentiation. The use of evolutionarily conserved signaling pathways to carry out developmental decisions in a range of animals is highlighted. Course work includes student participation in critical analysis of primary literature and a research proposal term paper.
W 1:30pm-3:20pm

MCDB 720a, NeurobiologyHaig Keshishian and Paul Forscher

Examination of the excitability of the nerve cell membrane as a starting point for the study of molecular, cellular, and intracellular mechanisms underlying the generation and control of behavior.
MWF 11:35am-12:25pm

MCDB 743b / GENE 743b / MB&B 743b, Advanced Eukaryotic Molecular BiologyMark Hochstrasser and Wendy Gilbert

Selected topics in transcriptional control, regulation of chromatin structure, mRNA processing, mRNA stability, RNA interference, translation, protein degradation, DNA replication, DNA repair, site-specific DNA recombination, somatic hypermutation. Prerequisite: biochemistry or permission of the instructor.
TTh 11:35am-12:50pm

MCDB 752b / CB&B 752b / CPSC 752b / MB&B 752b, Biomedical Data Science: Mining and ModelingMark Gerstein

Biomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. It represents a major practical application for modern techniques in data mining and simulation. Specific topics to be covered include sequence alignment, large-scale processing, next-generation sequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, normalization of microarray data, mining of functional genomics data sets, and machine-learning approaches to data integration. Prerequisites: biochemistry and calculus, or permission of the instructor.
MW 1pm-2:15pm

MCDB 900a / CBIO 900a / GENE 900a, Research Skills and Ethics IValerie Horsley

This course consists of a weekly seminar that covers ethics, writing, and research methods in cellular and molecular biology as well as student presentations (“rotation talks”) of work completed in the first and second laboratory rotations. 
M 4pm-5:30pm

MCDB 901b / CBIO 901b / GENE 901b, Research Skills and Ethics IIJoerg Bewersdorf

This course consists of a weekly seminar that covers ethics, writing, and research methods in cellular and molecular biology as well as student presentations (“rotation talks”) of work completed in the third laboratory rotation.
Th 4pm-5:30pm

MCDB 902a or b and MCDB 903b, Advanced Graduate SeminarStaff

The course allows students to hone their presentation skills through yearly presentation of their dissertation work. Two students each give thirty-minute presentations in each class session. Students are required to present every year beginning in their third year in the MCDB program. Each MCDB graduate student is expected to attend at least 80 percent of the class sessions. Two faculty members co-direct the course, attend the seminars, and provide feedback to the students.
HTBA

MCDB 911a / CBIO 911a / GENE 911a, First Laboratory RotationValerie Horsley

First laboratory rotation for Molecular Cell Biology, Genetics, and Development track students.
HTBA

MCDB 912a / CBIO 912a / GENE 912a, Second Laboratory RotationValerie Horsley

Second laboratory rotation for Molecular Cell Biology, Genetics, and Development track students.
HTBA

MCDB 913b / CBIO 913b / GENE 913b, Third Laboratory RotationValerie Horsley

Third laboratory rotation for Molecular Cell Biology, Genetics, and Development track students.
HTBA

MCDB 950a and MCDB 951b, Second-Year ResearchStaff

By arrangement with faculty.
HTBA