Sterling Hall of Medicine I313, 203.785.5846
M.S., M.Phil., Ph.D.
Directors of Graduate Studies
Professors Allen Bale, Susan Baserga (Molecular Biophysics & Biochemistry), W. Roy Breg, Jr. (Emeritus), Kristen Brennand (Psychiatry), Martina Brueckner (Pediatrics/Cardiology), Keith Choate (Dermatology), Lynn Cooley, Chris Cotsapas (Neurology), Daniel DiMaio, Casey Dunn (Ecology & Evolutionary Biology), Patrick Gallagher (Pediatrics), Joel Gelernter (Psychiatry; Neuroscience), Antonio Giraldez, Peter Glazer (Therapeutic Radiology), Valentina Greco, Jeffrey Gruen (Pediatrics), Murat Gunel (Neurosurgery), Ira Hall, Arthur Horwich, Yong-Hui Jiang, Mustafa Khokha (Pediatrics), Kenneth Kidd (Emeritus), Haifan Lin (Cell Biology), Maurice Mahoney (Emeritus), Shrikant Mane, Arya Mani (Internal Medicine), Michael Murray, Michael Nitabach (Cellular & Molecular Physiology), Valerie Reinke, Margretta Seashore (Emerita), Nenad Sestan (Neuroscience), Stefan Somlo (Internal Medicine/Nephrology), Berna Sozen, Peter Tattersall (Laboratory Medicine), Sherman Weissman, Hongyu Zhao (Public Health; Biostatistics)
Associate Professors Kaya Bilguvar, Sidi Chen, Daniel Greif (Internal Medicine/Cardiology), Marc Hammarlund, Smita Krishnaswamy, Peining Li, Janghoo Lim, Jun Lu, Stefania Nicoli (Internal Medicine/Cardiology), James Noonan, Sabrina Nunez, In-Hyun Park, Curt Scharfe, Zhaoxia Sun, Andrew Xiao
Assistant Professors Nadya Dimitrova (Molecular, Cellular, & Developmental Biology), Rama Kastury, Monkol Lek, Bluma Lesch, Mandar Muzumdar, Zachary Smith, Michele Spencer-Manzon, Kaelyn Sumigray, Siyuan Wang, Frederick Wilson (Internal Medicine/Oncology), Hui Zhang
Fields of Study
Molecular Genetics: chromosome structure and function, genetic recombination, viral genetics, DNA damage repair, ribosome biogenesis, protein folding, neurodegenerative diseases, non-coding RNA function, and the regulation of gene expression. Genomics: genome mapping, genome modification, high-throughput technology, evolutionary genetics, and functional genomics. Cellular and Developmental Genetics: limb development, kidney development, cilia function, stem cell development, genetic control of the cytoskeleton, cell death, aging, cell fate determination, cell cycle progression, cell migration, cell signaling, and growth control. Cancer Genetics: oncogenesis and tumor suppression, tumor progression and metastasis. Model Organism Genetics: forward genetic screens in Drosophila, C. elegans, yeast, zebrafish, frogs, and mouse, transposon and insertional mutagenesis, gene and protein trapping, mosaic genetics. Medical Genetics: genetic basis of human disease, chromosome rearrangements, population and quantitative genetics.
To enter the Ph.D. program, students apply to the Molecular Cell Biology, Genetics, and Development (MCGD) track within the interdepartmental graduate program in Biological and Biomedical Sciences (BBS), https://medicine.yale.edu/bbs.
Special Requirements for the Ph.D. Degree
The Ph.D. program in Genetics is designed to provide the student with a broad background in general genetics and the opportunity to conduct original research in a specific area of genetics. The student is expected to acquire a broad understanding of genetics, spanning knowledge of at least three basic areas of genetics, which include molecular, cellular, organismal, and population genetics. Normally this requirement is accomplished through the satisfactory completion of formal courses, many of which cover more than one of these areas. Students are required to pass at least five graduate-level courses that are taken for a grade. Advanced graduate study becomes increasingly focused on the successful completion of original research and the preparation of a written dissertation under the direct supervision of a faculty adviser along with the guidance of a thesis committee.
A qualifying examination is given during the second year of study. This examination consists of a period of directed reading with the faculty followed by the submission of two written proposals and an oral examination. Following the completion of course work and the qualifying examination, the student submits a dissertation prospectus and is admitted to candidacy for the Ph.D. degree. There is no language requirement. An important aspect of graduate training in genetics is the acquisition of communication and teaching skills. Students participate in presentation seminars and two terms (or the equivalent) of teaching. Teaching activities are drawn from a diverse menu of lecture, laboratory, and seminar courses given at the undergraduate, graduate, and medical school levels. Students are not expected to teach during their first year. In addition to all other requirements, students must successfully complete GENE900 and GENE901, Research Skills and Ethics I and II, prior to the end of their first year of study. In their fourth year of study, all students must successfully complete , RCR Refresher for Senior BBS Students. Students will typically take two to three courses each term and three research rotations (GENE 911, GENE 912, GENE 913) during the first year.
Students must meet the Graduate School’s Honors requirement by the end of the fourth term of full-time study.
M.D./Ph.D. students affiliate with the Department of Genetics graduate program via a different route than other incoming graduate students in the department, resulting in some modification of the academic requirements for the Ph.D. portion of the M.D./Ph.D. degree. Typically, one or more research rotations are done during the first two years of medical school (in many cases, the first rotation is done during the summer between years one and two). No set number of research rotations is required. M.D./Ph.D. students officially affiliate with the Department of Genetics after selecting a thesis adviser and consulting with the director of graduate studies (DGS). M.D./Ph.D. students interested in Genetics are required to consult with the DGS prior to formal affiliation to determine an appropriate set of courses tailored to the student’s background and interests.
The courses, rotations, and teaching requirements for M.D./Ph.D. students entering the Genetics graduate program (see below) are modified from the normal requirements for Ph.D. students. Besides the modifications in these three requirements, M.D./Ph.D. students in the Department of Genetics are subject to all of the same requirements as the other graduate students in the department.
Courses Four graduate-level courses taken for a grade are required. (Two Yale graduate-level courses taken for a grade during medical school may be counted toward this requirement at the discretion of the DGS.) Course work is aimed at providing a firm basis in genetics and in cellular molecular mechanisms, with graduate-level proficiency in genetics, cell biology, and biochemistry.
Required courses: In addition to the four graduate-level courses, all M.D./Ph.D. students must take: Graduate Student Seminar: Critical Analysis and Presentation of Scientific Literature (2 terms; GENE675 and GENE676, graded Satisfactory/Unsatisfactory); Responsible Conduct of Research (, graded Satisfactory/Unsatisfactory); and, in their fifth year of study, RCR Refresher for Senior BBS Students ().
Recommended courses: Advanced Eukaryotic Molecular Biology (GENE743); Biochemical and Biophysical Approaches in Molecular and Cellular Biology (MCDB630); Molecules to Systems (CBIO502); Science at the Frontiers of Medicine (CBIO601).
Electives: Other courses may be taken in a wide variety of fields relevant to the biological and biomedical sciences.
Laboratory rotations One or more rotations are necessary to identify a thesis adviser. No set number of research rotations is required.
Teaching One term of teaching is required. Previous teaching while enrolled at the Yale School of Medicine may count toward this requirement at the discretion of the DGS.
Qualifying exam M.D./Ph.D. students take their qualifying exam in the term following the completion of their course work. The structure of the qualifying exam is identical to that for other Ph.D. students in Genetics. Students read with three faculty members for five weeks, one of whom supervises the reading on the thesis research topic, but who is not the thesis adviser. The following two weeks are devoted to writing two research proposals, one on the student’s thesis research. An oral exam follows in the eighth week.
Prospectus M.D./Ph.D. students submit their prospectus once their qualifying exam has been completed, but no later than the 30th of June following their exam.
Candidacy M.D./Ph.D. students will be admitted to candidacy once they have completed their course work, obtained two Honors grades, passed their qualifying exam, and submitted their dissertation prospectus.
Thesis committee M.D./Ph.D. students are required to have one thesis committee meeting per year, beginning the term after passing their qualifying exam. However, students are strongly encouraged to consider having additional meetings if they feel their project could benefit from the assistance of members of the thesis committee.
M.Phil. See Degree Requirements under Policies and Regulations.
M.S. Students are not admitted for this degree. They may receive this recognition if they leave Yale without completing the qualifying exam but have satisfied the course requirements as described above, as well as the Graduate School’s Honors requirement. Students who are eligible for or who have already received the M.Phil. will not be awarded the M.S.
Prospective applicants are encouraged to visit the BBS website (https://medicine.yale.edu/bbs), MCGD Track.
GENE625a / MB&B625a / MCDB625a, Basic Concepts of Genetic Analysis Jun 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.
GENE645b / CB&B647b, Statistical Methods in Human Genetics Hongyu Zhao
Probability modeling and statistical methodology for the analysis of human genetics data are presented. Topics include population genetics, single locus and polygenic inheritance, linkage analysis, quantitative trait analysis, association analysis, haplotype analysis, population structure, whole genome genotyping platforms, copy number variation, pathway analysis, and genetic risk prediction models. Offered every other year. Prerequisites: genetics; BIS505; or equivalent; or permission of the instructor.
GENE655a / CBIO655a, Stem Cells: Biology and Application In-Hyun Park
This course is designed for first-year or second-year students to learn the fundamentals of stem cell biology and to gain familiarity with current research in the field. The course is presented in a lecture and discussion format based on primary literature. Topics include stem cell concepts, methodologies for stem cell research, embryonic stem cells, adult stem cells, cloning and stem cell reprogramming, and clinical applications of stem cell research. Prerequisites: undergraduate-level cell biology, molecular biology, and genetics.
GENE675a, Graduate Student Seminar: Critical Analysis and Presentation of Scientific Literature Mandar Muzumdar and Siyuan Wang
Students gain experience in preparing and delivering seminars and in discussing presentations by other students. A variety of topics in molecular, cellular, developmental, and population genetics are covered. Required of all second-year students in Genetics. Graded Satisfactory/Unsatisfactory.
GENE734b / MB&B734b / MBIO734b, Molecular Biology of Animal Viruses Brett Lindenbach
Lecture course with emphasis on mechanisms of viral replication, oncogenic transformation, and virus-host cell interactions.
GENE743b / MB&B743b / MCDB743b, Advanced Eukaryotic Molecular Biology Mark Hochstrasser, Wendy Gilbert, and Matthew Simon
Selected topics in transcriptional control, regulation of chromatin structure, mRNA processing including spliceosomal splicing, mRNA turnover, RNA interference, translational regulation, protein modification, and protein degradation. Emphasis is placed on how these processes are regulated and the experiments that led to their discovery and understanding. Prerequisite: biochemistry or permission of the instructor.
GENE760b, Genomic Methods for Genetic Analysis Steven Reilly and Siyuan Wang
Introduction to the analysis and interpretation of genomic datasets. The focus is on next-generation sequencing (NGS) applications including RNA-seq, ChIP-seq, and exome and whole genome sequencing. By the end of the course, each student will be able to process and analyze large-scale NGS datasets and interpret the results. This course is intended only for graduate students who are interested in applying genomic approaches in their thesis research. At a minimum, students must have basic familiarity with working in a UNIX/Linux computing environment. Prior experience with shell scripting or a scripting language such as Perl, Python, or Ruby is strongly recommended. Interested students must contact the instructor early in the fall term to discuss their prior experience and expectations for the course. Enrollment limited to twenty. Prerequisite: permission of the instructor.
GENE777b / MCDB677b, Mechanisms of Development Zhaoxia Sun
An advanced seminar on animal development focusing on conserved mechanisms during germline development, embryogenesis, and somatic differentiation in molecular details. The relationship between development and disease is also emphasized. The course format is one class comprised of a lecture and a paper discussion per week. Course work includes student participation in critical analysis of primary literature and biweekly take-home problems. Extensive class participation, especially in the discussion, is required. The course grade is based on 60 percent take-home problems and 40 percent class participation. There are no official prerequisites. However, some familiarity with concepts and techniques of modern biology is necessary to get the most out of the course.
GENE900a / CBIO900a / MCDB900a, Research Skills and Ethics I Shirin Bahmanyar
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.
GENE911a / CBIO911a / MCDB911a, First Laboratory Rotation Shirin Bahmanyar
First laboratory rotation for Molecular Cell Biology, Genetics, and Development track students.
GENE912a / CBIO912a / MCDB912a, Second Laboratory Rotation Shirin Bahmanyar
Second laboratory rotation for Molecular Cell Biology, Genetics, and Development track students.