Genetics

Sterling Hall of Medicine I313, 203.785.5846
http://medicine.yale.edu/genetics
M.S., M.Phil., Ph.D.

Chair
Antonio Giraldez

Director of Graduate Studies
Marc Hammarlund

Professors Allen Bale, Susan Baserga (Molecular Biophysics & Biochemistry), W. Roy Breg, Jr. (Emeritus), Lynn Cooley, Daniel DiMaio, Patrick Gallagher (Pediatrics), Joel Gelernter (Psychiatry; Neuroscience), Antonio Giraldez, Peter Glazer (Therapeutic Radiology), Jeffrey Gruen (Pediatrics), Murat Gunel (Neurosurgery), Karen Hirschi (Internal Medicine/Cardiology), Arthur Horwich, Kenneth Kidd (Emeritus), Haifan Lin (Cell Biology), Maurice Mahoney (Emeritus), Shrikant Mane, Michael Nitabach (Cellular & Molecular Physiology), Charles Radding (Emeritus), Valerie Reinke, Margretta Seashore (Emerita), Nenad Sestan (Neuroscience), Stefan Somlo (Internal Medicine/Nephrology), Joann Sweasy (Therapeutic Radiology), Peter Tattersall (Laboratory Medicine), Sherman Weissman, Hongyu Zhao (Public Health; Biostatistics)

Associate Professors Martina Brueckner (Pediatrics/Cardiology), Keith Choate (Dermatology), Chris Cotsapas (Neurology), Valentina Greco, Daniel Greif (Internal Medicine/Cardiology), Marc Hammarlund, Natalia Ivanova, Mustafa Khokha (Pediatrics), Peining Li, Janghoo Lim, Jun Lu, Arya Mani (Internal Medicine), James Noonan, In-Hyun Park, Curt Scharfe, Zhaoxia Sun, Andrew Xiao

Assistant Professors Kaya Bilguvar, Sidi Chen, Smita Krishnaswamy, Monkol Lek, Bluma Lesch, Mandar Muzumdar, Stefania Nicoli (Internal Medicine/Cardiology), Michele Spencer-Manzon, 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.

Special Admissions Requirements

The department welcomes applicants who have a bachelor’s or master’s degree in biology, chemistry, or a related field, with experience (from course work and/or research) in the field of genetics. GRE General Test scores are required. A pertinent Subject Test in Biochemistry and Molecular Biology, Biology, or Chemistry is recommended.

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), http://bbs.yale.edu.

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 at the TF-10 level. 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 GENE 901, First-Year Introduction to Research—Ethics: Scientific Integrity in Biomedical Research, prior to the end of their first year of study. In their 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.

M.D./Ph.D. Students

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 is 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: Genomic Methods for Genetic Analysis (GENE 760); Graduate Student Seminar: Critical Analysis and Presentation of Scientific Literature (2 terms; GENE 675 and GENE 676, graded Satisfactory/Unsatisfactory); Ethics: Scientific Integrity in Biomedical Research (as part of GENE 901, graded Satisfactory/Unsatisfactory).

Recommended courses: Advanced Eukaryotic Molecular Biology (GENE 743); Biochemical and Biophysical Approaches in Molecular and Cellular Biology (MCDB 630); Molecules to Systems (CBIO 502); Frontiers (CBIO 601).

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.

Master’s Degrees

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 (http://bbs.yale.edu), MCGD Track.

Courses

GENE 555a / CB&B 555a / CPSC 553a, Machine Learning for BiologySmita Krishnaswamy

This course introduces biology as a systems and data science through open computational problems in biology, the types of high-throughput data that are being produced by modern biological technologies, and computational approaches that may be used to tackle such problems. We cover applications of machine-learning methods in the analysis of high-throughput biological data, especially focusing on genomic and proteomic data, including denoising data; nonlinear dimensionality reduction for visualization and progression analysis; unsupervised clustering; and information theoretic analysis of gene regulatory and signaling networks. Students’ grades are based on programming assignments, a midterm, a paper presentation, and a final project.
TTh 11:35am-12:50pm

GENE 625a / MB&B 625a / MCDB 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

GENE 655a / CBIO 655a, Stem Cells: Biology and ApplicationIn-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.
Th 1:30pm-3pm

GENE 675a and GENE 676b, Graduate Student Seminar: Critical Analysis and Presentation of Scientific LiteratureValentina Greco

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.
W 2pm-3:30pm

GENE 743b / MB&B 743b / MCDB 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

GENE 760b, Genomic Methods for Genetic AnalysisJames Noonan

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.
HTBA

GENE 777b / MCDB 677b, 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

GENE 900a / CBIO 900a / MCDB 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

GENE 901b / CBIO 901b / MCDB 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

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

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

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

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

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

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