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

Chair
Valerie Reinke

Directors of Graduate Studies
Janghoo Lim
James Noonan

Professors Allen Bale, Susan Baserga (Molecular Biophysics and Biochemistry/Therapeutic Radiology), Kristen Brennand (Psychiatry), Martina Brueckner (Pediatrics/Cardiology), Keith Choate (Dermatology), Lynn Cooley, Daniel DiMaio, Casey Dunn (Ecology and Evolutionary Biology), Joel Gelernter (Psychiatry; Neuroscience), Antonio Giraldez, Peter Glazer (Therapeutic Radiology), Valentina Greco, Daniel Greif (Internal Medicine/Cardiovascular Medicine), Jeffrey Gruen (Pediatrics), Murat Günel (Neurosurgery), Ira Hall, Marc Hammarlund, Arthur Horwich (Emeritus), Yong-Hui Jiang, Kenneth Kidd (Emeritus), Peining Li, Janghoo Lim, Haifan Lin (Cell Biology), Maurice Mahoney (Emeritus), Shrikant Mane, Arya Mani (Internal Medicine/Cardiovascular Medicine), Margaret McGovern (School of Medicine), Michael Nitabach (Cellular and Molecular Physiology), James Noonan, Valerie Reinke, Clemens Scherzer (Neurology), Margretta Seashore (Emeritus), Nenad Sestan (Neuroscience), Stefan Somlo (Internal Medicine/Nephrology), Zhaoxia Sun, Sherman Weissman, Hongyu Zhao (Public Health; Biostatistics)

Associate Professors Sidi Chen, Nadya Dimitrova (Molecular, Cellular, and Developmental Biology), Smita Krishnaswamy, Monkol Lek, Bluma Lesch, Jun Lu, Mandar Muzumdar, Stefania Nicoli (Internal Medicine/Cardiovascular Medicine), Sabrina Nunez, In-Hyun Park, Michele Spencer-Manzon, Silvia Vilarinho (Medicine; Pathology), Siyuan Wang, Frederick Wilson (Internal Medicine/Oncology), Andrew Xiao, Hui Zhang

Assistant Professors Xin Bi, Grace Chen (Immunobiology), Maurizio Chioccioli (Comparative Medicine), Nada Derar, Salil Garg, Teodoro Jerves Serrano, Anupama Jha, Evan Koch, Nicole Lake, Stephen Lanno, Deqiong Ma, Diyendo Massilani, Steven Reilly, Trevor Sorrells, Kaelyn Sumigray, Lena Sweeney (Obstetrics, Gynecology, and Reproductive Sciences), Abhinav Thakral, Jia Di Wen, Chen Zhao

Human Genome Sciences Faculty
Professors Allen Bale, Kristen Brennand (Psychiatry), Martina Brueckner (Pediatrics/Cardiology), Keith Choate (Dermatology), Joel Gelernter (Psychiatry/Neuroscience), Jeffrey Gruen (Pediatrics), Ira Hall, Yong-Hui Jiang, James Noonan, Lucila Ohno-Machado (Biomedical Informatics and Data Science), Valerie Reinke, Clemens Scherzer (Neurology), Zhaoxia Sun, Jeffrey Townsend (Biostatistics), Roel Verhaak (Neurosurgery), Hongyu Zhao (Public Health; Biostatistics)
 
Associate Professors Sidi Chen, Monkol Lek, Bluma Lesch, Ping Mu (Urology), Maria Rodriguez Martinez (Biomedical Informatics and Data Science), Edward Stites (Laboratory Medicine), David van Dijk (Cardiovascular Medicine)
 
Assistant Professors Sarah Aitken (Pathology), David Alagpulinsa (Comparative Medicine/Cardiovascular Medicine), Haoyu Cheng (Biomedical Informatics and Data Science), Hoon Cho (Biomedical Informatics and Data Science), Matthew Girgenti (Psychiatry), Anupama Jha, Jihoon Kim (Biomedical Informatics and Data Science), William Kim (Urology), Evan Koch, Nicole Lake, Qiao Liu (Biostatistics), Diyendo Massilani, Emily Olfson (Child Study Center), Steven Reilly, Trevor Sorrells, Sai Zhang (Biomedical Informatics and Data Science)

The Genetics Ph.D. program consists of two subprograms: the General Genetics Subprogram and the Human Genome Sciences (HGS) Subprogram.

General Genetics Subprogram Fields of Study

Cancer genetics: oncogenesis and tumor suppression, tumor progression, and metastasis. Cellular and developmental genetics: the genetic basis of germline development, skin development, internal organ development, stem cell development, genetic control and the role of the cilium, cytoskeleton, cell fate determination, cell cycle progression, cell migration, cell signaling, growth control and cell death during development, homeostasis and aging. Molecular genetics: chromosome structure and function, genetic recombination, mosaic genetics, viral genetics, DNA damage repair, ribosome biogenesis, protein folding, neurodegenerative diseases, non-coding RNA function, and the regulation of gene expression. Model Organism Genetics: forward genetic screens and targeted genetic manipulations in Drosophila, C. elegans, zebrafish, frogs, mouse, organoids, and stem-cell-based embryo models.

To enter the General Genetics 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.

Human Genome Sciences (HGS) Subprogram Fields of Study:

Genomic analysis: genome mapping, genome modification and gene editing, genome stability, evolutionary genetics and genomics, functional genomics. Human genetics: genetic basis of human disease, genetic and genomic variation, population, quantitative and evolutionary genetics and genomics. Genome technologies: 3D genomics, transcriptomics, spatial transcriptomics, single-cell genomics, epigenomics. Applied genetics and genomics: stem cell genomics, cancer genomics, neurogenomics, precision medicine, immunoinformatics, cardiogenomics, metabolomics, mitochondrial disease genetics and genomics. Computational genomics and bioinformatics: systems genomics, biomedical informatics, network biology, data science, statistical modeling, deep learning, machine learning, artificial intelligence.

To enter the HGS Subprogram, students apply to the Human Genome Sciences Track within the interdepartmental graduate program in Biological and Biomedical Sciences (BBS), https://medine.yale.edu/bbs

Requirements for the Ph.D. Degree

The Ph.D. program in Genetics is designed to provide the student with general training in 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 as well as expertise relevant to their dissertation research. Normally this requirement is accomplished through the satisfactory completion of formal courses, many of which cover several fundamental topics in genetics, as well as the qualifying exam. 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.

Laboratory Rotations and Choosing a Thesis Adviser Students must complete rotations in at least three laboratories in their first year in the MCGD or HGS program before selecting a thesis adviser. In the General Genetics Subprogram, the student’s dissertation adviser must hold a primary or secondary appointment in Genetics in order for the student to join the department. In the HGS program, the students dissertation adviser must be affiliated with HGS in order for the student to join the department.

Courses Students in both the General Genetics and the HGS Subprograms typically take two to three courses each term and three research rotations (GENE 9110, GENE 9120, GENE 9130) during the first year.

Students in the General Genetics Subprogram are required to pass at least five graduate level courses that are taken for a grade. The required Graduate Student Seminar course (GENE 6750/GENE 6760, two terms, graded Satisfactory/Unsatisfactory) is taken in the second year. In addition to all other requirements, students must successfully complete GENE 9000 and GENE 9010, 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 MCDB 5040, RCR Refresher for Senior BBS Students. 

Students in the Human Genome Science Subprogram are required to pass at least four graduate-level courses that are taken for a grade, including three HGS core courses GENE 6500, GENE 7600, and CB&B 5750. Students may be granted course waivers on a case-by-case basis at the discretion of the DGSs; these decisions are final and may not be appealed. There is a required graduate-student seminar course for students within the HGS subprogram (two terms, graded Satisfactory/Unsatisfactory) which is taken in the second year. Students in the HGS subprogram will meet their requirements for research and ethics training by taking GENE 6500 and GENE 7600 in the fall of their first year and by taking GENE 9010, Research Skills and Ethics II, in the spring of their first year. In their fourth year of study, all students must successfully complete MCDB 5040, RCR Refresher for Senior BBS Students. 

Students in both subprograms must meet the graduate school’s Honors requirement by the end of the fourth term of full-time study. Students must also maintain a High Pass average as required by the graduate school.

Qualifying Exam The process and requirements for the qualifying exam are identical between the General Genetics and HGS Subprograms. The qualifying exam (informally, QE or Quals) is an essential step in graduate-student training. The overarching goal is to provide a launching pad for the student to embark on a successful thesis project. The qualifying exam typically spans eight weeks and must be completed by December 15 in the student’s second year. The exam consists of three parts:

1. A five-week reading period during which the student discusses a selection of primary research articles with each of three Qualifying Committee faculty readers. The adviser will not be a member of the Qualifying Committee and will not participate in the oral defense.
2. A two-week writing period during which the student writes an original research proposal modeled on the NIH F31 NRSA application and focused on the student’s planned thesis work.
3. A one-week presentation period during which the student prepares an oral defense of the research proposal. The exam culminates in a two-hour oral defense of the research proposal, during which the committee provides feedback on the student’s oral and written presentations and evaluates the readiness of the student to proceed with their proposed research.

Dissertation Prospectus and Admission to Candidacy The process and requirements for the dissertation prospectus and admission to candidacy are identical between the General Genetics and HGS Subprograms. By January 15 of their third year, each student must prepare a written summary of the proposed nature and scope of the thesis research, together with a provisional title for the dissertation, following the format described in the Genetics Department Handbook. This document should be written in clear, plain English with minimal jargon, abbreviations, or colloquialisms. The student’s adviser must review the prospectus and indicate their approval in writing via an email to the DGS. The student then sends the prospectus and the adviser’s approval to their DGS, who may require additional changes, for review. Once the DGS has approved the prospectus, the student sends the prospectus and approval emails to the Genetics registrar for their file and so it may be noted on their transcript. Students will not be admitted to candidacy nor will they be allowed to register for their fourth year of study without an approved prospectus.

In order to be admitted to candidacy, the student must fulfill (1) all course requirements, (2) the Honors requirement, (3) the qualifying examination, (4) the dissertation prospectus, and (5) holding a satisfactory Thesis Committee meeting, at the conclusion of which, the committee will give their assent for the student to be admitted to candidacy. Upon completion of these requirements, final approval for admission to candidacy is granted during a subsequent faculty meeting—usually in late spring of the third year of study.

Thesis Committee The role and requirements for assembling the Thesis Committee are identical between the General Genetics and HGS Subprograms, with exceptions noted below. The Thesis Committee normally comprises three to four faculty members, including the student’s adviser, and is assembled by the student in consultation with the thesis adviser. In the General Genetics Subprogram, at least two members (including the adviser) must have primary or secondary appointments in the Department of Genetics. In the HGS Subprogram, the adviser must be affiliated with HGS and at least one other member must hold a primary or secondary appointment in Genetics or Biomedical Informatics and Data Sciences (BIDS). If a committee member outside of Yale is included, the committee should consist of: the advisor, two Yale faculty members, and the outside committee member, making four members in total. Names of committee members should be submitted to the DGS for approval, with the Genetics registrar copied, within the first month of the spring semester of the student’s second year. Students in years two and three are required to meet with their committee at least once per year, while students in year four and beyond are required to meet with their committee every six months. 

Teaching and Departmental Presentations An important aspect of graduate training in genetics is the acquisition of communication and teaching skills. Students participate in departmental 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 until they pass their qualifying exam. Students are also expected to present in the departmental Research in Progress seminar.

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 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 directors of graduate studies (DGSs). M.D.-Ph.D. students may affiliate with the General Genetics or HGS Subprograms and are required to consult with the DGSs prior to formal affiliation to determine an appropriate set of courses tailored to the student’s training 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.

Laboratory Rotations and Choosing a Thesis Adviser One or more rotations are necessary to identify a thesis adviser. No set number of research rotations is required. The student’s dissertation adviser must hold a primary or secondary appointment in Genetics or HGS (if the student is affiliating with that subprogram) in order for the student to join the department.

Courses for M.D-Ph.D. Students in the General Genetics Subprogram Four graduate-level courses taken for a grade are required. Yale graduate-level courses taken for a grade during medical school may be counted toward this requirement at the discretion of the DGSs; these decisions are final and may not be appealed. Coursework 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 joining the department via the General Genetics Subprogram must take: Graduate Student Seminar (GENE 6750 and GENE 6760, two terms, graded Satisfactory/Unsatisfactory); Responsible Conduct of Research (B&BS 5501, graded Satisfactory/Unsatisfactory); and, in their fifth year of study, RCR Refresher for Senior BBS Students (MCDB 5040).

Electives: Other courses may be taken in a wide variety of fields relevant to the biological and biomedical sciences.

Courses For M.D.-Ph.D. Students in the HGS Subprogram Four graduate-level courses taken for a grade are required, including the three core HGS courses listed above. Graduate-level courses taken for a grade may be counted toward this requirement at the discretion of the DGSs; these decisions are final and may not be appealed. Coursework is aimed at providing a firm basis in human genetics and genomic analysis, with graduate-level proficiency in genomic analysis, quantitative and statistical methods used to study human genetics, and bioinformatics. 

Required courses: In addition to the four graduate-level courses, all M.D.-Ph.D. students joining the department via the HGS Subprogram must take: the HGS-specific Graduate Student Seminar (two terms, graded Satisfactory/Unsatisfactory); Responsible Conduct of Research (B&BS 5501, graded Satisfactory/Unsatisfactory); and, in their fifth year of study, RCR Refresher for Senior BBS Students.

Electives: Other courses may be taken in a wide variety of fields relevant to the biological and biomedical sciences.

Qualifying Exam M.D.-Ph.D. students take their qualifying exam in the second year in the Ph.D. program. The structure of the qualifying exam is identical to that for other Ph.D. students in genetics as described above.

Dissertation Prospectus and Admission to Candidacy The process and requirements for the dissertation prospectus and admission to candidacy for M.D.-Ph.D. students are identical between the General Genetics and HGS Subprograms. M.D.-Ph.D. students submit their prospectus in their second year in the Ph.D. program once their qualifying exam has been completed, but no later than April 30 following their exam. Each student must prepare a written summary of the proposed nature and scope of the thesis research, together with a provisional title for the dissertation, following the format described in the Genetics Department Handbook. This document should be written in clear, plain English with minimal jargon, abbreviations, or colloquialisms. The student’s adviser must review the prospectus and indicate their approval in writing via an email to the DGS. The student then sends the prospectus and the adviser’s approval to their DGS, who may require additional changes, for review. Once the DGS has approved the prospectus, the student sends the prospectus and approval emails to the Genetics registrar for their file and so it may be noted on their transcript. Students will not be admitted to candidacy nor will they be allowed to register for their fourth year of study without an approved prospectus.

In order to be admitted to candidacy, the student must fulfill (1) all course requirements, (2) the Honors requirement, (3) the qualifying examination, (4) the dissertation prospectus, and (5) the holding of a satisfactory Thesis Committee meeting, at the conclusion of which meeting the committee will give their assent for the student to be admitted to candidacy. Upon completion of these requirements, final approval for admission to candidacy is granted during a subsequent faculty meeting.

Thesis Committee The composition of the Thesis Committee for M.D.-Ph.D. students is the same as for Ph.D. students as described above. M.D-Ph.D. students are required to have one Thesis Committee meeting per year, beginning the term after passing their qualifying exam, and two meetings per year beginning in the fourth year in the Ph.D. program. 

Teaching and Departmental Presentations 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. Students are also expected to present in the departmental Research in Progress seminar.

Master’s Degrees

M.Phil. Students are not admitted for this degree. The M.Phil. is awarded only to students who are continuing for the Ph.D. Students must have completed all of their course requirements, their qualifying exam, and have been admitted to candidacy as described above to be awarded this degree. Students will be automatically petitioned by the university for an M.Phil. after successful completion of the requirements at the end of the third year. No additional action is required on the part of the student. See Degree Requirements under Policies and Regulations.

M.S. (upon withdrawal) 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 and HGS Tracks.

Courses