Microbiology
Boyer Center for Molecular Medicine 354F, 203.737.1087
http://medicine.yale.edu/micropath
M.S., M.Phil., Ph.D.
Director of Graduate Studies
Ya-Chi Ho
Professors Serap Aksoy (Epidemiology), Susan Baserga (Molecular Biophysics and Biochemistry; Genetics; Therapeutic Radiology), Choukri Ben Mamoun (Internal Medicine; Microbial Pathogenesis), Ronald Breaker (Molecular, Cellular, and Developmental Biology; Molecular Biophysics and Biochemistry), Richard Bucala (Internal Medicine; Epidemiology; Pathology), Michael Cappello (Pediatrics; Epidemiology; Microbial Pathogenesis), Yung-Chi Cheng (Pharmacology), Jason Crawford (Chemistry; Microbial Pathogenesis), Peter Cresswell (Immunobiology; Cell Biology), Daniel DiMaio (Genetics; Molecular Biophysics and Biochemistry; Therapeutic Radiology), Vanessa Ezenwa (Ecology and Evolutionary Biology), Erol Fikrig (Internal Medicine; Epidemiology; Microbial Pathogenesis), Richard Flavell (Immunobiology), Jorge Galán (Microbial Pathogenesis; Cell Biology), Wendy Gilbert (Molecular Biophysics and Biochemistry), Andrew Goodman (Microbial Pathogenesis), Eduardo Groisman (Microbial Pathogenesis), Margarett Hosstetter (Pediatrics), Akiko Iwasaki (Immunobiology; Molecular, Cellular, and Developmental Biology), Barbara Kazmierczak (Internal Medicine; Microbial Pathogenesis), Albert Ko (Epidemiology; Internal Medicine), Jun Liu (Microbial Pathogenesis), John MacMicking (Microbial Pathogenesis; Immunobiology), Ruslan Medzhitov (Immunobiology), I. George Miller (Pediatrics; Epidemiology; Molecular Biophysics and Biochemistry), Walther Mothes (Microbial Pathogenesis), Joseph Mougous (Microbial Pathogenesis), Noah Palm (Immunobiology), Melinda Pettigrew (Epidemiology), Carla Rothlin (Immunobiology; Pharmacology), Craig Roy (Microbial Pathogenesis; Immunobiology), Dieter Söll (Molecular Biophysics and Biochemistry; Chemistry), Richard Sutton (Internal Medicine; Microbial Pathogenesis), Jeffrey Townsend (Biostatistics; Ecology and Evolutionary Biology), Christian Tschudi (Epidemiology), Paul Turner (Ecology and Evolutionary Biology), Yong Xiong (Molecular Biophysics and Biochemistry)
Associate Professors Murat Acar (Molecular, Cellular, and Developmental Biology; Physics), Charles Dela Cruz (Internal Medicine; Microbial Pathogenesis), Nathan Grubaugh (Microbial Diseases), Ya-Chi Ho (Microbial Pathogenesis; Internal Medicine/Infectious Diseases), Farren Isaacs (Molecular, Cellular, and Developmental Biology), Priti Kumar (Internal Medicine/Infectious Diseases), Nikhil Malvankar (Molecular Biophysics and Biochemistry), Kathryn Miller-Jensen (Biomedical Engineering; Molecular, Cellular, and Developmental Biology), E. Hesper Rego (Microbial Pathogenesis), Christian Schlieker (Molecular Biophysics and Biochemistry; Cell Biology), Craig Wilen (Laboratory Medicine; Immunobiology)
Assistant Professors Amy Bei (Epidemiology of Microbial Diseases), Grace Chen (Immunobiology), Allison Didychuk (Molecular Biophysics and Biochemistry), Ellen Foxman (Laboratory Medicine; Immunobiology), Benjamin Goldman-Israelow (Medicine), Stavroula Hatzios (Molecular, Cellular, and Developmental Biology), Caroline Johnson (Environmental Health Sciences), Yelizaveta Konnikova (Pediatrics/Neonatology), Maudry Laurent-Rolle (Infectious Diseases), Caroline Lucas (Immunobiology), David Martinez (Immunobiology), Wei Mi (Pharmacology), Michael O’Donnell (Molecular, Cellular and Developmental Biology), Hualiang Pi (Microbial Pathogenesis), Kaitlin Schaefer (Microbial Pathogenesis), Esen Sefik (Immunobiology), Chantal Vogels (Epidemiology-Microbial Diseases), Jing Yan (Molecular, Cellular, and Developmental Biology)
Fields of Study
The Graduate Program in Microbiology is a multidepartmental, interdisciplinary Ph.D. program in training and research in the study of microorganisms and their effects on their hosts. This program does not offer direct admission to a master’s degree. The faculty of the program share the view that understanding the biology of microorganisms requires a multidisciplinary approach; therefore, the Microbiology graduate program emphasizes the need for strong multidisciplinary training. The program is designed to provide individualized education in modern microbiology and to prepare students for independent careers in research and teaching. Students can specialize in various areas, including bacteriology, virology, microbe-host interactions, microbial pathogenesis, cell biology and immunobiology of microbial infections, microbial genetics and physiology, structural biology, parasitology, microbiome, and microbial ecology and evolution.
Admissions Requirements
To enter the Ph.D. program, students apply to the Microbiology track within the interdepartmental graduate program in the Biological and Biomedical Sciences (BBS), http://bbs.yale.edu. An undergraduate major in biology, biophysics, biochemistry, microbiology, or molecular biology is recommended; the GRE General Test or MCAT is no longer required, and scores will not be considered if submitted. Substantial research experience in hypothesis-driven investigations in microbiology, microbial pathogenesis, molecular biology, or related fields is strongly encouraged.
Special Requirements for the Ph.D. Degree
Courses Students are required to take four courses for a grade in the graduate school. Required graded courses for first and second-year students are listed below.
| At least three of these microbiology-related courses: * | ||
| CBIO 6020 | Molecular Cell Biology | 1 |
| IBIO 5300 | Biology of the Immune System | 1 |
| MBIO 6850 | The Biology of Bacterial Pathogens II | 1 |
| MBIO 6860 | The Biology of Bacterial Pathogens I | 1 |
| MBIO 7340 | Molecular Biology of Animal Viruses | 1 |
| PATH 5690 | Molecular Mechanisms of Disease | 1 |
| * | At least one course must be MBIO 6850, MBIO 6860, or MBIO 7340. |
| Other elective studies can be (but aren't limited to): | ||
| CBIO 7701 | Illuminating Cellular Function | 1 |
| EEB 7729 | Microbial Ecology and Evolution | 1 |
| EMD 517 | Principles of Infectious Diseases I | 1 |
| EMD 518 | Principles of Infectious Diseases II | 1 |
| EMD 550 | Epidemiology and Control of Vector Borne Diseases | 1 |
| GENE 6250 | Basic Concepts of Genetic Analysis | 1 |
| GENE 7600 | Genomic Methods for Genetic Analysis | 1 |
| Required credit-only, nongraded courses for first-year students: | ||
| IBIO 6010 | Fundamentals of Research: Responsible Conduct of Research | 1 |
| MBIO 6700 | Laboratory Rotations | 1 |
| MBIO 6710 | Laboratory Rotations | 1 |
| MBIO 6720 | Laboratory Rotations | 1 |
| MBIO 7000 | Seminal Papers on the Foundations of Modern Microbiology | 0 |
| MBIO 7010 | Research in Progress | 1 |
| MBIO 7020 | Research in Progress | 1 |
| MBIO 7030 | Microbiology Seminar Series | 1 |
| MBIO 7040 | Microbiology Seminar Series | 1 |
Coursework generally occupies the first two years of study. Students choose courses after consulting the DGS and the thesis adviser. Students must receive a grade of Honors in two full-term courses. All students participate in three laboratory rotations (MBIO 6700, MBIO 6710, and MBIO 6720), with different faculty members, in their area of interest. Laboratory rotations ensure that students quickly become familiar with the variety of research opportunities available in the program. At the end of each rotation, students present their rotation project in a ten to twelve-minute seminar. Three rotations are required. There can be an optional fourth rotation. In rare occasions, after discussion with the DGS, a fifth rotation can be taken, if the student cannot join a thesis lab in the first four rotations. Students who are not able to obtain a thesis adviser selection form (signed by the thesis adviser) and join a thesis lab by July 31 during their first year of Ph.D. will be dismissed from the program.
Qualifying Exam and Advancement to Candidacy The qualifying exam is on-topic in both written and oral forms before the end of the second year. With supervision from the adviser, students assemble their own qualifying exam committee, consisting of faculty members from different expertise relevant to the dissertation research. Through multiple one-on-one discussions with their adviser and the thesis committee, students strengthen their thesis proposals. Students write an on-topic thesis proposal based on the NIH F31 fellowship format and defend orally in front of the qualifying exam committee. Students are required to defend their proposals in a chalk-talk format. In the third year, students organize their thesis committee and prepare a dissertation prospectus, which is submitted to the graduate school after approval by their committee. The student is then admitted to candidacy. Committee approvals for both the qualifying exam and the dissertation prospectus are required to advance to the fourth year of Ph.D.
Thesis Committee, Dissertation, and Seminar Students are required to have at least one thesis committee meeting per year and one oral presentation at the Research in Progress Seminar series. Upon completion of the research project, the student will write a dissertation, which will be evaluated and approved by three dissertation research (including at least two Yale readers and one external reader, typically faculty in academic research institutions). The student will give a thesis seminar and conclude their Ph.D.
Teaching Students are required to serve as a teaching fellow for two terms.
- Teaching two term-long science courses is required as a fulfillment of the Ph.D.
- First-year students do not teach.
- Only one teaching fellow assignment is allowed per semester
- Teaching for additional income is available after the completion of the two required teaching fellow assignments, when openings exist after those selected for credit are hired; approval signatures from the both the adviser and DGS are required.
- The maximum teaching allowed is one course per term.
A one-day seminar entitled Teaching at Yale is offered by the Yale Poorvu Center for Teaching and Learning at the start of each term. Attending this seminar is recommended prior to teaching.
Responsible Conduct of Research In addition to all other requirements, students must successfully complete IBIO 6010, Fundamentals of Research: Responsible Conduct of Research, prior to the end of their first year of study. This requirement must be met prior to registering for a second year of study. In their fourth year of study, all students must successfully complete B&BS 5502, RCR Refresher for Senior BBS Students.
Master’s Degrees
M.Phil. The M.Phil. degree can be awarded to Ph.D. students who have been admitted to candidacy. See Degree Requirements under Policies and Regulations.
M.S. The M.S. degree may only be granted to students who are withdrawing from the Ph.D. program prior to advancing to candidacy. To be eligible for this degree, a student must have completed at least four graduate-level term courses at Yale, including at least three from microbiology-related courses (MBIO 530, MBIO 6850, MBIO 6860, MBIO 7340, CBIO 6020, and PATH 5690) and including at least one of the three core courses. Students must have received at least one Honors or two High Pass grades. In addition, students must have received a Satisfactory grade in the following courses: IBIO 6010, MBIO 6700, MBIO 6710, MBIO 6720, MBIO 7010, and MBIO 7020. Students who are eligible for or who have already received the M.Phil. will not be awarded the M.S.
For more information, please visit https://medicine.yale.edu/micropath/microbiology-phd.
MBIO TBD-2a, Molecular Cell Biology Thomas Melia
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. Graduate Prerequisites: 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). Undergraduate Prerequisites: This is a graduate-level cell biology class. Any undergraduates wishing to enroll must have already taken MCDB 205. In addition, undergraduates are strongly encouraged to reach out to the course directors prior to enrollment.
MW 1:45pm-3pm
MBIO 6700a and MBIO 6710a and MBIO 6720b and MBIO 6740b, Laboratory Rotations Ya-Chi Ho
Rotation in three laboratories. Required of all first-year graduate students.
HTBA
MBIO 6850b, The Biology of Bacterial Pathogens II Hesper Rego
This interdisciplinary course focuses on current topics related to host-pathogen interactions. Each week a lecture is given on the topic, followed by student presentations of seminal papers in the field. All participants are required to present a paper.
MW 9:30am-11am
MBIO 6860a, The Biology of Bacterial Pathogens I Jorge Galan and Maria Lara-Tejero
The course provides an introduction to basic principles in bacterial pathogenesis. Topics focus on the bacterial determinants mediating infection and pathogenesis, as well as strategies to prevent and treat diseases. Each week a lecture is given on the topic, followed by student presentations of seminal papers in the field. All participants are required to present a paper.
TTh 10am-11:30am
MBIO 7000b, Seminal Papers on the Foundations of Modern Microbiology Ya-Chi Ho
A required course for Microbiology first-year students; not for credit. The course is offered every spring. Students present and discuss papers describing fundamental discoveries in areas related to microbiology. The goal is to familiarize students with the process of scientific discovery and with the history of major developments in the field. Topics include important discoveries involving major human pathogens, fundamental processes in molecular biology, and the development of technology that has a major impact on current biomedical research. 0 Course cr
W 5pm-6:30pm
MBIO 7010a and MBIO 7020b, Research in Progress Ya-Chi Ho
All students, beginning in their third year, are required to present their research once a year at the Graduate Student Research in Progress. These presentations are intended to give each student practice in presenting the student’s own work before a sympathetic but critical audience and to familiarize the faculty with the research.
M 3:30pm-4:30pm
MBIO 7030a and MBIO 7040b, Microbiology Seminar Series Ya-Chi Ho
All students are required to attend all Microbiology seminars scheduled throughout the academic year. Microbiologists from around the world are invited to describe their research.
Th 3:30pm-4:30pm
MBIO 7340b / GENE 7340b / MB&B 7340b, Molecular Biology of Animal Viruses Walther Mothes and Maudry Laurent-Rolle
Lecture course with emphasis on mechanisms of viral replication, oncogenic transformation, and virus-host cell interactions.
TTh 10am-11:30am