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Appendix A - Graduate Curricula for MD/PhD Students at the University of Rochester

The MSTP works with graduate programs to establish and regularly review curricular guidelines for MD/PhD students.  Students should use these guidelines in consultation with graduate program directors and thesis mentors to determine an optimal program of study.  Students committed to a particular program are encouraged to meet with departmental program directors as early as possible.

Biochemistry and Biophysics

Biochemistry

MD/PhD program students usually enter the PhD portion of their combined degree work after the basic science years of the MD curriculum.  During the second year of the MD program students should discuss the PhD Program with prospective faculty advisors and the Biochemistry Program Director.  It is optimal for the student to complete two research rotations before choosing a permanent advisor.

Curriculum:

1) All of the following courses are required:

BCH 412 (5)                Advanced Topics in Biological Macromolecules            Spring
IND 410 (4)                 Molecular Biology and Genomics                                    Spring
IND 501 (1)                 Ethics in Research                                                               Fall
BCH 501, 502 (1)       Biochemistry Seminar*                                                     (each semester)
BCH 595                     PhD Research                                                                      (each semester)
*includes yearly presentation

2) Additional requirement

IND 409 (4)                 Cell Biology                                                                          Spring

 Or

An (advisor and program director) approved alternative elective

NOTE:  MD/PhD students are granted 30 credits toward the 96 credit hour requirement for the PhD on the basis of their basic sciences curriculum.

Other requirements:

No Teaching Assistantship is required.

The Qualifying Examination is required at the end of the second year of PhD studies.

Thesis preparation and defense.

Updated July 2016
 

Biophysics

Students in the MD/PhD program who are considering a PhD in Biophysics are encouraged to meet with the Biophysics Program Director and potential thesis mentors as early as is convenient but no later than the middle of the second year of the MD program.

Curriculum:

All MD/PhD students in the Biophysics program must complete the following courses:

BPH 411          Methods in Structural Biology                                     5 credits
BPH 509         Molecular Biophysics                                                     5
IND 501           Ethics in Research                                                         1
BPH 571,572   Biophysics Seminar (each semester)                         1
BPH 595          PhD research (each semester)

Elective course: At least one elective course must be taken.  The choice must be approved by the PhD advisor and Program Director. Recommended courses are listed below.

IND 408           Advanced Biochemistry                                                5 credits
IND 409           Cell Biology                                                                     4
BCH 412         Advanced Topics in Biological Macromolecules        5                        

Other requirements:

Two research rotations should be conducted prior to joining a laboratory for dissertation research. Students are encouraged to complete these rotations during the first two years of the MD program.

The qualifying examination must be completed by the end of the second year of PhD studies.

The teaching assistant requirement is waived.

At least one meeting per year with the thesis advisory committee (normally held after the student’s Biophysics Seminar presentation).

A satisfactory thesis must be written and successfully defended.  Details of these requirements are given elsewhere in this handbook.

Updated July 2016
 

Biology

The Department of Biology at the University of Rochester offers PhD degrees in the areas of Molecular, Cellular and Developmental Biology and Evolutionary Biology. The Department is united by a common interest in genetic processes that creates a continuum of research interests among the different laboratories. For example, our evolutionary biologists use molecular biological approaches, and some of our cell biologists publish in the areas of development and evolution. The Biology Department is housed in Hutchison Hall, together with Earth and Environmental Sciences and the Chemistry Departments. The Department is only a five minute walk from the Medical Center which is home to the Departments of Biochemistry and Biophysics, Biomedical Genetics, Microbiology and Immunology, Neurobiology and Anatomy, the Cancer Center, and related medical service departments. The physical closeness of these groups facilitates intellectual exchange and collaboration among the graduate programs of the basic and biomedical disciplines. Interdepartmental programs such as the Office of the Graduate Education and Postdoctoral Affairs, the MD/PhD Program and the Genetics Program serve to increase communication and training opportunities for our students.

I. COURSE WORK

A. Credit Hours

90 credit hours are required for completion of the PhD degree. Credit hours include both coursework and research. Once a research advisor has been selected, students must register each semester for a sufficient number of credit hours in Biology 595 (PhD Research in Biology) to bring the total to 12 credits. After a total of 90 credits has been achieved, the student should register for Biology 999 (Doctoral Dissertation). Students do not formally register for credit during the summer, but are required to do full-time research during this period.

B. Course Requirements

Students whose interests are in cell, developmental or molecular biology must take a minimum of six courses during their graduate career, selected according to background and research interests. Each course must be > three credits. Students whose interests are in ecology and evolutionary biology are required to take five lecture or reading courses (each > three credits). Courses will be selected, in consultation with a faculty advisor, to assure appropriate depth and breadth of preparation.  A list of courses available in the Department is provided at the end of this document. 

Students who have taken graduate courses prior to entering the PhD program may petition the GAAC for a reduction in the number of required courses.  MD/PhD students typically take fewer courses because of their work in the first two years of medical school.

C. Laboratory Rotations

Rotations are not required. Students may rotate through research laboratories in order to become acquainted with faculty and to aid in selection of a research advisor.

D. Seminar Requirements

All students are required to participate in a minimum of four seminar courses in which they make oral presentations. EEB students will meet this requirement in BIO 584 and CMD students will meet this requirement by taking three BIO 516 seminars and presenting in BIO 517 every Spring semester. First year students and advanced students who will defend their dissertation by the end of the following Fall semester are not required to present in BIO 517. Both EEB and CMD students may petition the GAAC to have one oral presentation at a national or international meeting count towards the seminar requirement. Students must complete the seminar requirement by the end of their fourth year in order to avoid tuition charges.

II. TEACHING

MD/PhD candidates are exempt from teaching.

III. QUALIFYING EXAMINATION

The PhD Qualifying Examination consists of a written thesis proposal and an oral examination. The oral exam is intended to determine whether a student is prepared to pursue a professional career in science, as demonstrated by successful defense of the proposal. The exam also will test general knowledge of biology and, in greater depth, knowledge within the students' field of interest.

Preparation of the thesis proposal for the Qualifying Examination should be a realistic training experience that involves developing a feasible research project and presenting it in concise and cogent prose.  The suggested format for the thesis proposal is that used for a research grant. It should include an introduction providing a brief background to the research, a list of specific aims, a description of experimental procedures, and presentation of preliminary data that have been obtained by the student to demonstrate the feasibility of the approach. The advisor must sign the thesis proposal, indicating that (s)he is willing to allow the research to be carried out in her/his laboratory. The advisor should also indicate his/her level of input into the proposal. This might include, for example: provision of a recently submitted proposal or one in preparation; suggestions to expand and/or clarify specific parts of the proposal; discussions on the preliminary data to be included, and its interpretation; identification of missing background information; and text editing for grammar, syntax or clarity.

A copy of the thesis proposal must be distributed to the examining committee and filed with the secretary of the GAAC at least one week prior to the oral exam. The proposal should be less than or equal to 10 pages, single-spaced, excluding figures and references.

The examining committee is selected by the GAAC and approved by the Associate Dean of Graduate Studies of the College. It will consist of four members, one of whom may be from outside the Department. The student's advisor will not be present. The committee will be chaired by the most appropriate faculty member.

After the questioning is concluded, the candidate will be asked to leave the room and each committee member in turn will discuss the strengths and weaknesses of responses to his/her questions. The committee will also list major strengths and weaknesses of the research proposal. When discussion has been completed to everyone's satisfaction, an anonymous written, pass-fail vote will be taken.

IV. RESEARCH

The most important part of the work leading to the PhD degree is the independent research that leads to the preparation of a thesis. The following sections outline the formal mechanisms for guiding thesis research and monitoring its progress

A. Selection of a Research Sponsor

Students become familiar with the research of faculty through lab rotations, seminars, reading published work, and conversations with individuals.

B. Thesis Advisory Committee and Progress Reports

Following completion of the Qualifying Exam, the student will meet with his or her Thesis Advisory Committee (TAC), which need not include the same members as the Qualifying Examination Committee. The first meeting should be held by the end of the fifth semester. Subsequently, the Thesis Advisory Committee must meet at least once a year to review the candidate's progress. More frequent meetings may be held at the request of the student or any member of the Thesis Advisory Committee.

The Thesis Advisory Committee is normally selected by the student and the research advisor to include faculty members especially knowledgeable in the research area. The committee is formally appointed by the Associate Dean of Graduate Studies. It must include at least three faculty members from the Department (one of whom is the research advisor) and a faculty member from outside the Department. The outside member is usually from another department at the University of Rochester, but may be from another institution, if sufficient expertise is not available at the University.

At least one week before each meeting, the candidate will provide TAC members with a written report of work completed since the previous meeting. This report should be no more than five pages long (double-spaced, typed). A copy of the report should be filed with the secretary of the GAAC for retention in the student's record. Written assessments of the candidate's progress will be submitted to the GAAC by members of the Thesis Advisory Committee after every meeting. These reports will form the basis for the Department's recommendation regarding continuation in the PhD Program. If more than two semesters and one summer elapse without a progress meeting, the student will not be allowed to register for the next semester.

TAC meetings are intended to be a constructive mechanism to assist the student in his/her progress toward an outstanding thesis. They should be used as opportunities to review results and focus research plans. However, they are not the only mechanism. Students are encouraged to consult with their sponsor, with members of the TAC, and with any faculty member or student whose expertise is of use.

C. Preparation and Defense of the Thesis

Once a student has completed the work agreed upon by the advisor and TAC, he/she writes a thesis.  Students are strongly encouraged to begin writing sections of their theses dealing with completed work, even while final research projects are being carried out. The style of the thesis (e.g., chapters based on papers, or a continuous results narrative) should be agreed upon by the student and the TAC at least six months prior to the intended submission date.

The final version of the thesis (as approved by all members of the thesis advisory committee) must be registered with the Associate Dean for Graduate Studies of the School of Arts and Sciences at least fifteen full working days prior to the date of the final oral examination. The Dissertation Examining Committee will normally consist of the members of the student's Thesis Advisory Committee and a chairman to be appointed by the University Dean of Graduate Studies. If the Thesis Advisory Committee did not include an outside member of the Department, the student and advisor must select a faculty member from outside the Department to sit on the Dissertation Advisory Committee.

The final oral examination will consist of a one-hour public seminar, followed by an open question and answer period. The candidate and the examining committee will then meet in private for additional discussion and the formal defense.

Courses Offered by the Department of Biology

402  Molecular Biology
405  Evolution: Fundamentals of Evolution and Population Biology
420  Advanced Cell Biology
422  Biology of Aging
426  Developmental Biology
443  Eukaryotic Gene Regulation
453  Computational Biology
460  Animal Behavior
463  Ecology
468  Laboratory in Molecular, Cell and Developmental Biology
457  Applied Genomics
471/472/473/474. Advanced Ecology and Evolutionary Biology A-D

Revised: 2016

Biomedical Engineering

Students earning a PhD in Biomedical Engineering through the MD/PhD program will begin PhD training in the third year of graduate school after two years of medical school training. Unless explicitly stated below all requirements and definitions for the PhD in Biomedical Engineering (Section I) apply to students in the MD/PhD program.

A. Curricular requirements

Because the medical school training emphasizes biology and physiology, the BME PhD requirement for 11 credits of Approved Biology are waived. Additionally, only 4 credits of BME Intensives are required, and the preliminary exam is waived. A teaching assistantship is encouraged but not required. The BME faculty believe that experience and training in teaching is a valuable part of doctoral education for biomedical engineers, however the program does not require TA service in order to be consistent with MD/PhD requirements in other departments.  At least two rotations are required by the MD/PhD program and these are typically completed before beginning the PhD training. The following summarizes the full non-research requirements for BME PhDs in the MD/PhD program:

  • 12 credits of approved engineering
  • BST 467:  Applied Statistics in the Biomedical Sciences (4 credits)
  • 4 credits of Advanced BME
  • The proposals writing course (2 credits; spring term)
  • Research ethics (1 credit; fall term)
  • BME 496: Current Research Seminars (0 credit)
  • Three formal presentations in a public forum

A student should complete the curricular requirements in one academic year, and it is expected that 2-3 additional years will be required to complete the PhD thesis. Students must select a research advisor by the beginning of the spring term, and research should be underway by the spring term so that the proposal writing class is most effective. The qualifying exam should be taken in the fall of the second year of PhD study.

B. Clerkships

During the years of doctoral training, students will continue with clerkship activities for one afternoon each week to remain active in medical training.  The clerkship time accumulates as medical school credit, and enables the student to have a free block in the last year of medical training to pursue either additional elective or further research activities. 

Updated August 2016

Biostatistics and Computational Biology

The Department of Biostatistics and Computational Biology offers programs leading to the Doctor of Philosophy, Master of Arts, and Master of Science degrees. The department conducts a program of teaching and research in statistical theory and statistical methodology oriented toward the health sciences. Department faculty have research interests and expertise in virtually all areas of modern theoretical and applied statistics. Faculty are involved in wide-ranging collaborative activity with basic science and clinical departments in the School of Medicine and Dentistry. This environment is ideally suited for training in research in statistical methodology, collaborative research, and consulting.

The curriculum is designed to provide students with a thorough grounding in statistical theory, which provides the necessary foundation for the successful conduct of research in statistical methodology. Included are core courses in probability, stochastic processes, statistical inference, large sample theory, and Bayesian inference. The curriculum also provides students with an appreciation for applied problems in biomedical research and the skills necessary to succeed in collaborative research environments. Core courses focused on applications include Categorical Data Analysis and Design of Clinical Trials, in addition to formal training in the use of statistical software. Additional core courses including Linear Models, Generalized Linear Models, Survival Analysis, and Analysis of Longitudinal and Dependent Data provide a mix of theory and application.  Courses in High Dimensional Data Analysis, Computational Systems Biology, and Genomic Data Analysis are designed for those interested in a concentration in Bioinformatics and Computational Biology. Several elective courses are also offered. An important goal is to produce graduates with a command of technical skills and the ability and experience to use them appropriately.

Program for the Degree of Doctor of Philosophy in Statistics (Traditional)

The department administers the doctoral program in statistics. The department interprets the term “statistics” very broadly. The program permits specialization in probability, statistical theory and analysis, biostatistics, and interdisciplinary areas of application. Students have opportunities for supervised teaching and supervised consulting experience, requiring approximately 12 to 15 hours of effort per week.

A candidate for admission to the PhD program should have a strong background in mathematics, including advanced calculus or mathematical analysis (similar to MTH 265), a course in linear and/or matrix algebra (similar to MTH 165), and a year of probability and mathematical statistics (similar to STT 201 and STT 203). A course in statistical methods is also recommended; however, promising students may make up deficiencies after matriculation. A background in biology may be helpful for some research areas, but is not required.

Doctoral students are expected to attain some competence in each of the following (overlapping) areas: I. statistical inference; II. statistical analysis (theory and methods); III. probability and stochastic processes. In addition, each student is expected to qualify at a more advanced level in two areas, designated major and minor. Minor areas, in addition to those three above, include IV. mathematics; V. epidemiology; VI. biostatistics; and VII. a specific field of application, such as econometrics, psychometrics, computer science, genetics, computational biology, engineering, etc. Students are required to acquire some proficiency in statistical computation, using at least one high-level language and several statistical packages. There is no formal specific language requirement, but students undertaking certain areas of research may find it necessary to undertake appropriate language study.

Students are required to take a minimum of 16 formal courses, including:

  1. Basic courses: at least two courses in each of the areas I, II, and III and at least three in areas IV–VII combined.
  2. Major area: at least three additional courses (12 credits), ordinarily at the 500 level, in one of the areas I–III (or IV–VII with permission).
  3. Minor area: at least two additional courses in another one of the seven areas.

Beginning students should expect to spend all of their first year, most of their second year, and some of their third year taking formal courses. This includes a minimum of six semesters of BST 487, a one-credit seminar course designed to give students extensive practice in searching the statistical literature and preparing and delivering presentations. The balance of time is spent on reading and research. Students entering with advanced training in statistics may transfer credits at the discretion of their advisors and in accordance with University policy. A typical program for an entering student without previous advanced training is as follows:

Year 1: Fall

BST 401. Probability Theory (4 credits)

BST 411. Statistical Inference (4 credits)

BST 430. Introduction to Statistical Computing (4 credits)

BST 487. Seminar in Statistical Literature (1 credit)

BST 590. Supervised Teaching (2 credits)

IND 501. Ethics and Professional Integrity in Research (1 credit)

Year 1: Spring

BST 413. Bayesian Inference (4 credits)

BST 426. Linear Models (4 credits)

BST 466. Categorical Data Analysis (4 credits)

BST 487. Seminar in Statistical Literature (1 credit)

BST 590. Supervised Teaching (3 credits)

Year 2: Fall

BST 402. Stochastic Processes (4 credits)

BST 479. Generalized Linear Models (4 credits)

BST 487. Seminar in Statistical Literature (1 credit)

BST 590. Supervised Teaching (3 credits)

Elective (4 credits)

Year 2: Spring

BST 412. Large Sample Theory (4 credits)

BST 487. Seminar in Statistical Literature (1 credit)

BST 513. Analysis of Longitudinal and Dependent Data (4 credits)

BST 591. Reading Course at the PhD Level (3 credits)

Elective (4 credits)

Year 3+

Mostly reading and research, with some 400-level and 500-level courses

Notes:

  1. BST 487, Seminar in Statistical Literature (1 credit), is offered every semester. Topics covered vary. PhD students are required to register for at least six semesters.
  2. All PhD students are required to have at least four credits of supervised teaching and/or supervised consulting (BST 590, 592).
  3. All students in the doctoral program are required to take IND 501, Ethics and Professional Integrity in Research (1 credit), in their first semester in the program.
  4. Usually in year two, students begin exploring potential research topics by taking reading courses with faculty (BST 591). The structure, content, and number of credit hours for these courses are flexible and determined by mutual agreement between the students and faculty member.
  5. Advanced topics courses in statistical inference, data analysis, and biostatistics (BST 511, 512, 550, or 570), for varying numbers of credits, are offered depending on interests of students and instructors. Recent examples include:
  • Missing Data
  • Frailty Models in Survival Analysis
  • Causal Inference and Its Applications
  • Functional Data Analysis
  • Time Series
  • ROC Curve Analysis
  • Smoothing Methods
  • The Bootstrap, the Jackknife, and Resampling Methods
  • Advanced Bayesian Inference with an Emphasis on Computation
  • Model Selection and Validation

Students also have the option of taking relevant courses that are offered through other doctoral programs at the University, such as Mathematics (e.g., MTH 471–Real Analysis), Epidemiology (e.g., PM 416–Epidemiologic Methods), and Health Services Research (e.g., PM 472–Measurement and Evaluation of Research Instruments).

These requirements are to be interpreted as guidelines, rather than as regulations. A balanced program is worked out with the student’s advisor and the graduate advisor.

The examination requirement consists of:

  1. Written examination in two parts. The basic part covers basic material in areas I–III, based on undergraduate preparation and some of the first-year graduate courses. It is taken after one year of study. The advanced part covers advanced material from two to three core courses in each of areas I–III taken during the first two years of graduate study. This part is usually taken after two years of study.
  2. Qualifying examination (oral) on the general area of proposed research and other topics as necessary.
  3. Final examination on the completed dissertation.

The dissertation will consist of substantial scholarly contribution, worthy of publication, in one of the areas I–III or in any other area approved by the faculty committee.

Program for the Degree of Doctor of Philosophy in Statistics with Concentration in Bioinformatics and Computational Biology

The Bioinformatics and Computational Biology (BCB) concentration is designed to educate the next generation of biostatisticians with the knowledge required to address critical scientific and public health questions and, in particular, equip them with the skills necessary to both develop and use quantitative and computational methodologies and tools to manage, analyze, and integrate massive amounts of complex biomedical data. Students learn core statistical methods and obtain training in data analysis methodologies and computational skills and techniques necessary for handling big data in the biomedical and public health sciences. In addition to this training in core methods, the program also places great emphasis on cross-training: (1) training students with quantitative/computational science backgrounds to enhance their understanding of biological questions and biological interpretation; and (2) training students with biomedical science backgrounds to proficiently use bioinformatics and computational methods and tools to address scientific questions.

Entering PhD students need undergraduate preparation in mathematics, including advanced calculus or mathematical analysis (similar to MTH 265), a course in linear and/or matrix algebra (similar to MTH 165), and a year of probability and statistics (similar to STT 201 and STT 203). Basic courses in computer science and/or biology are also required. A course in statistical methods is also recommended; however, promising students may make up deficiencies after matriculation.

Formal course and examination requirements for students in the BCB concentration are essentially the same as those for students in the traditional program, with the main differences being in the courses taken in areas IV-VII (with a heavier focus on courses related to bioinformatics and computational biology) and in the material covered on the written examination (advanced part).

Beginning students should expect to spend all of their first year, most of their second year, and some of their third year taking formal courses. At the same time, students in the BCB concentration are expected to take both dry (computational) lab rotations and, ideally, wet lab rotations for the first two years until selecting one or two thesis advisors (ideally one statistics advisor and one basic science advisor). The balance of time is spent on reading and research. Students entering with advanced training in statistics, bioinformatics, or computational biology may transfer credits at the discretion of their advisors and in accordance with University policy. A typical program for an entering student without previous training is as follows:

Year 1: Fall

BST 401. Probability Theory (4 credits)

BST 411. Statistical Inference (4 credits)

BST 430. Introduction to Statistical Computing (4 credits)

BST 496. Wet/Dry Lab Rotation (1 credit)

BST 590. Supervised Teaching (2 credits)

IND 501. Ethics and Professional Integrity in Research (1 credit)

Year 1: Spring

BST 413. Bayesian Inference (4 credits)

BST 426. Linear Models (4 credits)

BST 466. Categorical Data Analysis (4 credits)

BST 496. Wet/Dry Lab Rotation (1 credit)

BST 590. Supervised Teaching (3 credits)

Year 2: Fall

BST 402. Stochastic Processes (4 credits)

BST 432. High Dimensional Data Analysis (4 credits)

BST 479. Generalized Linear Models (4 credits)

BST 496. Wet/Dry Lab Rotation (1 credit)

BST 590. Supervised Teaching (3 credits)

Year 2: Spring

BST 412. Large Sample Theory (4 credits)

BST 434. Genomic Data Analysis (4 credits)

BST 496. Wet/Dry Lab Rotation (1 credit)

BST 513. Analysis of Longitudinal and Dependent Data (4 credits)

BST 591. Reading Course at the PhD Level (3 credits)

Year 3+

Mostly reading and research, with some 400-level and 500-level courses.

Notes:

  1. All PhD students are required to have at least four credits of supervised teaching and/or supervised consulting (BST 590, 592).
  2. All students in the doctoral program are required to take IND 501, Ethics and Professional Integrity in Research (1 credit), in their first semester in the program.
  3. Usually in year two, students begin exploring potential research topics by taking reading courses with faculty (BST 591). The structure, content, and number of credit hours for these courses are flexible and determined by mutual agreement between the student and faculty member.
  4. As with the traditional PhD program, advanced topics courses in statistical inference, data analysis, and biostatistics (BST 511, 512, 550, or 570), for varying numbers of credits, are offered depending on interests of students and instructors.

The examination requirements for students in the BCB concentration are the same as for students in the traditional PhD program.

Considerations for Students in the MD/PhD Program

Students admitted to the MD/PhD program follow essentially the same course of study as students in the PhD program, except that coursework in statistics begins during the fall of the third year in the program. During the first year, students spend three months (June–August) with a mentor to begin the process of orientation toward research in statistical methodology. This may be implemented either as an informal (noncredit) reading course or as involvement in an applied project that may motivate a methodological research problem. This is repeated during the second year of the program (March–August) just prior to the start of coursework. The main goals of these interactions are to provide the student some insight regarding the process of research in statistical methodology and to facilitate the process of choosing a research advisor.

Reviewed: June 2016

Brain and Cognitive Sciences

The Department of Brain and Cognitive Sciences (BCS) offers a PhD degree that can be combined with the MD.  After two years of the MD curriculum, students complete two years of coursework in BCS and at least a 3rd year (or more) of dissertation research before returning to complete the MD.

The full complement of required courses in BCS has been reduced slightly to accommodate the additional coursework and training for the MD.  The requirements are listed below.

Core courses

Students must take three of the following six core courses (reduced from the normal requirement of four), with at least one core course from each of the three pairs.

BCS 501: Language
BCS 502: Cognition
BCS 504: Sensory Systems
BCS 505: Perception and Motor Systems
BCS 508:  Cognitive Neuroscience
NSC 531: Integrative and Systems Neuroscience

Experimental Design and Statistics.  One course from the following list:

BCS 510: Data Analysis I
BST 464: Applied Linear Regression
CSP 519: Data Analysis: General Linear Applications II
STT 422: Design of Experiments and STT 441: Applied Multivariate Analysis (together these 2 courses form one semester)

Methodology.  One course from the following list:

BCS 511: Behavioral Methods in Cognitive Science
BCS 512: Computational Methods in Cognitive Science
BCS 513: Intro to fMRI: Imaging, Computational Analysis and Neural Representations

Professional Development

Students must take all three courses below:

BCS 582: Grant Writing in BCS
BCS 599: Professional Development and Career Planning
IND 501: Ethics and Professional Integrity in Research Biomedical Sciences

Teaching Assistantship

A one-semester TA experience in a relevant undergraduate course in BCS or NSC (to be determined based on TA needs and the skills and background of the student), with simultaneous enrollment in BCS 598: Supervised Teaching

Elective Courses and Seminars

In addition to the above course requirements, the student must complete a minimum of 90 credit hours of formal coursework or readings/research courses.  Enrollment in the following courses should be used to meet the 90 credit-hour requirement for the PhD.

BCS 591: Readings at the PhD level
BCS 595: Research at the PhD level
BCS 999: Doctoral Dissertation

Research Activities

In contrast to other GEBS programs, BCS does not have a formal lab rotation requirement.  Students are encouraged to move as quickly as possible into a lab (after suitable negotiation with the faculty mentor) and engage in research activities for the entire duration of the 3 (or more) years spent in BCS fulfilling course requirements and completing the dissertation.

Students are also required to make a formal presentation about their on-going research to the Department (students, postdocs, and faculty) at the biweekly BCS Lunch no later than their third semester in the program.

Written Qualifying Exam

At the end of the second year, students must take a multi-day, open book, written examination based on their coursework and a custom reading list negotiated with their faculty mentor and two other BCS faculty of their choosing.  The qualifying exam for MD/PhD students is 2/3 the length of the normal BCS qualifying exam.  A passing grade on this exam enables the student to be formally admitted to candidacy in the University’s Graduate School for a PhD in BCS.

Dissertation

Once admitted to candidacy for the PhD, the student forms a dissertation committee consisting of the faculty mentor, two other faculty members in BCS, and one faculty member in a non-BCS department (or program).  A formal presentation of the dissertation proposal, both in written form and orally, is made to this dissertation committee well in advance of completion of the dissertation research.  Upon completion of the dissertation research, and having met all course and credit hour requirements, the written dissertation is filed with the Graduate Dean who schedules the final oral examination and appoints an outside Chair to monitor the examination.  This examination consists of a public lecture to the entire Department, followed by a closed oral exam by the dissertation committee.

Reviewed: 2016

Chemistry

1.   Course Requirements. All students enrolled in the PhD program must demonstrate breadth and depth in their coursework.  For graduate students matriculated into the PhD program, a total of 20 credit hours of coursework is required.  For MD/PhD students, courses taken during the first two years are taken into account and the required number of Chemistry course credit hours is reduced to 12.

Programs of study can be modified to best address a student's research needs and interests. For their first year in Chemistry, students develop a program of study in consultation with their research adviser, who is typically chosen in December of the student’s first year of Chemistry concentration. 

Courses within the department include those given below.

402.     Biophysical Chemistry I (4 credits)
404.     Biophysical Chemistry II (4 credits)
406.     Interface of Chemistry & Biology (2 credits)
411.     Inorganic Chemistry I (4 credits)
414.     Biological Inorganic Chemistry (4 credits)
415.     Group Theory (2 credits)
416.     X-ray Crystallography (2 credits)
421.     Basic Organometallic Chemistry (2 credits)
422.     Organometallic Chemistry (2 credits)
423.     Nuclear Magnetic Resonance Spectroscopy- Survey (2 credits)
425.     Physical Methods in Inorganic Chemistry (4 credits)
427.     Organic Structure Determination (2 credits)
433.     Advanced Physical Organic Chemistry I (4 credits)
434.     Advanced Physical Organic Chemistry II (4 credits)
435.     Organic Reactions (4 credits)
436.     Applications of Organometallic Chemistry to Synthesis I (2 credits)
437.     Synthetic Design: Strategy and Tactics (2 credits)
438.     Applications of Organometallic Chemistry to Synthesis II (2 credits)
440.     Bioorganic Chemistry and Chemical Biology (4 credits)
441.     Physical Chemistry I (4 credits)
444.     Advanced Nuclear Science Educational Laboratory (ANSEL) (4 credits)
451.     Quantum Chemistry I (4 credits)
455.     Thermodynamics and Statistical Mechanics (4 credits)
456.     Chemical Bonds: From Molecules to Materials (4 credits)
458.     Spectroscopy and Kinetics (4 credits)
462.     Biological Chemistry (4 credits)
469.     Computational Chemistry (2 credits)
470.     Computational Chemistry II: Electronic Structure Theory & Quantum Dynamics (2 credit)
475.     Chemistry of Poisons (4 credits)
476.     Polymer Synthesis and Characterization (4 credits)
477.     Advanced Numerical Methods: Theory to Implementation (4 credits)
486.     Energy: Science, Technology & Society (4 credits)
489.     Electrochemical Biosensor Design (4 credits)

2.     Seminar & Colloquium - All Chemistry students register each semester for graduate Seminar & Colloquium.  For the first year, students will register for CHM 511 & CHM 513 and will earn one credit per semester, accumulating a total of two (2) credit hours. After this, students continue to register for and attend seminars and colloquium, but register for CHM 583 for zero credits.

3.     1st Year Graduate Workshop- This course has been designed specifically to address topics of interest to our incoming graduate students.  All students entering the graduate program will register for CHM 585 for 1 credit for each of the first two semesters accumulating a total of two (2) credit hours.

4.     Teaching - All graduate students in Chemistry participate in the teaching program as teaching assistants in undergraduate and graduate courses for a total of three semesters.  Teaching time for MD/PhD students is decreased to one semester.

5.     PhD Research in Chemistry - Students register each semester for a sufficient number of credit hours of CHM 595 PhD Research in Chemistry to bring the total credit hours for the semester to 12, until a total of 90 credit hours has been achieved.

6.     Doctoral Dissertation -    After students accumulate 90 total credit hours, they register for CHM 999 Doctoral for zero credits, as well as for the appropriate seminar and colloquium courses.

Qualifying Examinations

1.     Written Qualifying Examinations - These examinations are based on material from undergraduate course work, first-year graduate course work, seminars, colloquia, and the literature. These examinations serve to stimulate review of past and current materials, and are designed to encourage reading of current literature.  First-year students entering in September must begin the Written Qualifying Examinations series between October and April of their first year.  They then have twelve consecutive months to obtain the necessary points to pass the Written Qualifying Examinations.

2.     Oral Qualifying Examination - The Oral Qualifying Examination for admission to PhD candidacy is based on, but not limited to, a written report of the student’s research problem outlining research objectives, important background (including key references) and progress to date.  The Oral Qualifying Examination must be completed by the end of the student’s second year in the program.

Seminar Presentation

During the third year of study, students present a departmental seminar on a research topic as defined by the requirements of the student’s sub-discipline.

Reviewed: May 2016

Epidemiology

INTRODUCTION

The School of Medicine and Dentistry at the University of Rochester Medical Center (URMC) seeks to improve health through caring, discovery, teaching and learning. Education has traditionally been the ‘centerpiece’ of the URMC; our history has been marked by the education of renowned academic leaders including Nobel Laureates and deans of prestigious universities throughout the U.S.  The University of Rochester remains committed to integrating excellence in education into the ever increasingly complex environment of health care.  Comprehensive educational programs are well established in the laboratory, clinical and public health sciences.

Scholarly research has also been a critical component in the history of URMC. Clinical advances emanating from today’s science require the knowledge and skills from a broad spectrum of independent, scientific disciplines including some outside of the ‘traditional’ basic sciences.  Such disciplines as epidemiology, biostatistics, health services research and behavioral sciences have a unique theoretical core while also possessing the tools and methodologies for significant applicability to the study of health. Epidemiology has a distinct philosophy and a unique set of scientific concepts and methods, which are utilized to conduct independent community and population research, focusing on the delineation of disease causation and the prevention of morbidity and mortality.  It also provides the principles and tools necessary for the practice of preventive medicine and the formulation of public health practice. 

Doctoral Program in Epidemiology

A PhD program in Epidemiology was established in 2002 within the Division of Epidemiology, Department of Public Health Sciences.  The primary objective of the epidemiology doctoral program is to train epidemiologists in a wide variety of skills and methods spanning the disciplines of psychology, social and behavioral health, statistics and biostatistics in addition to solid course offerings in advanced epidemiologic methods and specialized areas of epidemiologic and population health research.

Specific objectives are to:

  • Educate individuals in the basic science of Epidemiology;
  • Teach the skills required to conduct population research;
  • Provide intense mentoring to assure a productive, and satisfying educational and research experience;
  • Prepare students to successfully transition into a role of an independent investigator by providing opportunities for peer mentoring, writing grant proposals, publishing work in scientific journals, and reviewing the work of peers;
  • Provide educational role models and opportunities that encourage students to develop and cultivate their own teaching skills; and
  • Nurture a research environment in which accuracy, integrity and ethical practices are highly valued.

The educational experience within the doctoral program provides a comprehensive blending of a didactic curriculum of theory and methods for epidemiologic research with an intensive mentored research experience.  Epidemiology students have access to experiences and opportunities across numerous departments and scientific centers within the University.  Quality education is provided through innovative approaches in a supportive, integrated environment.

Research Opportunities

The research component of the doctoral training has been planned as an intense, carefully mentored process.  The program faculty represent the majority of clinical departments within URMC as well as basic science departments.  Also represented are government agencies such as the Health Department and private corporations such as Kodak, Xerox and Blue Cross/Blue Shield, each of which has expressed interest in public health/health care issues.  Collaborations with these institutions have been developed and nurtured by the Department of Public Health Sciences because of the diversity that they bring to the department activities as well as the rich data sources each holds.  The program faculty provides the primary source of research opportunities for students to share in during their training as well as serving as the foundation on which dissertation research investigations may be built.  The federally funded research studies led by program faculty provide ample options for doctoral students, however, students are not limited to these programs.

Combined MD/PhD in Epidemiology Program

This MD/PhD option in epidemiology extends the long commitment of the University and the Department to improve health through research and education, with a particular emphasis on community and population-based research.  The interest in epidemiology throughout both the medical education and graduate education programs at the University mirrors the growing need for epidemiologists nationally who can both act as independent investigators and make significant contributions to medical research.

This combined program may be integrated into the establish MD/PhD program at the University of Rochester School of Medicine & Dentistry and culminates in the award of both an MD and a PhD in Epidemiology. The overall goal of this program is to prepare individuals for an academic career in medicine, which will focus on the conduct of epidemiology-oriented, population-based research. 

The major components of the program design are outlined below:

  1. Students seeking admission to the Doctoral program in Epidemiology as part of the combined MD/PhD program are held to the same academic standards for admission and performance as the students in the established PhD Program.  Requirements for admission are similar.  Student interviews with the Executive Committee of the epidemiology program (responsible for program admissions) are integrated into the admission process as conducted by the MD/PhD program.  Faculty provide the MD/PhD Admissions Committee with an evaluation as to the student’s eligibility and potential contributions to the program.
  1. Given the year 1 and 2 medical school curriculum (and perhaps completed masters degrees), some of the epidemiology course requirements in the standard doctoral program may be ‘waived’ for the MD/PhD students.  A maximum of 30 credits may be waived.  Courses which may be waived are specified on the attached MD/PhD program worksheet below.
  1. The first 2 years of the medical school curriculum will be completed by the student.  During this time, as schedules allow, students will participate in selected Division of Epidemiology activities such as seminars, journal clubs, etc. Emphasis will be placed on integrating the epidemiology student in program and division activities as much as possible in order to maximize the student’s exposure to epidemiologic principles/methods and research opportunities.
  1. In year 3 of the program the student will transition to the doctoral program in epidemiology.  At this time he/she will complete the majority of the required coursework for the PhD program and will complete elected courses from the epidemiology-specific offerings.  It is expected that the student will complete 5 courses during each of the two semesters.  Due to scheduling an additional course may need to be completed in year 4.

After the student has completed the required coursework he/she will complete both written and oral qualifying examinations.  The written examination, which is developed each year by the Executive Committee of the program, is administered within a two-day ‘classroom’ setting.  The oral examination is administered by the Executive Committee.  Based on both the written and oral examination, a vote of the members to pass the candidate is required; all votes are recorded.  In the case of failure, approval may rarely be given to a second qualifying examination after a minimum period of 6 months has elapsed.  No further opportunities for examination are provided.  Any student not successfully completing the examination is counseled to complete the requirements for a Masters in Public Health

  1. During year 4 the student will focus on the development of his dissertation research, perhaps writing a pre-doctoral grant to support these research activities. Students are also encouraged to serve as a Teaching Assistant for 1 introductory course.
  1. In year 5 and 6 the student will complete the 3rd and 4th year of medical school.  Blocks of time will be available during these two years in which the student will be able to return intermittently to continue work on their data collection.  Since original data collection is required as part of the dissertation research, it is planned that these two years will provide a period for data ‘maturation’.
  1. In year 7 the student will return full-time to the Division of Epidemiology to close-out his study, analyze the data and complete writing of the dissertation.  Although this could take 6 to 12 additional months, it is anticipated that most students (with good planning and hard work) will complete the entire program in 7 years. 

The program director and steering committee in epidemiology work closely with the directors of the MD/PhD program to refine the educational process to allow for flexibility and integration of the two program missions.  Our program is committed to the development of strong clinical investigators with the research skills to contribute to the translation of scientific knowledge from the bench to the bedside and to the community.

REQUIRED COURSES

The doctoral program in Epidemiology includes 61 credits of required coursework.  According to University policies, MD/PhD students may receive up to 30 credits from the first 2 years of medical school curriculum that will be applied to the doctoral degree requirements.  Twenty-nine credits have been specifically waived for MD/PhD students in the epidemiology doctoral program, including six introductory courses.  They are therefore required to take a minimum of 32 additional credits of coursework specific to the doctoral degree.  The 32 required credits must include the 6 advanced courses and grantsmanship required of all doctoral students and 3 additional elective courses (or non-waived required courses) in epidemiology.

Expected time to completion: 4 yr. MD + 3 yr. PhD

Semester              Course (Credit)

Possible waiver    PM 410 Intro to Data Management and Data Analysis Using SAS (3)^
Waived                  PM 412 Survey Research (3)
_______                   PM 413 Field Epidemiology (3)
Waived                  PM 414 History of Epidemiology (3)
Waived                  PM 415 Principles of Epidemiology (3)
_______                   PM 416 Epidemiological Methods (3)
Waived                  PM 426 Social and Behavioral Medicine (3)
_______                   PM 469 Multivariate Models for Epidemiology (3)
_______                   PM 472 Measure and Evaluation of Research Instruments (3)
_______                   PM 438 Grantsmanship (3)
Waived                  BST 463 Introduction to Biostatistics (4)
_______                   BST 464 Statistical Methods (4)
_______                   BST 465 Design of Clinical Trials (4)
Possible waiver    IND 503 Ethics (1; preferably taken in 2nd year of medical school)
_______                   PM _ _ _ Epidemiology Content Course (3)
_______                   PM _ _ _ Epidemiology Content Course (3)
_______                   PM _ _ _ Epidemiology Content Course (3)
Waived                  PM _ _ _ Elective* (3)
Waived                  PM _ _ _ Elective* (3)
Waived                  PM _ _ _ Elective* (3)

Semester              Epidemiology Content Course (Credit)

_______                PM 417 Molecular Epidemiology (3)
_______                PM 418 Cardiovascular Epidemiology (3)
_______                PM 424 Chronic Disease Epidemiology (3)
_______                PM 442 Nutritional Epidemiology (3)
_______                PM 451 Infectious Disease Epidemiology (3)
_______                PM 466 Cancer Epidemiology (3)
_______                PM 470 Environmental & Occupational Epidemiology (3)
_______                PM 494 Injury Epidemiology & Emergency Care Research Methods (3)

Total Required Credits = 61

^Students are strongly encouraged to gain practical experience with data management and analysis prior to starting the PhD program (e.g. during summers)

*Additional courses within and outside of the department that are judged to significantly contribute to the student’s specific area of epidemiologic research may also be taken as electives with approval from the Epidemiology Program Director.  Related basic science courses are encouraged.

Revised 2016

Biomedical Genetics

MD/PhD program students usually enter the PhD portion of their combined degree work after the basic science years of the MD curriculum.  During the second year of the M.D. program, they should discuss the PhD Program with prospective faculty advisors and the Genetics Program Director.  It is optimal for the student to complete two research rotations before choosing a permanent advisor.

A total of 96 credit hours are required for the PhD. Program course requirements are meant to be sufficiently flexible to accommodate students with diverse backgrounds and career goals.

Curriculum

1.  All of the following courses are required:

  •             GEN 507 (4 credits)                 Advanced Genetics                                Fall
  •             IND 410  (4 credits)                 Molecular Biology and Genetics           Spring
  •             IND 501  (1 credit)                   Ethics in Research                                  Fall
  •             GEN 503/504 (1 credit)           Genetics Seminar*                                (each semester)
  •             GEN 595                                    PhD Research                                      (each semester)
  •             *Required each semester throughout the course of study and includes yearly presentations beginning at the end of year 2

2.   Additional requirement: One elective is required. Below is a list of approved electives. The advisor and the program director may approve other electives.

      Fall Semester

            BIO 426 (4 credits)                  Developmental Biology
            BPH 509 (5 credits)                Molecular Biophysics
            MBI 473 (3 credits)                 Immunology

      Spring Semester

            BCH 412 (5 credits)                Advanced Topics in Biological Macromolecules
            GEN 508 (4 credits)                Genomics and Systems Biology
            IND 407 (4 credits)                  Structure and Function of Cell Organelles
            IND 411 (5 credits)                  Methods in Structural Biology
            IND 443 (4 credits)                  Eukaryotic Gene Organization & Expression
            IND 447 (4 credits)                  Signal Transduction
            MBI 456 (4 credits)                 General Virology (odd numbered years)

 OTHER REQUIREMENTS

  • Two research rotations should be conducted prior to joining a laboratory for dissertation research. Students are encouraged to complete these rotations during the first two years of the MD program.
  • The Qualifying Examination is required at the end of the second year of the PhD studies.
  • The teaching assistant requirement is waived.
  • At least one meeting per year with the thesis advisory committee (normally held after the student’s Genetics Seminar presentation).
  • A satisfactory thesis must be written and successfully defended.

Reviewed: May 2016

Health Services Research and Policy Program

FIRST YEAR
 

2 Weeks Prior to Year 1, Fall
     2-week Mathematics and Statistics Review Course (Math Camp)

Year 1, Fall
      PM 421       US Health Care System:  Financing, Delivery, Performance (3.0 credits)
      PM 428       Health Services Research Seminar (1.0 credit) 
      PM 430       Psychology in Health Services Research (3.0 credits)
      PM 445       Introduction to Health Services Research and Policy (3.0 credits)
      PM 463       Introduction to Mathematical Statistics, Part I (3.0 credits) 
      IND 503      Ethics in Research (1.0 credit)

Year 1, Spring
     PM 428       Health Services Research Seminar (1.0 credit)
     PM 464       Introduction to Regression Analysis (3.0 credits)
     PM 472       Measurement & Evaluation of Research Instruments (3.0 credits)
     PM 484       Medical Decision Analysis & Cost Effectiveness Research  (3.0 credits)

Year 1, Summer
     PM 410       Introduction to Data Management and Analysis (3.0 credits)

SECOND YEAR

Year 2, Fall

     PM 412       Survey Research (3.0 credits)
     PM 420       American Health Policy & Politics (3.0 credits)
     PM 428       Health Services Research Seminar (1.0 credit)    
     PM 456       Health Economics I: Introduction to Health Economics (3.0 credits)
     PM 465       Stats III: Advanced models (3.0 credits)

Year 2, Spring

     PM 422       Quality of Care and Risk Adjustment (3.0 credits)
     PM 428       Health Services Research Seminar (1.0 credit)
     PM 472       Measurement & Evaluation of Research Instruments (3.0 credits)
     PM 483       Advanced Health Economics II (3.0 credits)
     PM 487       Fundamentals of Science Technology & Health Policy (3.0 credits)
     PM 494       Health Policy Analysis Lab

Reviewed 7/7/16

Microbiology & Immunology (MBI)

Departmental requirements for the MD/PhD degrees reflect the fact that most students enter the PhD program after completion of two years of the Medical Curriculum. 

Students must earn 24 credit hours of course work and 6 credit hours of PhD Research after consultation with his/her advisor for fulfilling the Qualifying Exam requirements.  An additional 66 credits must be earned after the Qualifying Examination to fulfill the PhD requirements.  MD/PhD students will not be allowed to enter the clinical years until their thesis has been written and registered.

Typical MD/PhD students enter the PhD portion of their combined degree program after the basic science years of the MD curriculum.  During their first and/or second year of the MD program, they should discuss the PhD program in Microbiology and Immunology with the departmental faculty including the director of graduate studies in this department.  During this period, they should also be considering possible dissertation research mentors.  Research rotations in two (or more) of the prospective labs are conducted, typically in the summers before their entry into the PhD program.  This results in a waiver for MBI 507 (Laboratory Rotations) and MBI 506 (Scientific Writing in Research).

Based on their basic science courses in the medical curriculum, MD/PhD students are granted 30 credits toward the 90-credit requirement for the PhD.  This results in a waiver for IND 408 (Advanced Biochemistry).  Of course, any portions of this course may be audited as needed.

Depending on their research focus, MD/PhD candidates, like all doctoral candidates in the Department of Microbiology & Immunology, enter either the Immunology Track, the Microbiology Track, or the Virology Track; required and elective course offerings in each track are described below.  In addition, each student is required to take the Microbiology & Immunology Student Research Seminar (MBI 501) given every semester, and Biomedical Ethics (IND 501).

PhD research training focuses on the following major topics of cluster faculty members' interest such as: microbial pathogenesis; molecular genetics; microbial physiology; oral microbiology; molecular virology; neurovirology; viral immunology; vaccine biology; autoimmunity, tumor immunology; lymphocyte biology; developmental immunology; cytokines and immune regulation; psychoneuroimmunology; immunogenetics; and phylogeny of immunity.  MD/PhD students typically begin their dissertation research upon entry into the PhD program.  Their research focus intensifies in subsequent years during which time there is also an emphasis on presentation of research results locally, at national and international scientific meetings, and in journal articles.  Didactic course work is usually completed before the end of the second year.  Additional required courses are typically small group seminars and journal clubs (1-2 credits) where students learn how to critically evaluate and orally present recent literature in their chosen field of study.

MD/PhD students must take an oral qualifying examination on their proposed thesis research by October 1 of their second year in the PhD Program. The qualifying exam tests both the baseline level of knowledge of the field of study and well as a working knowledge of areas such as genetics, cell biology and biochemistry. Additionally, and critically, the qualifying exam tests the student’s ability to integrate this knowledge in the design and interpretation of experiments.  See page 10 for instructions on the PhD oral qualifying exam.

The doctoral program typically takes four years for combined degree students to complete.

Course Requirements

(Students must earn 24 credit hours of course work)

Core Requirements common to all three tracks:

IND 501     Ethics in Research (Fall of first year only)      1 credit      
MBI 501    Student Seminar (All semesters)                      1 credit                  
MBI 595    PhD Research (All semesters)                          add # of credits needed to total 16

Track specific requirements:

Immunology Track

Track requirements:

MBI 515                       Advanced Immunology                                   4 credits
MBI 580                       Journal Club & Immunology                           1 credit
                                    Research-in-Progress Seminar
MBI 540                       Adv. Topics in Immunology                            2 credits

            (taken in 2nd semester of 1st year plus 2 seminars during the rest of the PhD program)

Electives

Chosen after consultation with the research advisor and PhD committee, to best serve the needs of the student's program, background, and interests.  Electives taken by students have included:

IND 447                       Signal Transduction:                                       4 credits
MBI 456                       General Virology                                             4 credits
MBI 414/515                Mechanisms of Microbial Pathogenesis         4 credits
                                    + Co-Seminar
MBI 421/521                Microbial Genetics and Physiology                4 credits
                                    + Co-Seminar
PTH 507                      Cancer Biology                                               3 credits
MBI 403                       Drug Discovery                                               2 credits

Virology Track

Track requirements:

MBI 456                       General Virology                                             4 credits
MBI 588                       Virology Research Seminar Series                1 credit
                                    taken each year starting second year
MBI 589                       Advanced Topics in Virology                          1 credit
                                    taken each year starting second year

Electives

Chosen after consultation with the research advisor and PhD committee, to best serve the needs of the student's program, background, and interests.  Electives taken by students have included:

IND 447                       Signal Transduction:                                       4 credits
MBI 421/521                Microbial Genetics                                          4 credits
                                    + Co-Seminar
MBI 473/573                Immunology + Co-Seminar                             5 credits
MBI 414/515                Mechanisms of Microbial Pathogenesis         4 credits
                                    + Co-Seminar
MBI 421/521                Microbial Genetics and Physiology                4 credits
                                    + Co-Seminar
MBI 403                       Drug Discovery                                               2 credits

Microbiology Track

Track requirements:

MBI 414/515                Mechanisms of Microbial Pathogenesis         4 credits
                                    + Co-Seminar
MBI 421/521                Microbial Genetics and Physiology                4 credits
                                    + Co-Seminar

Electives

Chosen after consultation with the research advisor and PhD committee, to best serve the needs of the student's program, background, and interests.  Electives taken by students have included:

IND 408                       Cell Biology                                                     4 credits
IND 410                       Molecular Biology and Genetics                     4 credits
MBI 581                       Oral Microbiology                                            2 credits
MBI 403                       Drug Discovery                                               2 credits

Reviewed: June 2016

Neuroscience Graduate Program

The primary goal of the Neuroscience Graduate Program (NGP) is to provide state-of-the-art research-intensive training for students seeking to obtain a PhD degree in the study of the nervous system.  Typical MD/PhD students enter the PhD portion of their combined degree program after the basic science years of the MD curriculum.  During their first and/or second year of the MD program, they should discuss the two PhD degree tracks in the NGP with the program faculty including the director of graduate studies.  During this period, they should also be considering possible dissertation research mentors.  Research rotations in two (or more) of the prospective labs are conducted, typically in the summers before their entry into the PhD program. Students usually have selected a dissertation research mentor at the time of matriculation into the graduate portion of their training.  At this same time, students chose one of two PhD degree tracks: Neuroscience or Neurobiology & Anatomy. 

Curriculum

Based on their basic science courses in the medical curriculum, MD/PhD students are granted 30 credits toward the 96-credit requirement for the PhD. 

a. Required CourseworkAll NGP students complete a core curriculum during their first year that includes: Cellular Neuroscience (NSC 512), Integrative and Systems Neuroscience (NSC 531), Ethics in Research (IND 501), and laboratory rotations of their own choosing if needed. During years 1 and 2, NGP students must also complete 4 semesters of NGP Journal Club (NSC 592) and Applied Statistics in the Biomedical Sciences (BST 467).  Students are also required to register for NGP Student Seminar (NSC 503) each semester they are in the program. 

At the end of the first year (if not done earlier), students formally declare whether they will follow the Neuroscience (NSC) or Neurobiology & Anatomy (NBA) PhD degree track. The two tracks accommodate distinct training objectives:

Neuroscience track – maximum flexibility to tailor advanced coursework to fit individual education and research objectives

NBA track – comprehensive exposure to human physiology and anatomy or medical neuroscience through participation in the medical school curriculum

b. ElectivesIn addition to the coursework listed above, students must complete a minimum of 10 elective credits of coursework.  MD/PhD students can use 10 credit hours of medical school coursework to fulfill the Electives requirement.  For most students, a maximum of 4 elective credits will come from Biochemistry (IND 408), Cell Biology (IND 409), Molecular Biology and Genetics (IND 410), or Foundations in Cellular and Molecular Biology (ANA 511).  The remaining 6 (or more) elective credits are earned in upper level graduate courses and are chosen in consultation with the NGP Director and/or the student’s thesis advisor.

1st Year Core Curriculum - both PhD Tracks

Fall Semester

      NSC 512 (5 credits)                                     Cellular Neuroscience
      NSC 592 (1 credit)                                       NSC Journal Club
      NSC 503 (1 credit)                                       NSC Student Seminar
      IND 501 (1 credit)                                        Ethics in Research
      NSC 590 (2-4 credits)                                  Lab Rotations (if necessary)
      NSC 595 (0-4 credits)                                  PhD research
      and/or (0-4 credits)                                      Electives

Spring Semester

      NSC 511 (1credit)                                        Human Brain Anatomy
      NSC 531 (6 credits)                                     Integrative & Systems Neuroscience
      NSC 592 (1 credit)                                       NSC Journal Club
      NSC 503 (1 credit)                                       NSC Student Seminar
      NSC 595 (0-6 credits)                                  PhD research
      and/or (0-6 credits)                                      Electives

2nd year—NBA track

The NBA PhD requires completion of Human Structure and Function (HSF) or Mind, Brain, and Behavior (MBB).  Since these courses were completed during the medical school coursework, students are strongly encouraged to take electives relevant to their thesis work.  Finally, while MD/PhD students are not required to complete a teaching tutorial, most do so in their third semester in either HSF or MBB.

Fall Semester  

      ANA 526 (16 credits)                                HSF (waived for MD/PhD students)
      or ANA 525 (12 credits)                            MBB (waived for MD/PhD students)
      ANA 581 or 583 (3 credits)                       Teaching Tutorial in HSF or MBB (optional)
      NSC 592 (1 credit)                                    NSC Journal Club
      NSC 503 (1 credit)                                    NSC Student Seminar
      ANA 595 (4-11 credits)                             PhD Research
      and/or   (0-8 credits)                                 Electives

Spring Semester

      NSC 592 (1 credits)                                  NSC Journal Club
      NSC 503 (1 credits)                                  NSC Student Seminar
      *BST 467 (4 credits)                                 Appl. Stats in Biomedical Science
      ANA 595 (0-14)                                         PhD Research
      and/or (0-8 credits)                                   Electives

2nd year—Neuroscience track

The Neuroscience PhD requires completion of a minimum 10 credits of elective coursework (see list below for choices).  In addition most Neuroscience track students complete a teaching tutorial in the undergraduate courses Basic Neurobiology (NSC 201, Fall semester) or Lab in Neurobiology (NSC 203, Spring semester), or the medical school course Mind, Brain and Behavior.

Fall Semester

      NSC 592 (1 credit)                                    NSC Journal Club
      NSC 503 (1 credit)                                    NSC Student Seminar
      NSC 595 (4-14 credits)                             PhD Research
      and/or (0-8 credits)                                   Electives                 

Spring Semester

      NSC 592 (1 credit)                                    NSC Journal Club
      NSC 503 (1 credit)                                    NSC Student Seminar
      BST 476 (4 credits)                                   Appl. Stats in Biomedical Science
      NSC 581 (3 credits)                                 Teaching Tutorial (optional)
      NSC 595 (4-11 credits)                             PhD Research
      and/or (0-8 credits)                                   Electives

Partial list of electives taken by current students and recent graduates

ANA 405

Hearing & Balance: Structure, Function & Disease

ANA 513

Neuroinflammation

ANA 518

Intro to Neuroengineering

ANA/NSC 591

PhD Readings

BCS 502

Cognition

BCS 511

Behavioral Methods in Cognitive Science

BCS 512

Computational Methods in Cognitive Science

BCS 513

Intro to fMRI: Imaging, Computational Analysis & Neural Representations-

BCS 521

Auditory Reception

BCS 532

Probabilistic theories of cognitive processing

BST 465

Design of Clinical Trials

GEN 507

Advanced Genetics

GEN 508

Genomics and Systems Biology

IND 412

Graduate Experience in Science Education

IND 447

Signal Transduction

MBI 403

Drug Discovery

MBI 456

General Virology 

MBI 473

Immunology

MBI 492

Science Communication Skills Development

MBI 515

Advanced Immunology

NSC 525

Biology of Neurological Disease

PHP 404

Principles of Pharmacology

PHP 550

Ion Channels

PTH 507

Cancer Biology

PTH 509

Pathways of Human Disease

PTH 571

Molecular Basis of Disease

TOX 521

Toxicology I

TOX 522

Toxicology II

Irrespective of track, students should strive to complete all coursework by the end of the fifth semester of study (i.e., before taking the Thesis Proposal/Qualifying Examination).

Other Requirements & Related Details- both PhD tracks

Advising committees: During the first year each student is assigned a first year advising committee comprised of two NGP faculty members and a senior NGP student. The goal of the first year advisory committee is to provide not only critical feedback to students on rotation report and oral presentations in student seminar, but also to provide advice on areas that include (but are not limited to): expectations in graduate school, balancing classes and lab work, study habits, choosing a rotation and eventually a thesis lab, reading the scientific literature, scientific writing, qualifying exams, interacting with faculty and students, networking and future career options.  By the start of the second year, this committee is replaced by the Part I Exam Committee and eventually by the Thesis Committee.

Rotation report: MSTP students will only be required to complete a fall written rotation report. The report can be written on a rotation completed earlier. Completion of the report will be required to obtain a passing grade in NGP Student Seminar (NSC 503).

Qualifying Exam (Part I): The student in consultation with his or her advisor selects a minimum of 50 papers relevant to the student’s scientific area of interest to be read by the student over a period of not more than 2 months.  At this time, the student meets with the committee, which will either approve the reading list or suggest further refinements to the scope of the exam.  At the end of the reading period, the student formulates and submits in writing 5 broad hypothesis-driven research questions to their committee based upon the readings. The exam begins when the Committee returns a subset of these questions along with one or more of its own to the student. The student then has 1 week (7 calendar days) to compose written answers to these questions. As a guideline, a thorough answer to each question typically requires 2-4 single spaced pages. Students should take the Part I exam during the spring semester of the 2nd year. The exam must be started before April 1st and be completed by June 1st of the summer between years 2 and 3.

Qualifying Exam (Part II): Thesis Proposal. After passing the Part I Exam, the student is expected to formulate a thesis proposal with the guidance of his/her Thesis Advisor. The written proposal should include the specific aims and overall significance of the proposed research, sufficient background for others to understand the research plan, key preliminary data that support the aims, and a description of the experimental design that will be used to accomplish the stated aims. The thesis proposal must be written and the Qualifying Examination taken BEFORE October 1st of the fifth semester of graduate study (i.e., fall semester in year 3).  Successful completion of the Thesis Proposal/Qualifying Exam advances the student to candidacy for the Ph.D. degree.

Examining committee: The University Council on Graduate Studies has designated rules for the Committee.  The student’s committee must consist of 4 tenured or tenure-track faculty of assistant professor or higher rank and is subject to approval from the NGP Director.  An expert from outside the University of Rochester may be invited to join the Committee as the external member with prior written approval from the NGP Director and Associate Dean for Graduate Studies.

Neuroscience track: Three of the 4 members are chosen by the student in consultation with their thesis advisor. Of these, 2 MUST be from the NGP faculty list and 1 MUST be from outside of the primary department of the advisor and co-advisor. Please notice that NGP faculty members can serve as external committee members for NGP students. Note that the thesis advisor is NOT a member of the Examining Committee for students in the Neuroscience track, although he or she is expected to attend the closed session as a silent observer. The final member of the Committee will be appointed by the NGP Director from the NGP core faculty and will be a member of the examining committee for the purpose of the thesis proposal only.

NBA track: At least 2 of the 4 members MUST have their primary appointment in NBA while the external member must be from outside the NBA primary faculty. The thesis advisor (who must have a primary or secondary appointment in NBA) is the fourth member of the Examining Committee.

PhD Dissertation and Defense: After completing the Qualifying Exam, the official Thesis Advisory Committee is formed and the remaining years of study are spent working on developing the research project that will form the PhD dissertation.  The Thesis Advisory Committee must consist of a minimum of 4 tenured/tenure-track faculty assistant professor or higher. One of these is the thesis advisor. While the Thesis Advisory Committee is distinct from and need not overlap with the Qualifying Exam Committee, often two to three of the members come from the student’s Qualifying Exam Committee.

        For neuroscience students, two of the remaining three members MUST be from the NGP faculty list and one must be from outside of the primary department of the advisor and co-advisor.  Please notice that NGP faculty               members can serve as external committee members for NGP students.

For NBA students, at least two of the four members MUST have their primary appointment in NBA while the external member must be from outside the NBA primary faculty. The thesis advisor (who must have a primary or secondary appointment in NBA) is the fourth member of the Advisory Thesis Committee.

It is an expectation that prior to the thesis defense, all students will have published or submitted for publication at least one first-author manuscript in a peer-reviewed journal describing their research findings.  Review articles or published meeting presentations are NOT sufficient to fulfill this requirement.  After the advisor and Thesis Committee approve the completion of the thesis research, the student submits a dissertation of his or her findings.  In the form of an open lecture, the student publicly presents his or her thesis research and in a closed exam defends those findings to the Thesis Committee.

Reviewed 05/2016

Optics

The Institute of Optics offers a PhD degree that can be combined with the MD.  The outline below illustrates a student’s progress in the PhD program.  Details are given in subsequent sections.

First Year

Full time coursework and study

Choose Thesis Advisor (by April 15th)

Summer Research

Preliminary Examination

Second Year

Advanced specialized coursework

Teaching Assistantship

Research

Third Year

Oral Qualifying Examination

Elective Courses

Research

Fourth Year and Beyond

Research

Elective Courses

Thesis submission

Oral Thesis Defense

Core courses

First-year financial support is usually in the form of a fellowship allowing the student to devote full time to course work.  The full load is 16 hours of credit per semester.  The purpose of this year's work is to provide a broad background in optical physics and engineering.  The following is recommended to provide a broad survey of optics.

Fall                                                                             Spring

OPT 411  Mathematical Methods for Optics          OPT 442  Instrumental Optics
OPT 425  Radiation & Detectors                               OPT 462  Electromagnetic Waves
OPT 441 Geometrical Optics                                     OPT 412  Quantum Mechanics for Optics
OPT 461  Fourier Optics                                            Elective

With the exception of the elective, these courses are core courses and are normally required for a PhD.  They can be waived by petition to the Graduate Committee in those cases where they seem inappropriate for a student with an unusual background or interests

Preliminary Exam

The examination consists of three segments and is given one or two weeks before classes start in the fall semester.  Faculty grade their respective exam questions. Thereafter, the scores are presented to a faculty review board.  Passing the preliminary exam is dependent not only on proficiency shown on the test, but also on the student's entire body of work including past course work, past and current research activity within The Institute, and recommendation from his/her advisor and other faculty.

Teaching Assistantship

During the second year, students usually fulfill their TA requirement, which is two semesters of service.  This service is required whether or not the student has received financial support from the University.  It is the intent of the Optics faculty that this teaching should be more than merely grading papers for a course and should include some sessions in the classroom.

Elective Courses and Seminars

In addition to the above course requirements, the student must complete 28 credit hours of formal coursework, and 30 credit hours of research, totaling 90 credit hours.

Research Activities

Students typically secure a position in a lab during the spring semester of their first year, and start performing research the summer after their first year.

Qualifying Exam

  1. The student finds a prospective thesis advisor and selects a topic for PhD research.
  1. The student prepares a written document, which describes the proposed research.  This Thesis Proposal shall be no longer than 12 pages in length, not counting additional page(s) for references.  It includes a brief literature survey and should convince the reader that the candidate is aware of the problems he or she is attempting to solve and has some inkling of how to solve them.
  1. The student prepares a 25-30 minute presentation for the oral examination. The committee members can ask questions during and following this presentation. The question session can take up to one and a half hours.

Dissertation

Once admitted to candidacy for the PhD, the student forms a dissertation committee consisting of the faculty mentor, two other faculty members in Optics, and one faculty member in a non-Optics department (or program).  Upon completion of the dissertation research, and having met all course and credit hour requirements, the written dissertation is filed with the Graduate Dean who approves the final oral examination.  This examination consists of a public lecture to the entire Department, followed by a closed oral exam by the dissertation committee.

Reviewed June 2016

Pathology

The Department of Pathology offers a program leading to a PhD in Pathology to students enrolled in the MD/PhD program. Degree requirements are somewhat modified to take into account the basic science curriculum completed by students during their first two years of medical school.

1. Laboratory rotations: MD/PhD students are expected to have completed 2-3 lab rotations during their first two years of medical school.

2. Course Requirements for MD/PhD Students: The following courses are required for a PhD degree in Pathology:

Group A          (Select 1 Pathology elective course in consultation with program director)

PTH 507          Cancer Biology                                   spring
PTH 571          Molecular Basis of Disease                fall

Group B          (Select 1 non-Pathology elective 4-credit course in consultation with program                              director. Most often selected, though not exclusive electives.)

BST 463          Introduction to Biostatistics                 IND 408           Adv Biochemistry
CVS 401          Cardiovascular Biology & Disease     IND 409           Cell Biology
MBI 473           Immunology                                        IND 410           Molec Biol & Genetics
IND 447           Signal Transduction                                       

Group C          (all are required)

PTH 504          Current Topics in Experimental Pathology – Student Seminar
IND 501           Ethics and Professional Integrity

Note: Additional courses may be considered depending on the background and future directions of the student.

3.         Departmental and Student Seminar Series: Attendance at the Student Seminar Series (PTH 504) is mandatory for all Pathology graduate students. Students writing their thesis are exempt from PTH 504 during their final semester.

4.         Oral qualifying exam: Students are expected to defend their thesis proposal before an oral exam committee by October 1st of their second year of graduate training. By this time, the student will have completed all course requirements and will have generated sufficient preliminary data in their chosen thesis laboratory to propose and defend before the committee the thesis question that they wish to pursue for the PhD.

5.         Monitoring progress: Students who have passed their qualifying exam must meet with their thesis advisory committee at least yearly. The purpose of the committee is to monitor the student’s progress and to provide advice and additional guidance to the student.

Revised June 2016

Pharmacology and Physiology

During their second year, MD/PhD students should discuss entry into the PhD program with the Director of Graduate Studies of the Department of Pharmacology and Physiology.  The PhD portion of their combined degree program will begin after successful completion of the first two years of the Double-Helix Curriculum.

MD/PhD students should expect to successfully complete 2-3 laboratory research rotations, at least one with a primary faculty member in the Department of Pharmacology and Physiology, during the first two years of the Double-Helix Curriculum.

The PhD portion of the MD/PhD program will build on previous background acquired in the Medical School curriculum.  Because of this, certain course requirements of the traditional PhD track will be waived and advanced courses may be substituted to provide depth in an area of specialization.

MD/PhD students are granted 30 credits toward the 96 credit requirement for the PhD on the basis of their basic science courses in the medical curriculum.  Students who consider that their background may permit exemption from other core curriculum courses in Pharmacology and Physiology should request such an exemption.

Each MD/PhD student must complete at least one of the following three Core Courses:

     IND408       Biochemistry (5 credits)
     IND409       Cell Biology (4 credits)
     IND410       Molecular Biology (4 credits)

MD/PhD students must complete each of the following additional courses:

     IND447       Signal Transduction (4 credits)
     PHP502      Seminar (4 semesters) (1 credit)
     IND501       Ethics and Professional Integrity (1 credit)

MD/PhD students must also complete a total of at least 4 credits of upper-level A/E credit selected from the following list of recommended courses:

     PHP 550     Ion Channels and Disease (2)
     MBI 473      Immunology (3)
     NSC 525     Biology of Neurological Diseases (3)
     BST 463     Introduction to Biostatistics (4)
     PTH 507     Cancer Biology (3)
     PTH 509     Pathways to Human Disease I (4)
     PTH 510     Pathways to Human Disease II (4)
     PTH 571     Molecular Basis of Disease (3)
     CVS 401     Cardiovascular Biology and Disease (3)

MD/PhD students must complete the Departmental Qualifying Examination by 10/1 of their 4th year of study in the MD/PhD program. After successful completion of the Qualifying Examination, MD/PhD students must meet with their Dissertation Advisory Committee at least once yearly.  During these meetings, the committee will discuss the student’s progress, clarify research problems, and outline priorities of future research directions.

(For information on thesis preparation and defense, see:

http://www.urmc.rochester.edu/education/graduate/phd/pharmacology-and-physiology/program/handbook.cfm )

Reviewed: June 2016

Toxicology

(http://www.urmc.rochester.edu/education/graduate/phd/toxicology/)

The program is housed in the Department of Environmental Medicine, which also oversees the Environmental Health Sciences Center, one of 22 such Centers of Excellence sponsored by the National Institute of Environmental Health Sciences.  This program consists of an interdisciplinary faculty, many of whom which are located in contiguous space, with basic science, translational and clinical expertise. Many faculty in this program serve as mentors in the Toxicology Training Program. In addition to providing research and training opportunities, this program supports a vibrant seminar series, journal club, and maintains a state-of-the art inhalation facility for exposing cells, animals, and human subjects to a variety of agents including infectious organisms, air pollutants, tobacco smoke, and other environmental agents. Finally, several Toxicology Training Program faculty and their trainees are involved in the Rochester Clinical and Translational Science Institute (CTSI).

Areas of strength include:

  • Neurotoxicology
  • Cardiovascular & Pulmonary Toxicology
  • Osteotoxicology
  • Nanotoxicology/Nanomedicine
  • Developmental Toxicology
  • Immunotoxicology
  • Stem cells and Epigenetics

CURRICULUM FOR THE PhD

The Toxicology graduate curriculum consists of several components: (1) core course requirements, (2) seminar requirements, (3) elective course requirements, and (4) experimental research. It is our belief that research is the most important part of this doctoral training program. As such, the PhD degree is awarded only after a student has conducted an independent, hypothesis driven research project and then written a dissertation that demonstrates a high level of intellectual competence.

A total of 96 credit hours are required to complete the PhD program, and The Graduate School requires an academic load of 16 credit hours per semester. A minimum of 30 graduate credit hours must be accumulated before taking the qualifying examination, with 24 credit hours being course work credit. These will come from core courses, electives, seminars, and research (TOX 595, PhD Research in Toxicology). Given that toxicology is highly interdisciplinary, our curriculum reflects that a thorough grounding in basic sciences is indispensable. To ensure that our trainees obtain broad and in-depth knowledge necessary for success, in addition to the Core Curriculum, 6 credit hours as electives are required, and at least 3 of these credits must be from toxicology (TOX) electives.

A.  Core Curriculum (required courses):

      Course No.      Course Title      Credits

      IND 408           Advanced Biochemistry                                              5
      IND 409           Cell Biology                                                                   4
      IND 410           Molecular Biology & Genetics                                    4
      PHP 403          Human Cell Physiology                                                4
      PHP 404          Principles of Pharmacology                                        4
      TOX 521          Biochemical Toxicology                                               4
      TOX 522          Organ Systems Toxicology                                          4
      TOX 558          Seminar in Toxicology                                                1 (taken 4 times)
      BST 467#             Applied Biostatistics in the Biomedical Sciences       3
      IND 501           Ethics and Professional Integrity in Research           1
      TOX 597          Intro Faculty Research in Toxicology                         0

# Includes a required ‘boot camp’ prior to the start of the course that serves as a refresher for students who may have already had some statistics/biostatistics, as well as providing fundamental information for students who are new to biostatistics. Students also receive hands-on training in the software that will be used during the course.

Exemptions from the Core Curriculum:  A student interested in an exemption from any core course listed above needs to discuss this with the Program Director, who will help determine whether an exemption is appropriate. Students need to come to this meeting with the Program Director prepared to provide details about the content of prior courses and the grade earned. Providing a comprehensive course description including lecture syllabus of a prior graduate-level course is required; therefore obtaining this in advance of meeting with the Program Director is strongly encouraged. After a review of prior course materials, either a decision will be made that the course needs to be taken, or the Program Director will have the student share prior course materials with the UR Course director for in-put on, and final approval of, the request. The request then needs to be reviewed and approved by the Senior Associate Dean of Graduate Education and Postdoctoral Affairs (GEPA).

MD/PhD Students in Toxicology 

Typical MD/PhD students enter the PhD portion after the basic science years of the MD curriculum.  During their first and/or second year of the MD program, they should discuss the PhD program in toxicology with departmental faculty and the Director of the Toxicology Graduate program.  During this period, they should evaluate possible dissertation research mentors.  Research rotations in two or three prospective labs are conducted, typically in the summer before their entry into the PhD program.

Based on their basic science courses in the medical curriculum, MD/PhD students are granted 30 credits toward the 96-credit requirement for the PhD.  Thus, many of the required courses for Toxicology PhD candidates (i.e., IND 408 – Biochemistry; IND 409 - Cell Biology; IND 410 -Molecular Biology and Genetics; PHP 403 and PHP 404 – Pharmacology and Physiology) are waived for most MD/PhD students.  30 credits can only be transferred IF the student earns more than 96 credit hours of PhD research.  Please refer to the University policy on credit sharing between 2 degrees.

PhD Qualifying Examination  

The Qualifying Examination consists of a closed session with the Thesis Advisory Committee, with one member selected by the Senior Associated Dean to serve as Chair of the Examination process.  The oral examination usually lasts between 2 to 3 hours. The candidate is judged on the following criteria:

(1) Written and oral presentation of the thesis proposal;

(2) Grasp of the fundamental issues and theoretical basis for the experimental approaches;

(3) Knowledge of alternate approaches to achieve the outlined goals; and

(4) Ability to critically evaluate a research area, to propose a relevant hypothesis, to design critical experiments to test the hypothesis, and to critically assess potential results of proposed experiments.

The Committee will meet separately at the conclusion of the oral examination, determine whether or not the student has passed, and formulate a report to the Senior Associate Dean’s office. Directly after this discussion, the committee, led by the committee Exam Chair, will meet with the student to discuss strengths and weaknesses of the exam, and may make specific recommendations. The student will be informed of the examination results at this time.

Thesis Defense

The final examination for the PhD portion of the degree requires a written dissertation, a public oral presentation of the research project, and a closed defense of this research before the Dissertation Advisory Committee. A faculty member from another graduate program at the University of Rochester serves as the official chair the final closed examination. The committee for the final examination decides on the acceptability of the quality of the research and the method of presentation (written and oral), following all University guidelines.

Reviewed: July 2016

Translational Biomedical Science

Professor Simpson-Haidaris, PJ

The goal of the PhD program in Translational Biomedical Science is to prepare individuals for independent careers along the translational research spectrum with in-depth knowledge of disease mechanisms. Participants in the program will receive in-depth co-mentoring to assure skills development and productive research training. The program aims to teach fundamental theory and knowledge in subject areas including systems biology, drug design, biostatistics and computational biology, epidemiology, molecular mechanisms of diseases, laboratory methods and analytical skills, human subjects research, regulatory science, and population science essential to translational research. The program aims to provide a critical environment fostering inquiry, integrity, academic scholarship, high productivity, and skills development to excel at multidisciplinary team science.

Curriculum

Core Courses include:

IND 501 Ethics and Professional Integrity in Research
PM 415 Principles of Epidemiology
BST 463 Introduction to Biostatistics or BST 467 Applied Biostats for Biomedical Science
IND 419 Introduction to Quantitative Biology or PM 486 Medical Ecology
IND 417 Workshop in Scientific Communication
IND 438 Practical Skills in Grant Writing (or equivalent workshops and seminars)

Student Seminar Courses

Training in Rigor and Data Reproducibility in Science

The additional core and elective coursework is highly tailored to the individual to accomplish discipline-specific research and career goal objectives while meeting the requirements for degree fulfillment. TBS students select courses from other PhD programs in the Schools of Medicine and Dentistry and Arts, Sciences and Engineering with guidance and approval from the TBS program director and steering committee. Additional course work information is available at the following PhD program sites:

Biochemistry and Molecular Biology

Biomedical Engineering

Biophysics, Structural, and Computational Biology

Cellular and Molecular Pharmacology and Physiology

Epidemiology

Genetics, Development and Stem Cells

Health Services Research and Policy

Immunology, Microbiology and Virology

Neuroscience (program of entry for Neuroscience and Neurobiology and Anatomy PhD programs)

Pathways of Human Disease

Statistics and Statistics with concentration in Bioinformatics and Computational Biology

Toxicology

Infection and Immunity: From Molecules to Populations (IIMP)

Professors Bennett, Nancy, Dewhurst, Stephen, Simpson-Haidaris, PJ

The Infection and Immunity: From Molecules to Populations (IIMP) is a transformative training focus in the Translational Biomedical Science Program. This program was selected for funding by the Burroughs Wellcome Fund and is co-directed by Nancy M. Bennett, MD, Director of the Center for Community Health and Co-Director of the UR Clinical and Translational Science Institute (CTSI), and Stephen Dewhurst, PhD, Chair of Microbiology and Immunology and Vice Dean for Research at the UR School of Medicine and Dentistry.

The goal of the TBS program is to prepare individuals for academic and clinical careers relating to the translation of basic biomedical research into clinical strategies to improve health. The mission of the IIMP training focus in TBS is to prepare the next generation of researchers who can lead interdisciplinary research combining population approaches with insights generated at the cellular and molecular level.

About the Program

Students in the IIMP training focus will cross-train in both population and basic sciences of infection and immunity. From the perspective of population scientists, basic science is playing a bigger role in understanding the patterns and causality of disease and health. For example, infectious disease surveillance will soon be based on whole genome sequencing and other advanced molecular detection techniques.

Knowledge of these methods and interpretation of the data they produce will be critical to understanding the patterns and transmission of disease. Similarly, basic scientists will need to understand and demonstrate the impact of their work on the health of the population. Thus, it will be essential that they understand the language and concepts of population health.

Curriculum

Our flexible, student-centric curriculum can be tailored to individual student needs, and all trainees will be overseen by dual mentors, one each from laboratory and population sciences. A number of new courses and innovative cross-training opportunities will provide training in team science, research collaboration and the soft skills important for career success. Furthermore, all trainees will conduct research in population science and in laboratory science through Immersive Cross-Disciplinary Internships and Externships under the mentorship of program faculty.

The program will have broad impact by promoting research on challenging contemporary questions that cross discipline boundaries at the interface of population and laboratory science, and will prepare students for high impact careers as research leaders in infection and immunity.

The core curriculum for all TBS PhD students is listed above. Additionally, students following the IIMP training focus take discipline specific courses in Microbiology, Immunology and/or Virology to align with the focus of their dissertation research.

The Translational Biomedical Science program office is located on the basement level of the Clinical and Translational Science Institute in the Saunders Research Building.

Email: katherine_libby@urmc.rochester.edu

Reviewed: July 2016