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Curriculum

Example Program of Study for T0-T4 training focus in the Translational Biomedical Science PhD program.

The core curriculum will provide the students with ~34-36 credit hours of didactic training in the first two years. We have designed the core curriculum to allow selection of the strongest courses available to provide fundamental and deep knowledge in basic, translational and population science disciplines so that TBS students emerge from the training program with the skills to translate this knowledge in a team science environment for a productive research career. Download Example Program of Study

Example Program of Study Infection and Immunity: From Molecules to Populations (IIMP) training focus in the Translational Biomedical Science PhD Program.

The core curriculum provides students with ~34-36 credit hours of didactic training in the first two years. The IIMP pathway-specific core curriculum allows a selection of the best courses available to provide fundamental and deep knowledge so that IIMP students emerge from the training program prepared for a productive academic career at the interface between laboratory and population science. Download Example Program of Study

Descriptions of required and some elective courses for TBS PhD Program training tracks.

Purpose Ethics and Professional Survival Skills
Inform students of the importance of ethics and integrity in research, working with human subjects and vertebrate animals, conflict of interest, and ethical grant and manuscript preparation and peer review.
  • IND 501 - Ethics and Integrity in Research (Fall). The required eight-week course consists of a one-hour lecture followed by a one-hour small group discussion with case studies each week to assess various examples of ethical issues in biomedical research. Lecture topics covered in the course include: Introduction to Ethical Issues of Biomedical Research, Human/Clinical Data & Conflict of Interest, Plagiarism, Animal Research, Team Science & Collaboration, Publication Process, Stem Cell Research, and Mentor-Mentee Relationships. Senior faculty and deans lead lectures and experienced mentoring faculty in URMC PhD training programs facilitate the small group discussions. Ongoing training in responsible conduct of research occurs through yearly seminars sponsored by the CTSI and the office of Graduate Education, as well as from regular interactions with research mentors. Topics such as conflict of interest in the publication and peer-review process, authorship and plagiarism are reviewed in the Workshop on Scientific Communications course (IND 417) and ethics in grant writing and grant reviewing are covered in the Practical Skills in Grant Writing course (IND 438). Training and certification in Human Subjects Protection and Use and Care of Vertebrate Animals is also required as needed.

Enhance skills to communicate science to peers and lay public in oral and written formats.

  • IND 417 - Workshop in Scientific Communications (Spring) (Required). Focuses on clear and concise scientific writing, submission to and publication in scientific and medical journals, learning about and how to use digital resources and bibliography software, building skills to give effective oral presentations and creating visually informative posters. This is a skills-based workshop aimed at improving scientific communication. 

Provide students in biomedical, behavioral and population sciences with skills to procure external support for research. 

  • IND 438 – Practical Skills in Grant Writing (Spring) (Required). Course content includes didactic lectures on grant-related topics, opportunities to examine grants that others have written, examination of tools and resources available to assist in grant writing, and the opportunity to write a grant application for the support of the trainee’s own research project and have it critiqued.  At the end of the course, the enrollee should be able to write and peer-review a research grant application.  This course will focus on how to find appropriate grant funding opportunities, the fundamentals of grant requirements in common with most all funding agencies including foundations, NIH, non-NIH federal agencies (DoD) and community-based population funding opportunities.

Seminars cover topics in translational research, team science and human subjects research.

  • CTSI Grand Rounds (all semesters, all years) (Recommended). A weekly seminar series throughout the academic year that will include presentations from UR training mentors, guest lecturers, experts in technological innovations in clinical, translational and population science research, as well as select trainee presentations. Monthly, one seminar is devoted to training in responsible conduct of research.

Informal forum to critically think about and discuss research ideas and plans and to troubleshoot problems encountered in their research; Provide experience giving oral presentations; students will gain experience communicating science to audiences with expertise in broad array of disciplines.  

  • IND 436 – Unifying Population & Laboratory Based Sciences (all semesters, all years) (1 credit) (Required). This student-led critical thinking in research and research in progress seminar series will provide Translational Biomedical Science (TBS) PhD students with a forum for presenting and discussing their planned and ongoing research projects in depth with student peers - including the underlying basis for their studies, experimental design, data interpretation, future studies, and challenges encountered in executing their studies and crossing discipline boundaries. The course will be facilitated by program faculty to provide students with a self-directed learning environment and to encourage participation in a lower-stakes setting. The students will meet 7 times each semester, for 90 min. First and Second year students will give informal work-in-progress presentations to build confidence and develop critical thinking skills; advanced students will give research seminar presentations, share career development strategies, and give insight on qualifying exams and writing F31 NRSA individual predoctoral fellowship awards. Because TBS students’ dissertation research projects cross multiple discipline boundaries and cover the translational spectrum from preclinical in animal models of disease to community and population health sciences, research and policy, each student will assign readings in advance that provide classmates with fundamental knowledge about the research discipline corresponding to the student’s dissertation research. This course is for TBS and TBS-IIMP PhD students.  With permission of course directors, other pre- and post-doc trainees may participate. Outside speakers may be invited to lead topical discussions on research, team science, application of “big data” to research, population science and other timely subjects selected by student input. This student-centric critical thinking in research and seminar series will complement the Career Stories seminar series sponsored by the URBEST program.

Selected Course Work in Computational, Qualitative, Health Policy and Population Science

Purpose Ethics and Professional Survival Skills

Principles & practices of infectious disease epidemiology and how communicable diseases and their control affects public health.

  • PM 451 - Epidemiology of Infectious Diseases (Spring). Introduces the basic methods for infectious disease epidemiology and case studies of important disease syndromes and entities. Methods include definitions and nomenclature, outbreak investigations, disease surveillance, case-control studies, cohort studies, laboratory diagnosis, molecular epidemiology, dynamics of transmission, and assessment of vaccine field effectiveness. Case studies focus on acute respiratory infections, pneumococcal infections, diarrheal diseases, hepatitis, HIV, tuberculosis, sexually transmitted diseases, and malaria, among other current topics. (Required IIMP track)

Provide basics of epidemiology and statistics for health and biomedical sciences.

 

  • PM 415 - Principles of Epidemiology (Fall). Overview of concepts dealing with the study of the distribution of diseases and their causes in populations; define epidemiologic terms, introduce methods used to describe diseases in populations, provide an overview of ways to determine the causes of disease, and apply epidemiologic principles to the evaluation of preventive and therapeutic interventions (Required all TBS tracks). 
  • BST 463 - Introduction to Biostatistics (Fall) OR BST 467 Applied Biostatistics for Biomedical Science (Spring). (One of 2 courses requires all TBS Tracks)
  • BST 463 - Intro to Biostatistics. Introduction to statistical techniques with emphasis on applications in the health sciences. Summarizing and displaying data; introduction to probability; Bayes’ theorem and its application in diagnostic testing; binomial, Poisson, and normal distributions; sampling distributions; estimation, confidence intervals, and hypothesis testing involving means and proportions; simple correlation and regression; contingency tables; use of statistical software.
  • BST 467 - Applied Biostatistics. Introductory biostatistics course designed for PhD students in the biomedical sciences. Topics include probability and probability distributions, sampling distributions, statistical inferences from small and large samples, analysis of categorical data, analysis of variance, correlation and simple linear and non-linear regression analysis. All analytical topics will be illustrated using examples from biomedical sciences areas. Objectives of this course are to provide a basic foundation of probability and probability distributions, instruction on how to formulate an appropriate hypothesis and make relevant inferences from quantitative and qualitative data, and how to apply modeling to real life data to identify the associated significant predictors to response variables.

Provide introduction to global health issues for students with focus in population sciences; introduction to high throughput biological data analysis for students with focus in lab-based sciences.

  • PM 486 - Medical Ecology OR IND 419 – Introduction to Quantitative Biology (Spring)

One of these courses required for all TBS Training Tracks

  • PM 486 - Medical Ecology. A systems approach to analyzing disease, with an emphasis on how change in environments relates to change in risk of exposure and incidence of disease. Many methods are used to generate and test medical ecological models, drawn from medical geography, epidemiology, biology, and the social sciences. Lessons from this course come from global health, health impact of colonial relationships, and diseases of lifestyle and modernization. This course is suited for students who wish a research-oriented, multidisciplinary approach to the study of environmental impacts (broadly defined) on human health. Students are expected to be comfortable with a multi-disciplinary approach (integrating social, biological, and physical sciences) to examining illness, injury, and disease.
  • IND 419 - Introduction to Quantitative Biology. A graduate-level survey course that introduces concepts for the analysis of high volume biological data in the context of important current biological questions. No previous computational experience is required. At the end of this course, students should have a deeper understanding of the computational tools involved in the analysis of high volume biological data, focusing on web-based resources but also introducing core approaches in bioinformatics. As an advanced-level course, we will emphasize critical thinking and reading of the primary literature to understand original experiments, rather than abstract facts and memorization.

Course selection for all TBS tracks made with individual student and Program Directors.

Provide learner with solid foundation and appreciation for disease prevention strategies on both an individual and population-wide basis. Provide skills on qualitative approaches to survey development and interpretation and methods for valid and reliable survey research or for the collection, analysis, and interpretation of social and cultural data. Introduction science and technology policy issues.

  • BST 465 - Design of Clinical Trials OR PM 458 - Qualitative Health Care Research OR PM 426 - Social & Behavioral Medicine OR PM 487 - Fundamentals of Science, Technology & Health Policy (Spring).
  • BST 465 - Design of Clinical Trials. Introduction to the principles of clinical trials; clinical trial protocols; overview of the drug development process; hypotheses/objectives; specification of response variables; defining the study population; randomization; blinding; ethical issues; factorial designs; crossover designs; equivalence trials; trial monitoring and interim analyses; sample size and power; data collection and management; issues in data analysis and reporting; evaluating clinical trial reports. (BST 463 or equivalent is prerequisite)
  • PM 458 - Qualitative Health Care Research. Qualitative methods allow for the collection, analysis, and interpretation of social and cultural data that quantitative methods cannot adequately reach and function as an essential adjunct to quantitative methods by hypothesis generation or identifying lay terminology for accurate survey developed. This course will cover standard qualitative methodologies through a discussion of relevant literature, class exercises, and a class project.
  • PM 426 - Social & Behavioral Medicine. The overall goal is to examine the public health impact of behavioral, psychosocial, cultural, and environmental factors on the development, prevention, and treatment of health problems. This is a survey course designed to introduce students to a wide range of social and behavioral determinants of health, health behavior change, and health disparities over the life course.
  • PM 487 - Fundamentals of Science, Technology & Health Policy. Science and technology continues to be an area of significant focus to drive innovation, improve public health and enhance national security in the U.S. and across the globe. This interactive course will offer students exposure to the interaction between science and technology and public policy, particularly exploring the role and impact of the Federal government in this process. Students will explore roles for scientists in the policy making process, while gaining the ability to objectively analyze science and technology policy issues and develop skills to provide policy recommendations and write policy memos (offered every other year).

Course selection for all TBS tracks made with individual student and Program Directors.

Provide fundamental knowledge in population science research skills in data management, survey design; health services and policy research; human subjects for research studies and clinical trials; therapeutic interventions to modulate disease; or introduction to regulatory affairs and protection of intellectual property for medical innovations.

  • PM 445 - Introduction to Health Services Research OR PM 410 - Intro Data Management and Analysis (SAS) OR PM 412 - Survey Research OR PM 420 - American Health Policy and Politics OR PM 419 - Recruitment & Retention of Human Subjects in Clinical Research OR PM 488 - Experimental Therapeutics OR BME 431 - FDA & Intellectual Property (Fall classes)
  • PM 445 - Introduction to Health Services Research. Introduction to field of health services research that includes: 1) review of the nature and scope of health services research; 2) discussion of conceptual frameworks for guiding health services research including systems-based approaches; 3) illustration and discussion of health services research topics (e.g. health system planning and policy, effectiveness and quality of care, efficiency of care, equity of care and disparities research, health care financing, the current US health care reform, and health care decision making); and 4) an ongoing review and discussion of current topics in health services research.
  • PM 410 - Intro Data Management and Analysis (SAS). Introduction to the SAS analytic software and a basic understanding of data management. Classes focus on the theories and practices associated with data management, database development and analysis. Through a mixture of lectures and applied lab sessions, students gain experience creating forms for data entry, database creation, data management and analyzing data. Building on linkages to the departments of biostatistics and epidemiology curriculum, this course emphasizes the integration of SAS into the research environment and the development of statistical computing skills. (Fall or summer)
  • Survey Research (PM 412). This course presents the elements of survey instrument development and survey research methods, with a focus on practical applications in health care research, epidemiology and social & behavioral science. The integrated. Students participate in all stages of the survey research process through application of homework assignments, survey development and research project design.
  • PM 420 - American Health Policy and Politics. Course examines the formation and evolution of American health policy from a political and historical perspective. Among topics covered are efforts to rationalize and regionalize health care institutions, periodic campaigns for national health insurance, the creation of Medicare and Medicaid and the further evolution of these programs among other current topics.
  • PM 419 - Recruitment & Retention of Human Subjects in Clinical Research. This course focuses on determining eligibility, minimizing risk to research subjects and designing protocols that are not overly burdensome for the subject or participant. Course focuses on strategies to recruit and retain subjects from groups known to be ‘hard to recruit’ such as individuals from disenfranchised communities (racial/ethnic minorities, homeless) and other sub-groups such as the elderly. Participants will critique and design recruitment strategies from published reports and local research, develop feasibility assessments and draft a recruitment plan (offered every other year).
  • PM 488 - Experimental Therapeutics. This course is designed for individuals interested in the process for identifying novel interventions for diseases, and for their eventual introduction into humans. Topic areas covered will include: preclinical assessment of an intervention's ability to modulate disease, the preclinical safety data needed before initiating human experimentation, the appropriate techniques for extrapolating dosages from animals to humans; types of human experimentation (Phase 1-Phase 3 clinical trials), the level of animal and human evidence necessary to progress from one phase of experimentation to the next, and the ethical underpinnings of human experimentation.
  • BME 431 - FDA Regulatory Processes and Intellectual Property. Students are exposure to the intellectual property (IP) and regulatory pathways for new medical innovations. Students will learn the terminology, processes and challenges involved in FDA regulations and the protection of IP for medical innovations. Emphasis placed on the ways knowledge of prior art and regulatory barriers can optimize concept selection, and early phase project planning to best identify projects suitable for commercialization. Instruction will include lectures, case studies, guest speakers and integrated assignments that will ask students to explore examples of IP and regulatory challenges, successes and failures.
  • BME 432 (Spring)- FDA & IP Commercialization: Implementing FDA Requirements and Practical Steps to Commercializing Medical Products. Building on the basics learned in BME 431, students learn about the processes (and barriers) to bringing a product such as a novel medical device through clinical trials. Lectures on regulatory and IP topics will alternate in order to allow students to understand the difficulty presented by balancing these two challenges in the innovation process. If BME 431 selected in Fall, recommend also take BME 432 in the next Spring semester.

Course selection for all TBS tracks made with individual student and Program Directors.

Selected Course Work in Laboratory Sciences: Biochemistry, Cell, Molecular Biology, Toxicology OR Infection & Immunity

Purpose

Ethics and Professional Survival Skills

Provide students with basics of molecular biology and genetics; provide advanced knowledge of mechanisms of chromatin-mediated regulation of gene expression.

Mostly chosen as electives

  • IND 410 - Molecular Biology and Genetics (Spring). Lecture topics include DNA replication; DNA repair and mutagenesis; regulation of eukaryotic RNA transcription, RNA processing and protein translation. Emphasis placed on biochemical and genetic approaches to the study of these problems. Special additional topics include genomics as an approach to regulation and mammalian genetic techniques of analysis. (Prerequisites: undergraduate Biochemistry and/or Molecular Biology).
  • IND 443 - Eukaryotic Gene Regulations & Recitation (Spring). This advanced course examines mechanisms of chromatin-mediated regulation of gene expression, relating molecular structures, dynamic interactions, nuclear processes, 3-D nuclear organization to biological functions. Topics include DNA structures, packaging and higher order chromatin organization in the nucleus, the transcription machinery, eukaryotic chromosome structure and its modifications, epigenetics and functional genomics, dynamics of nuclear processes, nuclear reprogramming, development and applications of genome manipulation technology. Lectures and readings draw heavily on primary literature both classic and most recent. (Prerequisites: Molecular Biology, Cell Biology and/or Developmental Biology).

Course selection for all TBS tracks made with individual student and Program Directors.

Prove fundamentals of biochemistry, cell biology or immunology as needed to tailor program of study for each student. Courses may substitute for other courses as required to develop individualized training programs for each student.

  • IND 408 - Advanced Biochemistry OR IND 409 - Cell Biology OR MBI 473/573 - Immunology & Seminar (Fall)
  • Advanced Biochemistry (IND 408). Covers selected topics in modern biochemistry, including analysis of protein and domain structure by classical and modern methods, including mass spectrometry, NMR, X-ray crystallography, and other biophysical techniques; protein-ligand and protein-protein interactions; enzyme kinetics and catalytic mechanisms; and, cellular energy production and utilization. In addition to lectures, workshops are held once a week, during which time selected papers from the literature are discussed. (Prerequisite: Introductory Biochemistry)
  • Cell Biology (IND 409). Topics include cell cycle and its breakdown during cancer and apoptosis; cytoskeleton; intracellular compartments and protein sorting; signal transduction and cell-cell communication; membrane structure and transport. In addition to the lectures, weekly interactive journal-club-style sessions explore the current cell biology literature. (Prerequisite: undergraduate Cell Biology)
  • Immunology (MBI 473). Lectures cover innate and adaptive immunity; structure and genetics of immunoglobulins and T cell receptors; lymphocyte development, immune regulation, immunological diseases, and tumor immunity. The Immunology seminar (MBI 573) discussion course covers a variety of topics that provide an overview of immunology with an emphasis on critical reading of original journal articles. (Prerequisite: Basic Biochemistry or Biology).

Course selection for all TBS tracks made with individual student and Program Directors; one of 3 courses required for IIMP track

Provide students with in depth knowledge on molecular mechanisms of host-pathogen interactions in microbial pathogenesis, genetics or virology and vaccine biology.

  • MBI 414/514 Microbial Pathogenesis & Seminar (Fall) OR MBI 421/521 - Microbial Genetics & Seminar (Spring) OR MBI 456 - General Virology (Spring)
  • Microbial Pathogenesis (MBI 414) & Seminar (MBI 514). Course examines host-parasite interactions and mechanisms by which microbes evade the host response and cause disease. Emphasis on understanding the molecular level of microbial pathogenesis, including colonization, invasion, antigen variation, and toxin production and mode of action. How host defense mechanisms interact with pathogenic microbes are examined. (Prerequisite: undergraduate Microbiology)
  • Microbial Genetics (MBI 421) & Seminar (MBI 521). Provides an in-depth examination of representative genetic systems in bacteria and bacterial viruses. Emphasizes methods of genetic analysis used to study biological function. Topics in course and concurrent seminar include: nature of bacterial variation, processes affecting gene synthesis and integrity, nature of gene transfer in bacteria, regulation of gene expression in prokaryotes and genomic approaches to study of microbial genetics. (Prerequisite: undergraduate Microbiology or Biology)
  • General Virology (MBI 456). Introduction to animal virology, with emphasis on human disease. Topics covered include the following: general properties of viruses, methods in viral research, virus structure, biochemistry of virus replication, virus-host cell interactions, pathogenesis, HIV/AIDS, emerging infections, vaccines, antivirals, and viral vectors and gene therapy. (Prerequisite: Basic Biochemistry or Molecular Biology).

Course selection for TBS-IIMP track made with individual student and Program Directors; Electives for TBS tracks

Elective courses providing in depth knowledge of toxicology, gene-environment interactions, epigenetics, placental physiology and implantation, forensic toxicology, and evidence-based decision-making in public health.

  • TOX 521 Biochemical Toxicology I (Spring). Lectures cover the history and principles of toxicology, toxicokinetics and biotransformation, xenobiotic metabolism and elimination, oxidants, anti-oxidants and glutathione homeostasis, hepatic and renal pathophysiology, receptor-mediated toxicology, principles of carcinogenesis, gene environment susceptibility, epigenetics, forensic toxicology, and evidence-based decision-making in public health.
  • TOX 522 Organ Systems Toxicology II (Fall). This course focuses on determinants of toxicity in the major organ system of the human body and in the developing organism. Introductory material will be presented within each lecture block regarding the basic structure and purpose of the organ systems as these relate to specific examples of toxicological responses.
  • TOX 530 Reproductive and Developmental Toxicology (Spring). Lectures include placental physiology and implantation, embryo culture, gene environmental interactions in birth defects, reproductive immunobiology, artificial reproductive technologies, labor and premature delivery, lactation and perinatal pharmacology, identification of susceptible populations in reproduction, and monitoring of populations and risk.

Prerequisite course in biochemistry and pharmacology may be required.

Elective Courses from many disciplines

  • Pathology, Neurology, Biomedical Engineering, Pharmacology and Physiology, Biostatistics, Public Health Sciences, Microbiology and Immunology, Genetics, Biochemistry/Biophysics, Toxicology, Health Services Research and Policy