Courses of the Morningside Graduate School of Biomedical Sciences

Research rotations are defined periods of research experience under the direction of a faculty member. They are intended to familiarize the student with concepts and techniques in several areas of research and to assist the student in evaluating research laboratories and projects that might be developed into a dissertation project. The student will participate in an ongoing research project, gain familiarity with concepts underlying the research, acquire a working knowledge of techniques used in the research, and write a report and present an oral summary of the results of the research.

Credits: 2-5

Fulfills an elective requirement: No

Course Director: Varies

Semester Offered: Fall, Spring

Last Taught: Taught every Fall and Spring semester

This is a required course for all third year Basic Sciences students and all MD/PhD students entering doctoral study but who are not on the CPHR track. The PARC course helps to center our students in areas that are foundational to success in research: responsible data management; management of intellectual property; the ethical use of research subjects; recognizing and resolving conflicts of interest, professionalism in peer review and publishing; engaging mentors; and career exploration and planning. The PARC course comprises faculty-led presentations and small group discussions with case studies and workshop material. An online learning module (CITI training program comprising many case studies) is also included and must be completed before the end of the fall semester. 

Credits: 1

Prerequisite(s): None

Fulfills an elective requirement: No

Course Directors: Anthony Imbalzano, Cynthia Fuhrmann

Semester Offered: Fall 

Last Taught: Fall 2023

This course will help prospective scientists in the biological and medical sciences communicate their work effectively, in writing, graphics, and oral presentations. The course teaches how to prepare a research paper using words, statistics, and figures; how to present science to a lay audience; how to write a grant proposal; and how to present orally to scientific peers.

Credits: 2

Prerequisite(s): None

Fulfills an elective requirement: No

Course Directors: Jill Zitzewitz, Daryl Bosco, and Nese Kurt Yilmaz

Semester Offered: Fall 

Last Taught: Fall 2023

This problem-based course provides learning opportunities through exploration of multidisciplinary areas of contemporary biomedical research, and creates a forum for practice in the skills required for research.

Credits: 6

Prerequisite(s): Matriculation in the PhD Program

Fulfills an elective requirement: No

Course Directors: Jill Zitzewitz, Neal Silverman, Elizabeth Shank

Semester Offered: Fall

Last Taught: Fall 2023

Chemical biology uses the power of chemistry to ask and answer questions of biological significance, typically using molecular tools designed to inhibit, activate, or report on the function of biomolecules. In this class we will cover a wide range of chemical biology topics. We will start with a basic chemistry review, then cover peptide and nucleic acid chemistry and synthesis, post-translational modification of proteins, optical imaging, chemoselective chemistry in water, and approaches to lead discovery for drug development. In the second half of the course, we will cover chemical genetics, orthogonal ligands and receptors, DNA recognition and modification, unnatural amino acids, enzyme inhibitors, rational drug design, nanoparticles, and synthetic biopolymers.

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Director: Stephen Miller

Semester Offered: Fall, odd years

Last Taught: Fall 2023

The goal of this course is to give students a strong foundation in physical principles that underlie the thermodynamic and mechanistic properties of biological macromolecules and macromolecular complexes. In addition to providing theoretical background, lectures and discussion groups will focus on the application of physical chemical principles in contemporary biomedical research. Topics will include spectroscopic and computational approaches to studying protein and nucleic acid structures, thermodynamics and kinetics of protein folding, the solution behavior of macromolecules and principles that govern molecular recognition.

Credits: 3

Prerequisite(s): Strongly recommended, but not required: undergraduate Physical Chemistry

Fulfills an elective requirement: Yes

Course Director: Francesca Massi, Sy Redding

Semester Offered: Fall, even years

Last Taught: Fall 2022

The goal of this course is to provide students with a theoretical and practical understanding of techniques used to determine the three-dimensional structures of biological macromolecules. The primary methods explored will be X-ray crystallography and Nuclear Magnetic Resonance (NMR), but also including discussions of computational methods and cryo electron microscopy (cryo-EM).  Emphasis will be placed on both structural determination and analysis of dynamics, which can be crucial for macromolecular function.

Credits: 2

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Directors: Brian Kelch

Semester Offered: Spring

Last Taught: Spring 2024

This course will cover current research in the general area of RNA biology. Topics include RNA synthesis; modification and processing pathways; RNA structure; RNA transport and subcellular localization; translational regulation; RNAi and microRNAs; RNA decay; RNA aptamers; RNA catalysts; RNA and early evolution; and RNA as a drug and/or drug target. The format of this course will center around group discussion of papers from the primary literature. Grading will be based on student attendance, performance in presentations and participation in group discussions.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: Yes

Course Directors: Phillip Zamore and Andrei Korostelev

Semester Offered: Spring, even years

Last Taught: Spring 2024

Cellular Biochemistry takes an inside-out approach to teaching the molecular biological underpinnings of DNA replication, gene transcription, translation, metabolism, secretion and cell signaling.

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Director: William Kobertz

Semester Offered: Spring

Last Taught: Spring 2024

The overall goal of the course is to expose students to the pathology of different types of cancers that occur in humans and the methods used for diagnosis, including histology, cytology, immunohistochemistry, flow cytometry and molecular diagnostics. The course will start with a review of normal tissue histology of all the major organ systems and an overview of diagnostic techniques. The remainder of the course will consist of organ-based lectures in tumor pathology along with a hands-on microscopic review of pathologic tumor samples. The general format of the 8-week course will consist of a one-hour lecture followed by a one-hour laboratory session, given 2 days per week.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: Yes

Course Director: Stephen Lyle

Semester Offered: Summer

Last Taught: Summer 2023

This course will provide students with a rigorous and comprehensive understanding of the mechanisms that underlie the genesis and progression of human cancers. It will build on the basic science knowledge acquired in the SIBR Course and establish an appreciation of cancer as a disease. The salient topics to be covered include cancer stem cells; oncogenes and tumor suppressor genes; tumor-host interactions, invasion and metastasis, cancer metabolism and anti-tumor immunity. A major theme of the course will be to integrate the biology of cancer with the clinical behavior of tumors and cancer therapy.

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Directors: Marcus Ruscetti, Jason Pitarresi

Semester Offered: Fall, Spring

Last Taught: Spring 2024

Principles and application of microscopy in biomedical research for graduate students at all levels. Demonstrations and laboratory exercises will be incorporated into some of the blocks of the instruction. This course is designed to teach the biologist how microscopes work and how to optimize image quality.

Credits: 2

Prerequisite(s): None

Fulfills an elective requirement: No

Course Directors: Greenfield Sluder, David Grunwald

Semester Offered: Spring, odd years

Last Taught: Has not been taught in the past 2 years

This course encompasses current topics in eukaryotic gene regulation including the discussion of current research articles. Within this context, we will also explore the role of epigenetic regulators in transcriptional control. Course goals include improving skills in reading, presenting, discussing, and critically analyzing research articles.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: Yes

Course Director: Craig Peterson

Semester Offered: Spring, odd years

Last Taught: Fall 2020

This course covers several important areas of modern bioinformatics and computational biology. The course is aimed not only at students specializing in bioinformatics, but also general biology students who would like to utilize bioinformatics tools in their daily research. The course will begin with an overview of modern sources of bioinformatics data, especially high-throughput sequencing data (RNA-seq, ChIP-seq, DNase-seq, ATAC-seq, Whole genome bisulfite sequencing, etc.), followed by a thorough presentation of an extensive set of statistical learning and machine learning algorithms and their application to analyzing biological data. The course will include 10 lectures each with a homework set, followed by individual or group projects, presented in lieu of the final exam. 

Credits: 2

Prerequisite(s): Familiarity with at least one programming language (e.g. Python, MatLab, R, etc.)

Fulfills an elective requirement: Yes

Course Director: Zhiping Weng, Jill Moore

Semester Offered: Fall, Even Years

Last Taught: Fall 2022

This intense 3-week course will expose students to a variety of topics related to cellular metabolism. The course will cover material ranging from foundational principles to current leading-edge research. The principles and mechanisms regulating metabolism will be explored from multiple perspectives, including biochemistry, biophysics, genetics, molecular biology and cell biology. 

Credits: 2

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Director: Brian Lewis

Semester Offered: Fall, Summer

Last Taught: Fall 2023

Infectious disease is among the strongest agents of natural selection, and adaptations constituting the armament of pathogens and the defense of the host involve many of the most fascinating mechanisms in biology. This course presents a modern view of the fundamental biology of bacterial and viral disease in the context of molecular mechanisms of host defense. A detailed knowledge of cellular and molecular components of the immune system will be integrated with current understanding of microbial virulence strategies, to provide a working understanding of biological mechanisms important in health and disease. The course is organized as three integrated sections focusing on the fields of immunology, bacterial pathogenesis, and virology. Students will obtain a background for advanced course work in each of these disciplines. We will focus on three themes; (1) basic properties of microbes and the innate and adaptive immune defenses that have evolved to respond to them, (2) the interplay—in both dynamic and evolutionary sense—between host defenses and microbial virulence, and (3) the mechanisms of pathogenesis during infection. Comparative clinical and epidemiological pictures of selected diseases will be presented, and will serve as a framework for development of key molecular, cellular, and physiological concepts. 

Credits: 4

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: Yes

Students may register for individual BBS755 modules (BBS 755a, BBS 755b, BBS 755c).  Completion of one or two individual modules does not fulfill an elective course requirement.

Course Director: Timothy Kowalik

Semester Offered: Spring

Last Taught: Spring 2024

This is the virology component of BBS 755 Infection and Immune Response.

Credits: 1

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: No

Course Director: Timothy Kowalik, Trudy Morrison

Semester Offered: Spring

Last Taught: Spring 2022

This is the bacteriology component of BBS 755 Infection and Immune Response

Credits: 1

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: No

Course Director:Timothy Kowalik, Javier Irazoqui

Semester Offered: Spring

Last Taught: Spring 2022

This is the immunology component of BBS 755 Infection and Immune Response

Credits: 2

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: No

Course Director: Timothy Kowalik, Micheael Brehm

Semester Offered: Spring

Last Taught: Spring 2024

This course covers genetic, biochemical and cellular mechanisms of cell cycle control. Topics include genetic screens for cell cycle regulators; cell cycle checkpoints; cell cycle regulation of DNA replication and chromosome structure; and the cell cycle in development and cancer. 

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Director: Nicholas Rhind

Semester Offered: Spring, odd years

Last Taught: Spring 2023

This course examines topics across four short modules within the broader scope of systems biology. These modules are Gene Regulation, Network Biology, Genome Organization, and Mathematical and Quantitative Methods. In addition, this course has a hands-on component that teaches programming in the MatLab coding environment to analyze data and generate insights through computational approaches. No prior knowledge of computation is assumed, and beginners are encouraged to enroll.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent or coordinator's approval.

Fulfills an elective requirement: Yes

Course Director: Hyun Youk, Manuel Garber

Semester Offered: Spring

Last Taught: Spring 2024

This course has two parts. Part I focuses on electrical properties of neurons, transmitters, receptors, and neurotransmitter release. Part 2 focuses on neurodevelopment. Videos, problem sets, paper discussions and take-home assignments are integrated with subject introductions by faculty for efficient, but active learning. Modern methods and research preparations are introduced along with subject matter to prepare students for thesis research.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: Yes

Course Director: Ann Rittenhouse

Semester Offered: Spring

Last Taught: Spring 2024

This advanced topics course will be an in-depth study of specific areas of the neurochemical, anatomical, cell biological and genetic basis of nervous system disease. It will teach students skills in critically reading, literature and presentation of research material. The course topics are divided into sections covering disorders of neuronal migration and development; neurodegenerative diseases; and behavioral disorders. These topics cover the cell and molecular biological processes of brain function in health and disease. 

Credits: 2

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent or permission from course coordinator

Fulfills an elective requirement: Yes

Course Director: Claudio Punzo

Semester Offered: Fall, even years

Last Taught: Fall 2022

The genetics of behavior represents a focal point in contemporary neuroscience research. Genetic screens have been conducted to identify mutants affecting behavior in model systems, and this has converged with advances in understanding the neurobiological basis of behavior. This course will synthesize the state of the art regarding the genetic basis of behavior in model organisms (worms, flies and mice), including discussion of learning and memory, circadian rhythms, and social behaviors. Lectures will include descriptions of systems for identifying mutations, genes that have been identified, and how identification of these genes contributes to understanding the underlying neural mechanisms of behavior. The course format will include faculty lectures, student presentations and discussion of assigned readings. 

Credits: 2

Prerequisite(s): BBS 760 Introduction to Neuroscience or permission from course director

Fulfills an elective requirement: Yes

Course Director: David Weaver

Semester Offered: Fall, even years

Last Taught: Fall 2021

The objective of this course is to introduce Morningside Graduate School of Biomedical Sciences graduate students to approaches used to understand the molecular causes of representative diseases and application of such knowledge toward the design and implementation of rational therapies. The course is divided into five-week sections covering neurodegenerative, cardiovascular, and metabolic diseases. Interspersed among these topics will be guest speakers who will discuss specific aspects of the drug design process and novel approaches to therapy, including gene-, RNA-, and cell-based interventions. Class discussions will also help prepare students to participate effectively in team-oriented translational science. Pairs of students will each write a research proposal addressing a disease mechanism or therapy development of interest and defend the proposal during the last two weeks of class.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: Yes

Course Directors: Pranoti Mandrekar, Chinmay Trivedi

Semester Offered: Spring

Last Taught: Spring 2024

Neuroscience Journal Club gives students the opportunity to present and discuss exciting new papers in neuroscience in an informal setting. Student presentations occur weekly (Wednesday 12-1). Students are also expected to attend the Neuroscience Program Seminar series (Thursday 12:15-1:15) and to meet with external speakers (Thursday 1:40-2:20). Program in Neuroscience students are required to take 2 semesters of BBS 808.  BBS 838 substitutes for 808.

Credits: 2

Prerequisite(s): None

Fulfills an elective requirement: No

Course Director: David Weaver 

Semester Offered: Fall, Spring

Last Taught: Fall 2021

Participants in this course will attend the Program in Neuroscience Seminar Series. Attendance at > 60% of seminars in a semester is needed for a passing grade. Two semesters of Neuroscience Seminar are required for Neuroscience Program students.

This Advanced Topics course will cover sensory and motor systems, Integrative neuroscience, motivated behaviors, and model organisms. The course will consist of lectures, student presentations, and paper discussions. Intended to follow BBS 780, but 780 is not a prerequisite. Strongly recommended for Program in Neuroscience students; others are welcome.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: Yes

Course Director: Patrick Emery

Semester Offered: Fall

Last Taught: Fall 2023

Some of the most active areas of current immunology are investigated through the reading and discussion of research papers. Students further develop the ability to pose questions and design experiments to answer them through writing a research proposal. Topics to be covered include: regulation of lineage specification/commitment and antigen receptor gene recombination; mechanisms of immunological tolerance and lymphocyte activation, cellular transactions and their consequences (e.g., APC:T cell); and immune responses in infectious diseases.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent and BBS755, Infection and Immune Response (or their equivalent)

Fulfills an elective requirement: Yes

Course Directors: Andrea Reboldi and Joonsoo Kang

Semester Offered: Fall

Last Taught: Fall 2023

This is a paper reading-based course discussing in depth new findings in animal virology, including viral biochemistry and molecular biology, genetics, oncogenesis, and pathogenesis. The course will be team-taught by UMass Chan faculty. The course will begin with introductory lectures to provide background for more advanced readings. Students will then cover different specific areas chosen by the professors in detail with paper readings. At the end of the course the students will write a research proposal and present it to the class and faculty. Course can be taken for three credits with proposal and presentation or for two credits without proposal.

Credits: 2-3

Prerequisite(s): BBS755, Infection and Immune Response, or their equivalent

Fulfills an elective requirement: Yes

Course Director: James Munro

Semester Offered: Fall

Last Taught: Fall 2023

This course introduces students to cutting-edge topics in bacterial pathogenesis in a class format designed to encourage both critical analysis and concentration on experimental design, which will aid students in preparation for qualifying exams. The course meets once per week for 2.5-3 hours. Depending on class size and on a rotating basis, individual students, or groups of two or three students lead discussions of selected topics. Presenting students are required to prepare PowerPoint presentations to focus the discussion, and the following week to produce a Specific Aims page modeled after NIH R01 applications. The bulk of class time is devoted to open discussion, critical analysis of the literature, and constructive feedback of student reviews. In the end, each student develops and presents a research proposal on one of the topics discussed. Students taking the course for 2 credits will not be required to prepare the research proposal. Grading is based on quality of presentations, Specific Aims pages, and class participation (all students) and on the quality of the research outline (students taking the class for 3 credits).

Credits: 2-3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent, BBS755, Infection and Immune Response, or permission from course coordinator

Fulfills an elective requirement: Yes

Course Directors: Javier Irazoqui, Beth McCormick

Course Offered: Fall

Last Taught: Fall 2023

Advanced Immunology & Microbiology Program graduate students present seminars on their thesis research.

Credits: 1

Prerequisite(s): BBS755, Infection and Immune Response

Fulfills an elective requirement: No

Course Director: Eric Huseby

Semester Offered: Fall

Last Taught: Fall 2023

Leading researchers present a weekly seminar on a basic or clinical immunology and virology topic. Prior to the seminar, students read papers suggested by the seminar speaker and discuss the papers in class. Following the seminar, graduate students meet with the speaker for a discussion of the formal seminar. This course surveys the most important areas of basic and clinical immunology and virology including, but not limited to, antigen presentation; gene rearrangements; and expression of the genes for antigen receptors, immune tolerance, cytokines, immune cell development, immunodeficiency diseases, autoimmune diseases, human immune system malignancies and immune response to infectious agents such as viruses, parasites and bacteria.

Credits: 2

Prerequisite(s): BBS755, Infection and Immune Response

Fulfills an elective requirement: No

Course Directors: Javier Irazoqui, Vanni Bucci, Kiera Clayton, Eric Huseby,  Lee Quinton, Neal Silverman

Semester Offered: Spring

Last Taught: Spring 2024

This course will demonstrate the major elements that distinguish a great presentation, and identify areas in which each student can improve their presentations through peer critiques and self-assessment. Importantly, this class will allow students many opportunities to see their skills improve throughout the course. Substitutes for Neuroscience Journal Club in meeting Neuroscience Program requirements.

Credits: 1

Prerequisite(s): Students conducting research in the neuroscience field will have priority if maximum enrollment is reached, but the course is open to students from other Programs and areas of research on a space-available

Fulfills an elective requirement: No

Course Director: David Weaver

Course Offered: Fall

Last Taught: Fall 2020

This course is designed to help first-year students prepare for the Immunology & Microbiology Program advanced topics courses in the fall, learn how to think critically about articles, and meet senior students in the program. Students in the class will read one primary and one review paper the week before each class. The topic, paper and review will be chosen by two student mentors. In a brief presentation; the mentors will describe the current state of the field and summarize the review. The class will then discuss the chosen article and critically analyze the positives and negatives of techniques, systems, conclusions, etc.

Credits: 1

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent

Fulfills an elective requirement: No

Course Director: Jillian Richmond

Semester Offered: Summer

Last Taught: Summer 2022

Tutorials offer the opportunity for one student or a small group of students to discuss research in a specific research area, or a series of selected papers, with one or more faculty members. The small group format allows extensive discussion and interaction. This course number allows faculty and students the flexibility to develop a syllabus of their making. The proposed syllabus must be approved by the Neuroscience Program director. Tutorials are arranged with individual faculty members. Students may re-enroll for multiple tutorials.

Credits: 1

Prerequisite(s): Permission from Neuroscience Program Director

Fulfills an elective requirement: No

Course Director: David Weaver

Semester Offered: Fall, Spring, Summer

Last Taught: Fall 2021

Research rotations are defined periods of research experience under the direction of a faculty member. They are intended to familiarize the student with concepts and techniques in several areas of research and to assist the student in evaluating research laboratories and projects that might be developed into a dissertation project. The student will participate in an ongoing research project; gain familiarity with concepts underlying the research; acquire a working knowledge of techniques used in the research; and write a report and present an oral summary of the results of the research.

In the summer term, only MD/PhD students may register.

Credits: 2-5

Fulfills an elective requirement: No

Course Director: Varies

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every Fall, Spring, and Summer

Summer Research – Year 1 is for first year BBS students.  Expectations are for students to (1) formulate initial hypotheses and/or goals, (2) design and begin to execute research plans, (3) Critically read and evaluate relevant literature.

Credits: 6

Fulfills an elective requirement: No

Course Director: Varies

Semester Offered: Summer

Last Taught: Taught every Summer

Students are required to register for this course in the fall semester of the academic year in which they are to pass their Qualifying Examination.

Credits: 1

Fulfills an elective requirement: No

Course Director: Mary Ellen Lane

Semester Offered: Fall

Last Taught: Taught every year 

All graduate students are required to have at least one Thesis Research Advisory Committee (TRAC) meeting each academic year. After passing their Qualifying Examination and selection of their TRAC, students are required to register for this course each fall semester until their Dissertation Advisory Committee is formed.

MD/PhD Goals: 1) To periodically review progress along thesis research project advised by content experts 2) To provide guidance for establishing a thesis research project consistent with the MD/PhD Program goals

MD/PhD Curricular Expectations: Two Thesis Research Advisory Committee (TRAC) meeting each academic year as define by the Professionalism Benchmark Checklist

Credits: 1

Fulfills an elective requirement: No

Course Director: Mary Ellen Lane

Semester Offered: Fall

Last Taught: Taught every year

This course is for students who have selected a program and thesis advisor but who have not yet passed the Qualifying Examination. 

Credits: 9

Fulfills an elective requirement: No

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Students register for Thesis Research fall term of year three of the program (MD/PhD Students: Fall term of year four in the program), after passing the Qualifying Exam.

Credits: 12

Fulfills an elective requirement: No

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Students register for Graduate Research fall term of year four (MD/PhD Students: Fall term of year five+) in the PhD Program and will continue to register each semester until they complete all remaining requirements.

Credits: 0

Fulfills an elective requirement: No

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Research rotations are defined periods of research experience under the direction of a faculty member. They are intended to familiarize the student with concepts and techniques in several areas of research and to assist the student in evaluating research laboratories and projects that might be developed into a dissertation project. The student will participate in an on-going research project; gain familiarity with concepts underlying the research; acquire a working knowledge of techniques used in the research; and write a report and present an oral summary of the results of the research.

Credits: 2-4

Course Director: Faculty member in whose research group the student is working

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every Fall, Spring, and Summer

Building on basic skills in epidemiology and scientific research methods, this course will cover research design, including hypothesis development, measurement, and analysis. Students will explore methodological strengths of various quantitative and qualitative techniques and designs. Students will have three examinations, weekly problem sets and assignments to develop original research approaches to specific scientific and clinical questions.

Credits: 3

Prerequisite(s): CTS605A or equivalent or permission from course coordinator 

Course Director: Anthony Nunes

Semester Offered: Spring

Last Taught: Spring 2024

The purpose of this class is to learn advanced epidemiologic techniques, to learn how and when to apply them, and to learn to design rigorous epidemiologic studies.  Students will gain experience in reading the primary epidemiologic methods literature. Course objectives will be met through class lecture, class discussion, problem sets, exams, application of selected principles to one’s research and the development of a mini-lecture.

Credits: 3

Prerequisite(s): CTS602A, CTS603A, CTS603B (corequisite)

Course Director: Anthony Nunes

Semester Offered: Fall

Last Taught: Spring 2023

This course provides an overview of multivariable analysis and advanced analytical strategies for clinical and population health research. Emphasis is on developing an understanding of multivariable modeling in the context of linear, logistic and Poisson regression. Computational lab assignments and two exams will be completed.

Credits: 4

Prerequisite(s): CTS605A, Introduction to Statistics or permission from course coordinator 

Course Director: JungAe Lee

Semester Offered: Spring

Last Taught: Spring 2024

Course provides a foundation for statistical thinking in clinical and population health research involving time to event data and longitudinal data. Students will learn statistical models used for estimation and inference; understand advanced statistical techniques; and develop modeling strategies and analysis plans for specific research questions.

Credits: 4

Prerequisite(s): CTS603A

Course Director: Jonggyu Baek

Semester Offered: Fall

Last Taught: Fall 2023

This course will provide structure and support for students completing their first major evaluation milestone.  Students come to the first day of class with a research study question approved by their mentor and an existing dataset to use to evaluate the study question. Students will develop a manuscript and write it up according to the instructions for authors for the target journal. Students will conduct their own data analysis and will be evaluated on summative competencies expected to be achieved by the end of their first year of CPHR core coursework and research experiences.  Students present their work in an open forum in the form of a 10-15 minute presentation followed by questions and answers. The manuscripts are sent out for review by three faculty.  Students have two weeks to write a rebuttal and prepare a revised manuscript.

Credits: 4

Prerequisite(s): CTS602A, CTS603A, CTS702

Course Director: Shao-Hsien Liu

Semester Offered: Summer

Last Taught: Summer 2023

This course reviews basic principles of epidemiology and biostatistics. The course reviews the application of various observational and experimental research designs and strategies to clinical, epidemiological, and translational research. Didactic instruction, readings, and problem sets (including lab-based analyses) are used to more fully understand epidemics and their causes, as well as various study designs, including cross-sectional studies, case-control studies, cohort designs, and randomized clinical trials. Students also will learn basic principles of biostatistics and will be introduced to STATA for statistical computing. Students are graded on exams, problem sets, and lab assignments.

Credits: 3

Prerequisite(s): None

Course Director: Maira Castaneda-Avila

Semester Offered: Fall

Last Taught: Fall 2023

Students will learn how to: create and sustain cohesive research teams; develop a productive program of research; develop good mentor and mentee relationships; engage in transdisciplinary science; understand the NIH Roadmap; and hear about different forms of clinical and community research from local investigators who conduct it. 

Credits: 2

Prerequisite(s): None

Course Director: Stephenie Lemon

Semester Offered: Spring

Last Taught: Summer 2021

The course considers the scientific and practical considerations in the design and conduct of observational studies and clinical trials. Topics to be covered include: study designs (cohort studies, case-control studies and clinical trials); confounding and bias; ethical considerations; patient recruitment and retention; interim analysis and safety monitoring; and analysis and reporting. Course objectives will be met through a combination of lecture, discussion and development of a proposal in the student’s area of interest.

Credits: 3

Prerequisite(s): CTS605A or permission from instructor 

Course Director: Bruce Barton

Semester Offered: Spring

Last Taught: Spring 2023

This course teaches students how to develop a peer reviewed scientific manuscript, through the review of elements of style, authorship and extent of information that needs to be incorporated into a scientific research paper. Students will learn how to develop the elements that go into a successful scientific manuscript, submit an article for peer review and respond to reviewers' concerns. During each session, students will critique the work of others enrolled in the course to obtain hands on experience in the write-up of the introduction, methods, results and discussion sections of a manuscript. This course will also teach students how to put together a successful oral, as well as poster, scientific presentation.

Credits: 3

Prerequisite(s): None

Course Director: Robert Goldberg

Semester Offered: Fall, Spring

Last Taught: Spring 2024

The purpose of this class is to teach students how to conduct a systematic review, including development of a question of appropriate scope and clinical relevance; development of abstraction tool; selection of articles; and drafting of all sections of the review, including tables and figures. The end product will be a journal style and length systematic review in the topic area of the student’s substantive interest area that is 75 percent ready for submission to a peer-reviewed journal. 

Credits: 2

Prerequisite(s): None

Course Director: Jeffrey Driban

Semester Offered: Fall

Last Taught: Fall 2022

This course is designed to provide students with a basic knowledge of ethics that will prepare them to understand and address problems in the ethical conduct of research involving human subjects, as well as understand and address scientific misconduct, including fraud, misrepresentation and conflict of interest. The course also addresses authorship guidelines, IRB regulations and UMass Chan Medical School Regulations. Students will also focus on how to design ethical research and evaluate treatment risk, placebo control, ethics of recruitment, dilemmas of informed consent, potential scientific contribution and issues for special populations and conducting research internationally. 

Credits: 2

Prerequisite(s): None

Course Director: Catherine Dube

Semester Offered: Fall

Last Taught: Fall 2023

Course will cover a focused set of issues in advanced epidemiology such as conducting community based, surveillance-based randomized controlled trial. Skills will be developed in the practical and scientific issues as well as analysis plans and presentation of results.

Credits: 3

Prerequisite(s): CTS602A, CTS602B, CTS603A, CTS603B, or permission from instructor

Course Director: Sarah Forrester

Semester Offered: Spring

Last Taught: Spring 2023

This course will cover an advanced topic in biostatistics (for example, multilevel models, longitudinal data analysis, survival analysis, graphical information systems and spatial statistics). The purpose of the course is to provide students with emersion in one particular area of biostatistics, providing the theoretical background necessary and the practical hands-on data-analyze experience.

Credits: 3

Prerequisite(s): CTS603A, CTS603B or permission from instructor 

Course Director: Jonggyu Baek

Semester Offered: Summer

Last Taught: Has not been taught within last two years

This advanced methods course is focused on learning methods for addressing confounding and bias. The goals for students taking this course are: to become comfortable recognizing and discussing bias and confounding; to gain experience in using a variety of techniques that help in identifying and minimizing bias and confounding; and to be able to assess the potential impact of residual bias and confounding on study results. This course is organized as topic lectures followed by applications of the topic. Students independently apply what is introduced in the lecture to their own data and share their learning with classmates. 

Credits: 3

Prerequisite(s): CTS602A, CTS602B, CTS603A, CTS603B

Course Director: Anthony Nunes

Semester Offered: Spring

Last Taught: Spring 2023

The purpose of this course is to provide opportunities for the student to understand the foundations of randomized clinical trials (RCTs) in behavioral medicine research. Topics related to theory, design, implementation, and evaluation of behavioral randomized clinical trials will be discussed. Students will develop a research project where concepts can be applied and practice reviewing behavioral RCTs in the published literature.

Credits: 2

Prerequisite(s): CTS702 or permission from instructor

Course Director: Catherine Dube

Semester Offered: Spring

Last Taught: Spring 2020

This course provides an in-depth look at the U.S. health care system. Students will apply constructs of structure, process, and outcomes of care to understanding and evaluating health care quality and cost, and learn how health care policies and payment practices impact the accessibility, effectiveness and cost of care. 

Credits: 2

Prerequisite(s): None, but an introductory-level  understanding of inferential statistics and research design is helpful.

Course Director: Alcusky, Matthew

Semester Offered: Fall, odd years

Last Taught: Fall 2023

The course will discuss fundamental concepts in chronic disease epidemiology; common research methods used in the design and conduct of studies of chronic disease epidemiology; and the application of these methods for the major chronic diseases affecting industrialized countries. Topics will include cardiovascular disease, cancer, cerebrovascular disease, diabetes and lifestyle practices to promote health.

Credits: 2

Prerequisite(s): CTS605A (corequisite) or permission from instructor 

Course Director: Mara Epstein

Semester Offered: Fall, odd years

Last Taught: Fall 2023

Students will become familiar with existing population-based public health, electronic medical record and claims data. Topics include advantages and disadvantages, complex sampling and weighting, and obtaining limited-access data. Using a population-based dataset, students will develop and implement an analytic plan to answer a research question of their choosing.

Credits: 2

Prerequisite(s): CTS 605A or permission of the course director

Course Director: ShaoHsien Liu

Semester Offered: Spring, even years

Last Taught: Spring 2024

This course will provide students with fundamental knowledge of psychiatric epidemiology. We will cover epidemiological principles specific to psychiatric epidemiology such as assessment and diagnostic validity in the absence of a gold standard. Students will be given the opportunity to conduct original research and will gain knowledge of particular psychiatric illnesses through student preparation of course presentations.

Credits: 2

Prerequisite(s): CTS 605A or permission of the course director

Course Director: Mayra Tisminetzky

Semester Offered: Spring, odd years

Last Taught: Spring 2023

We will cover the main societal causes implicated in affecting the health of human populations, including class hierarchy, racism, gender hierarchy, heteronormativity and ableism. We will focus on methodological approaches to measuring and interpreting these forces and their effects, on both minority and dominant populations.

Credits: 2

Prerequisite(s): CTS 605A or permission of the instructor

Course Director: William Jesdale

Semester Offered: Fall, even years

Last Taught: Fall 2022

The purpose of this class is to learn models of disease prevention; multilevel determinants of health behaviors; and major theories of health behavior change and their application to interventions to address major public health problems. 

Credits: 2

Prerequisite(s): None

Course Director: Stephenie Lemon

Semester Offered: Fall, even years

Last Taught: Spring 2024

This course examines use of qualitative methods in qualitative studies or mixed-qualitative/quantitative studies. Essential qualitative research components are explored: theory, rigor, research questions, data collection methods, data collection using open-ended techniques, sampling, data coding and analysis (focusing on thematic analysis), publishing and writing proposals. Students apply concepts covered in class by developing an original qualitative study.

Credits: 2

Prerequisite(s): None

Course Director: Catherine Dube

Semeter Offered: Spring, odd years

Last Taught: Spring 2023

The purpose of this class is to learn pharmacoepidemiology, including: rigorous methodologic approaches to the measurement of medication exposure, adherence and adverse events; pharmacoepidemiologic study design; choices for pharmacoepidemiology data resources; and the role of quality of life measurements and pharmacoeconomics.

Credits: 2

Prerequisite(s): CTS 602A or equivalent

Course Directors: Anthony Nunes

Semester Offered: Summer, odd years

Last Taught: Spring 2022

In this class, we will explore the influence of place on population health, including physical environment (e.g., air, water, soil, food), built environment (e.g., neighborhood structure, traffic, green space), social environment (e.g., cohesion, safety, deprivation, segregation), and legal and civic structure (e.g., policy, law, representation). We will also learn to implement (and critique) methodologic approaches that are particularly adapted to understanding how individuals and places interact, specifically multilevel thinking and modeling, and spatial analytic methods. 

Credits: 2

Prerequisite(s): CTS 605A (corequisite) or permission of the course director

Course Director: William Jesdale

Semester Offered: Spring

Last Taught: Fall 2021

This class provides an introduction to what is often referred to as translational, dissemination or implementation research, as well as the broad field of implementation science. Students will learn about the significance and major initiatives associated with moving research into practice, and will be introduced to conceptual and analytic tools (e.g., theories, frameworks) to support work in this area.

Credits: 2

Prerequisite(s): None

Course Directors: Jamie Faro and Daniel Amante

Semester Offered: Summer

Last Taught: Summer 2022

The purpose of an independent study elective is to gain in depth knowledge of a specific topic by working closely with a faculty member with expertise in that area. Typically independent studies cover areas not addressed in the core curriculum and advanced topics or other electives. However, the level of effort and objectives for an independent study must be equivalent to that of a regular three-credit course. The student and sponsoring faculty member must propose a framework and outcome for the independent study, in the semester prior to the semester in which the student will be enrolled, to the program director for prior approval. 

Credits: 1-6

Prerequisite(s): Permission of Associate Dean for PHS and Course Director 

Course Director: Varies

Semester Offered: Fall, Spring, Summer

Last Taught: Spring 2024

Research rotations are defined periods of research experience under the direction of a faculty member. They are intended to familiarize the student with the theory, background, concepts and techniques in several areas of research and to assist the student in evaluating projects and areas that might be developed into a dissertation project. The student will participate in an ongoing research project; gain familiarity with a field of study; acquire a working knowledge of techniques used in the research; and write a report and make an oral presentation on the results of their work. 

Credits: 4

Course Director: Student's advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

This course number is used for students sitting for the written qualifying exam—an evaluation milestone typically conducted in Spring of their second year of graduate study. 

Credits: 1

Course Director: Kate Lapane

Semester Offered: Spring, Summer

Last Taught: Taught every year

This course number is used for students who will defend their dissertation proposal. Students should register for this either in the Spring or Summer of their second year of graduate studies. 

Credits: 1

Course Director: Kate Lapane

Semester Offered: Spring, Summer

Last Taught: Taught every year

All graduate students are required to have a TRAC meeting each academic year in the Fall. After passing their Written and Oral Qualifying Exams in January of the second year, students are required to register for this course each Fall semester until their Dissertation Examination Committee is formed.

Credits: 1

Course Director: Kate Lapane

Semester Offered: Fall Spring

Last Taught: Course taught every year

This course is for students who have selected a program and thesis advisor but who have not yet passed their Qualifying Examination.

Credits: 3-9

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

The purpose of this course is to allow CPHR PhD students to gain experience writing grant proposals in a systematic fashion under faculty guidance. The course includes overviews of the grant process, participation in a mock proposal review session, and the completion of each of the written scientific components of proposals. 

Credits: 3

Prerequisite(s): CTS702, CTS602A, CTS 602B, CTS603A, CTS603B or permission of instructor

Course Director: Mara Epstein

Semester Offered: Spring

Last Taught: Spring 2024

Students register for Thesis Research after passing a Qualifying Examination. They will take Thesis Research each semester until they have accumulated 90 credits.

Credits: 7-12

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Students register for Graduate Research after completing the requisite number of credits to meet graduation requirements. They will take this course each semester until they complete all remaining requirements.

Credits: 0

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Goals:  This course is designed to help students discern study design approaches appropriate to the area of inquiry, consider biological variability in study design, prospectively design and select valid data collection instruments, prospectively identify appropriate statistical methodologies and alternative analytical approaches, identify data sharing and publication strategies, accurately communicate facts and interpret results, and fairly acknowledge specific contributions to research studies. As part of the course, students are expected to achieve a minimum competency in the programming language “R”.  These course activities will be conducted in a manner that enables the student’s intellectual contribution to the University’s academic and research functions.

Objectives:

•Review the elements of experimental design, tools, and standards

•Provide an overview of quality procedures for biomedical research, including authentication procedures

•Review reporting guidelines used for manuscript preparation

•Present a workflow that promotes transparency including detailed record keeping and data management

•Demonstrate understanding of how to conduct reproducibility/replication studies and effectively communicate results

•Basic of downloading data and essential dataset manipulation

•Basics of descriptive visualizing data once cleaned

•Basics of most common statistical analyses

•Basics of visualization and graphing

Goals: Facilitate application of standards and requirements for rigor and responsibility and research as applied to the student’s potential thesis project.  In coordination with identified Thesis advisor, the student will elaborate thoughts on questions/problems to be analyzed, approaches to hypothesis generation, strategy for hypothesis testing, and strategy for data storage, analysis, and reporting.  These course activities will be conducted in a manner that enables the student’s intellectual contribution to the University’s academic and research functions.

 Objectives:

•Identify the question or problem that is the topic of the research

•To enumerate current hypotheses related to the research question

•To justify the need for further hypothesis generation

•To explain how specific hypotheses will be derived from hypothesis generating approach

•To define the timeline for hypothesis generation

•To describe specific assays to test specific hypothesis

•To describe and justify statistical tests that will be used

•To escribe how reproducibility will be ensured

•To describe where and how data will be stored

•To describe anticipated timelines for reporting and publication

Credits: 1

Prerequisite(s): None

Course Director: Jonathn Kay

Semester Offered: Fall, Spring

Last Taught: Taught every fall and spring

Goals: The goal for the course is to continue to support MD/PhD student connection to research activities during their Core Clinical Experiences (CCE).  This will allow the student to conduct research in a manner that enables their intellectual contribution to the University’s academic and research functions.  The second goal is to support students in preparing to apply to research intensive residency programs.  These activities will involve a minimum of one hour per week over the course of the semester (15 hours total). 

 Objectives:

•Propose an approach to investigate novel research questions arising from their clinical observations

•Continue interactions with Thesis lab to conclude potential in progress research publications

•In consultation with MD/PhD mentors, explore potential areas of specialization that will be compatible with long term research career goals

•In consultation with MD/PhD mentors and Thesis advisor, work on Personal Statement appropriate for application to residency programs

Curricular Expectations: The student will develop a presentation appropriate for the requirement for the Capstone Scholarship Discovery Program.

Credits: 1

Prerequisite(s): None

Course Director: Jonathan Kay

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Goals: The MD/PhD program stresses the importance of maintaining clinical involvement during students’ dissertation research.  The first goal of this course is to allow students to maintain clinical skills in a variety of clinical settings.  The second goal is to help students identify an appropriate specialty in which to pursue residency training.  Sessions should reinforce clinical skills learned during the first two years of medical school, as well as during the first 16 weeks of Core Clinical Experiences (CCE). 

Curricular Expectations: Students will engage in a minimum 15 hours of clinical experiences during each of the fall, spring, and summer terms. Students will also participate in the Physician Scientist Forum, which is held weekly on Monday evenings.  Students will be evaluated by their designated Learning Community MD/PhD mentor at the end of each term.

Prior to the end of each term during their dissertation research, students will record their clinical hours in the OASIS system using a dedicated form that will include the date, time, term, preceptor, and number of hours. 

Preceptors must have a faculty appointment at UMass Chan Medical School, and clinical sessions must take place at a facility that is affiliated with UMass Chan Medical School.  The student’s designated Learning Community MD/PhD mentor must approve the choice of preceptor.

Credits: 1

Prerequisite(s): Open only to MD/PhD Students in PhD Portion of Degree

Course Director: Jonathan Kay

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Goal: To maintain HIPAA and OHSA qualifications while enrolled in the research portion of the combined degree program.

Curricular Expectations: Complete the certification module of HIPPA and OSHA online course/assessment in Black Board Learn annually (within the first two weeks of the Morningside Graduate School of Biomedical Sciences fall semester) each year. This is an online class that can be accessed by each MD/PhD student registered for this course in PeopleSoft.  The scores will be monitored by the MD/PhD Program Administrator during the student's PhD years.

Credits: 1

Prerequisite(s): None

Course Administrator: Praneet Mann

Semester Offered: Fall

Last Taught: Taught every fall

Goals: Preparation of MD/PhD students to enter Morningside Graduate School of Biomedical Sciences full-time research in fall term after completing 16 weeks of clinical clerkships from May through August prior to Morningside Graduate School of Biomedical Sciences start.  This includes meetings with the future PI, literature review, and, when scheduling permits, attendance at lab meetings.  For students who have not yet selected a PI the requirements are to work with MD/PhD Advisors and Morningside Graduate School of Biomedical Sciences leadership to target and meet with potential lab rotation mentors during the summer term.

Curricular Expectations: For students who have selected an advisor:  Attend meetings with intended mentor, literature review, and attendance at lab meetings.  Work on development of life skills needed to balance clinical and research obligations. 

For students who have not selected a thesis mentor they should be meeting with potential rotations, talking to MD/PHD advisor and attending research seminars from potential labs.  Outcome should be a signed lab rotation form submitted to the Morningside Graduate School of Biomedical Sciences by late August in time to start the rotation day one of Fall term.

Credits: 1

Prerequisite(s): MDP 740A, MDP 740B, MDP 740C

Course Director: Jonathan Kay

Semester Offered: Summer

Last Taught: Taught every summer

Objectives: 

•To foster skills that MD/PhD students need to be maximally competitive for research intensive residency programs.

•To guide MD/PhD students regarding postgraduate training opportunities through interactions with residents, fellows, and faculty.

•To highlight connections between basic and clinical science through the presentation and discussion of patient cases.

•To expose postgraduate trainees to research conducted by MD/PhD students and promote opportunities for potential collaboration.

Curricular Expectations: This seminar is offered weekly for 1.5 hours every Monday evening.  It is organized by MD/PhD students, and participation is required of students in all years of the MD/PhD program who are not otherwise scheduled for clinical rotations.

Credits: 1

Prerequisite(s): None

Course Director: Jonathan Kay

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Students enrolled in the MD/PHD Program who have completed their requirements for the PhD degree will register for this Morningside Graduate School of Biomedical Sciences course each semester while completing their T.H. Chan School of Medicine requirements. Students enrolled in this course will participate in and assist with the teaching/evaluation of the MDP Seminar course (MDP800). This course is the MD/PhD equivalent of the Morningside Graduate School of Biomedical Sciences course - BBS 990 or CTS 990, Graduate Research. All students must be in good standing in the MD/PhD program to pass.

Credits: 0

Prerequisite(s): Completion of all the PhD requirements in the Graduate School of Biomedical Sciences

Course Administrator: Praneet Mann 

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester