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Principles of Research Methodology

MEDI N135: Principles of Research Methodology

August 16, 2017 – December 20, 2017
Wednesdays 5 PM – 6 PM
Lecture Hall 2

Calendar »

Course Director:

Phyllis G. Supino, EdD
Professor of Medicine, College of Medicine
Adjunct Professor of Public Health, School of Public Health
Director, Clinical Epidemiology and Clinical Research
Division of Cardiovascular Medicine
Chair, Institutional Review Board
SUNY Downstate Medical Center


  • Jeffrey Borer, MD
  • Joseph Franciosa, MD
  • Kathleen Powderly, CNM, PhD
  • Phyllis Supino, EdD
  • Jeremy Weedon, PhD

Recommended text:

Principles of Research Methodology: a Guide for Clinical Investigators. Phyllis G. Supino, Jeffrey S. Borer (eds); Springer June 2012

This course is intended for physicians, medical students and other members of the Downstate Medical Center (DMC) academic community who are designing research projects, writing grant proposals, or conducting research for publication as a journal article or presentation at a medical society meeting. Its purpose is to familiarize participants with the:

  • principles of problem definition and hypothesis construction;
  • logic of research design and statistics;
  • rationale and procedures for generating and validating self-reported data;
  • fundamentals of writing and submitting a research protocol; and
  • guidelines for assembling and interpreting results, evaluating and writing scientific papers, and publishing studies.

The course consists of 18 one-hour sessions. Its faculty includes senior members of the DMC Departments of Medicine, School of Public Health, Scientific Computing Center, and John Conley Division of Medical Ethics and Humanities.

The course is an approved elective for MS1 and MS2 students, and is CME approved for a maximum of 18 AMA/PRA Category 1 Credits™ (1 credit per lecture).

For more information please contact, x2201.


  1. Identifying and Developing the Research Problem

    Dr. Supino

    Overview of the research process; importance of the research plan; identifying and refining the problem; characteristics of good research problems; role of the literature review.

    Recommended reading: Principles of Research Methodology (PRM), Chapters 1- 2

  2. The Role of the Hypothesis in Research

    Dr. Supino

    The role of the hypothesis in a research investigation; relation to the research question; logical underpinnings; hypothesis testing vs. hypothesis generating studies (important distinctions); characteristics of well-defined hypotheses; types of hypotheses

    Recommended reading: PRM, Chapter 3

  3. Constructing the Research Hypothesis

    Dr. Supino

    Identifying and labeling variables in a hypothesis (independent, dependent, control, moderator; intervening); methodology for developing testable hypotheses (role of the operational defini

    tion; operationalizing the hypothesis); real case examples

    Recommended reading: PRM, Chapter 3

  4. Cohort Studies

    Dr. Weedon

    The nature and purpose of cohort and cross-sectional studies; estimation of effect size; statistical testing

    Recommended reading: PRM, Chapter 4: pp 55-63

  5. Case-Control Studies

    Dr. Weedon

    Introduction to the methodology of the case control study; selection of cases; selection of controls; case/control ratio; estimation of effect size; statistical testing; confounding; sources of bias; relative strengths and weaknesses of this approach relative to cohort and cross-sectional methods

    Recommended reading: PRM, Chapter 4: pp 64-77

  6. Sources of Bias in Studies about Impact of Interventions (Pre-Experimental Designs)

    Dr. Supino

    Distinctions between internal and external validity of a study; common threats to validity (selection, history, maturation, regression, experimental mortality and other sources of bias); examples of pre-experimental designs found in the literature; ethical implications.

    Recommended reading: PRM, Chapter 5: pp 79-91

  7. Control of Bias in Studies about Impact of Interventions (True-Experimental Designs)

    Dr. Supino

    Controlling internal and external bias in a study; the concept of blinding in an experimental design; advantages/disadvantages of 4 common alternative true experimental designs (pretest only, pretest-posttest, factorial, and cross-over parallel group designs); examples from the literature; strengths and limitations of controlled clinical trials.

    Recommended reading: PRM, Chapter 5: pp 91-100

  8. Control of Bias in Studies about Impact of Interventions (Quasi-Experimental Designs)

    Dr. Supino

    Limitations of randomized designs; practical alternatives for determining intervention effects ("quasi-experimental designs); time series and equivalent time samples designs in preclinical research, the "N-of-1" study in the clinical setting, the non-equivalent control group design; literature examples.

    Recommended reading: PRM, Chapter 5: pp 100-11

  9. Estimation and Confidence Limits

    Dr. Weedon

    Relation of the sample to the population; point estimates (proportions and means); the confidence interval (CI): interpretation of CI using probability concepts, construction (upper and lower limits), relation of sample size and degree of confidence to CI width.

    Recommended reading: PRM, Chapter 11: pp 207-217

  10. Evaluating Differences between Means and Proportions

    Dr. Weedon

    Understanding/choosing between tests of hypotheses about differences between means (the one sample, two sample, and paired t-test; analysis of variance [ANOVA], nonparametric analogues) and proportions (the chi-square, Fisher's exact and McNemar's tests); assumptions, limitations, real case examples.

    Recommended reading: PRM, Chapter 11: pp 217-223

  11. Correlation and Regression

    Dr. Weedon

    Testing hypotheses about correlation and linear regression; assumptions; limitations; real case examples

    Recommended reading: PRM, Chapter 11: pp 226-227

  12. Survival Analysis

    Dr. Weedon

    Understanding censored data; how to construct, compare and interpret Kaplan-Meier Product Limit ("survival") curves; Cox regression

    Recommended reading: PRM, Chapter 11: pp 227-231

  13. Logistic Regression

    Dr. Weedon

    The concept of odds, the logistic regression model, interpretation of coefficients, multiple logistic regression

    Recommended reading: PRM, Chapter 11: pp 227-231

  14. Evaluation of Diagnostic Tests

    Dr. Weedon

    Sensitivity, specificity, positive and negative predictive values; ROC curves; biases in assessing diagnostic tests

    Recommended reading: PRM, Chapter 11: pp 223-226

    NO CLASS – 11/22/2017 – THANKSGIVING EVE

  15. Surveys & Psychometric Instruments

    Dr. Weedon

    Purpose of psychometric instruments: how they work and how they are validated; the distinction between psychometric instruments and general surveys; basics of writing good survey items; principles of sampling frames/subject selection and the primacy of maximizing return rate.

    Recommended reading: PRM, Chapter 8

  16. Promoting Science While Protecting Human Subjects: Why do we have IRBs?

    Dr. Powderly

    Historical context; historical abuses of human subjects and present safeguards; how to promote access while protecting human subjects; ethical issues in selection and treatment of human subjects; informed consent and voluntariness; ethical issues in research involving animals (time permitting)

    Recommended reading: PRM, Chapter 12

  17. Research Protocols for Industry

    Dr. Franciosa

    Purpose of the institutional research protocol; ethical underpinnings; format of the introduction and methods sections; human subjects issues (e.g., informed consent, risk/benefit, protection of privacy)

    Recommended reading: PRM, Chapter 6

  18. How to Prepare, Present, and Publish a Scientific Paper

    Dr. Borer

    The role of the scientific paper in the research process; general characteristics of scientific writing; organization of the scientific paper (IMRAD format); how to: prepare a title, list authors, write the IMRAD sections, cite references, prepare tables, figures, and illustrations; general linguistic requirements; how/where to submit a manuscript; the review process; ethical principles.

    Recommended reading: PRM, Chapter 13


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