BINF G6002 Methods III: Research Methods

Course Description: The course provides an overview of research methods relevant to biomedical informatics, with a specific focus on interventions research. The overall goal of the course is to prepare the student to participate in and perform scientific research.


Lena Mamykina, PhD

Teaching Assistant

Amanda Moy

Course Schedule

This class has two weekly lectures, held Tuesday and Thursday from 10:30 am - 12 pm. It also has a weekly lab Friday at 9 am.

By the end of the course, the students will be able to:

  • Identify opportunities for innovative informatics interventions for improving health and medicine
  • Formulate research questions relevant to the identified opportunities
  • Conduct literature review and identify gaps in existing scholarship related to the research questions
  • Critique published research in relation to the research questions
  • Identify research methods appropriate for research questions of interest
  • Plan and carry out a qualitative study on a topic of interest to biomedical informatics
  • Plan and carry out a quantitative study on a topic of interest to biomedical informatics
  • Write a research proposal on a topic of interest to biomedical informatics
  • Write a research proposal for review by Institutional Review Board
  • Complete certification in Responsible Research Conduct

The course material is covered through in-class lectures and discussions, on-line lectures, assigned readings, assignments, and labs.  Assignments and labs are intended to reinforce the other learning materials. 


Primary texts: 
Designing Clinical Research: An Epidemiologic Approach, Hulley SB, Cummings SR, Browner WS, Grady DG, Newman TB.  Third edition, 2006.

Secondary texts: 
The Practice of Nursing Research: Appraisal, Synthesis and Generation of Evidence, Burns N, Grove SK. Sixth edition, 2008.
Basics of Qualitative Research: Techniques and Procedures for Developing Grounded Theory, Juliet Corbin, Anselm Strauss, SAGE Publications, Inc; 3rd edition (November 19, 2007)
Evaluation Methods in Biomedical Informatics. Freidman CP, Wyatt J. Second edition, 2010. 

Supplemental readings will also be required.


The grading is divided up into three parts.

Part 1:  The first part is the weekly assignments, based on the material covered in class.  Assignments are intended to provide “hands-on” experience to reinforce concepts and strengthen research skills, and to prepare for the labs.  Assignments and labs will account for 30% of the final grade.

Part 2: The second part of the course is the exams.  There will be both a midterm and final exam for the course. The midterm will be a take-home midterm paper in which the students will be asked to critique a research paper. The paper for critiquing will be announced two weeks prior to the deadline, and students will have two weeks to complete their critique.  The schedule for the final is TBD; it will most likely happen during regular class hours.  The midterm and final each account for 20% of the final grade. The final will be comprehensive of the course material.

Part 3:  The final project for this course is for groups of 2-3 students to develop a quality research proposal. This is a major focus of the course, and much of the course is organized around this activity.  The proposal is due at the beginning of the final exam, and accounts for 30% of the grade. 

SYLLABUS (subject to change)

DateTopicReading AssignmentAssignmentsProposal Milestones
1/21Introductory MaterialLecture 1: Intro/Basic components of researchDesigning Clinical Research (Ch.1-2)Assignment 1 (due 01/24): critique research paper
1/23Specific Aims Lecture 2: Interventions in biomedical informatics1. Henrik Skaug Sætra, Science as a Vocation in the Era of Big Data: the Philosophy of Science behind Big Data and humanity’s Continued Part in Science, Integrative Psychological and Behavioral Science, December 2018, Volume 52, Issue 4, pp 508–522.
2. Sittig DF, Wright A, Osheroff JA, Middleton B, Teich JM, Ash JS, et al. Grand challenges in clinical decision support. Journal of Biomedical Informatics. 2008 Apr 1;41(2):387–92.
3. Middleton B, Sittig DF, Wright A. Clinical Decision Support: a 25 Year Retrospective and a 25 Year Vision. Yearbook of Medical Informatics. 2016 Aug 6;25(S 01):S103–16.
1/24no lab
1/28Lecture 3: Philosophy of scienceLaplane, L., Mantovani, P., Adolphs, R., Chang, H., Mantovani, A., McFall-Ngai, M., Rovelli, C., Sober, E., and Pradeu, T., Opinion: Why science needs philosophy, PNAS March 5, 2019 116 (10) 3948-3952; 2 (due 01/29): debate
1/30Lab 1: Debate1) Holliday R. The incompatibility of Popper’s philosophy of science with genetics and molecular biology. Bioessays 1999;21:890–891
2) Jonathan Bard, Popper’s philosophy of science: a practical tool for the working biologist. BioEssays 22:205
3) Nick Smith The utility of Popper's philosophy in biology. BioEssays 22:205
4) Aubrey D.N.J. de Grey. Biologists abandon Popper at their peril BioEssays 22:206
1/31Lab 2: Critiquing Research I
2/4Lecture 4: Writing proposals I
“Summary” from Initial National Priorities for Comparative Effectiveness Research, Institute of Medicine, 2009.
Assignment 3 (due 02/07: critique a paper)
2/6Significance/InnovationLecture 5: Assessing research quality /literature review1) Knopf, J.W. 2006 Doing a Literature Review, Political Science and Politics, Vol. 39, No. 1 (Jan., 2006), pp. 127-132;
2) Hannan EL. Randomized clinical trials and observational studies: guidelines for assessing respective strengths and limitations. JACC Cardiovasc Interv. 2008 Jun;1(3):211-7;
3) Akobeng AK. Assessing the validity of clinical trials. J Pediatr Gastroenterol Nutr. 2008 Sep;47(3):277-82.
2/7Lab 3: Critiquing research IIDiscuss paper critiques
2/11Lecture 6: Formulating research questions: Qualitative I1) Ploeg, J., Identifying the best research design to fit the question. Part 2: Qualitative designs, Evid Based Nurs 1999;2:36-37 (
2) Holloway, I., and Wheeler, S., Qualitative Research in Nursing and Healthcare, Chapter 1, The Nature and Utility of Qualitative Research (the book is available online through Google Books)
3) MacLean, A.M., Two Weeks in Department Stores, The American Journal of Sociology, Vol. 4, No.6 (May 1899), 721-741.
4) Ash JS, Gorman PN, Lavelle M, Payne TH, Massaro TA, Frantz GL, et al. A cross-site qualitative study of physician order entry. J Am Med
Assignment 4 (Due 02/14): Design a plan for a qualitative study (participants, recruitment strategies, interview guide)
2/13Lecture 7: Qualitative II – Analysis 1) Banks, S., Louie, E., Einerson, M., Constructing personal identities in holiday letters, Journal of Social and Personal Relationships, Vol.17(3):299-327, 2000.
2) Braun, V., & Clarke, V., Using thematic analysis in psychology, Qualitative Research in Psychology 2006; 3: 77/101
2/14Lab 5: Discuss qualitative study plan, interview guides
2/18ApproachLecture 8: Frameworks I (DiCog, Activity Theory, Situational Awareness)Required Reading:
1) Hutchins, E., 1995. How a cockpit remembers its speeds. Cognitive Science, 19(3), 265–288.
2) Halverson, K., 2002. Activity Theory and Distributed Cognition:
Or What Does CSCW Need to DO with Theories? Computer Supported Cooperative Work B: 243–267, 2002.
3) W. Pratt, M.C. Reddy, D.W. McDonald, P. Tarczy-Hornoch, J.H. Gennari. Incorporating Ideas from Computer Supported Cooperative Work. Journal of Biomedical Informatics. 2004; v37:1p.28-137.
Assignment 5 (due 2/21): conduct qualitative study, analyze results
2/20Lecture 9: Frameworks II (informatics)1) Davis, F. D.; Bagozzi, R. P.; Warshaw, P. R. (1989), "User acceptance of computer technology: A comparison of two theoretical models", Management Science 35: 982–1003
3) Donabedian, A. (1997). The quality of care. How can it be assessed? 1988. Archives of pathology & laboratory medicine, 121(11), 1145-1150.
2/21Lab 6: Qualitative coding, identify major common themes and requirements
2/25Lecture 10: Design I1) Beyer, H., Holtzblatt, K, Contextual Design, Chapters 5 and 6.Assignment 6 (due 02/28): Develop 2 work models for the conference room scheduling task (flow model, information model), identify 5 different design ideas for the new conference reservation system
2/27Lecture 11: Design II
2/28Lab 7: Develop design concepts for the new website, storyboard, mockupsIdentify project groups; make arrangements for an exploratory study
3/3Lecture 12: Hypothesis testing1) Designing Clinical Research, Chapters 5 and 6
2) Regina Nuzzo, Scientific method: Statistical errors, Nature, 2014 (
3) The ASA's statement on p-values: context, process, and purpose
Assignment 7 (due 03/06): critique a framework paper
3/5Lecture 13: Basic research designs I (observational)Designing Clinical Research, chapters 7-9
3/6Lab 8: apply theoretical framework to the designConduct exploratory study, identify research questions and specific aims
3/10Class cancelled Designing Clinical Research, chapters 7-9Assignment 8, design an observational study
3/12Midterm distributedLecture 14: Basic research designs II (experimental)Designing Clinical Research, chapters 7-9
3/13Lab 9: design an observational Discuss assignment 8
3/16 - 3/20Spring Break
3/24Class cancelled
3/26Lecture 15: Research data analysis Designing Clinical Research, Chapters 3-6
3/27Specific Aims are due;
Initial design of an intervention
3/31Lecture 16: Power and SamplingDesigning Clinical Research, Chapter 6
4/2Lecture 17: Validity IDesigning Clinical Research, Chapter 4
4/3Midterm DueLab 10: Design an experimental studySignificance due
4/7Lecture 18: Validity II
4/9Lecture 19: Writing proposals II
4/10Lab 11: Summarizing research findingsInnovation due
4/14Lecture 20: Ethics/IRBDesigning Clinical Research, Chapter 14NIH proposal for review during Friday lab
4/16Lecture 21: Research Data Management Designing Clinical Research, Chapter 16
4/17Lab12: Mock grant panelApproach due
4/21Lecture 22: Final reviewInitial feedback on Approach
4/23Lab 13: Writing limitations sections
4/24Lab 14: Review the actual scoring of NIH proposal; preparing resubmissionProposals posted for critiquing
4/28Presentation of research projects
4/30Presentation of research projects
5/1Presentation of research projects
5/5 - 5/7Study Week
5/8FinalFinal (open book)Final proposals are dueFinal proposals are due