1

Introduction (Peter Szolovits)

(PDF - 1.3MB)

[Text] Chapter 1, and 2

2

Nature of clinical data (Peter Szolovits)

(PDF)

[Text] Chapter 12

3

Standards (Peter Szolovits)

(PDF)

(PDF)

4

Data in narrative text (Peter Szolovits)

(PDF)

[Text] Chapter 8

5

Gene, expression and protein data (Alvin Kho)

[Text] Chapter 22

6

Genes and modeling (Alvin Kho)

MAQC Consortium. "The MicroArray Quality Control (MAQC) Project Shows Inter- and Intraplatform Reproducibility of Gene Expression Measurements." Nature Biotechnology 24, no. 9 (2006).

7

Building models (Peter Szolovits)

(PDF - 1.2MB)

8

Probabilistic and graphical models (Peter Szolovits)

[Text] Chapter 3

9

Information theoretic metrics (Gil Alterovitz)

10

Decision support via probabilities and utilities (Peter Szolovits)

(PDF - 1.2MB)

11

Decision support via expert systems (Peter Szolovits)

(PDF - 1.0MB)

[Text] Chapter 20

Pople, H. E., Jr. "Heuristic Methods for Imposing Structure on Ill-Structured Problems: Medical Diagnostics." 1982.

12

Using the healthcare enterprise for research (Isaac Kohane)

13

Personally controlled health records (Kenneth Mandl)

Mandl, Kenneth D., and Isaac S. Kohane. "Tectonic Shifts in the Health Information Economy." New England Journal of Medicine 358, no. 16 (2008).

———. "No Small Change for the Health Information Economy." New England Journal of Medicine 360, no. 13 (2009).

MIT Sana (PDF) (Courtesy of Leo Anthony Celi. Used with permission.)

14

Modeling with bayesian networks (Peter Szolovits)

(PDF)

Pearl, Judea. "Causal Inference in the Health Sciences: A Conceptual Introduction." Health Services & Outcomes Research Methodology 2, no. 3-4 (2001).

A tutorial on learning with Bayesian networks

Szolovits, Peter. "Uncertainty and Decisions in Medical Informatics."Methods of Information in Medicine 34, no. 1-2 (1995).

15

Patient monitoring and intensive care (Leo Celi)

(PDF)

(PDF - 3.9MB)

(Courtesy of Leo Anthony Celi. Used with permission.)

Celi, Leo Anthony G., et al. "A Clinical Database-Driven Approach to Decision Support: Predicting Mortality Among Patients with Acute Kidney Injury." Journal of Healthcare Engineering 1, no. 2 (2011).

16

HIT in the developing world (Hamish Fraser)

(PDF - 3.6MB)(Courtesy of Hamish Fraser. Used with permission.)

Mamlin, Burke W., et al. "Cooking up an Open-Source EMR for Developing Countries: OpenMRS – A Recipe for Successful Collaboration." AMIA Annu Symp Proc (2006).

Amoroso, Cheryl L., et al. "Using Electronic Medical Records for HIV Care in Rural Rwanda." Studies in Health Technology and Informatics 160 (2010).

Were, Martin C., et al. "Leapfrogging Paper-Based Records using Handheld Technology: Experience from Western Kenya." Studies in Health Technology and Informatics 160 (2010).

17

Learning bayesian networks (Peter Szolovits)

(PDF)

18

Informatics in radiology (Ronilda Lacson)

[Text] Chapters 9, and 18

Branstetter, Barton F. "Basics of Imaging Informatics: Part 1." Radiology243, no. 3 (2007).

———."Basics of Imaging Informatics: Part 2." Radiology 244, no. 1 (2007).

19

Predictive genomics (Michael McGeachie)

Sebastiani, Paola, et al. "Genetic Dissection and Prognostic Modeling of Overt Stroke in Sickle Cell Anemia." Nature Genetics 37, no. 4 (2005).

Allocco, Dominic J., et al. "Geography and Genography: Prediction of Continental Origin Using Randomly Selected Single Nucleotide Polymorphisms." BMC Genomics 8, no. 68 (2007).

Lewis, Cathryn M. "Genetic Association Studies: Design, Analysis and Interpretation." Briefings in Bioinformatics 3, no. 2 (2002).

McGeachie, Michael, et al. "Integrative Predictive Model of Coronary Artery Calcification in Atherosclerosis." Circulation 120 (2009).

20

Patient data privacy (Peter Szolovits and Chris Cassa)

(PDF)

Meystre, S. M., et al. "Automatic De-Identification of Textual Documents in the Electronic Health Record: A Review." BMC Medical Research Methodology 10 (2010): 70.

21

Public health informatics (John Brownstein)

[Text] Chapter 15

22

Computer science challenges from health care (Peter Szolovits)

(PDF)

Stead, W. W., and H. S. Lin, editors. Computational Technology for Effective Health Care: Immediate Steps and Strategic Directions. Committee on Engaging the Computer Science Research Community in Health Care; National Research Council. National Academies Press, 2009. (PDF)

23

Networks (Gil Alterovitz)

Suggested Reading

 Alterovitz, Gil, and Marco F. Ramoni, editors. Chapters 1 and 7 in Systems Bioinformatics. Artech House Publishers, 2007. ISBN: 9781596931244.

24-25

Final project presentations

1

Clinical databases

2

Extracting meaning from text

3

Gene expression and mathematical foundations

4

Project proposals:

Please submit proposals for projects for the class. Students may complete the project alone or pair up with one or two other students. It is generally quite helpful for each team to include students with different backgrounds. Topics for projects can include anything that is relevant to the class material. Your proposal should include a list of the people who will be working on the project, a title, and a one-page description, with enough detail that the instructor can provide feedback to help direct your work.