HST.950J | Fall 2010 | Graduate

Biomedical Computing

Lectures and Readings

[Text] = Shortliffe, Edward H., and James J. Cimino, eds. Biomedical Informatics: Computer Applications in Health Care and Biomedicine. 3rd ed. Springer, 2006. ISBN: 9780387289861.

See Supplemental Readings below for additional reading material.

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)



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 - 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 Pro_c (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.” Radiology 243, 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    

Supplemental Readings

“What is HL7?” by Altis, Inc., 2010.

Adida, Ben, and Isaac S. Kohane. “GenePING: Secure, Scalable Management of Personal Genomic Data.” BMC Genomics 7, no. 93 (2006).

Health Care Industry Pays Steep Price for Ignoring IT.” OR/MS Today, August 13, 2005.

EHRs are the Problem, Not the Solution.” Healthcare IT News, March 10, 2006.

Alterovitz, Gil, and Marco F. Ramoni. “Topological Analysis of Biomolecular Networks.” Chapter 7 in Systems Bioinformatics: An Engineering Case-Based Approach. Artech House Publishers, 2007. ISBN: 9781596931244.

Brownstein, John S., Cecily J. Wolfe, and Kenneth D. Mandl. “Empirical Evidence for the Effect of Airline Travel on Inter-Regional Influenza Spread in the United States.” PLoS Medicine 3, no. 10 (2006).

Bouchie, Aaron. “Clinical Trial Data: To Disclose or Not to Disclose?Nature Biotechnology 24 (2006).

Alvarez, George, and Enrico Coiera. “Interruptive Communication Patterns in the Intensive Care Unit Ward.” International Journal of Medical Informatics 74_,_ no. 10 (2005).

———. “Interdisciplinary Communication: An Uncharted Source of Medical Error?Journal of Critical Care 21, no. 3 (2006).

Fellegi, Ivan P., and Alan B. Sunter. “A Theory for Record Linkage.” Journal of the American Statistical Association 64, no. 328 (1969).

Ramoni, M., and P. Sebastiani. “Bayesian Methods.” Chapter 4 in Intelligent data analysis: An Introduction. Edited by M. Berthold, and D. J. Hand. Springer, 2007. ISBN: 9783540430605.

Frantz, Simon. “How to Avoid Another ‘Vioxx’.” Nature Reviews Drug Discovery 4 (2005).

Schachter, Asher D., and Marco F. Ramoni. “Clinical Forecasting in Drug Development.” Nature Reviews Drug Discovery 6 (2007).

Fraser, Hamish, et al. “Evaluating the Impact and Costs of Deploying an Electronic Medical Record System to Support TB Treatment in Peru.” AMIA Annual Symposium Proceedings (2006).

Glaser, John. “Assessing the IT function in Less Than One Day.” Healthcare Financial Management 60, no. 1 ( 2006).

———. “Wired for Success.” Healthcare Financial Management 60, no. 2 (2006).

HIMSS Analytics. 2009 Annual report of the U.S. hospital IT market. Healthcare Information and Management Systems Society, 2009. (PDF - 2.4MB) Also see https://foundation.himss.org

Harrison, Michael I., Ross Koppel, and Shirly Bar-Lev. “Unintended Consequences of Information Technologies in Health Care—An Interactive Sociotechnical Analysis.” Journal of the American Medical Informatics Association 14, no. 5 (2007).

Kohane, Isaac S., Daniel R. Masys, and Russ B. Altman. “The Incidentalome: A Threat to Genomic Medicine.” Journal of the American Medical Association 296, no. 2 (2006).

Wolberg, W. H., and G. L. Mangasarian. “Multisurface Method of Pattern Separation for Medical Diagnosis Applied to Breast Cytology.” Proceedings of the National Academy of Sciences 87, no. 23 (1990).

Kohane, Isaac S., et al. “Reestablishing the Researcher-Patient Compact.” Science 316, no. 5826 (2007).

Blaya, J., B. Holt, and H. S. Fraser. “Evaluations of the Impact of eHealth Technologies in Developing Countries: A Systematic Review.” Presented at “Making the eHealth Connection” in Bellagio, Italy, 2008. (PDF)

Halamka, John, et al. “Health care IT collaboration in Massachusetts: The Experience of Creating Regional Connectivity.” Journal of the American Medical Informatics Association 12, no. 6 (2005).

Halamka, John D., Kenneth D. Mandl, and Paul C. Tang. “Early Experiences with Personal Health Records.” Journal of the American Medical Informatics Association 15, no. 1 (2008).

Hirschhorn, Joel N., and Mark J. Daly. “Genome-Wide Association Studies for Common Diseases and Complex Traits.” Nature Reviews Genetics 6 (2005).

Dudley, Joel T., et al. “Disease Signatures are Robust Across Tissues and Experiments.” Molecular Systems Biology 5, no. 307 (2009).

Reis, Ben Y., Isaac S. Kohane, and Kenneth D. Mandl. “Longitudinal Histories as predictors of future diagnoses of domestic abuse.” British Medical Journal 339 (2009).

Murphy, Shawn, et al. “Instrumenting the Health Care Enterprise for Discovery Research in the Genomic Era.” Genome Research 19 (2009).

Alterovitz, Gil, et al. “Ontology Engineering.” Nature Biotechnology 28, no. 2 (2010).

Schneider, Thomas D. “Information Theory Primer.” Originally chapter II from PhD thesis. The Information Content of Binding Sites on Nucleotide Sequences. University of Colorado, 1984.

Mandl, Kenneth and Isaac Kohane. “No Small Change for the Health Information Economy.” New England Journal of Medicine 360 (2009).

Pople, Harry E., Jr. “Heuristic Methods for Imposing Structure on Ill-Structured Problems: The Structuring of Medical Diagnostics.” Chapter 5 in Artificial Intelligence in Medicine. Edited by Szolovits, Peter. Westview Press, 1982. ISBN: 9780891589006.

Mandl, Kenneth D., et al. “Indivo: A Personally Controlled Health Record for Health Information Exchange and Communication.” BMC Medical Informatics and Decision Making 7, no. 2 (2007).

Health care blog: http://thehealthcareblog.com/

Aliferis, Constantin F., Alexander Statnikov, and Ioannis Tsamardinos. “Challenges in the Analysis of Mass-Throughput Data: A Technical Commentary from the Statistical Machine Learning Perspective.” Cancer Informatics 2 (2006).

Bosworth, Martin H. “VA Loses Data on 26 Million Veterans: Employee Claims Laptop with Sensitive Data was Stolen.” Consumer Affairs, May 22, 2006.

Freudenheim, Milt. “Medical Data on Empire Blue Cross members May Be Lost.” New York Times, March 14, 2007.

Wikipedia, “United Kingdom National DNA Database.”

Butte, A. J., and I. S. Kohane. “Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements.” Pacific Symposium on Biocomputing 5 (2000). (PDF)

Alterovitz, Gil. “System-Wide Peripheral Biomarker Discovery Using Information Theory.” Pacific Symposium on Biocomputing 13 (2008). (PDF)

Gawande, Atul. “The Checklist.” The New Yorker, December 10, 2007.

Clifford, G., et al. “Robust Parameter Extraction for Decision Support Using Multimodal Intensive Care Data.” Philosophical Transactions of the Royal Society A 367 (2009). (PDF)

Stead, William W., and Herbert S. Lin, eds. “Computational Technology for Effective Health Care: Immediate Steps and Strategic Directions.” National Academies Press, 2009. (PDF)

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

May, Robert M. “Uses and Abuses of Mathematics in Biology.” Science 303, no. 5659 (2004).

Wolberg, William H. Breast Cancer Wisconsin (Original) Data Set: http://archive.ics.uci.edu/ml/datasets/Breast+Cancer+Wisconsin+(Original) 
This data set about patients with breast cancer is available from the UCI machine learning data repository. The repository is a very valuable resource of real data that have been contributed for public access and use, and in the case of medical data have been sufficiently de-identified that privacy considerations do not prevent its broad dissemination. As a result, these data have been used often to help develop or test new modeling techniques.

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