Biomedical Informatics for Cancer Research

Section 1. Concepts, Issues, and Approaches

1. Biomedical Informatics for Cancer Research: Introduction
Michael F. Ochs, John T. Casagrande, Ramana V. Davuluri

2. Clinical Research Systems and Integration with Medical Systems
Joyce C. Niland, Layla Rouse

3. Data Management, Databases, and Warehousing
Waqas Amin, Hyunseok Peter Kang, Michael J. Becich

4. Middleware Architecture Approaches for Collaborative Cancer Research
Tahsin Kurc, Ashish Sharma, Scott Oster, Tony Pan, Shannon Hastings, Stephen Langella, David Ervin, Justin Permar, Daniel Brat, T. J. Fitzgerald, James Purdy, Walter Bosch, Joel Saltz

5. Federated Authentication
Frank J. Manion, William Weems, James McNamee

6. Genomics Data Analysis Pipelines
Michael F. Ochs

7. Mathematical Modeling in Cancer
Robert A. Gatenby

8. Reproducible Research Concepts and Tools for Cancer Bioinformatics
Vincent J. Carey, Victoria Stodden

9. The Cancer Biomedical Informatics Grid (caBIG‚): An Evolving Community for Cancer Research
J. Robert Beck

Section 2. Tools and Applications

10. The caBIG‚ Clinical Trials Suite
John Speakman

11. The CAISIS Research Data System
Paul Fearn, Frank Sculli

12. A Common Application Framework that is Extensible: CAF-É
Richard Evans, Mark DeTomaso, Reed Comire, Vaibhav Bora, Jeet Poonater, Aarti Vaishnav, Scott Catherall, John T. Casagrande

13. Shared Resource Management
Matt Stine, Vicki Beal, Nilesh Dosooye, Yingliang Du, Rama Gundapaneni, Andrew Pappas, Srinivas Raghavan, Sundeep Shakya, Roshan Shrestha, Momodou Sanyang, Clayton Naeve

14. The caBIG® Life Sciences Distribution
Juli Klemm, Anand Basu, Ian Fore, Aris Floratos, George Komatsoulis

15. MeV: MultiExperiment Viewer
Eleanor Howe, Kristina Holton, Sarita Nair, Daniel Schlauch, Raktim Sinha, John Quackenbush

16. Authentication and Authorization in Cancer Research Systems
Stephen Langella, Shannon Hastings, Scott Oster, Philip Payne, Frank Siebenlist

17. Caching and Visualizing Statistical Analyses
Roger D. Peng, Duncan Temple Lang

18. Familial Cancer Risk Assessment Using BayesMendel
Amanda Blackford, Giovanni Parmigiani

19. Interpreting and Comparing Clustering Experiments Through Graph Visualization and Ontology Statistical Enrichment with the ClutrFree Package
Ghislain Bidaut

20. Enhanced Dynamic Documents for Reproducible Research
Deborah Nolan, Roger D. Peng, Duncan Temple Lang

Keywords: Medicine & Public Health, Health Informatics, Popular Science, general, Cancer Research, Molecular Medicine, Oncology, Bioinformatics