Kristopher J. Kosmatka - Curriculum Vitae

5765C Medical Sciences Center

1300 University Ave

Madison, WI 53706-1510

kosmatka@cs.wisc.edu

http://cs.wisc.edu/~kosmatka

517 Troy Drive

Madison, Wisconsin 53704

mobile: 608.338.5110

kjkosmatka@gmail.com

Objective

A full-time position in software engineering

Interests

Distributed Systems, Web Application Platforms, Scalability, Location-based Services, Bioinformatics, Medical Image Processing

Education

University of Wisconsin – Madison

M.S. in Computer Sciences, expected May 2011

Special Student, January 2006 to December 2007

B.S. in Mathematics, May 2001

Graduate GPA 4.0/4.0
Coursework in Operating Systems, Distributed Systems, Databases, Artificial Intelligence, Natural Language Processing, Bioinformatics
Post-baccalaureate coursework including Biochemistry, Genetics, Organic Chemistry - GPA 4.0/4.0
Undergraduate coursework including Programming, Data Structures, Machine Organization, Mathematics - GPA 3.7/4.0

Work Experience

September 2010 –
present
Research Assistant

University of Wisconsin – Madison

Dewey Lab, Prof. Colin Dewey
- Designed a new Hidden Markov Model for alignment of whole genome optical maps
- Analyzed and evaluated performance and accuracy of alignment predictions
- Implemented front end, visualization, and workflow automation tools in C and Python
May 2010 –
September 2010
Software Engineering Intern

Locomatix, Inc. – Madison, WI
- Designed and implemented a RESTful API for a location-based database server platform
- Developed database backend features using C++ and Python
- Built location-aware web applications using latest HTML5 web standards
September 2009 –
May 2010
Research Assistant

University of Wisconsin – Madison

Wisconsin Alzheimer's Disease Research Center – Imaging Core
- Implemented distributed medical image processing and analysis pipeline using Condor
- Built a Ruby on Rails application used to schedule and monitor image processing tasks
- Debugged and upgraded legacy physiological signal processing software in Python
August 2007 –
August 2009
Research Specialist

University of Wisconsin – Madison

Johnson Neuroimaging Lab
- Developed custom software for functional MRI image processing and analysis using Python, Matlab, and R
- Designed novel image analysis methods for a large cross-institutional study later published in Science
- Coordinated management of medical imaging data for a multidisciplinary team of researchers
May 2006 –
August 2007
Student Researcher

University of Wisconsin – Madison

Johnson Neuroimaging Lab
- Automated structural and functional MRI data analysis pipelines using Ruby and Python
- Built several public and internal lab web applications using Ruby on Rails
- Administered lab computing resources, network configurations, authentication services, data backup, and a 15TB RAID file server

Technical Skills

Platforms

Linux, MacOSX, Windows

Languages

C/C++, Java, Python, Ruby, Bash, Matlab, R, SQL, LaTeX

Web

Javascript, jQuery, Ruby on Rails, HTML, CSS

Publications

Journal Articles

[1] R.J. Colman, R.M. Anderson, S.C. Johnson, E.K. Kastman, K.J. Kosmatka, T.M. Beasley, D.B. Allison, C. Cruzen, H.A. Simmons, J.W. Kemnitz, and R. Weindruch. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science 10 July 2009: Vol. 325. no. 5937, pp. 201 - 204 DOI: 10.1126/science.1173635

[2] I.A. Humbert, M.E. Fitzgerald, D.G. McLaren, S.C. Johnson, E. Porcaro, K.J. Kosmatka, J. Hind, and J. Robbins. Neurophysiology of swallowing: effects of age and bolus type. Neuroimage, 44:982–991, Feb 2009. Epub Oct 28. doi:10.1016/j.neuroimage.2008.10.012; PMID 19010424.

[3] D.G. McLaren, K.J. Kosmatka, Kastman E.K., Bendlin B.B., and Johnson S.C. Rhesus macaque brain morphometry: a methodological comparison. Methods, Oct 2009. doi:10.1016/j.ymeth.2009.10.003.

[4] D.G. McLaren, K.J. Kosmatka, T.R. Oakes, C.D. Kroenke, S.G. Kohama, J.A. Matochik, D.K. Ingram, and S.C. Johnson. A population-average MRI-based atlas collection of the rhesus macaque. Neuroimage, 45:52–59, Mar 2009. Epub Nov 14. doi:10.1016/j.neuroimage.2008.10.058.

Conference Posters

[5] E.K. Kastman, B. Bendlin, G. Xu, M. Ries, D.G. McLaren, M. Fitzgerald, B. Jabbar, K.J. Kosmatka, and Johnson S.C. Rate of whole brain volume decline in a cohort of cognitively normal participants with family history of Alzheimer’s Disease: A longitudinal study. International Conference on Alzheimer’s Disease, July 2008.

[6] K.J. Kosmatka, E.K. Kastman, A.A. Willette, E. Canu, D.G. McLaren, and S.C. Johnson. Hand dominance modulates interhemispheric gray matter asymmetry in rhesus macaques. Organization for Human Brain Mapping Annual Meeting, June 2009.

[7] K.J. Kosmatka, D.G. McLaren, C. Kroenke, S. Kohama, J. Matochik, D. Ingram, and S.C. Johnson. Adult and elderly rhesus macaque atlas template for functional and structural imaging. Organization for Human Brain Mapping Annual Meeting, June 2007.

[8] D.G. McLaren, M. Ries, B. Bendlin, E.K. Kastman, K.J. Kosmatka, G. Xu, B. Jabbar, L. Newman, M. Fitzgerald, and S.C. Johnson. Memory formation in middle-aged adults: Dynamics of the BOLD signal across repetitions. International Conference on Alzheimer’s Disease, July 2008.