Richard Craig Pelikan

5260 Centre Avenue #817 Pittsburgh, PA 15232 Home Phone: (412) 681-2265
PERSONAL: Born in Trenton, NJ, USA (1980). EDUCATION: Ph.D. Candidate, Intelligent Systems 2005-Present, University of Pittsburgh, Pittsburgh PA o Currently enrolled in the Ph.D. program with a 4.0 GPA overall. M.S. Computer Science, 2005, University of Pittsburgh, Pittsburgh PA o Completed a Master of Science degree within the department of Computer Science. Graduated with a 3.3 GPA overall. B.S. Computer Science, 2002, University of Pittsburgh, Pittsburgh PA o Completed a Bachelor of Science degree with a major in Computer Science. Graduated summa cum laude with a 3.82 GPA overall, as well as with departmental honors. AWARDS AND HONORS Departmental Honors (Computer Science, 2002) FAS Research Fellowship (Intelligent Systems Program, 2005-2006) NLM Research Training Fellowship (Department of Biomedical Informatics, 2006-2010) A&S Research Fellowship (Intelligent Systems Program, 2010-2011) RESEARCH INTERESTS: Since August 2003, I have been working under the supervision of Dr. Milos Hauskrecht at the University of Pittsburgh. My research interests include statistical modeling in the presence of uncertainty as well as pattern discovery and recognition. BOOK CHAPTERS M. Hauskrecht, R. Pelikan, M. Valko and J. Lyons-Weiler. Feature selection and dimensionality reduction in genomics and proteomics. In W. Dubitzky, M. Granzow, and D. Berrar, editors, Fundamentals of Data Mining in Genomics and Proteomics, pages 149172. Springer, 2007. R. Pelikan, M. Lotze, J. Lyons-Weiler, D. Malehorn and M. Hauskrecht. Serum Proteomic Profiling and Analysis. In Lotze MT, Thomson AW, eds. Measuring Immunity: Basic Biology and Clinical Applications, Elsevier, London, 2004.

Website: http://www.cs.pitt.edu/~pelikan E-mail: pelikan@cs.pitt.edu Office Phone: (412) 624-9182

JOURNAL PUBLICATIONS R. Pelikan and M. Hauskrecht . Efficient peak labeling algorithms for whole-sample mass spectrometry proteomics. IEEE Transactions on Computational Biology and Bioinformatics, 2009 7(1):126-37. R. Pelikan, W.L. Bigbee, D. Malehorn, J. Lyons-Weiler and M. Hauskrecht. Intersession Reproducibility of Mass Spectrometry Profiles and its Effect on Accuracy of Multivariate

Pelikan, Richard C.

Classification Models. Bioinformatics, 2007 23(22):3065-3072. M. Hauskrecht, R. Pelikan, W.L. Bigbee, D. Malehorn, M.T. Lotze, H.J. Zeh, D.C. Whitcomb, and J. Lyons-Weiler. Feature Selection for Classification of SELDI-TOF-MS Proteomic Profiles, Applied Bioinformatics , 4(3), 2005. J. Lyons-Weiler, R. Pelikan, H.J. Zeh III, D.C. Whitcomb, D.E. Malehorn, W.L. Bigbee and M. Hauskrecht. Assessing the Statistical Significance of the Achieved Classification Error of Classifiers Constructed Using Serum Peptide Profiles and a Prescription for Random Resampling Repeated Studies for Massive High-Throughput Genomic and Proteomic Studies, Cancer Informatics,1(1), 2005.

CONFERENCE PUBLICATIONS AND POSTERS R. Pelikan and M. Hauskrecht. Automatic Preprocessing of Mass Spectrometry Protein Profiles. AMIA 2010, Washington, DC, November 15-17, 2010. M. Valko, R. Pelikan and M. Hauskrecht. Learning predictive models for multiple heterogeneous proteomic data sources. In the proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 10-12, 2008. M. Hauskrecht and R. Pelikan. Inter-session reproducibility measures for high-throughput data sources. In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 10-12, 2008. Timo Jahnukainen, David Malehorn, Gaurav Gupta, Mai Sun, James Lyons-Weiler, William Bigbee, Parmjeet Randhawa, Richard Pelikan, Milos Hauskrecht and Abhay Vats. Proteomic Analysis of urine in kidney transplant patients with BKV nepropathy. Submitted to the Clinical and Translational Science Day, University of Pittsburgh, 2006. William L. Bigbee, David E. Malehorn, Talal El-Hefnawy, Milos Hauskrecht, James LyonsWeiler, Richard C. Pelikan, Mai Sun, Rodney J. Landreneau, James D. Luketich, Joel L. Weissfeld, Pierre P. Massion, and Jill M. Siegfried. Intersession Reproducibility and Independent Clinical Cohort Evaluation of Lung Cancer Serum Proteomic Profiling and Classification Using SELDI-TOF-MS. AACR: Advances in Proteomics in Cancer Research, January 2006. William Bigbee, David Malehorn, Anna Lokshin, Talal El-Hefnawy, Milos Hauskrecht, Doug Landsittel, James Lyons-Weiler, Richard Pelikan, Hiran Fernando, Rodney Landreneau, James Luketich, Joel Weissfeld, Jill Siegfried. Serum SELDI-TOF-MS protein expression and Luminex xMAP marker panel profiling for lung cancer detection and classification. AACR: Advances in Proteomics in Cancer Research, Key Biscayne, FL, October 6-10, 2004. James Lyons-Weiler, Milos Hauskrecht, Richard Pelikan, David Malehorn, Doug Landsittel, Bill Bigbee, Herb Zeh, David C. Whitcomb. Permutation Achieved Classification Error (PACE): A Significance Test for Assessing the Statistical Significance of Classifiers for Peptide Profiling via MALDI/SELDI-TOF Mass Spectrometry. The EDRN workshop on the analysis of proteomic spectral data including SELDI/MALDI-TOF-MS applications, Seattle, WA, March 15-17, 2004. M. Hauskrecht, R. Pelikan, and J. Lyons-Weiler. Techniques for Analyzing Proteomic Mass Spectrometry Data. The Early Detection Research Network (EDRN) workshop on the analysis of proteomic spectral data including SELDI/MALDI-TOF-MS applications, , Seattle,

Pelikan, Richard C.

WA, March 15-17, 2004. M.Hauskrecht, R. Pelikan, J.Lyons-Weiler. Comparative Analysis of Statistical Learning Techniques for Classification of Proteomic Profiles. APIII 2003, Pittsburgh, PA.

RESEARCH EXPERIENCE: Proteomic Data Analysis o Currently working with Dr. Milos Hauskrecht in the analysis of proteomic profiles from Time-of-Flight mass spectrometry. Our primary focus is on feature extraction of biomarkers which signal the presence or lack of a condition. Text Classification and Subjectivity Mining o Worked with Dr. Janyce Wiebe in developing models used to extract subjective information from world-news text articles. RELEVANT COURSEWORK: Methodology in Artificial Intelligence, Design and Analysis of Algorithms, Advanced Techniques in Machine Learning, Reasoning Under Uncertainty, Pattern Recognition, Graph Theory, Biostatistics. SKILLS: Programming Languages: C++, Java, MATLAB, Perl Spoken Languages: English, Spanish, German, Japanese Strong familiarity with all common software suites on any operating system.

Pelikan, Richard C.