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BIOGRAPHICAL SKETCH Steven Skiena Distinguished Teaching Program Director/Principal Investigator (Last, First, Middle): BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES. NAME POSITION TITLE Steven Skiena Distinguished Teaching Professor eRA COMMONS USER NAME (credential, e.g., agency login) Dept. of Computer Science Stony Brook University EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) University of Virginia, Charlottesville, VA B.S. 05/83 Computer Science University of Illinois at Urbana-Champaign Ph.D 05/88 Computer Science A. Personal Statement I have worked in computational biology / bioinformatics for almost twenty years, since the very start of the genomics revolution. My interests over the years have ranged from genome assembly algorithms, microrarray design and analysis, and meta-genomic sequence analysis. My primary interest lies in sequence design algorithms for synthetic biology. My students and I pioneered the study of algorithms coding for given protein sequencing while optimizing specific criteria such as RNA secondary structure, pattern placement / avoidance, and coding in alternate reading strands. This work forms the foundation of my current collaborations on sequence design for live attenuated vaccines, multiplex sequence design algorithms for large-scale synthesis technologies, and design/synthesis approaches to signal-detection in coding sequences. B. Positions and Honors Positions and Employment 2009-date Distinguished Teaching Professor of Computer Science, Stony Brook University 2008-2009 Visiting Professor of Computer Science, Hong Kong University of Science and Technology 2001-2009 Professor of Computer Science, Stony Brook University Affiliated faculty, Dept. of Biomedical Engineering and Graduate Program in Genetics 1994-2001 Associate Professor of Computer Science, Stony Brook University. 1994-1995 DIMACS visitor, Rutgers University, special year in Computational Biology 1988-1994 Assistant Professor of Computer Science, Stony Brook University Honors Editorial Board, IEEE/ACM Transactions on Computational Biology/Bioinformatics (TCBB), 2003-2006. Fulbright Scholar, Haifa, Israel, 2001-2002. IEEE National Computer Science and Engineering Undergraduate Teaching Award, 2001. President's and Chancellor's Award for Excellence in Teaching, SUNY Stony Brook, 2000. ONR Young Investigator Award, 1993. EDUCOM Higher Education Software Award for Distinguished Mathematics Software, 1991. NSF Research Initiation Award, 1991. First Place, Apple Personal Computer of the Year 2000 Competition, 1988. PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): C. Selected Peer-reviewed Publications (Selected from 124 peer-reviewed publications) Most relevant to the current application 1. S. Mueller, R. Coleman, D. Papamichail, C. Ward, A. Nimnual, B. Futcher, and E. Wimmer. (2010). Live Attenuated Influenza Vaccines by Computer-Aided Rational Design. Nature Biotechnology 20 723-726. 2. V. Sitaraman, P. Hearing, C. Ward, D. Gnatenko, E. Wimmer, S. Mueller, S. Skiena, and W. Bahou. (2011) Computationally-recoded AAV Rep 78 is Efficiently Maintained within an Adenovirus Vector. Proc. National Academy of Sciences (PNAS), 108 14294-14299. 3. J.R. Coleman, D. Papamichail, B. Futcher. S. Skiena, S. Mueller, and E. Wimmer (2008). Virus attenuation by genome-scale changes in codon-pair bias. Science, 320 1784-1787. 4. B. Cohen and S. Skiena. (2003). Natural selection and algorithmic design of mRNA (2003). Journal of Computational Biology 10, 635-652. 5. S. Skiena (2001). Designing Better Phages. Bioinformatics 17, S253-261. Additional recent publications of importance to the field (in chronological order) 1. S. Skiena. (2012) Redesigning Viral Genomes., IEEE Computer (invited paper/cover article), March 2012. 2. Y.-L. Lin, C. Ward, and S. Skiena (2012) Synthetic Sequence Design for Signal Location Search , Proc. 16th International Conf. on Computational Molecular Biology (RECOMB 2012) Barcelona Spain. 3. S. Hossain, N. Azimi, S. Skiena (2009). Crystallizing Short-Read Assemblies Around Seeds. BMC Bioinformatics 10 S15. 4. C. Lesaulnier. D. Papamichail, S. McCorkle, B. Ollivier, S. Skiena, S. Taghavi, D. Zak, and D. van der Lelie (2008). Elevated CO2 Affects Soil Microbial Diversity Associated with Trembling Aspen. Environmental Microbiology 10, 926-941. 5. B. Wang, D. Papamichail, S. Mueller, and S. Skiena. (2007) Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences Natural Computing 6 359-370. 6. S. Skiena (2008), The Algorithm Design Manual, second edition, Springer-Verlag. 7. S. Pyne, B. Futcher, and S. Skiena (2006). Meta-analysis based on control of false discovery rate. Bioinformatics 20, 2516-22. 8. S. Mueller, D. Papamichail, J. Coleman, S. Skiena, and E. Wimmer (2006). Reduction of the rate of poliovirus protein synthesis through large scale codon deoptimization causes virus attenuation of viral virulence by lowering specific infectivity. J. of Virology 80, 9687-96. 9. A. Oliva, A. Rosebrock, F. Ferrezuelo, S. Pyne, S. Skiena, B. Futcher, and J. Leatherwood (2005) The Cell Cycle Regulated Genes of Schizosaccharomyces pombe. PLOS Biology 3 e225. 10. S. Pyne, S. Skiena, and B. Futcher (2005). Copy Correction and concernted evolution in the conservation of yeast genes. Genetics. 170 1501-1513. D. Research Support Ongoing Research Support NSF DBI-1060572 Skiena (PI) 03/1/11-2/28/11 Synthetic Sequence Designs for Real Biology This project seeks to develop improved sequence design algorithms for signal search, embedding patterns in coding sequences, and constructing diverse libraries of sequences. Role: PI NSF III-1017181 Skiena (PI) 07/01/10-08/30/13 Better Sentiment Analysis Through Forecasting This project seeks to develop forecasting-based approaches to evaluating and improving text-based sentiment detection methods. Role: PI PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): NIH 5R01AI07521903 Wimmer (PI) 07/15/08-03/31/13 Synthetic Viral Genome Design for Rapid Vaccine Development This study exploits the power of design algorithms optimizing codon-pair bias to design attenuated viral strains for vaccines in poliovirus and influenza. Role: Co-Investigator Completed Research Support NSF DBI-044815 Skiena (PI) 07/01/05-06/30/09 Sequence Assembly for High-Throughput Technologies The goal of this project was to develop novel sequence assembly algorithms for next-generation, short-read sequencing technologies. Role: PI NSF EIA-035123 Skiena (PI) 01/01/03-9/30/07 Gene Design for Vaccines and Therapeutic Phages The goal of this project was to develop gene design algorithms for novel applications in synthetic biology. Role: PI PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page .
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