Dimitris Papamichail Assistant Professor Department of Computer Science University of Miami P.O. Box 248154 Coral Gables, FL 33124-4245  USA Tel: (+1) 305-284-4189 Fax: (+1) 305-284-2264 E-mail: dimitris AT cs DOT miami DOT edu

Vita (pdf)    Teaching     Publications    Software    Pizza_Seminars

Education

Work Experience

Teaching

Office hours (Spring 2013)

Recent Publications (2005-present)

Publications in Peer-Reviewed Journals

• Designed reduction of Streptococcus pneumoniae pathogenicity via synthetic changes in virulence factor codon-pair bias (with J. R. Coleman, M. Yano, M. d. Garcia-Suarez and L. Pirofski), Journal of Infectious Diseases, 1;203(9):1264-73, May 2011.

• Live Attenuated Influenza Vaccines by Computer-Aided Rational Design (with S. Mueller, J. R. Coleman, C. B. Ward, A. Nimnual, B. Futcher, S. Skiena and E. Wimmer), Nature Biotechnology, 28:7, 723-726, 13 June 2010.

• In the news: Calaway, E. Weekened flu virus proves ideal vaccine, New Scientist, June 22, 2010.

• Call admission control algorithm for pre-stored VBR video streams (with C. Tryfonas, A. Mehler and S. Skiena), Journal of Multimedia, Vol 4, No 4 (2009), 169-181, Aug 2009.

• Improved algorithms for approximate string matching (with G. Papamichail), BMC Bioinformatics , Vol. 10 (Suppl. 1):S10, January 2009.

• Virus attenuation by genome-scale changes in codon-pair bias (with J. R. Coleman, S. Skiena, B. Futcher, E. Wimmer and S. Mueller), Science, Vol. 320, 1784-1787, 27 June 2008.

• Featured in the News of the Week: VIROLOGY: 'Biased' Viruses Suggest New Vaccine Strategy for Polio and Other Diseases, Science, Vol. 320, 1709, 27 June 2008.
• Featured in Nature Reviews: Silent mutations cause a stir, Nature Reviews Microbiology 6, 574-575, August 2008 
• Also featured in NewsWise: Team Designs customized 'Wimpy' Polioviruses -- A New Path to Vaccines? and picked up by ScienceDaily, ScienceCentric and others.
• Covered by Reuters Top News: Fake virus could make safe New Vaccines and picked up by Scientific American, Yahoo News, AOL News, News Daily, National Post, ABC News, MSNBC, Comcast, Impact Lab, and many other newscasters around the globe.
• Featured in ScienceNews: Viruses rewritten

• Towards a Taxonomical Consensus: Diversity and Richness Inference from Large Scale rDNA Analysis (with C. C. Lesaulnier, S. Skiena, S. McCorkle, B. Ollivier, S. Taghavi and D. van der Lelie), submitted.

• Elevated CO2 Affects Soil Microbial Diversity Associated with Trembling Aspen (with C. C. Lesaulnier, S. McCorkle, B. Ollivier, S. Skiena, S. Taghavi, D. Zak and D. van der Lelie), Environmental Microbiology, Vol. 10 (4), 926-941, April 2008.

• The k-means range algorithm for personalized data clustering in e-Commerce (with G. Papamichail). European Journal of Operational Research, Vol. 177 (3), 1400-1408, March 2007

• Reduction of the rate of poliovirus protein synthesis through large scale codon deoptimization causes virus attenuation of viral virulence (with S. Mueller, J.R. Coleman, S. Skiena and E. Wimmer), Journal of Virology, October 2006, p. 9687-9696, Vol. 80, No. 19

• In the news: Aldhous, P. 'Alien code' leads to faster vaccines, New Scientist, June 3, 2006

• Two proteins for the price of one: The design of maximally compressed coding sequences (with B. Wang, S. Mueller and S. Skiena), Lecture Notes in Computer Science 2006, Vol. 3892, pp. 387-398

• Also in Natural Computing, Vol. 6 (4), 359-370, December 2007

• Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens (with N. Delihas), Biology Direct 2006, 1:12

Publications in Peer-Reviewed Conferences & Workshops with Proceedings

• Rational Design of Orthogonal Libraries of Protein Coding Genes (with D. Ryan), ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2012, Orlando, Florida, October 7-10, 2012.

• Gene Variant Library Design for High-Throughput Experimentation (with D. Ryan), Fourth International Workshop on Bio-Design Automation (IWBDA 2012), San Francisco, June 3-4, 2012.
  

• Incorporating miRNA target sites in protein-coding RNA (with G. Papamichail), Workshop for Bioinformatics for MicroRNA and Disease, IEEE International Conference on Bioinformatic & Biomedicine (BIBM 2010), Hong Kong, December 18-21, 2010.

• Improved Algorithms for Approximate String Matching (with G. Papamichail), Seventh Asian Pacific Bioinformatics Conference (APBC) 2009, Beijing, China, 13-16 January 2009.

• Two proteins for the price of one: The design of maximally compressed coding sequences (with B. Wang, S. Mueller and S. Skiena), 11th International Meeting on DNA Computing (DNA11) 2005.

• Bacterial population assay via k-mer analysis (with D. van der Lelie, S. R. McCorkle and S. Skiena), Third Asian Pacific Bioinformatics Conference (APBC) 2005: 299-308

• Synthetic Biology: Synthesis and Modification of a Chemical Called Poliovirus (with S. Mueller, J. Coleman, J. Cello, A. Paul, S. Skiena and E. Wimmer), Future Trends in Microelectronics: Up the Nanocreek, Wiley Interscience, 2007.

Publications in Conferences and Workshops without Proceedings

• Genomic Coding Sequence Characterization for Heterologous Host Expression (with G. Bonilla), 9th Asian-Pasific Bioinformatics Conference (APC 2011), Seoul, South Korea, December 11-14, 2011.

• Design and Synthesis of Minimal and Persistent Protein Complexes (with V. Patsalo, S. Skiena and D. Green), Chemistry Research Day 2007, SUNY at Stony Brook

• Computational Limitations Associated with Large DNA Datasets for Comparative Community Profiling (with C. Lesaulnier, S. McCorkle, S. Skiena, B. Ollivier and D. van der Lelie), Computational Biology Workshop, SUNYSB 2006.

• Population Dynamics in the Rhizosphere: How Elevated CO₂ Transforms Microbial Community Composition (with C. Lesaulnier, S. McCorkle, D. Zak, B. Ollivier, S. Skiena, S. Taghavi and D. van der Lelie),  American Society for Microbiology (ASM) 106th General Meeting 2006

• N-158 Phylogenetic Identification of the Rhizosphere of Poplar: Effects of Elevated CO₂ on Microbial Community Composition (with C. C. Lesaulnier, S. McCorkle, B. Ollivier, S. Taghavi, S. Skiena and D. van der Lelie), American Society for Microbiology (ASM) 105th General Meeting 2005

Software

• CoSeChar: Coding Sequence Characterization
• Ribosomal RNA sequence classifier (work in progress)
• SeEd - Sequence Editor (work in progress)
• String edit distance algorithm implementations

Extracurricular Activities

• Member of the executive director board of the Archimedean Academy.

• For the period 2005-2007 I have served as the president of the Graduate Table Tennis club at the University of Stony Brook. In Fall 2006 I organized the 1st SUNY at Stony Brook campus wide table tennis tournament, the finalists of which made up the teams which competed on the 12th of November against several other universities/colleges in the New York City division. I secured funding for both the enrollment to NCTTA and our tournament trips. I was the intramural singles table tennis champion at the University of Miami in the academic year 2007-08. I was also the doubles winner (with Yuki Kasamo) at the FIU Intercollegiate tournament in Fall 2007, the runner-up of the faculty singles at the Barry University Intercollegiate tournament in Spring 2008 and won 1st place in the faculty singles and the team event at the same tournament in Spring 2009.

• Studied the classical guitar since the age of 9. Acquired the classical guitar degree in Greece on January 1996. Performed in several concerts, including three in Stony Brook, for the Adult Chamber Music Workshop, accompanying flute, soprano or combination.

Name in Greek: Δημήτρης Παπαμιχαήλ

Erdös number: 3 (Paul Erdös -> Mark K. Goldberg -> Steven S. Skiena -> me!)

Last updated: January 13, 2013