Dimitris Papamichail Associate Professor Department of Computer Science The College of New Jersey P.O. Box 7718 Ewing, NJ 08628-0718 USA Tel: (+1) 609-771-2268 Fax: (+1) 609-637-5190 E-mail: papamicd AT tcnj DOT edu

Teaching    Office hours   Education   Publications    Software    C.V.

Teaching

Office hours

Education

Selected Publications

• Live Phylogeny with Polytomies: Finding the Most Compact Parsimonious Trees
  
• (with A. Huang, E. Kennedy, , J.-L. Ott, A. Miller, G. Papamichail), 14th Asian Pacific Bioinformatics Conference (APBC 2017), Shenzhen, China, January 14-16, 2017.

• Codon Context Optimization in Synthetic Gene Design
• (with H. Liu, V. Machado, N. Gould, J. R. Coleman, G. Papamichail), IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. PP, no. 99, pp. 1, March 23, 2016.
  

• Computational Tools and Algorithms for Designing Customized Synthetic Genes
  
• (with N. Gould and O. Hendy), Frontiers in Bioengineering and Biotechnology, Vol. 2, October 6, 2014.

• Rational Design of Orthogonal Libraries of Protein Coding Genes
  
• (with D. Ryan), ACS Synthetic Biology, 2 (5), pp 237-244, February 27, 2013.

• 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.

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

• 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.

• 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.

• 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

• Two proteins for the price of one: The design of maximally compressed coding sequences
  
• (with B. Wang, S. Mueller and S. Skiena), Natural Computing, Vol. 6 (4), 359-370, December 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

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

• 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

Software

• Level Ancestor algorithm implementations (to appear)

• Degenerate Codon calculator
  

• Codon Context Analysis Tool (CCTool) (Under Repair)
  

• CoSeChar: Coding Sequence Characterization

• String edit distance algorithm implementations

• TCHISLA solver by Luke Kurlandski

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