Computer Science Design
Resume:
Curriculum Vitae
Dimitris Papamichail
Assistant Professor
Department of Computer Science
University of Miami
P.O. Box 248154
Coral Gables, FL 33124-4245, USA
Phone (office): 305-***-****
e-mail: ********@**.*****.***
webpage: www.cs.miami.edu/~dimitris
RESEARCH INTERESTS
Computational biology, algorithms and data structures.
EDUCATION
Ph.D. Computer Science, SUNY at Stony Brook, USA, 8/02-8/07
M.S. Computer Science, University of Arizona, USA, 8/96-5/98
B.E. Computer Engineering and Informatics, University of Patras, Greece, 9/91-6/96
WORK EXPERIENCE
Assistant Professor, Department of Computer Science, University of Miami, 8/07 - date
Research Assistant, Brookhaven National Laboratory, Upton, USA, 10/04 - 8/07
Research Assistant, Computer Science department, SUNY at Stony Brook, Stony Brook,
USA, 9/03 - 8/07
Teaching Assistant, Computer Science department, SUNY at Stony Brook, Stony Brook,
USA, 8/02 - 7/03
Computer Programmer, Division of Research and Informatics, Greek Army, Greece, 9/00 -
3/02
Site Engineer, Modular Mining Systems Inc., Tucson, Arizona, USA, 8/98 - 4/00
Teaching assistant, Computer Science department, University of Arizona, Arizona, USA, 8/97
- 5/98
Programmer, Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA,
1/97 - 6/97
Programmer, National Electric Company of Greece, Athens, Greece, 6/94 - 8/94
Systems Operator, Computer Institute of Technology, Patras, Greece, 6/92 - 9/93
AWARDS/DISTINCTIONS
University of Miami Faculty Learning Community (FLC) Fellow, 2010.
Best paper award, Graduate Research Conference 2004, Computer Science Dept. SUNY at
Stony Brook.
State fellowship, Department of Computer Science, Stony Brook University, 2002-03.
Academic merit tuition scholarship, Department of Computer Science, University of Arizona,
1996-97.
PUBLICATIONS IN PEER-REVIEWED JOURNALS
1. D. Ryan and D. Papamichail, Gene Variant Library Design for High-Throughput
Experimentation, submitted.
2. J. R. Coleman, D. Papamichail, M. Yano, M. d. Garcia-Suarez, L. Pirofski, Designed
reduction of Streptococcus pneumoniae pathogenicity via synthetic changes in virulence
factor codon-pair bias, Journal of Infectious Diseases, 1;203(9):1264-73, May 2011.
3. S. Mueller, J. R. Coleman, D. Papamichail, B. Futcher, S. Skiena and E. Wimmer, Live
Attenuated Influenza Vaccines by Computer-Aided Rational Design, Nature
Biotechnology, Vol. 28, pp. 723-726, 13 June 2010.
4. C. Tryfonas, D. Papamichail, A. Mehler and S. Skiena, Call admission control algorithm
for pre-stored VBR video streams, Journal of Multimedia, Vol. 4 (4), pp. 169-181, August
2009.
5. D. Papamichail and G. Papamichail, Improved algorithms for approximate string
matching, BMC Bioinformatics, Vol. 10 (Suppl. 1):S10, January 2009.
6. J. R. Coleman, D. Papamichail, S. Skiena, B. Futcher, E. Wimmer and S. Mueller, Virus
attenuation by genome-scale changes in codon-pair bias: a novel method for developing
viral vaccines, Science, Vol. 320, no. 5884, pp. 1784 - 1787, 27 June 2008.
Featured in News of the Week: VIROLOGY: 'Biased' Viruses Suggest New
o
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
o
Microbiology 6, 574-575, August 2008
o Covered by Reuters: 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 NewsWise: Team Designs customized 'Wimpy' Polioviruses A
o
New Path to Vaccines? and picked up by ScienceDaily, ScienceCentric and
others.
Featured in ScienceNews: Viruses rewritten.
o
7. C. C. Lesaulnier, D. Papamichail, S. McCorkle, S. Skiena, B. Ollivier, S. Taghavi, D. Zak and
D. Van Der Lelie, Elevated CO2 Affects Soil Microbial Diversity Associated with
Trembling Aspen, Environmental Microbiology, Vol. 10 (4), 926-941, April 2008.
8. B. Wang, D. Papamichail, S. Mueller, and S. Skiena, Two Proteins for the Price of One:
The Design of Maximally Compressed Coding Sequences, Natural Computing, Vol. 6 (4),
359-370, December 2007.
9. G. Papamichail and D. Papamichail, The k-means range algorithm for personalized data
clustering in e-Commerce, European Journal of Operational Research, Vol. 177 (3),
pp.1400-1408, March 2007
10. S. Mueller, D. Papamichail, J.R. Coleman, S. Skiena and E. Wimmer, Reduction of the rate
of poliovirus protein synthesis through large scale codon deoptimization causes virus
attenuation of viral virulence, Journal of Virology, Vol. 80, No. 19, pp. 9687-9696, October
2006.
In the press: Aldhous, P. 'Alien code' leads to faster vaccines, New Scientist,
o
June 3, 2006
11. D. Papamichail and N. Delihas, Outer membrane protein genes and their small non-
coding RNA regulator genes in Photorhabdus luminescens, Biology Direct 2006, 1:12
12. G. Papamichail and D. Papamichail, Personalized Trust Management in Decision Making:
A dynamic clustering approach, Journal of Computing and Information Technology, Vol 12
(1), 47-53, 2004.
13. G. Papamichail and D. Papamichail, Towards using computational methods for real-time
negotiations in electronic commerce. European Journal of Operational Research, Vol 145
(2), pp. 3-9, March, 2003.
PUBLICATIONS IN BOOKS
14. 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: The Nano, the Giga, the Ultra, and the Bio, Wiley Interscience, 2007.
PUBLICATIONS IN PEER-REVIEWED CONFERENCES AND WORKSHOPS
15. D. Papamichail and G. Papamichail, The Level Ancestor Problem in Practice, submitted.
16. D. Ryan and D. Papamichail, Rational Design of Orthogonal Libraries of Protein Coding
Genes, to appear in the ACM Conference on Bioinformatics, Computational Biology and
Biomedicine 2012, Orlando, Florida, October 7-10, 2012.
17. D. Ryan and D. Papamichail, Gene Variant Library Design for High-Throughput
Experimentation, Fourth International Workshop on Bio-Design Automation (IWBDA
2012), San Francisco, June 3-4, 2012.
18. D. Papamichail, G. Papamichail, Incorporating miRNA target sites in protein-coding
RNA, IEEE International Conference on Bioinformatics & Biomedicine Workshops (BIBM
2010), Hong Kong, December 18-21, 2010.
19. D. Papamichail, Design Tools and Algorithms for Synthetic Biology, 2010 CMOS
Emerging Technologies Workshop, Whistler, BC, Canada, May 19-21, 2010.
20. D. Papamichail and S. Skiena, Design Tools for Synthetic Virology, First International
Workshop on Bio-Design Automation (IWBDA 2009), San Francisco, June 27, 2009.
21. D. Papamichail, G. Papamichail, Improved Algorithms for Approximate String Matching,
7th Asian-Pasific Bionformatics Conference (APBC 2009), Beijing, China, 13-16 January
2009.
22. S. Mueller, J. R. Coleman, D. Papamichail, S. Skiena, B. Futcher and E. Wimmer, Whole
Viral Genome Synthesis in Synthetic Biology, 4th International Meeting on Synthetic
Biology (SB 4.0), Hong Kong, October 10-12, 2008.
23. D. Papamichail, S. McCorkle, D. van der Lelie, and S. Skiena, Bacterial Population Assay
via k-mer Analysis. Third Asia-Pacific Bioinformatics Conference (APBC 2005), Singapore,
January 17-21, 2005. Series on Advances in Bioinformatics and Computational Biology 1
(2005) 299-308.
24. B. Wang, D. Papamichail, S. Mueller, and S. Skiena, Two Proteins for the Price of One:
The Design of Maximally Compressed Coding Sequences, 11th International Meeting on
DNA Computing (DNA11), June 6-9, 2005. Lecture Notes in Computer Science 2006, Vol.
3892, pp. 387-398.
25. G. Papamichail and D. Papamichail, Real-Time Concept Creation in distributed e-learning
systems. 3rd IASTED Conference on Web-Based Education, Innsbruck, Austria, 16-18
February, 2004.
26. G. Papamichail and D. Papamichail, Supporting small groups in distributed cooperative
reasoning tasks. Proceedings of the European Conference on Intelligent Management
Systems in Operations, Salford, England, March 25-27, 1997.
27. G. Papamichail and D. Papamichail, SOCRATES: A methodology for translating group
decision making needs into groupware products. International Joint Conference of the
European Oprational Research Society and the INFORMS EURO XV INFORMS XXXIV,
Barcelona, July 14-17, 1997.
28. G. Papamichail and D. Papamichail, Intelligent Facilitation in Small Group Decision
making: Experience from the lab. International Informs Conference managing Services in
the next millennium, San Diego, USA, May 4-7, 1997.
29. G. Papamichail and D. Papamichail, Distributed group decision support: An experiment
with small groups carrying out Business Process Reengineering tasks. 7th Mini Euro
Conference: Bruges, Belgium, March 24-27, 1997.
30. G. Papamichail and D. Papamichail, Knowledge effects of the impact of mediated group
memory on Group Decision Making. Euroconference on Management Information Systems,
Porto, Portugal, September, 1996.
31. G. Papamichail and D. Papamichail, Application of the cross rectangle intersection
method in negotiation decision making. Proceedings of the European-Hellenic Conference
on Mathematics and Informatics, Athens University of Economics and Business, 630-635,
September 1996.
32. G. Papamichail and D. Papamichail, An experimental investigation of the impact of
mediated group memory on collaborative Small Group Decision Making. Proceedings of
the 7th meeting of the European Working Group on Decision Support Systems, 89-102, Ispra,
Italy, 6-8 June, 1996.
POSTERS
33. G. Bonilla, D. Papamichail, Genomic Coding Sequence Characterization for Heterologous
Host Expression, 9th Asian-Pasific Bioinformatics Conference (APBC 2011), Seoul, South
Korea, January 11-14, 2011.
34. V. Patsalo, D. Papamichail, S. Skiena, and D. Green, Designing the World's Shortest Gene.
Synthetic Biology 4.0, Hong Kong, October 10-12, 2008.
35. V. Patsalo, D. Papamichail, S. Skiena and D. Green, Design and Synthesis of Minimal and
Persistent Protein Complexes, Chemistry Research Day 2007, SUNY at Stony Brook.
36. D. Papamichail, C. C. Lesaulnier, S. McCorkle, S. Skiena, B. Ollivier and D. van der Lelie,
Computational Limitations Associated with Large DNA Datasets for Comparative
Community Profiling, Computational Biology Workshop 2006, SUNY at Stony Brook.
37. C. C. Lesaulnier, D. Papamichail, S. McCorkle, D. Zak, B. Ollivier, S. Skiena, S. Taghavi and
D. van der Lelie, Population Dynamics in the Rhizosphere: How Elevated CO2
Transforms Microbial Community Composition, American Society for Microbiology
(ASM) 106th General Meeting 2006.
38. C. C. Lesaulnier, D. Papamichail, S. McCorkle, B. Ollivier, S. Taghavi, S. Skiena and D. van
der Lelie, Phylogenetic Identification of the Rhizosphere of Poplar: Effects of Elevated
CO2 on Microbial Community Composition, American Society for Microbiology (ASM)
105th General Meeting 2005.
BOOK REVIEWS
39. D. Papamichail, Review of Introduction to Computational Proteomics by Golan Yona,
1st ed., 767p. ACM SIGACT News, to appear.
40. D. Papamichail, Review of Design Theory by C. C. Lindner and C. A. Rodger, 2nd ed.,
272p. ACM SIGACT News 43(1): 35-37, March 2012.
41. D. Papamichail, Review of Applied Combinatorics by Fred S. Roberts and Barry
Tesman, 2nd ed., 848p. ACM SIGACT News 42(3): 29-32, 3 September 2011.
THESIS
42. Analysis and Design of Genomic Sequences (Doctoral Dissertation), advisor: Steven S.
Skiena, Department of Computer Science, Stony Brook University, Stony Brook, NY, August
2007
PROFESSIONAL ACTIVITIES
NSF Panel reviewer, 2012.
Editorial board member of the Computational Biology Journal.
Book reviewer for the Book Review Column of the ACM SIGACT News.
Book reviewer for Jones and Bartlett publishing, for preparation of next edition:
o Review of Essentials of Software Engineering by Frank Tsui and Orlando Karam,
2nd Edition, 2009, 416p.
Book reviewer for Choice Current Reviews for Academic Libraries, in the algorithms,
computational biology, and software engineering areas:
o D. Papamichail, review of Computer science: the hardware, software and heart
of it, ed. by Edward K. Blum and Alfred V. Aho, Springer, 2011, 468p.
o D. Papamichail, review of. Data clustering in C++: an object-oriented approach
by Gan, Guojun, CRC Press, 2011, 520p.
o D. Papamichail, review of Design of modern heuristics: principles and
applications by Rothlauf, Franz, Springer, 2011. 267p.
o D. Papamichail, review of Software modeling and design: UML, use cases,
patterns, and software architectures by Gomaa, Hassan, Cambridge, 2011, 550p.
o D. Papamichail, review of Elements of scientific computing by Aslak Tveito et al.
Springer, 2010, 459p.
o D. Papamichail, review of Natural computing: DNA, quantum bits, and the
future of smart machines by Dennis Shasha and Cathy Lazere, W.W. Norton, 2010,
268p.
o D. Papamichail, review of Designing and engineering time: the psychology of
time perception in software by Seow, Steven C., Addison-Wesley, 2008, 198p.
o D. Papamichail, review of Software testing and quality assurance: theory and
practice by Kshirasagar Naik and Priyadarshi Tripathy, Wiley, 2008, 616p.
Article referee for the journals:
o Bioinformatics
o In Silico Biology
o Bioinformatics and Biological Insight
o INFORMS Journal on Computing
o International Journal of Computational Biology and Drug Design
o Lecture Notes in Social Networks
o International Journal of Foundations of Computer Science
Member of bioinformatics.org.
TALKS AND PRESENTATIONS
Gene Variant Library Design for High-Throughput Experimentation, Fourth International
Workshop on Bio-Design Automation (IWBDA 2012), San Francisco, June 3, 2012.
Incorporating miRNA target sites in protein-coding RNA, IEEE International Conference
on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong, December 18-21, 2010
GPU Computing Architecture, Algorithmic Techniques and Programming, Computer
Science Department Pizza Seminar, Coral Gables, FL, US, November 10, 2010 (Joint seminar
with Scott Baker, Division of Marine Geology and Geophysics, University of Miami).
Design Tools and Algorithms for Synthetic Biology, 2010 CMOS Emerging Technologies
Workshop, Whistler, BC, Canada, May 19-21, 2010.
Design Tools for Synthetic Virology, First International Workshop on Bio-Design
Automation (IWBDA 2009), San Francisco, USA, June 27, 2009.
Analysis and Design of Genomic Sequences, Computer Science Department, Athens
University of Economics and Business, Athens, Greece, July 2, 2009.
Improved Algorithms for Approximate String Matching, 7th Asian-Pacific Bioinformatics
Conference (APBC 2009), Beijing, China, January 15, 2009.
Networks in Genomic Sequence Design, UM Symposium on Networks, University of
Miami, Miami, USA, October 11, 2008.
Design and Classification of Genetic Sequences, Biomedical Research Foundation of the
Academy of Athens, Athens, Greece, June 20, 2008.
Opportunities at the borders of Biology, Computer Science and Mathematics, Computer
Science Department, University of Miami, Miami, USA, November 28, 2007.
Analysis and Design of Genomic Sequences, Computer Science Department, University of
Texas at San Antonio, San Antonio, Texas, USA, April 3, 2007.
Analysis and Design of Genomic Sequences, Ohio St. Jude s Medical Center, Columbus,
Ohio, USA, March 26, 2007.
Analysis and Design of Genomic Sequences, Computer Science Department, University of
Miami, Miami, Florida, USA, March 19, 2007.
Analysis and Design of Genomic Sequences, College of Information Science and
Technology, Peter Kiewit Institute, Omaha, Nebraska, USA, January 31, 2007.
Bacterial Population Assay via k-mer Analysis, Asia-Pacific Bioinformatics Conference
2005, Singapore, January 20, 2005.
Short sequence distribution statistics for bacterial identification in homogeneous and mixed
samples, Graduate Research Conference 2004, Computer Science Department, SUNY at
Stony Brook, May 7, 2004.
FUNDING
PI in the grant CAREER: Algorithms for Synthetic Gene Design, NSF, AF-CCF, pending.
Co-PI in the grant Online Short Courses on Bioinformatics Skills for Biologists, Short
Courses on Mathematical, Statistical, and Computational Tools for Studying Biological
Systems, (PIs: H. Kocak, E. Martin), NIH, pending.
Faculty participant in the grant IGERT: A systems biology approach to elucidate the
mechanisms that generate and maintain tropical diversity, (PI: J.A.C. Uy), NSF, pending.
Faculty Learning Community (FLC) Fellow, Effective use of digital technology and
information literacy concepts in the Bioinformatics Tools course, University of Miami, 2010,
$12,000.
PI in the grant Genetic Sequence characterization and clustering using oligonucleotide
distribution classification, General Research Support Awards, University of Miami,
02/06/2008-01/06/2009, $6,009.
Supporting personnel in the grant: Synthetic Viral Genome Design for Rapid Vaccine
Development (PI: E. Wimmer), NIH, 4/1/08-3/31/13, $2,867,678.
PATENTS
Attenuated influenza viruses and vaccines (with Wimmer, E., Skiena S., Mueller S.,
Futcher B. Coleman R., and Cello J.), PCT/US2010/052188, pending.
Attenuated viruses useful for vaccines (with Wimmer E., Skiena S., Mueller S., Futcher B.,
Coleman R., and Cello J.), US 2010/0209454 A1.
TEACHING EXPERIENCE
Data Structures and Algorithms Analysis, Fall 2012.
Computer Programming I (Java), Fall 2011.
Bioinformatics Tools, Fall 2010.
Computer Science Project Planning and Implementation, Fall 2010/11/12.
Computing for Scientists, Spring/Fall 2009/10/11/12.
Bioinformatics Algorithms, Fall 2008/09, Spring 2011.
Software Engineering, Spring 2008/09/10/11/12.
Bioinformatics, Fall 2007.
THESIS AND DISSERTATION ADVISING/SUPERVISION
Ph.D. advisor of Faisal Sikder, Fall 2011-date.
Ph.D. advisor of Gracia Bonilla, Spring 2011.
Dissertation committee member of Wen Ji.
Dissertation committee member of Zhouyi Xu.
Dissertation committee member of Indika Kuruppu Appuhamilage.
UNIVERSITY COMMITTEE AND ADMINISTRATIVE RESPONSIBILITIES
University of Miami Singer and Stamps scholarship interviewer, 2012.
Member of the Mixed Media Education Committee, Spring 2011-date.
Member of the Parking Appeals Committee, Fall 2008-11.
Member of the Admissions and Academic Standards Committee, Fall 2008-11.
Advisor of the University of Miami Table Tennis club, Spring 2008-date.
Advisor of the University of Miami Anime club, Fall 2010-date.
UM Citizens Board Research & Creativity Forum (RCF) judge, 2008/09/10/11/12.
Judge for The Miami Dade STEM Expo s South Florida Regional Science and Engineering
Fair, January 22, 2011.
Organizer of Department of the weekly Computer Science seminars, Spring 2011-date.
EXTRACURRICULAR ACTIVITIES
Member of the Archimedean Academy Charter Schools Board of Directors since August
2009.
Classical guitar diploma, 1996: Studied classical guitar since the age of 9. Acquired the
classical guitar degree in Greece on January 1996. Performed in numerous concerts in Greece
and the US.
President of the Stony Brook University Table Tennis club, 2004-2007. In Fall 2006 I
organized the 1st SUNY at Stony Brook campus wide table tennis tournament, the finalists of
which formed the teams that competed in the NYC division of NCTTA. I secured funding for
both the enrolment to NCTTA and our tournament trips. I was the intramural singles
champion in the University of Miami in 2007, won 1st position in doubles at the FIU
tournament in Fall 2007 and 1st position in faculty singles at the Barry University tournament
in Spring 2009.
REFERENCES
Dr. Eckard Wimmer
Dr. Steven Skiena
Distinguished Professor
Professor
Department of Molecular Genetics and
Department of Computer Science
Microbiology
Stony Brook University
Stony Brook University
Stony Brook, NY 11794-4400, USA
Stony Brook, NY 11794, USA
Phone: 631-***-****
Phone: 631-***-****
Fax: 631-***-****
Fax: 631-***-****
E-mail: ******@**.******.***
E-mail: *******@**.**.******.***
Dr. J. Robert Coleman Dr. Christos Tryfonas
Assistant Professor CTO, Cloud and Big Data Analytics
Department of Biology VMware
SUNY - Farmingdale State College 3401 Hillview Ave
2350 Broadhollow Rd, Palo Alto, CA 94304, USA
Farmingdale, NY 11735-1021 Phone: 650-***-****
Phone: 631-***-**** Fax: 650-***-****
Email: ********@***********.*** Email: *********@******.***
Dr. Sean McCorkle
Bioinformaticist
Biology Department,
463 Brookhaven National Laboratory
Upton, NY 11973-5000, USA
Phone: 631-***-****
Fax: 631-***-****
E-mail: ********@***.***
Contact this candidate