Christos Kozanitis

PhD Candidate

University of California San Diego

Computer Science and Engineering

email: <my_user_name> at cs <dot> ucsd <dot> edu

Education

2006-current: PhD student in Computer Science and Engineering at UCSD

Thesis Advisor: George Varghese
Thesis CoAdvisor: Vineet Bafna

2009: MS from Computer Science and Engineering at UCSD
2006: Diploma (5 year degree) from the ECE Department of the Technical University of Crete, Greece

Thesis Advisor: Apostolos Dollas

Work Experience

2006-present: Graduate Student Researcher
summer 2009: Summer intern at Illumina, Bioinformatics Department

manager: Semyon Kruglyak
collaborator: Chris Saunders

summer 2007: Summer intern at Cisco, Research Center Department

manager: Flavio Bonomi
collaborator: Sushil Singh

Interests

Computational Biology
Genomics
Internet Algorithmics

Publications

Using Genome Query Language to Uncover Genetic Variation C. Kozanitis, A. Heiberg, G. Varghese, V. Bafna Bioinformatics, June 2013 supplemental source code
Abstractions for Genomics V. Bafna, A. Deutsch, A. Heiberg, C. Kozanitis, L. Ohno-Machado, G. Varghese Communications of the ACM, January 2013 video
Compressing Genomic Sequence Fragments Using SLIMGENE C. Kozanitis, C. Saunders, S. Kruglyak, V. Bafna, G. Varghese, RECOMB 2010

Also in the Journal of Computational Biology Vol 18, Issue 3 draft

Leaping multiple headers in a single bound: Wire-Speed Parsing Using the Kangaroo System C. Kozanitis, J. Huber, S. Singh, G. Varghese, Infocom 2010

Older Publications

Rapid Prototyping of a System-on-a-Chip for the BLAST Algorithm Implementation, E. Sotiriades, C. Kozanitis, G. Chrysos, A. Dollas, RSP 2006
FPGA Based Architecture for DNA Sequence Comparison and Database Search, E. Sotiriades, C. Kozanitis, A. Dollas, RAW 2006
Some Initial Results on Hardware BLAST Acceleration with a Reconfigurable Architecture, E. Sotiriades, C. Kozanitis, A. Dollas, HiCOMB 2006