Mihailo Kaplarevic, Ph.D.

Dr. Mihailo Kaplarevic is a well-rounded individual with broad technical knowledge in project planning and management, data management, and system performance analysis. He has over 10 years of experience in large-scale relational, non-relational, and object-oriented databases; applied algorithms and applications; data mining and analysis; and high performance computing. Dr. Kaplarevic has published scientific articles in pier-reviewed journals in the areas of bioinformatics, cross-platform optimizations, and sequential and parallel computer architectures. Specifically, Dr. Kaplarevic is considered a subject matter expert in large-scale data storage and mining, cloud computing, high-performance cluster computing, and cross platform porting. This expertise has been called on frequently by the National Science Foundation through participation in their biotechnology and information science panels. Dr. Kaplarevic has hands-on expert-level knowledge of a wide range of computational platforms from Windows/Linux servers to high-performance clusters to shared-memory systems.

• Programming languages: C, C++, Java, Php, Perl (BioPerl), Linux scripting
• 10 years of experience on profiling diverse applications, pinpointing performance bottlenecks and making cross-platform optimizations
• 10 years of experience in analyzing, processing and storing large datasets
• 10 years of experience in project planning and management, and system performance analysis
• Expert knowledge of sequential and high-performance parallel computer architecture
• Excellent background and strong problem-solving capability in entity-relational databases, object oriented databases, applied algorithms and applications, and high-performance computing
• Expert knowledge of high performance computing (PVM, MPI, OpenMP, pthread), Linux clusters, shared memory systems, and porting applications to different platforms
• Operating Systems: Windows (admin level), LINUX (admin level), MAC OSX (admin level)
• MySQL, Postgres and ORACLE database design and administration
• Web Platforms: HTML, Dreamweaver, Macromedia Flash, LIMP servers, and dynamic portals
• Extensive experience in technical writing
• Excellent oral and written communication in multiple languages

• Professional Masters in Bioinformatics – Worked to develop the program, curriculum and policy for University of Delaware’s new masters program
• Distributed data security and selective access (protocol development and implementation)
• Optimization In High-Capacity Genomic Data Storage and Retrieval (DB structure and SQL optimization)
• Environmental Genome Informational Utility System (EnGENIUS) – A complete web based metagenome analysis system: http://ocean.dbi.udel.edu (Case study: Metagenome Alvinella Pompejana Dataset)
• UPSTREAMER (Upstream Speculative Promoter Sequence Search Tool and Database)
• GRACEST (Gene Recognition and Comparison Using ESTs)
• Various research projects in compilers and compiler optimizations (available upon request)

Sep. 2001 – May 2006

Research Assistant

University of Delaware

• Research in the area of parallel and high-performance computing
• Teaching appointments

Aug. 2002 – Jan. 2007

Metagenome research group team leader

Computer Architecture and Parallel Systems Laboratory (CAPSL), University of Delaware

University of Belgrade, School of Electrical Engineering

Combined B. Sc. and M.S. in Electrical and Computer Engineering

Thesis: "Object Oriented Database Modeling and Optimization Techniques"

• Frequent grant review panelist at Directorate for Biological Sciences, National Science Foundation
• Peer reviews for accredited journals in the area of parallel computing and bioinformatics (list of journals available upon request)
• Participated in the Graduate Program Planning - Professional Masters In Bioinformatics University of Delaware Faculty Senate

• Hammond, S., Swanberg, J., Kaplarevic, M., and Lee, H.K., Genomic sequencing and analysis of a Chinese Hamster ovary cell line using Illumina sequencing technology, BMC Genomics (Accepted on 01/17/11)
• Kaplarevic, M., Mahaling, G.,Meyers B., Distributed Databases Applications in Next Generation Sequencing (in review)
• Kaplarevic, M., Murray, A.E., Environmental Genome Informational Utility System (EnGENIUS), Journal of Bioinformatics and Computational Biology (Dec. 2008.)
• Mahalingam, G., Mayers, B., and Kaplarevic, M., Application of distributed database methodology in high-throughput large-scale genomic datasets. Bioinformatics (In review)
• Grzymski, J.J., Murray, A.E., Campbell, B.J., Kaplarevic, M.,Gao, G., Lee, C., Daniel, R., Ghadiri, A., Feldman, R., and Cary, S.C., Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proceedings of the National Academy of Science USA (In press)
• H. Wu, M. Kaplarevic, L. Li, G. Gao, SOS: Segment-based Optimization Search – A New Empirical Methodology. (PLDI 2007)
• Kaplarevic, M., Design and development of a metagenome database and annotation pipeline, American Society for Microbiology General Meeting, New Orleans, LA (May 2004.)
• Cary, S.C., Kaplarevic, M., Murray, A.E., Exploring genomes of non-model microbial systems: A meta-genome level analysis of a complex microbial symbiosis from an extreme environment. Ecological, Evolutionary, and Functional Genomics - Gordon Conference, New London NH, (Aug. 2003.)
• Kaplarevic, M., Gao, G., UPSTREAMER (Speculative promoter search tool) IEEE Computer Society Bioinformatics Conference (CSB2002), Stanford University, Palo Alto, CA