Resume

Electrical Engineering

Location:

Newark, DE

Posted:

January 28, 2013

Contact this candidate

Resume:

Mihailo Kaplarevic, Ph.D.

Personal Info

Professional Profile

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.

Technical Skills

Programming languages: C, C++, Java, Php, Perl (BioPerl), Linux scripting10 years of experience on profiling diverse applications, pinpointing performance bottlenecks and making cross-platform optimizations10 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 architectureExcellent background and strong problem-solving capability in entity-relational databases, object oriented databases, applied algorithms and applications, and high-performance computingExpert knowledge of high performance computing (PVM, MPI, OpenMP, pthread), Linux clusters, shared memory systems, and porting applications to different platformsOperating Systems: Windows (admin level), LINUX (admin level), MAC OSX (admin level)MySQL, Postgres and ORACLE database design and administrationWeb Platforms: HTML, Dreamweaver, Macromedia Flash, LIMP servers, and dynamic portalsExtensive experience in technical writingExcellent oral and written communication in multiple languages

Key Projects

Professional Masters in Bioinformatics Worked to develop the program, curriculum and policy for University of Delaware s new masters programDistributed 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)

Work Experience

July 2008 - PresentResearch Assistant Professor Computer and Information Science Department, University of DelawarePropose, develop, and manage projects with faculty, customers, and vendors that utilize large-scale research data and knowledge baseLead research teams of up to 15 graduate studentsDevelop model concepts and approaches as an individual researcher and act independently on technical mattersMake authoritative decisions and recommendations that have a major impact on scientific research activities such as defining project timelines, selecting computational hardware, leading research teams etc.Prepare competitive grant proposals to obtain funding in support of research activitiesServe as a primary investigator or co-investigator on projects of complexity and scope consistent with above criteriaPrepare analysis, reports, and other documentation for publicationPresent findings at local, national and/or international meetings

Jan. 2007 presentBioinformatics Associate ScientistDelaware Biotechnology InstituteConceptualize and implement algorithms and approaches to create solutions for complex computational/informational challengesLead and participate in planning, organizing, and guiding extensive research programs and activitiesInterpret, organize, execute, and coordinate diverse computational assignments concerned with unique and highly complex problemsMaintain an expert, broad knowledge of state-of-the-art technology, software, and systemsAdminister and maintain diverse OS computational systems and deploy required servicesProvide network support, monitoring and maintenanceOversee installation, training, and maintenance of the software and hardware used across the Institute (computational and database cluster)

Sep. 2001 May 2006 Research AssistantUniversity of DelawareResearch in the area of parallel and high-performance computing

Research

Jan. 2007 - present

Computational Core Center, Delaware Biotechnology Institute, University of Delaware

Sep. 2001 Dec. 2006

Bioinformatics Group, Computer Architecture and Parallel Systems Laboratory

Department of Electrical and Computer Engineering

Advisor: Professor Guang R. Gao

Co-advisor: Professor Craig Cary, College of Marine Studies, University of Delaware

Co-advisor: Professor Alison Murray, Desert Research Institute, Reno Nevada

Nov. 2004 - Dec. 2004

http://www.ceoe.udel.edu/extreme2004/mission/divemission/index.html

Aug. 2002 Jan. 2007

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

Education

University of Delaware Ph.D. in Electrical and Computer Engineering with the concentration in Biomedical Engineering, GPA 3.9/4.0

Dissertation: "Advanced Informational System Framework for Analysis of Incomplete Environmental Metagenome Datasets"

University of Belgrade, School of Electrical EngineeringCombined B. Sc. and M.S. in Electrical and Computer Engineering

Thesis: "Object Oriented Database Modeling and Optimization Techniques"

Services

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

Key Publications

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

Extended list available upon request.

References

Dr. Karl V. Steiner