Developing methods and tools for analysis of raw sequencing data.- Developing and maintaining the mapping and alignment tool capable of accounting for various sequencing errors (TMAP)- Designed, implemented, and continuing development and maintanence of the long duplication variants (ITD) detection tool.- Designed, implemented, and continuing to improve the back-end components for variant calling performance optimization framework.

- Led development of SciDM, zero-maintenance high performance object-relational NoSQL database engine, capable of handling practically unlimited volumes of data.- Developed QSimScan, an ultra-high performance sequence similarity search algorithm, operating 10-100 times faster than industry standard tools with comparable sensitivity. (available on GoogleCode under open license)- Led development of EmbeDB, an open-source, lightweight, high performance embedded database engine (back-end for SciDM; available on GoogleCode)

Developed the research platform for comparative phylogenetic analysis of environmental survey sequencing (16S) data. This platform includes:- database of sequence reads clustered into OTUs and placed on the taxonomic tree; - pipeline for initial population and incremental updates of this database;- middleware that provides a high-level WEB API for querying this database. The update pipeline operates on a cluster at NERSC super-computing facility, but capable of scaling down to a small network or even single host for smaller data volumes. Developed original tools and algorithms for sequence comparison and clustering, artifact detection and taxonomic assignment which overcome limitations of industry standard methods and allow to process extreme data volumes generated at JGI. Carried out full research, design and prototyping cycle for the platform; using developed platform, performed initial analysis of full set of environmental survey data at JGI (over 75 million reads from over 1.7K samples)Helped with normalization of Strain data in Genomes Online Database.

- Created high performance mapping technology for a Next Gen sequencing data, from strategy evaluation and algorithm design to performance optimization and quality control.- Increased mapping performance by an order of magnitude by customization of alignment algorithms and inventing of automated selection of best search strategies based on input composition.

Providing on-demand solutions in computational biology and software engineering.Major clients and projects:(2011) InfoWeb Corp, Potomac, MD. Subcontract for Hughes/EchoStar. - Developed software system for real time satellite position mapping.(2008) DOE Joint Genome Institute, Walnut Creek, CA- Carried performance analysis of DNA sequence comparison tools for metagenomics research.(2006-2008) Integrated Genomics Inc, Chicago. IL- Redesigned Information Processing Pipeline for the company's flagship product – ERGO(tm) to accommodate for the rapid growth of data volume. Achieved up to 100-fold increase in pipeline performance by re-implementation and refactoring of bottleneck components.(2006-2011) Ariadne Genomics Inc., Rockville, MD- Designed high-performance software pipeline for normalization and elimination of redundancy in chemical structure databases; successfully applied the new pipeline to large-scale data sets, including PubChem database.- Developed data conversion and format customization tools for metabolic pathway databases.(2006-2011) EMPProject, Naperville, IL- Created parsing technology for EMPProject’s pathway database (MPW).- Developed quality assurance, validation and automated correction tools for encoded metabolic pathways.

- Leading a team of scientists and software engineers, created a novel technology for Sequence–Based Metabolic Reconstruction.- Led development of software pipeline for High Throughput Metabolic Reconstruction, a production system for Tissue-Specific Metabolic Databases, the main company product.Managed production of Human Tissue-Specific Metabolic Databases.- Obtained grant funding to support technology development.- Coordinated data analysis and data mining services.

- Led development and support of company's core software product – ERGO(tm) genome annotation suite, a pioneer in genomic biology.- Managed a team of up to seven developers; performed resource management and strategic planning; managed collaborations and client support.- Maintained constant enrichment of company's proprietary annotated genome database, processing 12 to 20 new genomes a month.- Provided support, including development of custom solutions, for Sequencing, Genome Assembly, Genome Annotation, and Marketing departments.

- Completed full cycle of development of CORBA API for the core company product (ERGO) from idea to production. - Introduced support for human and other higher eukaryotic genomes into ERGO. - Designed and deployed software tools, including high performance contamination filtering pipeline and modular toolkit for gene expression data analysis.

Established and managed the Bioinformatics Group at the University of Illinois, operated under the contract with Quark Biotech. Managing annual budget of over $1M, led a team of up to 8 scientists and software engineers in development of:- A solution for bioinformatics data management- An EST analysis package- A suite of gene expression data analysis tools- Technology and tools for biomedical literature mining.

(subcontract at Panasonic Factory Automation)- Managing a team of 5 engineers, led development of PCB assembly optimization sub-system for PanaPRO(tm) software suite. - Established and supported beta-sites; organized training for customer support staff; provided off-site and on-site customer support for critical problems.

Pioneered development of world-first hardware accelerated DNA sequence analysis suite.