Software developer in the Bioinformatics Group, Advanced Technologies, R&D, Life Science Group.

Data Science Group Leader in the Advanced Development Group responsible for creating innovative natural-language-processing and machine-learning tools, methods and best practices around scientific literature.

Nuclear Power Plant Safety and Performance Analysis• Computational modeling and simulation of nuclear reactor thermal-hydraulics during transients and severe accidents.• COMPASS (Core Meltdown Progression Accident Simulation Software) code development.• Implementation of modular computational models with Python’s Numpy, Scipy and Matplotlib.• Model testing/validation and core meltdown simulation.

• Functional annotation of gene families in the Plant Genomics Program.• Implementation of text mining technologies for gene information acquisition. ◦ Aggregated data from numerous genomic and literature databases, implemented variousmachine learning analysis pipelines for finding relationships between biological entities. ◦ Utilized various direct and custom NLP solutions (primarily Python’s NLTK-based) for entity andphrase extraction used for extended search and machine learning (Relationship Networks and Naïve Bayes) algorithm feature selection. ◦ Developed a dynamic UI for data exploration based on the Relationship Networks technology. Implemented all solutions with Python, R, jQuery, MySQL and MongoDB. ◦ Enhanced the Relationship Networks approach, making it more scalable, faster and flexible.

• Design and implement a knowledge discovery pipeline at LLNL’s Biodefense Knowledge Center.• Large-scale implementation of text mining, machine learning and bioinformatics tools. ◦◦ Utilizing Java, Python, R, and jQuery, set up automated knowledge discovery pipeline with targeted web crawling, entity recognition, DNA and protein sequence extractor and analyzer, feature and topic extraction, with results available through an interactive, analyst-focused UI. ◦◦ System capabilities included custom implementations of Non-negative Matrix Factorization(NMF) and R’s Dirichlet allocation (LDA) for feature and topic extraction and clustering.

• Development and upgrades of Symyx Isentris® decision support software for access, analysis and reporting of scientific information across a broad range of scientific disciplines in the pharma, oil and energy, and consumer products industries.• Formulation of product requirements documents that include business cases, requirements and use cases supporting the product release cycles.• Work in an agile development environment to ensure timely delivery to market of products that areeasy to use, easy to install and provide high scientific value.

• Led development of R&D 100 Award winning, biomimetic algorithms for context-based search,knowledge discovery and relevance ranking. ◦◦ Extensive research into search and recommendation technologies. ◦◦ Implemented customized search indexing and developed Relationship Networks approach forcontext-based search, discovery and recommendation applications.• Co-inventor of four patents in search and recommendation methods with heavy focus on music.• Developed vertical search and discovery applications in automatic playlist generation, targeted adplacement, as well as finance, online commerce and genomics.

• Responsible for life science database feature development, user support and training. Guideddatabase feature development based on understanding of customer needs in drug development andmedical professions.• Developed a biomedical literature text mining application utilizing Oracle Text and Oracle DataMining algorithms, including document search, clustering and classification as part of a full lifescience workflow demo. Analysis methods included Non-negative Matrix Factorization, SVMclassification, K-means clustering and semantic analysis using thematic ontologies.• Developed a flexible BLAST application utilizing Oracle Data Mining BLAST algorithms, allowing for dynamic creation of query and target sequence sets based on a broad combination of metadatafeatures (date, annotation, sequence fragment match).• Participated in Oracle Life Sciences User Group (OLSUG) board meetings and organization ofannual, international user meetings and workshops. Conducted workshops at meetings. Assisted insetup and administration of the OLSUG website in the areas of database object design, CGI scriptsand page layout.• Presented and demonstrated Oracle technologies to life science professionals at conferences andcustomer sites. Hosted and presented e-seminars on life science applications of Oracle technology.

• Developed SureGene, a large scale, literature-based, gene name disambiguation strategy andsystem, presented at the CSB 2004 conference. ◦◦ Co-developed strategy, implemented, tested and validated system with Java, Perl, Apache Lucene search and ReelTwo’s Classification System.• Collaborated with cancer research scientists in various aspects of data and information, management, analysis and visualization.• Investigated and developed heatmap-based data visualization tools for analysis and correlation ofgene expression, transcription factor and annotation data sources.• Developed a web-based project literature management system, allowing shared access to an auto-updating project knowledge base with multi-level annotation capability. Provided continued support and feature enhancement based on user feedback and requests. System built on Apache, Oracle database, Perl, JavaScript, and APIs for literature database access.• Evaluated text mining application vendors and products for licensing and integration within theexisting text analytics system.

• Developed a context-based, biological literature knowledge discovery tool.• Lead developer of X-Reporter, a gene information extraction tool supporting a microarray expressiondata analysis system.• Developed visual and statistical tools for gene expression microarray data reliability.

• Created a novel human protein domain database from genomic sequences obtained from Celera'shuman genome project and Incyte clones.• Extracted the sequences and assembled multiple alignments of novel protein domains.• Analyzed domain properties and potential functional features.

• Conducted performance analyses of boiling water reactors, code validation and development.

Nuclear Power Plant Performance Analysis.• Conducted safety and performance analyses of various nuclear power plant system designs.• Developed performance analysis models and codes.

• QA of submarine heat exchanger construction process.