Raf Podowski Email & Phone Number

Pleasant Hill, CA, US

Hercules, CA, US

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

Hercules, CA, US

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.
• 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.

Dallas, TX, US

• 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.
• System capabilities included custom implementations of Non-negative Matrix Factorization(NMF) and R’s Dirichlet allocation (LDA) for feature and topic extraction and clustering.

US

• 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.
• 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.

US

• 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.

Austin, Texas, US

• 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..
• 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.
• 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.
• 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.

Cambridge, Cambridgeshire, GB

• 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.
• 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.

Phd, Bioinformatics

Fil.Lic., Molecular Biology

Ms, Engineering Physics

Bs, Mechanical Engineering