Doug Hershberger's Email Addresses & Phone Numbers

Associate Director, Bioinformatics @ Algenol Biofuels Inc. Leading a bioinformatics team for biofuel producing strain development using systems biology methods Fort Myers, FloridaSoftware Developer @ TeselaGen * Programmed components of the graphical user interface for the premier, commercial synthetic biology design and automation platform* Wrote reusable, object oriented HTML5 code in Javascript using ExtJS and MongoDB* Conformed...

Associate Director, Bioinformatics @ Algenol Biofuels Inc. Leading a bioinformatics team for biofuel producing strain development using systems biology methods Fort Myers, FloridaSoftware Developer @ TeselaGen * Programmed components of the graphical user interface for the premier, commercial synthetic biology design and automation platform* Wrote reusable, object oriented HTML5 code in Javascript using ExtJS and MongoDB* Conformed to industry standard software development practices including MVC architecture, revision control (git), unit testing/behavior driven development (Jasmine) and issue tracking From February 2013 to April 2013 (3 months) San Francisco Bay AreaAssociate Director @ Intrexon Corporation * Established Laboratory Information Management Systems (LIMS) for high throughput screening of Industrial Products. * Led a team which constructed the computational biology infrastructure to support the Design, Build, Test synthetic biology cycle. * Recruited, interviewed and hired senior personnel, coached and aided them to attain prominent positions where they made significant contributions to the company's core businesses. * Exerted influence across multiple departments within the company, making a major impact on their research programs. * Contributed to programs which led to increases in the efficiency of critical integral processes by 50% or more. From July 2011 to February 2013 (1 year 8 months) San Carlos, CABioinformatics Scientist @ LS9, Inc. * Established high throughput screening data management, reducing screening cycle times 50%* In collaboration with expert, senior software developer, designed and built a three tiered database application for tracking detailed strain information including lineage, and combining that data with results from the lab in an integrated LIMS * Filed invention disclosure outlining gene discovery for new product development From November 2009 to July 2011 (1 year 9 months) South San Francisco, CAScientist @ Codexis Summary: * The founder and driving force behind a bioinformatics team for biofuel producing strain development using systems biology methods* Multiple invention disclosures* 3 Employee Recognition Awards for outstanding work on LIMS development, genome analysis and biofuel strain development- Identified targets for improved resistance to biofuel toxicity through the analysis of systematic deletion/survival and microarray response experiments- Assembled libraries through the analysis of public and proprietary microarray data- Designed libraries which resulted in the improved secretion of heterologous proteins- Identified promoters which resulted in greatly enhanced protein production and improved expression profiles- Optimized production of proteins through bioinformatics approaches- Established genome database with a user friendly web interface- Managed next generation sequencing project - Annotated a novel eukaryotic genome - Led group which developed system for shake flask and fermentation data storage and analysis- Co-led high throughput strain evolution LIMS group- Co-led group mapping high throughput protein and strain evolution process level flow and systems architecture- Led systems biology architecture group to design and install integrated fermentation and systems biology analysis database- Organized a team of bioinformatics experts and directed their efforts to address systems biology needs- Aided in recruiting a top notch systems biology team, including personally recruiting a senior level bioinformatician as a direct report- Oversaw goal setting, goal completion, progress reporting and performance evaluations for reports- Effectively resolved disputes over the performance of direct reports, engaged in process review ensuring that project goals were met, the customers were satisfied and that employees learned from the experience From January 2008 to August 2009 (1 year 8 months) Research Specialist @ The Dow Chemical Company Summary: Improved microbial protein expression using bioinformatics and systems biology methods. Published two patent applications and over twenty peer reviewed research reports.• Strain Improvement/Systems Biology: Analyzed microarray data to identify strain improvement targets. Developed of an array of mutants for improved expression of heterologous proteins. • Pathway/Metabolic Flux Analysis and Strain Engineering: Curated metabolic pathways and performed in silico metabolic flux analyses to identify targets for strain engineering.• Systems Biology• Bioinformatics Expert• Genomics: Developed a high quality, functional genome annotation. • Project Management: Led project to implement bioinformatics infrastructure involving four developers in addition to myself.• Outsourcing Project Management: Managed a project with the Indian contract research firm, Syngene.• Programming and Databases: many languages. From December 2000 to January 2008 (7 years 2 months) Lead Developer @ The University of Minnesota Biocatalysis/Biodegradation database Research topic: Developing a web based application for the study and prediction of biodegradation pathways.• Pathway Analysis: Assembled models of biodegradation and biocatalysis pathways from the primary literature.• Pathway Prediction: Developed rules for predicting the biodegradation of highly recalcitrant compounds. Collected rules from the literature as well as interviews with biodegradation experts.• People Management Advised graduate students, directing their daily work and helping them set and work towards long term goals aligned to the project aims.• Web Applications: Maintained and improved a dynamic object oriented database connected web application using Java servlets. http://umbbd.msi.umn.edu/index.html From 1998 to 2000 (2 years) Graduate research assistant @ University of Illinois College of Medicine Research topic: Regulation of alginate in Pseudomonas aeruginosa controlled by the alternate sigma factor E. • Assay Development: Developed a protocol for in vitro transcription using a novel sigma factor. Detected protein/protein complex formation by glycerol gradient sedimentation. Detected protein/DNA complex formation by gel shift analysis. Determined in vivo transcriptional levels by lacZ transcriptional fusion assays. • Protein Biochemistry: Purified proteins using His-Tag, GST, conventional ion exchange, affinity and size exclusion column chromatography. Prepared samples for crystallization. Determined Km and Vmax for wild type and mutant enzymes.• Cloning, PCR and DNA Sequencing: Cloned from plasmid and chromosomal DNA. Performed site directed mutagenesis. Prepared target DNAs by PCR. Cloned using degenerate primers. Performed overlapping extension mutagenesis. Sequenced both single stranded and double stranded DNA with high G/C content. From 1991 to 1998 (7 years)