Project Manager Quality Assurance

Edward Elhauge

**** ********* ******, *** *********, CA 94107

415-***-**** ******.*******@*****.***

PROFILE

Lead computational-biology researcher and engineer with proven ability to synthesize

solutions to problems independently. Education in and aptitude for Physics, Biology,

Mathematics and Statistics, including vast experience as a developer, enabling a creative

and systematic approach to solving problems as they arise. Intensely curious pioneer and

quick learner of cutting-edge technology. A 15-year passion for all things biological,

supported by an analytical base with deep knowledge of scientific and medical trends and

techniques. Strong track record in Discovery Research and Product Delivery with completed

projects in biotech/biology, statistics, robotics, process control and WebApps. Recognized

for synergistic teamwork with top scientists, doctors, and engineers.

PROFESSIONAL EXPERIENCE

(see Technology Addendum for Implementation and Technical Details)

Lawrence Livermore National Laboratory, Livermore, CA 2009-Current

Computational and Statistical Biologist (level MTS4)

National Security work for Global S Program (DOE Q clearance). Part of Pathogen

Bioinformatics Group, doing our part to keep us all safe. Identifying hostile bugs, both

natural and not.

1.1 Detection: Computational tools to detect and identify organisms and virulence using

likelihood mixture model.

1.2 Phylogenetics: Phylogenetic genotyping, forensic classification and visualization.

1.3 miRNA Assay: Analytical support for development of assays for miRNA discovery,

expression, and diagnostics.

1.4 Modeling & Visualization: Modeling and visualization projects for biological research

(e.g. visualization of seasonal rhythms of bacterial and viral strains).

1.5 Protein Hybridization: Analysis of controls and signal.

1.6 Microbial Forensic Encyclopedia: Worked on synchronization and automated curation

with NCBI data store.

Roche Molecular Systems, Pleasanton, CA 2001-2009Principal Bioinformatics Specialist

Conducted key research projects with scientists by providing information, analysis,

methodologies and tools. Advanced key research programs and commercial product

development. Served as architect, team leader, and project developer.

2.1 SNP Interference: Delivered to scientists studying breast/leukemia/bladder cancer a

risk assessment of mutations in the assay regions for acceptance review.

2.2 SNPexplorer: Created SNPexplorer, a suite of WebApp data-mining tools for SNP,

mutation analysis, genetics and disease study, fusing in-house Roche data and NCBI dbSNP

for all scientists in the global-Roche network.

2.3 HCV Assay: Developed a dual-target assay for HCV (Hepatitis C) with the goal of

recovering market share in the HCV testing market by improving inclusivity of HCV4.

2.4 Rational Assay Design: Initiated a methodology for PCR/Taqman assay design using

thermodynamic modeling and statistical analysis of the HCV genome swarm (or similar

organism). The goal, a much shorter time to market for new diagnostics and predicting

problems with approved assays to extend their market life.

2.5 Neisseria gonorrhoeae Assay: Analyzed the Neisseria Gonorrhoeae genome, performing

due diligence analyses incorporated into Roche s FDA submission.

2.6 Assay Inclusivity WebApp: Wrote Assay Inclusivity WebApp tools now part of quarterly

product workflow, resulting in reduction of FDA PLR (Post-Launch Review) effort from six

weeks to less than a week per organism.

2.7 System Integrator: Provided consulting services and mentored other bioinformatics

team members on R-language, Python, Java, Perl, Apache, Linux, sequence alignment, biology

DBs, SQL, Agile development, etc.

2.8 Culture Collection: WebApp to monitor, report and audit mission-critical cultures,

cell lines and vectors held at RMS, including USDA-regulated select agents.

Edward Elhauge 415-***-**** ******.*******@*****.*** Page 2 of 4

Uncanny, Inc., San Francisco, CA

Principal/Owner

Established a software consulting firm specializing in network-aware and database-aware

scientific and industrial project development. Representative projects and results follow.

Consulting - Genentech, South San Francisco, CA 1998-2001

Contracted with Genentech, the world pioneer in biotechnology, creating new

bioinformatics applications and porting standard ones to a thin-client, in-house

environment.

3.1 Bio Tools: Overhauled GSeqWeb, a suite of undocumented, biological data and analysis

tools, into a modern Java/Jython framework.

3.2 Java Libraries: Wrote infrastructure code to implement user profiles and speed

optimizations (caching); used by the entire development team.

3.3 BLAST Visualization: Delivered an enhancement to the in-house BLAST farm. BLAST

homology results saved to an object DB. A Java Applet to visualize the results.

3.4 Pipelining: Delivered a data-flow tool that permits scientists to run, share and peer-

review their own genomic analysis suites by pipelining together modules.

Consulting - Other Relevant Experience

4.1 Other: Pioneered many technological efforts, including: devising new methods,

adapting to changing frameworks/tools, applying human factor analysis, interview and

requirement gathering, and use of a wide range of computer languages and hardware.

Projects at Wells Fargo, Mayo Clinic, LTV Steel, US Steel, Fujitsu, BP Telecom, Teknekron;

follow-on callback work at SGI (Silicon Graphics), Ampex, Applied Materials.

Project manager: Designed Bill Payment for Wells Fargo Internet Banking, the first

Internet Banking and first Bank Internet Bill Pay systems deployed.

Cutting-edge Project: Contracted by Colossal Pictures (a leading animation and creative

shop) as technical liaison for the Time-Warner Orlando, Pay-Per-View rollout and to write

an interface to TV Guide Online.

Medical Imaging and Modeling: Developed cardiac X-ray image recorder for the Mayo Clinic

using Ampex devices.

Algorithms: Invented new algorithms for the closed-loop control of non-linear flow-valves

at Applied Materials and new techniques for precision temperature, pressure and RF servos

for CVD and etch chambers.

Robotics: Worked with mechanical and electrical engineers to design a robot system for

semi wafer handling at Applied Materials, with a Unimation PUMA robot and closed-loop

control software.

Imaging: Delivered a vision system that optimized cutting operations for LTV Steel.

Robotics: Designed/installed robotic controls and industrial automation for US Steel.

Pioneer: Started early ISP/Web hosting, Lever Industries, part of The Little Garden.

Networking: Developed telecom network switches for Fujitsu, Teknekron and BP.

Visualization: Delivered 3D Visualization tools at SGI and Wells Fargo.

AFFILIATIONS and PUBLICATIONS

EDUCATION AND CERTIFICATIONS

B.Sc. Physics, B.Sc. Mathematics Carnegie Mellon University, Pittsburgh, PA

Mathematics, Graduate Coursework - University of California, Berkeley, CA

Biochemistry, Graduate Course - UC Berkeley Extension

Molecular Biology, Graduate Course - UC Berkeley Extension

Statistical Learning and Data Mining, Seminar - Hastie & Tibshirani, Stanford

ISMB Conference yearly - Intelligent Systems for Molecular Biology, with tutorials in SVM

Classifiers for Hypothesis Models, Bayesian Analysis of Networks, Next-Gen Seq.

Roche Seminars, gave annual presentations, attended weekly seminars on assay chemistry

and disease markers.

Edward Elhauge 415-***-**** ******.*******@*****.*** Page 3 of 4

TECHNOLOGY ADDENDUM

IMPLEMENTATION AND TECHNICAL DETAILS

1.1 Detection: Phylogenetics, Statistics, R language, Python, Perl, ORM, RDBMS,

Parsimony, ML, Regression. Public information available via Internet Search.

1.2 Phylogenetics: Phylogenetic trees generated and visualized for forensic work.

1.3 miRNA Assay: Probability density analysis of miRNA microarray response. Sensitivity,

specificity, ROC curves. Analysis of sticky probes, dark probes. Multi-variate regression

modeling of microarray response.

1.4 Modeling & Visualization: Used R and Python to perform analysis, modeling and

presentation graphics of biological problems.

2.1 SNP Interference: In-house BLAST DBs built from selected genomic and RNA sequences.

Perl scripting and BioPerl used to drive sim4, BLAST and MegaBLAST for ePCR modeling.

Results correlated with dbSNP, RefSeq and GoldenPath assembly.

2.2 SNPexplorer: dbSNP data and Schema. Perl scripting to process NCBI Schema changes.

Perl scripting and BioPerl to map in-house SNPs to the GoldenPath Assembly. Java coding

and XSLT to generate on-the-fly queries from an XML description; XML configured output

description with raw rows, functions for synthetic rows, cross-linked queries, user

selectable sorting, and suppression and enabling of columns. XSLT capabilities used to

output report pipeline to HTML, XML or CSV. Assign functional tagging to SNPs using a

multitude of in-house and public DBs.

2.3 HCV Assay: Used open-sourced PrimerHunter software that implements nearest-neighbor

thermodynamics to find PCR amplification primers. Modified PrimerHunter program to also

pick probes. Performed global alignment of HCV genomes via MAFFT. Perl scripting to manage

alignment process, and chop alignments into segments manageable by PrimerHunter. Perl post-

processing script to filter using Roche Molecular proprietary amplification techniques.

Java Application modified to view HCV conservation for the purposes of assay design.

Reported literature search of HCV genome biology.

2.4 Rational Assay Design: Perl scripting to drive DNAsoftware OMP server and ThermoBlast

server (thermodynamic modeling). Automated workflow for Tm values computed for all oligo

bindings on all known sequences for existing Roche assays.

2.5 Neisseria gonorrhoeae Assay: Perl scripting to perform ePCR against all known NG

variants and all commensal organisms (N. meningitidis). ePCR performed against non-

redundant DB to guard against non-specific response. Perl scripting to search for

Neisseria DUS uptake sequences and Neisseria Correia sequences near assay binding to

evaluate risk of lateral gene transfer. Used HMMER to find set of possible unknown Correia

element motifs. Perl scripting to analyze GC and graph GC content of assay NG and the

assay binding sites. Analysis of stability and age of assay binding site using features of

GC analysis.

2.6 Assay Inclusivity WebApp: Perl preprocessing of ClustalW alignments. Python routines

to slice/dice, filter and sort inclusivity data. Python/TurboGears and AJAX UI.

2.7 System Integrator: Specified, ordered and built four rackmount Linux servers from

bare-metal; use dedicated to1) production WebApps, 2) development staging, 3)

biostatistics and 4) seamless prototyping and upgrade. Deployed Trac issue server for

project use and configured for Agile development. Supported Apache and R-language

installation and modules (including Bioconductor). Installed 100s of open source tools

including all major alignment tools. Installed and configured BioPerl, BioPython, Mason,

Postgres, MySQL and Oracle.

2.8 Culture Collection WebApp: Java, Cocoon, DB and Javascript.

3.1 Bio Tools: Java, Jython, Python, EJB. Supported BLAST, ClustalW, HMMER, +.

3.2 Java Libraries: Java, Java object serialization and marshalling. Introduced extensive

use of CSS. Oracle schema and queries.

3.3 BLAST Visualization: BLAST, Java parsing and HTML display. Java Applet.

3.4 Pipelining: HTML, Forms, Oracle DB, Jython, Java libraries.

4 Other: C or C++. PID loops, Kalman Filtering. OpenGL, Java Swing, Perl CGI. HTML,

Javascript, CSS.

Edward Elhauge 415-***-**** ******.*******@*****.*** Page 4 of 4

TECHNOLOGY EXPERIENCE AND CAPABILITIES (SELECTED)

Languages:

Python Java Jython Perl R-Lang Javascript C / C++ SQL

Biology:

NCBI / Entrez / dbSNP/ GoldenPath / RefSeq / BioProject EMBL / Emboss BioPerl / BioPython

SwissProt PCR Taqman Alignment BLAST / CLUSTALW / MAFFT HMMER sim4 Sanger / 454 sequencing

DNA / RNA structure Pathway Analysis Expression Analysis Detection/Tiling Arrays RaxML/

FastTree / PHYLIP

Analysis:

Regression Modeling SVM Methods Bootstrap Methods Maximum Likelihood Cluster Analysis ROC

Curves Principal Components False Positive Estimation ANOVA N-Fold Validation Independent

Components (area of interest) Visualization Visual OMP Thermodynamic Modeling Heat Maps

Systems:

Linux Debian / RedHat / Ubuntu BSD Unix Family FreeBSD / OpenBSD Mac OS X / Win XP VMware

/ Xen Solaris / IRIX VRTX Pyramid / Pylons Bottle JSP Templating: Mako / Genshi Oracle /

Postgres / MySQL / SQLite Apache / Tomcat

Project and Product Design:

Team Leadership Project Management Requirements Architecture Agile Programming Hands-On

Delivery Quality Assurance Trac / Confluence Rational Unit Testing Coverage Integration

Testing

2012-03-22-v

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