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Jennifer Meneghin
517 NW 25th St.  Gresham, OR 97030
(503) 703-4063  [email protected]
Recent Experience
Reysenbach Lab, Biology Department, Portland State University, Portland, OR
Bioinformatics Research Associate, 2003-2004, 2005-2007, 2008-2011, 2012-2013
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Designed, developed and used a protocol for de novo assembly of genomes using Illumina reads
(http://alrlab.research.pdx.edu/aquificales/genometools_content.html).
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Designed, developed and used a protocol for preliminary analysis of metatranscriptome (cDNA pyrosequenced) data
(http://alrlab.research.pdx.edu/aquificales/genometools_content.html).

Designed, developed and used a protocol for clustering data into operational taxonomic units (OTUs) using 16S rRNA
pyrosequencing data (http://alrlab.research.pdx.edu/aquificales/genometools_content.html).

Designed and developed a MySQL database on a Linux system to house data for all known Aquificales species.
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Designed and developed the Aquificales Data Warehouse website using Perl, JavaScript, SQL and HTML on a Linux system
which allows users to browse and submit new data to the Aquificales database (http://alrlab.research.pdx.edu/aquificales).

Designed and developed 60 Perl scripts, one Java script and two Python scripts for genomic sequence analysis that have been
made publicly available on the Aquificales Data Warehouse website
(http://alrlab.research.pdx.edu/aquificales/bioinformatics_scripts.html).

Designed and developed a web-based data mining tool, using Java servlets and HTML on a Linux system, for analyzing the
lab’s microbial diversity data that performs Kruskal-Wallis and Wilcoxon Rank Sum tests.

Designed and developed a database to house all of the lab’s samples and experimental data. The system was implemented in
MySQL on a Linux server.
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Designed and developed a web-based data entry tool for sample data collected in the field that uses a CGI script written in
Perl to error check the data and import it into the MySQL database.
Mitchell Lab, Computer Science Department, Portland State University, Portland, OR
Research Assistant, 2006-2008

Implemented the AdaBoost algorithm, a boosting algorithm intended to work over another base algorithm, on an evolutionary
learning algorithm that evolves cellular automata to perform a classification task. Performed and tracked experiments
comparing the performance of the evolutionary algorithm with and without AdaBoost. The AdaBoost algorithm has been
implemented in C++ on a Linux system.

Designed and developed a user interface for visualizing one-dimensional cellular automata using C++ and Java.
Goodman Lab, Vollum Institute, Oregon Health & Science University, Portland, OR
Bioinformatics Research Associate, 2004-2005

Designed and developed an Oracle database used to compare a full spectrum of annotated genomic data to specific
transcriptional regulatory regions of interest to the lab for human, mouse and rat genomes.

Designed and developed a web-based tool, using Java servlets and HTML, that allows researchers to import locations of
transcriptional regulatory regions of interest into the database and run any of several reports comparing these locations to
previously annotated genomic regions for human, mouse and rat genomes.
Gartner/Griggs-Anderson Research, Portland, OR
Senior Software Engineer, 2000-2002

Designed and developed an application in Java on Linux that sends out bulk e-mails, tracks the e-mails in a Sybase database,
then parses, forwards, and tracks any replies received, including extensive decision making to automatically deal with
bounced e-mails.

Worked on a team that designed and developed an application in Java on Linux that automatically generates trended
graphical reports (bar charts, pie charts, etc.) from survey data housed in a Sybase database. It included a graphical user
interface, and the ability export reports to HTML.

Worked on a team that designed and developed a large-scale panel application in Java on Linux. This project included a web
survey engine, bulk e-mailing, e-mail tracking, multiple graphical user interfaces and extensive reporting.

Designed a “win/loss” application for the statistics department. Worked on a team that developed the back-end database and
analysis side of the application in Java on Linux.
Software Engineer, 1997-2000

Designed and developed an application in Java on UNIX for the statistics department that searches for latent classes by
estimating maximum likelihood for various types of data distributions.

Developed many web surveys using Perl, connected to a Sybase database, on a UNIX system.
Unpaid Experience
Department of Biology, Portland State University, Portland, OR
Teaching Assistant, 2012
 Taught two Python programming classes for Computing for Biologists class. Participated and answered questions weekly.
Biostatistics and Bioinformatics Shared Resource, Oregon Health & Science University, Portland, OR
Practicum, 2004
 Used JSP and Java servlets to develop a general purpose query tool for an Oracle database that houses Affymetrix microarray
data.
Publications
Hamamura, N., Meneghin, J. & Reysenbach, A. L. 2013. Comparative community gene expression analysis of Aquificales-dominated
geothermal springs. Environmental Microbiology, 15, 4: 1226-1237
Flores, G., Shakya, M., Meneghin, J., Yang, Z. K., Seewald, J. S., Geoffwheat, C., Podar, M. & Reysenbach, A. L. 2012. Inter-field
variability in the microbial communities of hydrothermal vent deposits from a back-arc basin. Geobiology, 10, 4: 333-346.
Flores, G., Campbell, J. H., Kirshtein, J. D., Meneghin, J., Podar, M., Steinberg, J. I., Seewald, J. S., Tivey, M. K., Voytek, M. A.,
Yang, Z. K. & Reysenbach, A. L. 2011. Microbial community structure of hydrothermal deposits from geochemically different vent
fields along the Mid-Atlantic Ridge. Environmental Microbiology, 13, 8: 2158-2171.
Education
 Graduate Certificate, Biomedical Informatics (GPA 4.0)
Oregon Health and Science University, Portland, OR, 2003-2004
 Computer Science/Electrical Engineering Classes, 16 graduate credit hours: Computability Theory I & II,
Genetic Algorithms, Programming Languages and Artificial Intelligence
Portland State University, Portland, OR, 1993-1994, 2003, 2007
 Computer Science Classes, 36 undergraduate credit hours
Portland State University, Portland, OR, 1991-1993
 Bachelor of Science, Major in Mathematics with an emphasis on Statistics, Minor in Psychology
Portland State University, Portland, OR, 1987-1990, Graduated in three years
 Sherwood High School, Sherwood, OR 1984-1987, Graduated in three years
Skills
 Programming Languages: Perl, Python, JavaScript, HTML, Java (RMI, JDBC, JavaMail, JSP, Servlets, JUnit), C/C++
 Bioinformatics Tools: BLAST, Primer, RDP Pipeline, Mothur, ESPRIT, GenePix, Ecosim, SPSS, MS Excel, SolexaQA,
Euler, Velvet, Geneious, SOAP, BioPerl
 Database Management Systems: SQL, Sybase, MySQL, Oracle, PostgreSQL, MS Access
 Operating Systems: UNIX, Linux, Windows
Interests
Bioinformatics, Metagenomics, Biostatistics, Data Mining, Data Modeling, Evolutionary Computation, Genetic Algorithms