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									                                                                                                Shiran Pasternak
                                                                                                            Irvington, NY

   Excellent software engineering skills and a solid commitment to software process and best practices. Thorough
    expertise in the software life-cycle and the pragmatic application of agile software principles.
   Demonstrated computational biology and bioinformatics expertise. Deep understanding of biological systems and a
    marked aptitude for addressing challenges in biological research with appropriate computing solutions.
   Principal engineer and project manager for several highly successful team-oriented projects. Detailed involvement with
    all project phases. Demonstrated courage and perseverance in tackling project challenges. Provide ongoing mentoring
    and guidance to team members.
   Thorough experience and interest in the management, analysis, and interpretation of very large data sets, with a keen
    eye for designing informative data visualizations.
   Comprehensive expertise and continual self-enrichment in web technologies.
   Played a pivotal role in the Human Genome Project, delivering tools that identified outstanding issues and refined the
    quality of the published genome sequence.
   Other relevant areas: object-oriented systems, data management systems, information retrieval and mining, artificial
    intelligence, operating systems, distributed systems, computer graphics, interface design, data visualization, computer
    vision, cryptography and network security.
   Foreign languages: Hebrew and Russian.

Programming Languages. Java, C, C++, Objective C, Perl, Ruby, Python, Lisp, Unix shell
Software Process. Extreme Programming, Test-Driven Development, UML, Requirements Analysis, Analysis patterns,
Design patterns, Refactoring, Configuration Management, Object-oriented Architecture and Design, Quality Assurance and
Metrics, Change Management
Cloud Computing. Map/Reduce, Hadoop, HBase, HDFS, Pig, Hive, SGE, LSF, PBS, Amazon AWS, TeraGrid/TACC.
Configuration Management. Git, Subversion, Perforce, Mercurial, CVS, RCS.
IDEs. NetBeans, Eclipse, Xcode, TextMate, vi, Emacs.
Development Tools. Apache Ant, Maven, Make, JUnit.
Platforms. Linux, Mac OS X, Windows.
Web Technologies. JavaScript, AJAX, JSON, XML, web services, JSP, JSF, portlets, Ruby on Rails, Spring Framework,
Django, Catalyst, Apache, Tomcat.
Web Design. HTML, HTML5, CSS.
Data Stores. SQL, Oracle, MySQL, MongoDB, CouchDB, FastBit, HDF, object-relational mapping frameworks (Java
Hibernate, Perl Moose, Ruby ActiveRecord).
Data Statistics and Visualization. R, MATLAB, Processing, OpenGL, GD, Java3D, Circos.
Bioinformatics. EnsEMBL, BioMart, Tuxedo tools (Bowtie, Cufflinks, Tophat), sequence alignment (BLAST, BLAT), De
novo genome assembly (ABySS, Velvet), next-generation sequencing (Illumina, 454, SOLiD, PacBio), gene prediction and
building, genome browsers (EnsEMBL, Gbrowse, Circos).

Bioinformatics Analyst, Cold Spring Harbor Laboratory; Cold Spring Harbor, NY – July, 2005-Present
Project Manager for analysis and visualization for the Maize Genome Sequencing Project. Led a 5-member team in
building a robust automated pipeline for analyzing sequenced data and computing complex genetic annotations as well as
an open-source, public genome portal ( that provides up-to-date project data and mining tools
for biological research.
Technical lead for management and analysis of other genomes such as wheat, rice, tomato, sugarcane, and grape. Actively
collaborated with other groups to import raw data, analyze genomic content, and present the data for public consumption on
interactive web portals. Prototyped various cloud computing technologies, such as Map/Reduce and non-relational data
stores, for management and analysis of large-scale genome project data sets.
Presented work at various conferences, meetings, and seminars. Authored published research papers and grant proposals.
Generated compelling data visualizations for scientific publications and conference presentations.
Shiran Pasternak                                                                                                       Page 2

Directed hiring of team members. Introduced labwide use of software best practices such as defect tracking, unit testing,
and wiki-based project documentation. Conducted code reviews and technical mentoring of junior developers. Collaborated
with the systems group to establish a high-performance computing cluster, developed benchmarking protocols, and
encouraged institution-wide use.
Lead Scientific Programmer, Human Genome Sequencing Center, Baylor College of Medicine;
Houston, TX – October, 2001-June, 2005
Bioinformatics Lead for sequence assembly and finishing for the Human Genome Project. Built an automated pipeline for
validating sequenced chromosomes and mapped genetic data. Created tools that facilitate assemblers and annotators by
providing quality metrics and rapid feedback. Architected web-enabled, user-interactive genome browsers and reports for
public data visualization.
Institutional Bioinformatics Lead for The International HapMap Project. Built a web-enabled Laboratory Information
Management System (LIMS) for managing a substantial set of genotypes, genetic markers, and patient data. Delivered a
software pipeline for statistical analysis and data submission.
Principal Engineer: Enterprise-level Java system for laboratory tracking and management applications. Designed a robust,
generic database for intuitive barcode tracking. Architected an MVC-based infrastructure, featuring a rich set of custom
components, that enables rapid prototyping of specific laboratory use-cases.
Conceived and implemented a program to adopt XP across the organization and to improve its CMMI from Level I (ad
hoc) to Level II (Repeatable). Introduced a defect and feature management system for project tracking. Standardized
department-wide use of version control for source code and pertinent data. Established project management activities,
including requirements analysis and use of UML.
Initiated and implemented an internal training program to educate developers about technologies and software best
practices, such as code reuse, unit testing, and design patterns. Delivered weekly lectures, technology exchanges, and
Lunch-and-Learns on relevant topics. Mentored developers through design and programming sessions.
Principal Engineer: Web content management system for organizational internal and public websites. Assessed the existing
system and identified the need for its replacement. Architected a system that allows privileged users to publish documents
effortlessly while ensuring security and accountability.
Systems-Software Liaison and Coordinator. Identified and addressed concerns about system resources. Conducted web,
code, and security audits and identified solutions for potential flaws. Administrator for: Tomcat, Java, Perforce, and the
organization’s intranet.
Advisor and Bioinformatics Consultant for various software projects and initiatives in the organization.
Software Engineer, New York Times Digital; New York, NY – June, 2000-July, 2001
Architect for back-end applications for in Perl, C/C++, and Java. Automated content distribution to
subscribers and partners. Developed Java-based customer-service tools for account management. Architected data-
warehousing and decision support systems for managing web access logs. Designed relational databases for customer
registration and content management. Conducted extensive software security audits and developed automatic user-ban

The Association for Computing Machinery
New York Academy of Sciences

Johns Hopkins University, Baltimore, MD
Master of Science in Engineering, Computer Science, 2001
Thesis: RAPID: A Robust Programming Approach to Dynamic Interaction and Robotics

Johns Hopkins University, Baltimore, MD
Bachelor of Arts in Computer Science, 1999
Bachelor of Arts in Biology, 1999

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