Updated, maintained, and developed analytical tools and processes for assembly and analysis of genome sequence data. Focus on new tool development and adapting existing tools and processes for the Genome Assembly and Analysis Pipeline. Maintained local copies of externally developed tools using dotkits.• GATK-Queue: Grid Engine Integration – Developed and implemented Grid Engine support for GATK-Queue (https://github.com/broadgsa/gatk) using the Java DRMAA API from within a Scala codebase.• AllPaths-LG: BAM output of read-pair alignments used in scaffolding – Wrote AllPathsToBAM, using OpenMP for parallelization, to generate a BAM file of the read-pair to assembly alignments used by AllPaths-LG (http://www.broadinstitute.org/software/allpaths-lg/blog) to generate scaffolds.

Utilized software and databases to assemble and analyze genome sequence data. Served as point person for groups across the program to identify and resolve technical problems relating to the assembly and analysis of genome data, proposed and implemented upgrades to existing tools and processes to enhance analysis techniques and the quality of results, and developed and implemented innovative analytical tools and processes.• Subversion migration: Lead – Organized the team's internally developed sequence and assembly manipulation and analysis tools. Managed their migration to a source control system (Subversion).• Telomere Assembly: The Means To An End: Poster presented at the 2010 SFAF conference in Santa Fe, NM – Developed standardized de novo method of identifying telomere subunit motifs. Leveraged this into the construction and extension of telomeres in existing assemblies. Method published in: Rhind, et al. (2011). Comparative Functional Genomics of the Fission Yeasts. Science, 332(6032), 930-936. doi:10.1126/science.1203357• Arachne: Improved Algorithm for Hybrid Assembly, Usage Expert – Updated the HybridAssemble module for the Arachne tool suite (http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page), resulting in a significant improvement in contig and scaffold N50s. Developed the team's hybrid assembly process for Sanger-NGS projects utilizing the updated module. Served as worldwide point-of-contact for Arachne usage issues.• Genome Assembly and Analysis – Completed multiple assembly projects of genomes ranging from megabase to gigabase scale (bacterial, fungal, and metazoan). Utilized Sanger and NGS (454 and Illumina) data, as well as tools such as optical maps, genetic maps, and FISH mapping to improve assemblies.

Wyeth Consumer Healthcare: Developed, documented, tested, and migrated LabWare LIMS master data objects for lab implementation as project team member.• Inductively Coupled Plasma Optical Emission Spectrometer (ICP-OES) Interface: Developer – Designed, developed, and implemented the first LIMS/ICP-OES bidirectional software interface in the Wyeth network, eliminating the need for manual data entry and reducing the possibility of human error.

Assisted gifted high school students within an accelerated AP Computer Science course both in and out of the classroom. Supervised residential students.

Taught recitations for Introduction to Programming in Java. Tutored students in Java and Logic Design.