Sean Sykes

Managed maintenance and enhancement of Django-based high-throughput sequence assembly pipeline and analysis tools. • Developed flexible read data processing tool to filter contamination, trim low quality bases or remove data artifacts. Software helped analysts obtain high-quality assembly results on the most difficult datasets. • Diagnosed software bugs and investigated analysis failures using JIRA. Work allowed continuous processing of thousands of deliverables per month.

Supervised software engineering team delivering novel solutions to assembly and analysis problems. • Led development and implementation of a Python-based, modular, assembler-agnostic assembly analysis software package (GAEMR). Software collected the output of many disparate bioinformatics tools into one easily digestible format. • Designed and developed automated Multi-Locus Sequence Tag (MLST) analysis that accurately identifies MLST without prior knowledge of organism. Tool removed need to run manual internet search across two different sites. • Collaborated in development of multi-center Human MicroBiome Consortium’s protocol for reference-alignment of sequencing data. Work determined best alignment method given the requirements. • Presented assembly analysis instruction to work community to show scientists how to look at their data. Instruction received high peer score ranking. • Supervised and provided training and expertise to junior team members.

Devised innovative solutions to interrogate assembly and read data. Presented results to scientific directors. • Developed tools to manipulate large sequence datasets, model read lengths in different sequencing technologies, locate possible contamination, and create randomized input read sets for assembly coverage experiments. Work presented to scientific conference on two occasions. • Assembled genomic sequence using classic and next generation sequencing technologies. Effort resulted in 8 assembly publications. • Analyzed all aspects of the assembly process including bias, variation detection, and laboratory and algorithm errors to quickly diagnose problems and implement solutions.

Supported effort to create finished, complete genome data. • Assigned to most challenging projects. Met or exceeded set monthly goals. • Developed essential Perl scripts to increase team efficiency and project accuracy. • Supervised and provided training and expertise to junior team members.

Collaborated in identifying potential targets for plant genomics experiments. • Utilized literature searches and data mining to further understand the role of a given gene family in plants. Effort led to nominated genes for a Functional Genomics pipeline. • Verified gene boundaries (Met1 and ter*) and performed gene modeling using computational methods. Analysis ensured accurate identification of gene product.

Supervised multi-dimensional research finishing effort. • Managed full-length cDNA project for Corn Functional Genomics pipeline, Soybean BAC project for a Strategic Genetics pipeline, and large-scale genomic finishing efforts. Work led to 2 publications. • Recognized and rewarded three times for exceptional work.

Worked within a group responsible for the maintenance and operation of a cutting-edge, high-throughput sequencing lab. • Trained fellow Research Associates in automated DNA sequencing and in editing/assembling raw sequence data.