Shane Sanders Email and Phone Number

Architect, implement, and manage information technology solutions serving faculty and research staff.Manage staff and technical contract staff for excellent performance.Review and evaluate performance of existing systems to determine operating costs, productivity levels, and upgrade requirements.Communicate metrics, milestones and goals to IT leadership, organization executives, department heads, research faculty, staff, and end users.Contribute to budget planning, business case justifications, new technology evaluations, and cost/benefit analyses for spending and initiatives.

Identified and recommended innovative solutions and integrated proposals for server, storage, and network systems, including hardware and software acquisition, installation and administration based on the scientific needs of the community.Installed and updated scientific and research applications in the HPC environment, documented system changes, authored and maintained documentation for end users.Investigated application issues, documented findings: communicated with scientists to answer questions, troubleshoot problems and develop appropriate computational strategies to process and analyze their data.Benchmarked applications, pipelines and workflow performance, and determined areas for improved efficiencies.Created system design proposals: Stayed current with new trends and emerging information technologies and informatics tools, advocated for and lead the adoption of these technologies.

Institute for Genomics, Biocomputing, and Biotechnology:Planned, designed and executed experiments to evaluate the evolutionary biology of numerous species within the Genus Gossypium (cotton) through the use of next-generation sequencing techniques in collaboration with researchers at Mississippi State University, University of Georgia, Iowa State University, US Department of Agriculture (USDA), and Cotton, Inc.Planned, designed and executed experiments to sequence, assemble, and annotate the genome of the plant parasitic nematode, Rotylenchulus reniformis (the reniform nematode) using Illumina and Roche 454 nucleic acid sequencing technologies and proteomics analysis in collaboration with researchers at Mississippi State University and the US Department of Agriculture (USDA).Lead the effort to sequence and assemble the genome of the timber rattlesnake (Crotalus horridus), coordinating researchers across multiple institutions including Mississippi State University, University of Arkansas, University of Southern Mississippi, University of Missouri, and the U.S. Army Engineer Research and Development Center (Vicksburg, MS).Designed and planned analysis of RNA-seq (transcriptome) expression data to evaluate the effects of freeze-thaw effects on boar spermatozoa and improve fertility outcomes.Installed, maintained, and optimized software (performance analysis) for use on a number of high performance compute (HPC) systems.Developed software tools and pipelines for analysis of genomic data on HPC systems using published research software and novel programs and driver scripts developed in Perl, C, and Bash.Taught workshops, courses, and seminars on computational biology techniques and genome sequencing and assembly.Authored and assisted in the writing of grant proposals.Authored research reports and presentations. Presented at scientific conferences and forums.Supervised and trained visiting scientists and student workers.

Institute for Genomics, Biocomputing, and Biotechnology:Identified, developed (Perl), and installed software packages for identification and analysis of short sequence repeats (SSRs) for various organisms. Analysed and interpreted results.Installed and utilized MPI-based genome assembly algorithms and tools on high-performance compute (HPC) clusters for genome assembly for plant parasitic organisms. Analysed and interpreted results.Assisted with the analysis and interpretation of mass spectrometry (proteomics) results.

Institute for Digital Biology / Department of Computer Science & Engineering:Developed machine learning classifiers and data sets to predict peptides observable using mass spectrometry (proteomics).Implemented mapping and machine learning algorithms and developed pipelines for structural genome annotation using proteomics data (proteogenomic mapping) in C/C++/Java/Perl.Developed machine learning classifiers and data sets to predict cell penetrating peptides, then experimentally validated peptides predicted to be penetrating and non-penetrating via tissue culture.Refined and refactored pipelines for statistical validation of peptide-spectra-matches (PSMs) using C++, Perl, and MySQL.Designed and conducted experiments, both computational and with mass spectrometry and tissue culture.Authored research reports and presentations. Presented at scientific conferences and forums.Mentored undergraduate and summer students on computational biology research projects. Taught Python and Perl, along with various other bioinformatics tools, to graduate and undergraduate students.

Department of Biochemistry & Molecular Biology:Operated and maintained MALDI-TOF mass spectrometer for both protein and nucleic acid analysis.Operated and maintained numerous HPLC and GC based mass spectrometers for analysis of lipid based biofuels.Established and maintained tissue culture for numerous eukaryotic cell lines used for experiments.Developed and maintained departmental chemical inventory database (SQL), including material specifications sheets for each item.Designed and deployed computer resources (file servers, FTP servers, etc.) for document sharing, collaboration, and transfer among collaborating lab groups and researchers.Developed data analysis and visualization programs and scripts in C and Perl.

Department of Biochemistry & Molecular Biology:Instructed graduate and undergraduate students in laboratory and data analysis techniques for protein purification, liquid chromatography, electrophoresis, and enzyme kinetics.Assisted in the creation and grading of in-class assignments, homework, quizzes, exams and other assignments. Developed online course webpages detailing laboratory assignments and experimental techniques used in the course.

Diagnosed and repaired computers (MS-DOS, MS Windows 3.11/NT/95/98, MacOS, OS/2) and computer network environments (Novell NetWare, Microsoft Windows NT).Delivered and deployed solutions to customer sites.Installed and configured various software packages.Assisted in sales of computers and computer peripherals to retail, commercial, and educational customers.