10 Discovery Drive Farmington, CT 06032 (860) 837-2054 [email protected]

William S. Sanders

Employment

Manager - Information Technology Department Jan-2018 to Present Research Cyberinfrastructure The Jackson Laboratory Farmington, CT

Systems Analyst - Information Technology Department Feb-2016 to Jan-2018 High Performance Computing The Jackson Laboratory Farmington, CT

Section Editor (Bioinformatics) Genomics, Proteomics, and Bioinformatics Apr-2014 to Jun-2015 Beijing Institute of Genomics Chinese Academy of Sciences Beijing, China

Postdoctoral Associate - Institute for Genomics, Biocomputing, and Biotechnology Oct-2011 to Feb-2016 Peterson Laboratory Mississippi State University Starkville, MS

Programmer / Analyst Institute for Genomics, Biocomputing, and Biotechnology May-2011 to Oct-2011 Mississippi State University Starkville, MS

Graduate Research Assistant Department of Computer Science & Engineering Jan-2007 to May-2011 Mississippi State University Starkville, MS

Graduate Research Assistant Department of Biochemistry & Molecular Biology Jan-2004 to Dec-2006 Mississippi State University Starkville, MS

Teaching Assistant Department of Biochemistry & Molecular Biology Jun-2002 to Feb-2003 Mississippi State University Starkville, MS

Computer & Network Technician Computers Plus Jul-1998 to Jun-1999 Oxford, MS

Education

Ph.D. Computer Science Mississippi State University In Progress High Performance Computing Advisor: Dr. Ioana Banicescu

Ph.D. Molecular Biology Mississippi State University 2011 Computational Biology & Machine Learning Advisor: Dr. Susan Bridges

B.S. Computer Science Mississippi State University 2003

B.S. Biochemistry Mississippi State University 2003

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Publications

A genomic resource for the sedentary semi-endoparasitic reniform Journal of Nematology In press nematode, Rotylenchulus reniformis Linford & Oliveira ​ ​

Five life stage specific transcriptome assemblies for Rotylenchulus Journal of Nematology In press ​ reniformis

Insights into the evolution of the New World diploid cottons Genome Biology and Evolution 2018 (, subgenus Houzingenia) based on genome sequencing ​ ​ ​ ​

Comparative genomics of an unusual biogeographic disjunction in Genome Biology and Evolution 2017 the cotton tribe () yields insights into genome downsizing

Independent Domestication of Two Old World Cotton Species Genome Biology and Evolution 2016

Comparative Analysis of Fresh and Cryopreserved Boar Reproduction, Fertility, and Development 2015 Spermatozoa Using RNA Sequencing

Repeated polyploidization of Gossypium genomes and the evolution Nature 2012 ​ ​ of spinnable cotton fibres

Prediction of Cell Penetrating Peptides by Support Vector Machines PLoS Computational Biology 2011

Machine Learning and Mapping Algorithms Applied to Proteomics ProQuest/UMI Dissertation Publishing 2011 Problems

The Proteogenomic Mapping Tool BMC Bioinformatics 2011

Prediction of peptides observable by mass spectrometry applied at BMC Bioinformatics 2007 the experimental set level

Funding

Total Funding: $68,461.28

Role Title Agency Amount Date Status

PI Campus Champion Allocation for The NSF-XSEDE 905,500-SUs 27-Jun-2016 Funded Jackson Laboratory (~$45,275.00)

PI Finishing the Crotalus horridus (Timber 1. MSU-IGBB $10,224.28 21-May-2015 Funded ​ ​ Rattlesnake) Draft Genome with the 2. MSU-CSE MidSouth Computational Biology and 3. MSU-CVM Bioinformatics Society

PI Sequencing and Assembling a Draft 1. MSU-IGBB $12,962.00 20-Mar-2015 Funded Genome of drynarioides, a 2. ​ ​ Gossypium Outgroup USDA-FAS-Borlaug ​

Co-PI Developing Resources and Tools to USDA-NIFA $448,158.00 02-May-2014 Not Funded Facilitate Discovery of Disease-Associated microRNAs in Farm Animals

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Service

Technical Committee Member Practice and Experience in Advanced Research 2017-2018 CyberInfrasctructure (PEARC) Conference - 2018 ​ Pittsburgh, PA

Organizing Committee Member MidSouth Computational Biology and Bioinformatics Society 2017-2018 Annual Conference - 2018 ​ Starkville, MS

XSEDE Campus Champion Extreme Science and Engineering Discovery Environment 2016-Present The Jackson Laboratory (XSEDE) National Science Foundation

Workshop Organizer - Evolution of and Animal Genome Conference 2016-Present Genome Size San Diego, CA

Project Leader - Crotalus horridus MidSouth Computational Biology and Bioinformatics Society 2012-2018 ​ (Timber Rattlesnake) Genome Project

Session Chair - Proteomics Session MidSouth Computational Biology and Bioinformatics Society 2012 Annual Conference Oxford, MS

Certifications, Training, & Licensures

Scaled Agile Certified SAFe 4 DevOps Practicioner 2018

Scaled Agile Leading SAFe (Certified SAFe 4 Agilist) 2018

The Jackson Laboratory Frontline Leadership Training 2018

Karrass Effective Negotiating 2017

Karrass Negotiating Effectively Within Your Own Organization 2017

American Red Cross Adult CPR/AED, Infant CPR, and First Aid 2017-2019 (GVCZ9G)

Software Carpentry Foundation Software Carpentry Certified Instructor 2016

ROI Training Google Cloud Platform Fundamentals Certificate (CP100A) 2016 ​ ​

Bagley College of Engineering Information Assurance Certificate 2010 Mississippi State University (NSTISSI #4011 & NSTISSI #4014 Certified Program)

Federal Communications Commission Amateur Radio Technician License 2009 Amateur Radio Service (Callsign: KF5CZK)

Bruker Daltonics FLEX Series MALDI-TOF MS Operator Course 2006

Bagley College of Engineering Computational Biology Certificate 2007 Mississippi State University

Microsoft Microsoft Certified Professional 1998-2001 Windows NT 4.0, Networking Essentials

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CompTIA CompTIA A+ Certified Professional (COMP10072148) 1998 ​

Awards & Honors

JAX Champion - Excellence in Quality The Jackson Laboratory 2018 and Innovation Award Bar Harbor, ME | Farmington, CT | Sacramento, CA

st 1 ​ Place Postdoctoral Oral Presentation MidSouth Computational Biology and Bioinformatics Society Mar 13-14 2015 ​ Annual Conference Little Rock, AR

rd 3 ​ Place Student Oral Presentation MidSouth Computational Biology and Bioinformatics Society Feb 23-24 2008 ​ Annual Conference Oklahoma City, OK

st 1 ​ Place Student Poster Presentation MidSouth Computational Biology and Bioinformatics Society Feb 1-3 2007 ​ Annual Conference New Orleans, LA

University Honors Program - Phase I Mississippi State University May 2000 Scholar Starkville, MS

Teaching Experience

Instructor Introduction to High Performance Computing Workshop 2016-2018 The Jackson Laboratory

Instructor Excel, OpenRefine, Python 2017 Data Carpentry Workshop The Jackson Laboratory

Instructor Cloud Computing for Genomics 2017-2018 Data Carpentry Workshop The Jackson Laboratory

Instructor R for Reproducible Scientific Analysis 2016 Software Carpentry Workshop The Jackson Laboratory

Mentor Day One Leadership Community 2013-2015 Mississippi State University

Guest Lecturer High Throughput Sequence Analysis (CSE 6990) 2015 ​ ​ Department of Computer Science & Engineering Mississippi State University

Mentor Norman E. Borlaug International Agricultural Science and Technology Fellowship Program 2014-2015 Foreign Agricultural Service United States Department of Agriculture

Mentor Research Experience for Undergraduates 2007-2015 Undergraduate Research in Computational Biology Mississippi State University

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Lecturer Biochemistry Boot Camp 2014-2015 Department of Chemistry Mississippi State University

Guest Lecturer Genomes & Genomics (BCH 8653) 2012 ​ ​ Department of Biochemistry & Molecular Biology Mississippi State University

Student Tools for Teaching Introductory Computer Science (CSE 8990) 2010 ​ ​ Department of Computer Science & Engineering Mississippi State University

Guest Lecturer Essentials of Molecular Genetics (BCH 4113) 2009 ​ ​ Department of Biochemistry & Molecular Biology Mississippi State University

Teaching Protein Methods (BCH 4414/6414) 2004 ​ ​ Assistant Department of Biochemistry & Molecular Biology Mississippi State University

Teaching Biochemical Methods (BCH 4805/6805) 2002 ​ ​ Assistant Department of Biochemistry & Molecular Biology Mississippi State University

Reviewing Activities

Gene Nucleic Acids Research Bioinformatics

Interdisciplinary Sciences: Genomics, Proteomics, and BMC Genomics Computational Life Sciences Bioinformatics

PLoS One BMC Bioinformatics Journal of Translational Medicine

Journal of Biocomputing BioSystems

Software Tools

The Proteogenomic Mapping Tool. A Java-based implementation of the Aho-Corasick string searching algorithm http://www.agbase.msstate.edu/tools/pgm/ which takes peptides observed by mass spectrometry and maps them onto a source genome.

PepOut – A Distance Based Peptide A Perl/MySQL-based program that uses the k-nearest neighbor algorithm ​ Validation Tool. combined with Bayesian probabilities to perform mass spectrometry peptide http://www.agbase.msstate.edu/cgi-bin/tools/ validation using target and decoy databases.

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Skills

Software Skills Programming Languages: Perl, C/C++, Python, Java, MPI Statistical Analysis: R, SAS Other: MySQL, WEKA Machine Learning Toolkit, Apache, BioPerl, BioPython, ABySS Sequence Assembler, Velvet Sequence Assembler, Roche 454 GS De Novo Assembler, CLC Genomics Workbench

Research Skills Genomics, Genome Sequence Assembly & Analysis, Proteomics, Mass Spectrometry, Machine Learning, Data mining, Algorithm Analysis & Design, Eukaryotic Tissue Culture, High Performance Computing, High Performance Liquid Chromatography, Gas Chromatography, Gel Electrophoresis

Miscellaneous German (minimal professional proficiency), Grant Writing, Accounting, Marketing, Financial Management, Principles of Management

Presentations

MCBIOS Timber Rattlesnake Genome MidSouth Computational Biology and Bioinformatics Society Mar 31 2018 Project: Current Status & Lessons Annual Conference Learned Starkville, MS

Making It Work: Facilitating Collaboration University of Mississippi Medical Center Mar 28 2018 between IT and Researchers for Jackson, MS Computation-Intensive Programs Invited Presentation

A Mitochondrial Genome of the Timber MidSouth Computational Biology and Bioinformatics Society Mar 3-5 2016 Rattlesnake (Crotalus horridus) and a Annual Conference ​ ​ Reptilian Mitochondrial Phylogeny Memphis, TN

Genome size evolution among closely Plant and Animal Genome Conference XXIV Jan 9-13 2016 related species in Gossypium San Diego, CA ​

Genome Assembly & Analysis – From Southern Section of the American Society of Plant Biologists Mar 28-29 2015 “Gold-Standard” Assemblies to “Base (SS-ASPB) Metals” Dauphin Island, AL Kriton-Hatzio Symposium Keynote Address

Assembly and molecular MidSouth Computational Biology and Bioinformatics Society Mar 13-14 2015 characterization of a draft genome Annual Conference sequence and annotation of the Little Rock, AR plant-parasitic nematode Rotylenchulus ​ reniformis

Update on the Timber Rattlesnake MidSouth Computational Biology and Bioinformatics Society Mar 13-14 2015 Genome Collaborative Project Annual Conference Little Rock, AR

Draft Genome Assembly and Plant and Animal Genome Conference XXIII Jan 10-14 2015 Comparative Genomic Analysis of the San Diego, CA Plant-Parasitic Nematode Rotylenchulus ​ reniformis

Molecular Insights into the Rotylenchulus Plant and Animal Genome Conference XXIII Jan 10-14 2015 ​ reniformis transcriptome San Diego, CA ​

MCBIOS Timber Rattlesnake Genome MidSouth Computational Biology and Bioinformatics Society Mar 6-8 2014 Project Collaboration Annual Conference

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Stillwater, OK

Sequencing, Assembly, and MidSouth Computational Biology and Bioinformatics Society Mar 6-8 2014 Characterization of the Genome of Annual Conference Rotylenchulus reniformis Stillwater, OK

SABRe – Sequence Assembly By MidSouth Computational Biology and Bioinformatics Society Mar 6-8 2014 Reference Annual Conference Stillwater, OK

Assembly, Annotation and Plant and Animal Genome Conference XXII Jan 11-15 2014 Proteogenomic Mapping of San Diego, CA Rotylenchulus reniformis

Unveiling the Molecular Arsenal within Annual Meeting of the Society of Nematologists Jul 14-17 2013 Rotylenchulus reniformis via de novo Knoxville, TN ​ ​ Transcriptome Assembly.

Identification of Protein Coding Genes in MidSouth Computational Biology and Bioinformatics Society Apr 5-6 2013 the Plant-parasitic Nematode Annual Conference Rotylenchulus reniformis through Columbia, MO ​ Comparative Proteogenomic Mapping with Caenorhabditis elegans ​

The Genome of Reniform Nematode, MidSouth Computational Biology and Bioinformatics Society Apr 5-6 2013 Rotylenchulus reniformis Annual Conference Columbia, MO

De Novo Transcriptome Assembly of the MidSouth Computational Biology and Bioinformatics Society Apr 5-6 2013 ​ Plant-Parasitic Nematode Rotylenchulus Annual Conference ​ reniformis Columbia, MO

Genome Size Evolution In Gossypium Plant and Animal Genome Conference XXI Jan 12-16 2013 ​ (Cotton): Progress and Prospects San Diego, CA

Assembling and Annotating the Genome MidSouth Computational Biology and Bioinformatics Society Feb 17-18 2012 of a Plant Parasitic Nematode, Annual Conference Rotylenchulus reniformis, with Oxford, MS ​ Sequences Obtained Using 2nd ​ Generation Sequencing Technologies

The Rotylenchulus reniformis Genome: Plant and Animal Genome Conference XX Jan 14-18 2012 ​ ​ Sequencing, Assembly, and Annotation San Diego, CA

Sequencing and Analysis of the Plant and Animal Genome Conference XX Jan 14-18 2012 Rotylenchulus reniformis Transcriptome San Diego, CA ​

Proteogenomic Mapping of Gallus gallus MidSouth Computational Biology and Bioinformatics Society Apr 1-2 2011 ​ Serum Annual Conference College Station, TX

Experimental genome annotation by Workshop on Nanotechnology, Proteogenomics and Visual Dec 14-18 2010 proteogenomic mapping: experimental Analytic Applications for Schistosomiasis Control evidence for predicted proteins, novel Abuja, Nigeria proteins and protein structure

Metrics for Mass Spectrometry Dataset MidSouth Computational Biology and Bioinformatics Society Feb 19-20 2010 Quality Validation Annual Conference Jonesboro, AR

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A Staged Search Strategy for Plant and Animal Genome Conference XVIII Jan 9-13 2010 Proteomics Based Structural Annotation San Diego, CA in Chicken

Proteomics Based Genome Annotation Mississippi State University Digital Biology Learning Community Oct 21 2009 in Gallus gallus Starkville, MS ​

Features Predictive of Cell Penetrating Research in Computational Molecular Biology (RECOMB) 2009 May 18-21 2009 Peptides Validated by Machine Learning Tucson, AZ Classifiers

Prediction of Cell Penetrating Peptides Intelligent Systems for Molecular Biology (ISMB) 2008 Jul 19-23 2008 by Machine Learning Classifiers Toronto, ON

Proteomics Based Structural Genome Avian Genomics and Gene Ontology Annotation Workshop May 19-20 2008 Annotation in Chicken Starkville, MS

Prospecting for new genes in the Cold Spring Harbor Laboratory - Genome Informatics Meeting Nov 1-5 2007 chicken genome using proteomics Cold Spring Harbor, NY

Pepfly: A Tool for the Prediction of MidSouth Computational Biology and Bioinformatics Society Feb 1-3 2007 Peptides Observed by Mass Spectra Annual Conference New Orleans, LA

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