Thomas Nate Person Email & Phone Number

Huntsville, Alabama, Us

University Park, Pa, Us

Working to implement a pipeline utilizing the AI algorithm for detecting horizontal gene transfers utilizing the PlantTribes (https://github.com/dePamphilis/PlantTribes) pipelineDeveloped a python application for detecting paralogous genes via k-means clustering of blast scores. Currently working on analyzing results to determine sensitivity and specificity as compared to other published algorithmsAssisted in R code standardization of analysis program MethylIT https://git.psu.edu/genomath/MethylIT for Bioconductor submission

Murray , Ut, Us

Design and implement a RESTful API for interfacing with an Azure Spark interface to perform CRUDoperations on Parquet files.Design and implement a Parquet schema for efficient storage and rapid retrieval of variant andphenotypic dataDesign and implement an ETL pipeline for transforming VCFs to and from ParquetDesign and build an Azure Spark system for running bioinformatic tools and pipelinesWrite dockerfiles for containerization of bioinformatic tools and deploy them into Azure

Danville, Pa., Us

Lead bioinformatician in a multifaceted multiyear project shepherding 2500 samples from research grade sequencing to CLIA confirmation and ingratiation into our EPIC EHR systems Genomics module.Python implementation of the RIFTEHR algorithm ( https://github.com/thomasperson/riftehr)Designed and implemented a FHIR enabled GPACS system for storing 150k simulated variant call files and integration with a SMART on FHIR HSCPBuilt a custom GPACS database system with a RESTful API and a SMART-on-FHIR system for integration with the HSPC virtual EHR system and our corporate collaborators https://simulconsult.com/Expanded and improved a relational database schema designed to store variants called from the MyCode exome sequencing project to successfully store and query variants, quality metrics, and annotations from over one hundred and fifty thousand vcf filesDeveloped of a query pipeline for extraction of medically actionable high-quality variants on dozens ofvariables and option from our custom built genomic database to facilitate CLIA conformation of our NGSdata set for returning results to our MyCode participantsImplementation and execution of the GATK 3.x best practices pipeline for use on the DNAnexus cloudplatform for variant calling on over ninty thousand exome capture bam filesAssisted in development of an annotation program, PharmCAT, to annotate variants according to CPICguidelines

Marshfield, Wisconsin, Us

Creation of programs and NoSQL Cassandra tables for annotation of variants against the UCSC RefGene and custom built database tables. GWAS on data from Illumina, Affymetrix, and Sequenom platforms on the Personalized Medicine Research Project (PMRP) biobank.Processing and analyzing whole genome sequence data from Complete Genomics taken from hundreds of individuals in the PMRP biobank.Assisting in developing novel research tools and processes to facilitate and speed research on a Hadoop cluster. Analyze targeted exome capture genetic data for a pharmacogenetic study.Pipeline development.

Dallas, Texas, Us

Assist PI's in Biomedical Informatiatic research question through the use of Natural Language Processing from Epic EMR system.NGS processing with tools such as GATK, Samtools, BICseq, and PicardSet up, manage, maintain a bioinformatic Galaxy server. Setup, testing, cluster configuration, and deployment of newly created tools for a Galaxy bioinformatics server

Dallas, Texas, Us

Responsible for building and maintaining a microarray database to contain microarray data in such a way as to allow for datamining, collaborative efforts, and ensure proper backupsAssists researchers in Affymetrix and Illumina microarray analysis through statistical calculations and pathway analysis in programs such as Ingenuity, DAVID, Partek and SpotfireMaintains all research computers including computers connected to research equipment. Coordinates backup and storage of research dataReran basic processing NGS applications, such as cufflinks, on our Ubuntu Linux processing serverAssisted researchers in planning for and analyzing NGS data sets

Dallas, Texas, Us

Metabolic network creation and curation with the Biocyc Pathway Tools program in a MySQL database on a RedHat Linux system Metabolic network comparison from genomic data of multi-drug-resistant M. tuberculosis and drug-susceptible M. tuberculosis Integration of M. tuberculosis and H. sapien metabolic networks for in silico modeling of infection and identification of drug targets Analysis of networks via Java scripts and visualization through Cytoscape. Representation of networks with SBML and other formats. Maintaining and creation of a MySQL database to contain data.

Los Alamos, Nm, Us

Bioinformatic Intern at Los Alamos Nation Laboratory, where I worked on Metabolic Network creation with Biocyc/Pathway Tools program for the OralGen Project, focusing on unique pathways and reactions in P. gingivalis

Richardson, Texas, Us

Responsible for maintaining that UT Dallas wireless environment, focusing primarily on student housing

Falls Church, Virginia, Us

System Administrator employed with General Dynamics contracted to the USAF at Goodfellow AFB.Complete administration, of a Secure Windows 2000 and a Windows 2003 Domain combined totaling over 20 servers, 1100 workstation, 1400 user accounts and 30 TB of NetApp NAS space all over a Gig-E network and integrated with a Solaris 10 network

Bethesda, Md, Us

System Administrator employed with Lockheed Martin contracted to the USAF at Goodfellow AFB.Administration of 2 separate secure networks of 30 NT Servers, 1100 NT Workstations, over 1700 users and two Raid Array’s totaling 6.5TB over an ATM fiber network

Randolph Afb, Tx, Us

Network Systems Administrator - Continual configuration of three separate Windows NT and 2000 domain networks for use with Windows 95, 98 and NT 4.0, and 2000 clientsHelp Desk Technician - Technician leader in charge of three trainees while providing expert technical support for over 7600 users and assisted in conversion of 11 File servers and 13 Exchange servers from Novell 3.2 to Microsoft NT 4.0Computer Technician - Lead technician for 7,000 computer assets for 2 separate networks for all repair and troubleshooting from switch to keyboardData Base Administrator - Daily update and maintenance of four separate databases running on UNIX, Microsoft SQL 7.0, Sybase SQL 5.0, and Microsoft Access 2000 ensuring accurate and current records

Doctor Of Philosophy - Phd, Genomics And Bioinformatics

Master’S Degree, Bioinformatics And Computational Biology

Bachelor’S Degree, Biochemistry

3C0X1 Communications - Computer Systems Operations

Integrity First, Service Before Self, And Excellence In All We Do

High School