Stephen Bolaris Email & Phone Number

Pleasanton, California, United States

Bulk Transcriptomics- Develop Nextflow pipeline to analyze data generated from Bio-Rad RNAseq kits- Support RD efforts for chemistry kits to develop bespoke analysis solutions - Turn key solutions for deployment of bioinformatics solutions Assay Development- Identify bioinformatics targets - Design Primers and various types of probes to assist in finding suitable assays for kit development- Bioinformatics and machine learning analysis solutions - Down stream analysis solution to meet the needs of customers AWS infrastructure- Help foster better understanding of AWS infrastructure- Incorporate software toolkits in AWS infrastructure for use in the cloud- Set up toolkits for use with AWS and APIs for democratization of HPC- Automation of additional infrastructure using continuous integration (CI) frameworks- Data lake development (backend and infrastructure)

Davis, California

Genomics and Microbiome Project LeadResponsible for integrating multiple data types including genotypic, phenotypic and microbiome data to contribute to the discovery and development of microbes for improving agricultural productivity.Building a bioinformatics pipeline to transform raw "-omics" data in to meaningful, digestible results. Managing the genomics / microbiome budget while still accomplishing goals set by the executive team, including being cost efficient for the use of AWS infrastructure for analysis. Genomics Whole genome sequencing of various microbial isolatesAssembly, annotation and identification of whole genomes using a custom built pipeline with multiple steps of QC built to ensure genome quality Creation of R shiny applications to allow other scientist to interact with genomics resultsTesting annotations of genomics results through mode of action studies invitro and invivoHelping understand isolates through phylogenetics and comparative genomicsInforming field trial selections and possible hazards before consortia go the fieldHelping to guide product testing by narrowing down the microbial library in to isolates of interestImplementation of straightforward lab QC such as QR code samplesUsing technology to increase efficiency and timeliness of samples throughputImage processing of Arabidopsis experiment to show direct effects of microbes in a plant system using genomic predictions Included the use of PacBio long read sequencing for high impact isolates using hybrid sequencingMicrobiomeCollection of samples from both the field and the labAnalysis for data to provide for regulatory purposesAnalysis of microbiome samples to guide testing and product developmentConstantly working on improving workflows to improve data qualityWorking with other bioinformatics for statistics and QC of the data prior to presenting results.

Riverside, Ca

Bioinformatics Research with the Larsen Lab - Graduating in June 2018Data Management Officer - NSF award number 1539638Communication skills:- Yearly presentations to Program symposium- Yearly presentations to committees for updates and performance evaluation- Presentations to elementary children for educational outreach- Conference presentations both poster and oral: Plant Genome Stability and Change (PGSC) 2014, PGSC 2016, Alucidate Confrence 2018 Wet lab responsibilities:- Molecular cloning- Bacterial transformations - Protein expression and purification- DNA / RNA library preparation for sequencing- Electrophoretic mobility shift assay (EMSA)- PCR, primer design, genotyping- Radio labeling of DNA- DNA and RNA extractions of plant tissue- Media production- Managing various plant lines and bulking seeds- quantitative real time PCR (qPCR)Bioinformatics responsibilities:- Data management - Managing software required for data analysis- Using R pipelines and developing novel scripts to tailor the analysis for specific objectives- DNA sequencing analysis (Variant Analysis)- RNA sequencing analysis (Transcriptome Analysis)- Develop basic websites Administrative responsibilities:- Managing and ordering supplies- Managing / Mentoring undergraduate researchers in the lab- Identifying and working with vendors to find solutions to lab problemsGraduate Student Mentor (Sep 2016- Jun 2018) - Hold weekly meetings with first year graduate students - Help mentees to navigate and transition to grad school life- Provide resources to mentees, and aid in professional developmentTeaching:- BIO 119 - Introduction to Bioinformatics- BIO 5LA - Introduction to Molecular Biology (Lab)- BIO 020 - Dynamic Genome

Santa Clara, Ca

Sample Management-Maintaining Clinical Trial Material Retain inventory -Performing Clinical Trial Material Retain inspections -Stability Management, scheduling and pulling samples for distribution to testing labs-Sample receipt and distribution, including the use of Laboratory Information Management System for sample tracking-Special request and shipping of samples to Outside Testing LaboratoriesPotency Lab-Maintaining lab equipment -Prepare GMP reagents-Stock Lab-Perform cell based potency assayRaw Materials-Inspection, sampling and Testing of GMP Raw MaterialsQC Microbiology (Environmental Monitoring)-USP water: daily sampling, perform bioburden, conductivity and total organic carbon testing-USP clean steam: quarterly sampling, perform bioburden, conductivity and total organic carbon testing -Non USP water: preform conductivity and total organ organic carbon testing-Static Environmental Monitoring of both Clinical and Commercial manufacturing facilities-Dynamic Environmental Monitoring of product fill environment, and personnel-Clean Dry Air and specialty gas testing -Autoclaving of testing materials-Gown qualification of clean room personnel-Mold identification of isolatesShipping and Receiving- Shipping and verification of Validated QC sample shipments- Packing validated shipmentsSupplementary Role- Participate and support regulatory audits- Support Site closure activities including+Decommissioning and decontamination of equipment+Validated System Change Requests (VSCRs) initiation and execution

Morgan Hill, Ca

Responsible for member check-inPoint of salesResponsible for member service, as well as minor clean up to the facilities

Tucson, Arizona

Perl programming, curation of genes present in the database, some web development using Mason HTML, minor direct database usage, creation a machine learning quality assessment algorithm.

Tucson, Arizona

Responsible for the emotional welfare and physical safety of 30 residents Use creative thinking to solve challenges that developManage flow of communication and support of team workGained experience in dealing with conflicts between othersHelp to manage groups comprised of other staff members

San Jose, Ca

Responsible for setting up, configuring and monitoring multiple servers in development environmentResponsible for setting up network, including security and remote access for usersConfigured and updated servers and applications according to engineering requirementsProvided input and helped develop design of logo and websiteTook part in research and development type projects and assisted CEO in other odd jobs relating to system analysis

San Jose, Ca

Uploaded files to designated space on specific seversResponsible for monitoring and converting Library video materials to MPEG format for storage and use as streaming videoHelped the assistant Tech. director with various odd jobsGained basic understanding of streaming video and managing content Added memory to computersKept inventory of schools computers and other related items

San Jose, Ca

Minor first aidTaping of athletes prior to athletic eventsAssist at sporting events where requiredVarsity Letter

Doctor Of Philosophy (Phd), Bioinformatics

Activities and Societies: Improv Anonymous at UC Riverside GGB GSA Vice President 2015 GGB GSA President 2017Genetics, Genomics.

B.S., Molecular And Cellular Biology, Computer Science

Activities and Societies: Sigma Alpha Lambda Honors fraternityDean's List (2009) Arizona Excellence (2005 - 2009)

High School

Activities and Societies: Bellarmine Gaming Club, Sports Medicine: Soccer, Football and Lacrosse, Dead language Society