John Caskey Email & Phone Number

Madison, Wi, Us

Madison, Wi, Us

Madison, Wi, Us

Create Machine Learning models to predict sepsis outcomes in patient clinical data, using NLP from patient clinical notes for COVID contact tracing, build and maintain LabKey database with genetic variants related to cancerous phenotypes, build and run variant calling workflows on patient genetic data, perform statistical analyses on variant calling

Madison, Wi, Us

Key responsibilities include:- Writing code in Python and R to conduct analyses on NGS Biological datasets- Conducting statistical analyses in R and SAS JMP for experiments; example work: https://gist.github.com/disulfidebond/8197de960054cfcec754cdd273aaeb76- Using Machine Learning to create a novel approach to string matching on NGS Biological data, example here: https://github.com/disulfidebond/MHC_Automation_ML- Instructing technicians on best practices for computer use and data managementOther responsibilities include:- Managing computing resources for research lab- Data management and archival of research data, including proper submission to NCBI and EBI- Creating python notebooks to access and utilize local High Throughput Computing resources- Coding iOS App that provides a GUI for researchers

Baton Rouge, La, Us

Applied string-matching algorithms to Machine Learning (ML) in the area of RNASeq and Bioinformatics. Developed and Evaluated Deep Learning Models. Created novel algorithms for genomic analyses of Next Generation Sequencing (NGS) datasets. Conducted core analysis work in Biostatistics and Genomics analysis. Managed a High Performance Computer. Conducted statistical analysis of biological data, and creates analysis pipelines to optimize accuracy of work and efficiency of workflow. Enhanced experimental designs to incorporate wet lab and computational aspects. As an expert in Biology and Computer Science, I facilitated communication and translated information between Biologists and Computational Scientists, to ensure cohesiveness and accuracy across multiple projects. I managed complex assignments/projects with cross-functional project teams, typically 5-15 projects simultaneously. Software Utilized to Develop Pipelines and Develop Applications included:✔ Data Analysis: BWA, Tophat, Cufflinks, Hadoop in HPC environment✔ RNASeq/DNASeq: DNASTAR, Partek Flow, Partek GS, IBM Platform App Manager, Perl, Bash★ Key Accomplishments ★ • Wrote iOS (Swift) and Android (Java) App for yearly LSU conference• Wrote software in Java, Python, and Bash for researchers that allowed them to accurately and independently run analysis instead of outsourcing it. Made research more cost efficient/scalable, reduced turnaround time. • Managed complex assignments/projects with cross-functional project teams; typically 5-15 projects simultaneously.• Designed/taught highly reviewed workshops on the new IBM Power8 High Performance Computer.• Developed machine learning algorithms.Specialties: Bioinformatics ✔Project Management ✔Deep Learning Engineering ✔Genomics ✔Electronic DNA Sequencing ✔Statistics ✔Biostatistics/Genomics Analysis ✔Deep Learning ✔BioChemistry ✔Mathematics ✔Cross-Functional Collaboration ✔Code Review ✔Neural Networks ✔Data Science

New Orleans, La, Us

Used analytical software for RNAseq analysis and wrote customized Perl, Python, and Bash scripts to assist in analysis of RNASeq data. Wrote comprehensive protocol for extraction, processing, and preparing RNA tran-scripts from Bacterial RNA for RNASeq using Life Technologies Ion Torrent. Created RNAseq database with searchable Borrelia burgdorferi genome. Prepared biological samples for Next Generation Sequencing (NGS) and RNASeq. Conducted experiments to examine the phenotypic change of Borrelia burgdorferi.★ Key Accomplishments ★ • Developed and utilized iOS App for Cell Counting (MultiCell).• Wrote customized Perl, Python, and Bash scripts to assist in analysis of RNASeq data.• Performed statistical analyses (Pearson's Chi-Squared, t-test, and Bayesian) for published research. • Invited by the U.S. Embassy to produce and deliver a guest lecture at Belgrade University in Serbia on using computer programs to analyze scientific medical data.Specialties: ✔Bioinformatics ✔Project Management ✔Genomics ✔Electronic DNA Sequencing ✔Statistics ✔Biostatistics/Genomics Analysis ✔BioChemistry ✔Writing Software ✔String Matching ✔Mathematics ✔Cross-Functional Collaboration ✔Version Control ✔Reporting/ Documentation Architecting ✔Software Engineering/Management ✔Code Review ✔Data Science ✔Systems Administration ✔Server Maintenance/Security ✔Base-Calling ✔Burrows-Wheeler Alignment ✔Tophat ✔Cufflinks ✔Perl ✔Bash ✔C ✔C++ ✔Swift ✔Java ✔Blender ✔Adobe Photoshop ✔MySQL ✔iLife ✔Final Cut ✔XCode ✔R

Cupertino, California, Us

• Trained team members on new software and products at launch days.• Assisted customers in troubleshooting iPhone, Mac, iPod, and software issues.• Performed Basic Troubleshooting on iOS devices.• Taught customers Apple software, including iWork, iLife, and Final Cut. • Set up imaging computers with demo software.Specialties: ✔Writing Software ✔Mathematics ✔Cross-Functional Collaboration ✔Version Control ✔Software Engineering/Management ✔Cloud Infrastructure & Computing ✔Systems Administration ✔Customer Service ✔Training ✔Server Maintenance/Security

Doctor Of Philosophy (Phd), Biomedical Sciences

Bachelor Of Science (B.S.), Biology

Bachelor Of Arts (B.A.), European History