Jainy Thomas, Phd Email & Phone Number

• Responsible for the development and implementation of pipelines, and analysis of long read whole genome sequence (WGS) HIFI data as part of Invitae’s collaboration with PacBio to improve Epilepsy diagnostics • Developed pipelines to analyze, annotate, visualize and prioritize structural variant (SV) data from PacBio WGS data based on Human Phenotype Ontology terms • Developing a pipeline to view methylation data from repeat expansions from long read data• Explored multiple tools… Show more • Responsible for the development and implementation of pipelines, and analysis of long read whole genome sequence (WGS) HIFI data as part of Invitae’s collaboration with PacBio to improve Epilepsy diagnostics • Developed pipelines to analyze, annotate, visualize and prioritize structural variant (SV) data from PacBio WGS data based on Human Phenotype Ontology terms • Developing a pipeline to view methylation data from repeat expansions from long read data• Explored multiple tools for analysis, annotation and prioritization of variants from WGS• Devised a new approach to efficiently analyze SV events for which breaktypes are not defined • Set up the pipeline and led the analysis of long read sequencing data from adaptive sequencing from Oxford Nanopore Technologies (ONT).• Troubleshot experimental issues in collaboration with the wet lab to improve assay performance• Bioinformatics analyst for novel experimental approaches for the development of new products• Collaborated and communicated with multiple internal and external teams to identify and solve issues during the development, implementation, and analysis. Show less

Salt Lake City

• Developed a novel computational approach to mine and analyze variations in retroviral insertions in hundreds of human genomes, a challenging problem to solve • Collaborated with researchers at Cornell, John Hopkins University and University of Michigan in the design, development, testing, validation, and publishing of a computational tool that genotypes polymorphic mobile element insertions (MEIs) in reference human population datasets• Obtained funding as a principal investigator to… Show more • Developed a novel computational approach to mine and analyze variations in retroviral insertions in hundreds of human genomes, a challenging problem to solve • Collaborated with researchers at Cornell, John Hopkins University and University of Michigan in the design, development, testing, validation, and publishing of a computational tool that genotypes polymorphic mobile element insertions (MEIs) in reference human population datasets• Obtained funding as a principal investigator to identify pathogenic CNVs in whole genome sequences (WGS) of patients with neurological autoimmune disease (multiple sclerosis) • As a principal investigator, led the analysis on the detection of pathogenic CNVs in WGS of individuals with pancreatic autoimmune disease (Type 1 diabetes) • Developed a pipeline to assemble and characterize non-reference insertions in WGS of three-generational families • Developed a pipeline to generate a consensus sequences of non-reference MEIs from WGS of diverse human populations • Currently developing a computational pipeline to perform a genome-wide analysis of MEIs of high impact in families with diseases and assessing their impact through multi-omics approach (ATAC-Seq / ChiP-Seq / RNA-Seq)• Identified and analyzed variants in WGS of families with rare genetic disorders • Completed training for Machine learning for Healthcare, and Data Visualization from the Department of Biomedical Informatics, University of Utah Show less

Salt Lake City

• Identified and analyzed different mechanisms that generate CNVs of genes • Analyzed RNA-Seq for novel transcripts, isoforms, and fusion transcripts, and identified the impact of various CNVs on transcriptome• Properly classified a mis-identified group of repeats facilitating their exact annotation • Collaborated in the genome annotation of three different species• Mentored graduate students

Fayetteville, Arkansas Area

• Culturing of marine and freshwater algae including diatoms• Nucleic acid staining and fluorescence microscopy• Light microscopy• Genome size estimation using flow cytometer• Experience in using Transporter Classification Database for membrane transport protein analyses• Setting up, maintaining and managing laboratory• Training graduate students

Arlington

• Investigated the presence of specific MEIs in a variety of species using bioinformatic and various molecular biology techniques • Identified pervasive horizontal transfer of mobile elements through sequence analysis

Doctor Of Philosophy (Ph.D.), Quantitative Biology, 4.00

Master Of Science - Ms, Nematology, Molecular Biology And Biotechnology