Jayashree Kumar Email & Phone Number

Cambridge, Massachusetts, United States

Cambridge, Massachusetts, United States

Chapel Hill, North Carolina

PhD Student in Bioinformatics and Computational Biology CurriculumThesis Advisor: Alain LaederachDissertation: The effect of variants on alternative splicing through the lens of pre-cursor messenger RNA structure- Built & trained regression models in R incorporating RNA sequence & structural features around an exon-intron junction to successfully predict alternative splicing changes caused by single nucleotide variants- Developed novel methodology in Python to visualize changes caused by variants to structural ensembles of RNA sequences incorporating chemical structure probing data- Investigated positional distributions of over 200,000 human disease-associated variants using R & Python- Analyzed RNA-Seq data from GTEx database using bioinformatic packages in Terra cloud computing environment for 20 tissues to quantify cassette-exon splicing for over 1000 exon-intron junctions

Chapel Hill, Nc

Bioinformatics Research Technician in Daniel McKay Lab, University of North Carolina, Chapel Hill, NC - Built reusable shell script pipeline to process FAIRE-Seq reads and RNA-Seq reads - Utilized Bioconductor tools DiffBind and EdgeR to pull out differential peaks called using MACS2 - Performed motif analysis on differential peaks using MEME suite - Wrote functions in R and Python to analyze and visualize differential peak data and RNA-Seq data - Dissected Drosophila melanogaster wings and wing imaginal discs at different stages of development and performed FAIRE on them - Cloned potential enhancer regions of the genome identified from FAIRE-Seq data and performed immunofluorescence staining experiments on dissected wings of injected flies to visualize enhancer activity

New York, Ny

Masters Student in Duncan Smith Lab, New York University, New York, NYThesis: Genome-wide impact of Pif1 family helicases on replication fork progression in Saccharomyces cerevisiae - Developed methods in R and Python to integrate sequenced Okazaki fragment read densities and genomic data - Designed clustering algorithm to classify and quantify differences in fork progression in different strains - Built a reusable pipeline for the lab to align and process sequencing reads - Trained and advised lab members on bioinformatics strategies and tools to use in their projects - Built shell scripts to utilize High Performance Computing environment to run large-scale batch jobs - Created yeast strains using genetic techniques and prepared libraries for sequencing Okazaki fragments

- Teaching Adjunct for graduate level course Statistics In Biology- Lead weekly recitation and instruct students in R and help with problem sets- Grade homework sets, midterm and final

- Developed new features for Expenses and Budget product offerings using proprietary language Xpresso.- Designed and implemented class models for features using UML

- Led automated testing effort for Financials Application- Added over a hundred additional automated tests for Workday Financials- Built, executed and debugged functional and back-end tests using WATS and SOAPUI - Developed front-end user interface tests using Selenium- Worked closely with development and quality-assurance teams to make decisions around areas to automate- Diagnosed problems and reported bugs and enhancements to Development

- Used Workday Automated Transaction System (WATS), an automation tool, to automate regression testware- Tested the User Interface of Workday Software manually- Used SoapUI to test Workday Web Services- Wrote test scripts for conversion between two different software updates- Updated the Integration Section of Workday's User Guide- Compiled a glossary of useful Workday acronyms for future interns to reference- Awarded Exemplary Student Ambassador for experience with Workday

Doctor Of Philosophy - Phd, Bioinformatics And Computational Biology

Master Of Science (M.S.), Bioinformatics And Systems Biology

Bachelor Of Science - Bs, Electrical And Computer Engineering