Marra Lab

Along with my interest in teaching, I also develop and maintain the lesson, Intro to R and RStudio for Genomics (https://github.com/datacarpentry/genomics-r-intro)

I am an instructor for both Software and Data Carpentry workshops. My main goal is to introduce biologists and geneticists to the importance of utilizing R and other computer programming languages for bioinformatics analysis.Through this role, I have been invited as an instructor at the BC Cancer Research Institute, The Jackson Laboratory, and the Comparative and Experimental Approaches to Aging Biology Research Course at MDI Biological Laboratory.

Along with co-organizers, we create a community for gender and ethnic minorities in data science to share their R programming skills and build professional networks. We host monthly meet-ups in downtown Vancouver (https://www.meetup.com/rladies-vancouver/) and always look for new folks to share their skills. Please let me know if you are interested!

As a PhD candidate under Dr. Marco Marra's supervision, I developed an in-silico tool (GRETTA; https://github.com/ytakemon/GRETTA) to identify genetic networks (including synthetic lethal interactions) that can be used to infer functions and vulnerabilities of cancer-associated genes.

Patients diagnosed with Alport Syndrome (AS) are known to vary widely in disease severity despite similar genetic mutations. It is acknowledged by the AS research community that these variations are caused by genetic modifiers. We have created a new model for AS in a genetically diverse outbred mouse model to identify modifier genes through bioinformatic analysis. I am the lead coordinator for this project from generating experimental cohorts, data collection, to bioinformatic analysis. I have created various interactive query tools using an R based Shiny application to make QTL analysis and results accessible to the Korstanje Lab.Apps developed:https://www.jax.org/research-and-faculty/tools/do-as-cohort-datahttps://www.jax.org/research-and-faculty/tools/gfr-calculatorIn addition to my role in research, I am also an active member of the Korstaneja Lab journal club as a frequent presenter and discussion participant. Utilizing this platform I have been able to help generate new ideas and directions that have been actively pursued leading to RO1 submissions.I am also a Data Carpentry and Software Carpentry instructor helping to enrich the scientific community at The Jackson Laboratory through knowledge in R programming. I have taught both two-day workshops and short workshops on Reproducible Research in R and Introduction to Shell and Cloud Computing .

I worked as a summer research fellow for the Genome Technologies (GT) under the direct guidance of Dr. Chia-Lin Wei. My project that summer was the analysis of high-resolution whole genome structural variations in Neurofibromatosis Type II (NF2) using the high-throughput linked read sequencing. Patients diagnosed with NF2 have mutations in the NF-2 gene, however, patients are known to vary widely in tumor aggression. This study was conducted to identify modifier genes in a whole-genome approach.In collaboration with Dr. Daniel Roberts from the University of Connecticut Health Center, tumor biopsy samples from Neurofibromatosis Type II patients were sequenced using the Illumina 10X Genomics in-silico long read sequencer. As this technology was just coming into the market, my role was to QC generated sequence output files and understand the "black box" read alignment LongRanger pipeline. Additionally, I have also analyzed the in-silico long reads and identified novel large structural variations with ample literature results support its role in modifying tumor aggression. As a conclusion of my fellowship, I was given the opportunity to present my results to our collaborators consisting of medical doctors and researchers. As of 2017, these modifier genes are being pursued further by Dr. Wei's team.

I am working on two different projects at the Korstanje Lab. My primary project focuses on the effects of diabetic condition on aspartoacylase activity in podocytes of mice (Mus musculus). I have worked with podocyte cell cultures, RNA extraction, bioinformatics analysis, primer design, protein extraction, lowery protein assays, western blots, RT-PCR, and qPCR. My secondary focus is on the identification of non-coding RNA related to albuminuria, a common marker for chronic kidney dysfunction. I have been sequencing non-coding regions, performing bioinformatics analysis, and northern blots.40 hours/ week

Humpback whale ID worker, and genetic analysts for cetacean biopsy sample.Created lab space and opportunity for students to work on projects related to genetics.This project used skin and blubber biopsy samples collected from various cetaceans in the Gulf of Maine for PCR work, which used unique X and Y specific markers to identify their sex.

Worked for Trish De Graaf, the Maine marine resource management coordinator, to map their 10- year management plan put in place in 2012 for the Maine scallop fishery. The 2012 management plan separated the state waters into 21 separate regions each allocated to one of three zones. The three zones open to fishing in different years to reduce over fishing in certain areas. I used GIS to help predict the amount of landings in each allocated locations for different years using historical landings data. 6 hours/ week.

Research assistance for Dr. Bram Lutton Ph.D. Our topics was identifying vascular stem cell niches in the epigonal organ of Little Skates (Leucoraja erinacea). This research is translational to human bone marrow transplantation. I approached the subject through immunohistochemistry, whereby the wax embedded epigonal tissues were sectioned and mounted onto slides, then stained with BrdU and PCNA stains. 40 hours /week

Worked closely with Dr. Carla Guenther, science and leadership advisor, on managing Maine’s scallop fishery. We organized Community Fisheries Action Roundtable (C-FAR) programs in 7 locations in Maine to bring local fishing communities together to identify key problems and ideas that need to be addressed at the Maine state-wide Stakeholder Advisory Committee meeting. In addition, GIS maps were made of substrate, size, and density of scallops from information provided by local fishermen at the C-FAR meetings. 40 hours/week.