I am a graduate student at the Washington University in St.Louis, studying computational and systems biology in the DBBS program.

Previously, I was a Computational Scientist at The Pennsylvania State University, where I worked with Frank Pugh and Shaun Mahony at the Center for Eukaryotic Gene Regulation (CEGR) to build an automated Galaxy pipeline that utilizes high performance computing clusters to analyze ChIP-exo datasets.

I design and develop web infrastructure for knowledge discovery platforms, mostly for large scale genomic projects. I also create and maintain conda packages for bioinformatic software in the bioconda channel.

I received my Master's in Computer Science and the Graduate Certificate in Bioinformatics from Ohio University. Here is my timeline and résumé.

Publications

1. A high-resolution protein architecture of the budding yeast genome
   

   Matthew J. Rossi, Prashant K. Kuntala, William K. M. Lai, Naomi Yamada, Nitika Badjatia, Chitvan Mittal, Guray Kuzu, Kylie Bocklund, Nina P. Farrell, Thomas R. Blanda, Joshua D. Mairose, Ann V. Basting, Katelyn S. Mistretta, David J. Rocco, Emily S. Perkinson, Gretta D. Kellogg, Shaun Mahony & B. Franklin Pugh. [Nature, 2021].



2. ChExMix: A Method for Identifying and Classifying Protein–DNA Interaction Subtypes
   

   Naomi Yamada, Prashant K. Kuntala, B. Franklin Pugh & Shaun Mahony. [Journal of Computational Biology, 2020].

Projects

1. Yeast Epigenome Project (YEP) is a comprehensive DNA-centric structural view of how proteins are organized into complexes across the yeast genome, including the architectural basis of fundamental gene classes.




2. Protein Capture Reagents Program (PCRP) Validation is a community resource of renewable, high-quality protein capture reagents to understand the critical role the multitude of cellular proteins play in development, health, and disease.




3. Exo is a collection of command-line utilites for the Yeast Epigenome Project and ChIP-exo data analysis.




4. Locusplotter is an experimental visualization tool for discovering protein binding & co-binding patterns at interested genomic loci.




5. Stencil is a web templating engine that lets your share life-science datasets.

Some of the bioconda recepies I maintain --

1. ChExMix aims to characterize protein-DNA binding subtypes in ChIP-exo experiments.

2. ChExAlign is used for alignment and quantification of ChIP-exo crosslinking patterns.
3. SeqUnwinder is a framework for characterizing class-discriminative motifs in a collection of genomic loci that have several (overlapping) annotation labels.