Jiun Y. Yen, PhD

Software Engineer / Data Scientist / Computational Biologist / Amateur Finance Modeler

CV

Software Engineer
Since joining Presto in 2019, I've been building and maintaining numerous APIs that allow our Presto (Android) devices to communicate with a diversed set of point-of-sale systems. Functionalities includes sending orders, getting checks, making payments, etc.
Postdoctoral Fellow
At Carnegie Institute of Science, I built machine learning pipelines to classify functions. One main focus is to predict compartmentalization of cellular metabolism. I also used the preliminary results from this work in a proposal that received over $2 million of funding. Advised by top scientist in the field, Dr. Sue Rhee
Graduate School
For both my MS and PhD at Virginia Tech, I developed algorithms and computational pipeliens to predict genetic modifications that can lead to industrally useful new traits. These include, greater biomass, elevated sugar yield, and targeted amino-acid enrichment. Advised by outstanding PIs, Dr. Ryan Senger and Dr. Glenda Gillaspy (Dep. Biochem. head)
Redtide (Github repo)
Motivates by the question of "how to model stock movement?" I built Redtide to scrape stock history and company financial data. I'm improving it continuously. Most recent change is adding a tradebot that trades on Robinhood. Please check it out, and let me know what you think! Redtide repo
Kaggle datasets
There's a huge community on Reddit that's interested in modeling the stock market, r/algotrading. I often share the data that I obtained with Redtide on Kaggle and Reddit so we can all explore how we can predict stock market's future. Please checkout my datasets, thanks! Stock data on Kaggle

Publications

Co-suppression of AtMIPS demonstrates cooperation of MIPS1, MIPS2 and MIPS3 in maintaining myo-inositol synthesis
Author Fleet, C. M., Yen, J. Y., Hill, E. A., Gillaspy, G. E.
Journal Plant Molecular Biology
Year 2018
Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
Author Yen, J. Y., Gillaspy, G. E., Senger, R. S.
Journal Virginia Tech Doctoral Dissertations
Year 2017
SyM-GEM: A Biosynthetic and Metabolic Pathway Builder and Genome-Scale Model Database
Author Nazem-Bokaee, H., Yen, J. Y., Athamneh, A. I. M., Apte, A. A., McAnulty, M. J., Senger, R. S.
Journal Advances in Biochemistry and Biotechnology
Year 2017
Designing metabolic engineering strategies with genome-scale metabolic flux modeling
Author Yen, J., Tanniche, I., Fisher, A., Gillaspy, G., Bevan, D., Senger, R.
Journal Advances in Genomics and Genetics
Year 2015
A review of genome-scale metabolic flux modeling of anaerobiosis in biotechnology
Author Senger, R. S., Yen, J. Y., Fong, S. S.
Journal Current Opinion in Chemical Engineering
Year 2014
Deriving metabolic engineering strategies from genome-scale modeling with flux ratio constraints
Author Yen, J. Y., Nazem-Bokaee, H., Freedman, B. G., Athamneh, A. I. M., Senger, R. S.
Journal Biotechnology Journal
Year 2013
Are we ready for genome-scale modeling in plants?
Author Collakova, E., Yen, J. Y., Senger, R. S.
Journal Plant Science
Year 2012
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
Author McAnulty, M. J., Yen, J. Y., Freedman, B. G., Senger, R. S.
Journal BMC Systems Biology
Year 2012
Minimum requirements of flagellation and motility for infection of agrobacterium sp. strain H13-3 by flagellotropic bacteriophage 7-7-1
Author Yen, J. Y., Broadway, K. M., Scharf, B. E.
Journal Applied and Environmental Microbiology
Year 2012

Conference Talks

A genome-scale algorithmic approach for metabolic engineering of plants
Author Yen, J., Gillaspy, G., Senger, R.
Conference Great Lakes Bioinformatics and the Canadian Computational Biology Conference
Location Toronto, Canada
Year 2016
Systems Metabolic Engineering of Arabidopsis for Increased Cellulose Production
Author Yen, J., Gillaspy, G., Senger, R.
Conference American Society for Biochemistry and Molecular Biology - Experimental Biology
Location Boston, MA
Year 2015
Systems metabolic engineering of Arabidopsis for increased cellulose production
Author Yen, J., Gillaspy, G., Senger, R.
Conference Gordon Research Seminar – Plant Metabolic Engineering
Location Waterville Valley, NH
Year 2013
The utilization of genome-scale model to explore mutations that increase cellulose in Arabidopsis thaliana
Author Yen, J., Gillaspy, G., Senger, R.
Conference The Southern Section of the American Society of Plant Biologists
Location Myrtle Beach, SC
Year 2012

Contact

Jiun

1 (757) 274-5235

jiunyyen@gmail.com