Mentor: Hui Shen, Ph.D.

Research Focus: Research focus to be determined.

Experience: Before joining VAI, James was a research assistant on multiple projects over two years at Calvin University. In 2018, he studied the effects of anthropogenic noise on eastern bluebirds nestling health and parental feeding behavior. This project introduced him to programming on Arduino RFID monitors that tracked bird movement through nest boxes. He also worked on a project studying the effect of climate change on native plant flowering periods. In 2019, he studied the effect of dam removal on macroinvertebrate populations in the Boardman River in Northern Michigan. After graduating in 2020, he worked in the Guerreiro and Bras labs at Van Andel Institute as a data analyst and software developer, writing and maintaining genomic data analysis tools. His graduate research focuses on bioinformatics software development and application to understand cell identity in the Fallopian tube. This includes an R/C++ package for fast and memory efficient BED file reading and an R package for inferring chromatin compartments from single-cell gene expression.

Undergraduate Institution: Calvin University

Hometown: Cochin, India

Publications

*Completed during time as a VAI graduate student

*House RJ, Eapen J, Shen H, Graveel CR, Steensma MR. 2024. ceas: An R package for Seahorse data analysis and visualization. Bioinformatics 40(8):btae503.

*Zhou W, Johnson BK, Morrison J, Beddows I, Eapen J, Katsman E, Semwal A, Habib WA, Heo L, Laird PW, Berman BP, Triche TJ Jr, Shen H. 2024. BISCUIT: An efficient, standards compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single cell studies. Nucleic Acids Res 52(6):e32.

*Gouveia C, Gibbons E, Dehghani N, Eapen J, Guerreiro R, Bras J. 2022. Genome wide association of polygenic risk extremes for Alzheimer’s disease in the UK Biobank. Sci Rep 12:8404.

Pandit MM, Eapen J, Pineda Sabillon G, Caulfield ME, Moreno A, Wilhelm J, Ruyle JE, Bridge ES, Proppe DS. 2021. Anthropogenic noise alters parental behavior and nestling developmental patterns, but not fledging condition. Behav Ecol 32(4):747–755.