Segmentation of occluded hematopoietic stem cells from tracking. - Walter C. Mankowski; Mark R. Winter; Eric Wait; Mels Lodder; Ton N. Schumacher; Shalin H. Naik; Andrew R. Cohen (EMBC, 2014)

Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. - Joost B. Beltman; Jos Urbanus; Arno Velds; Nienke van Rooij; Jan C. Rohr; Shalin H. Naik; Ton N. Schumacher (BMC Bioinform., 2016)

Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system. - Tom Serge Weber; Mark Dukes; Denise C. Miles; Stefan P. Glaser; Shalin H. Naik; Ken R. Duffy (BMC Syst. Biol., 2016)

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. - Luyi Tian; Shian Su; Xueyi Dong; Daniela Amann-Zalcenstein; Christine Biben; Azadeh Seidi; Douglas J. Hilton; Shalin H. Naik; Matthew E. Ritchie (PLoS Comput. Biol., 2018)

Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. - Grace E. Lidgerwood; Anne Senabouth; Casey J. A. Smith-Anttila; Vikkitharan Gnanasambandapillai; Dominik C. Kaczorowski; Daniela Amann-Zalcenstein; Erica L. Fletcher; Shalin H. Naik; Alex W. Hewitt; Joseph E. Powell; Alice Pébay (Genom. Proteom. Bioinform., 2021)

Self-Organizing Nebulous Growths for Robust and Incremental Data Visualization. - Damith A. Senanayake; Wei Wang 133; Shalin H. Naik; Saman K. Halgamuge (IEEE Trans. Neural Networks Learn. Syst., 2021)