Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. - Viraj Deshpande; Eric D. K. Fung; Son Pham; Vineet Bafna (WABI, 2013)

ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. - Egor Dolzhenko; Viraj Deshpande; Felix Schlesinger; Peter Krusche; Roman Petrovski; Sai Chen; Dorothea Emig-Agius; Andrew Gross; Giuseppe Narzisi; Brett Bowman; Konrad Scheffler; Joke J. F. A van Vugt; et al. (Bioinform., 2019)