Efficient construction of an assembly string graph using the FM-index. - Jared T. Simpson; Richard Durbin (Bioinform., 2010)

Copy number variant detection in inbred strains from short read sequence data. - Jared T. Simpson; Rebecca E. McIntyre; David J. Adams; Richard Durbin (Bioinform., 2010)

Exploring genome characteristics and sequence quality without a reference. - Jared T. Simpson (Bioinform., 2014)

MinION Analysis and Reference Consortium: Phase 1 data release and analysis. - Camilla L. C. Ip; Matthew Loose; John R. Tyson; Mariateresa de Cesare; Bonnie L. Brown; Miten Jain; Richard M. Leggett; David A. Eccles; Vadim Zalunin; John M. Urban; Paolo Piazza; Rory J. Bowden; et al. (F1000Research, 2015)

On the Representation of De Bruijn Graphs. - Rayan Chikhi; Antoine Limasset; Shaun Jackman; Jared T. Simpson; Paul Medvedev (J. Comput. Biol., 2015)

Nanocall: an open source basecaller for Oxford Nanopore sequencing data. - Matei David; L. J. Dursi; Delia Yao; Paul C. Boutros; Jared T. Simpson (Bioinform., 2017)

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. - Hasindu Gamaarachchi; Wai Chun Lam; Gihan Jayatilaka; Hiruna Samarakoon; Jared T. Simpson; Martin A. Smith; Sri Parameswaran (BMC Bioinform., 2020)