Resolving Multicopy Duplications de novo Using Polyploid Phasing. - Mark J. P. Chaisson; Sudipto Mukherjee 001; Sreeram Kannan; Evan E. Eichler (RECOMB, 2017)

lra: A long read aligner for sequences and contigs. - Jingwen Ren; Mark J. P. Chaisson (PLoS Comput. Biol., 2021)

HQAlign: aligning nanopore reads for SV detection using current-level modeling. - Dhaivat Joshi; Suhas N. Diggavi; Mark J. P. Chaisson; Sreeram Kannan (Bioinform., 2023)