Efficient Indexed Alignment of Contigs to Optical Maps. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (WABI, 2014)

Misassembly detection using paired-end sequence reads and optical mapping data. - Martin D. Muggli; Simon J. Puglisi; Roy Ronen; Christina Boucher 001 (Bioinform., 2015)

Disentangled Long-Read De Bruijn Graphs via Optical Maps. - Bahar Alipanahi; Leena Salmela; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (WABI, 2017)

Succinct colored de Bruijn graphs. - Martin D. Muggli; Alexander Bowe; Noelle R. Noyes; Paul S. Morley; Keith E. Belk; Robert Raymond; Travis Gagie; Simon J. Puglisi; Christina Boucher 001 (Bioinform., 2017)

A Succinct Solution to Rmap Alignment. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (WABI, 2018)

Kohdista: an efficient method to index and query possible Rmap alignments. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (Algorithms Mol. Biol., 2019)

Building large updatable colored de Bruijn graphs via merging. - Martin D. Muggli; Bahar Alipanahi; Christina Boucher 001 (Bioinform., 2019)

Fast and accurate correction of optical mapping data via spaced seeds. - Leena Salmela; Kingshuk Mukherjee; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (Bioinform., 2020)

Metagenome SNP calling via read-colored de Bruijn graphs. - Bahar Alipanahi; Martin D. Muggli; Musa Jundi; Noelle R. Noyes; Christina Boucher 001 (Bioinform., 2021)