SemanticGenomeGraphs. - Simon Heumos; Jerven T. Bolleman (SWAT4HCLS, 2019)

Efficient dynamic variation graphs. - Jordan M. Eizenga; Adam M. Novak; Emily Kobayashi; Flavia Villani; Cecilia Cisar; Simon Heumos; Glenn Hickey; Vincenza Colonna; Benedict Paten; Erik Garrison (Bioinform., 2021)

ODGI: understanding pangenome graphs. - Andrea Guarracino; Simon Heumos; Sven Nahnsen; Pjotr Prins; Erik Garrison (Bioinform., 2022)

Wheeler Maps. - Andrej Baláz; Travis Gagie; Adrián Goga; Simon Heumos; Gonzalo Navarro 001; Alessia Petescia; Jouni Sirén (LATIN (1), 2024)

Rapid GPU-Based Pangenome Graph Layout. - Jiajie Li; Jan-Niklas Schmelzle; Yixiao Du; Simon Heumos; Andrea Guarracino; Giulia Guidi; Pjotr Prins; Erik Garrison; Zhiru Zhang (SC, 2024)

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. - Gisela Gabernet; Susanna Marquez; Robert Bjornson; Alexander Peltzer; Hailong Meng; Edel Aron; Noah Y. Lee; Cole G. Jensen; David Ladd; Mark Polster; Friederike Hanssen; Simon Heumos; et al. (PLoS Comput. Biol., 2024)