TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. - Jesper Eisfeldt; Francesco Vezzi; Páll Ísólfur Ólason; Daniel Nilsson; Anna Lindstrand (F1000Research, 2017)

Loqusdb: added value of an observations database of local genomic variation. - Måns Magnusson; Jesper Eisfeldt; Daniel Nilsson; Adam Rosenbaum; Valtteri Wirta; Anna Lindstrand; Anna Wedell; Henrik Stranneheim (BMC Bioinform., 2020)

pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing. - Jessada Thutkawkorapin; Jesper Eisfeldt; Emma Tham; Daniel Nilsson (BMC Bioinform., 2020)

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. - Maxime Garcia; Szilveszter Juhos; Malin Larsson; Páll Ísólfur Ólason; Marcel Martin; Jesper Eisfeldt; Sebastian DiLorenzo; Johanna Sandgren; Teresita Diaz de Ståhl; Philip Ewels; Valtteri Wirta; Monica Nistér; et al. (F1000Research, 2020)

Ecosystem Models Based on Artificial Intelligence. - Claes Strannegård; Niklas Engsner; Jesper Eisfeldt; John A. Endler; Amanda Hansson; Rasmus Lindgren; Petter Mostad; Simon Olsson; Irene Perini; Heather Reese; Fulya Taylan; Simon Ulfsbäcker; et al. (SAIS, 2022)