Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. - Pierre Nicolas; Aurélie Leduc; Stéphane Robin; Simon Rasmussen; Hanne Jarmer; Philippe Bessières (Bioinform., 2009)

Reads2Type: a web application for rapid microbial taxonomy identification. - Dhany Saputra; Simon Rasmussen; Mette V. Larsen; Nizar Haddad; Maria Sperotto; Frank Aarestrup; Ole Lund; Thomas Sicheritz-Pontén (BMC Bioinform., 2015)

A genomic history of Aboriginal Australia. - Anna-Sapfo Malaspinas; Michael C. Westaway; Craig Muller; Vitor C. Sousa; Oscar Lao; Isabel Alves; Anders Bergström; Georgios Athanasiadis; Jade Yu Cheng; Jacob E. Crawford; Tim H. Heupink; Enrico Macholdt; et al. (Nat., 2016)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. - Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; Jette Bork-Jensen; et al. (Nat., 2017)

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. - Maria Luisa Matey-Hernandez; Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; et al. (BMC Bioinform., 2018)

Mapache: a flexible pipeline to map ancient DNA. - Samuel Neuenschwander; Diana I Cruz Dávalos; Lucas Anchieri; Bárbara Sousa da Mota; Davide Bozzi; Simone Rubinacci; Olivier Delaneau; Simon Rasmussen; Anna-Sapfo Malaspinas (Bioinform., 2023)

FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data. - Mikaela Koutrouli; Katerina C. Nastou; Pau Piera Líndez; Robbin Bouwmeester; Simon Rasmussen; Lennart Martens; Lars Juhl Jensen (Bioinform., 2024)

Taxometer: Improving taxonomic classification of metagenomics contigs. - Svetlana Kutuzova; Mads Nielsen; Pau Piera Líndez; Jakob Nybo Nissen; Simon Rasmussen (Zenodo, 2024)