BioWish: a molecular biology command extension to Tcl/Tk. - Thomas Sicheritz-Pontén (Comput. Appl. Biosci., 1997)

GenePublisher: automated analysis of DNA microarray data. - Steen Knudsen; Christopher T. Workman; Thomas Sicheritz-Pontén; Carsten Friis (Nucleic Acids Res., 2003)

Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins. - Francesca Diella; Scott Cameron; Christine Gemünd; Rune Linding; Allegra Via; Bernhard Küster; Thomas Sicheritz-Pontén; Nikolaj Blom; Toby J. Gibson (BMC Bioinform., 2004)

InterMap3D: predicting and visualizing co-evolving protein residues. - Rodrigo Gouveia-Oliveira; Francisco S. Roque; Rasmus Wernersson; Thomas Sicheritz-Pontén; Peter Wad Sackett; Anne Mølgaard; Anders Gorm Pedersen (Bioinform., 2009)

Addendum: Enterotypes of the human gut microbiome. - Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R. Mende; Gabriel R. Fernandes; Julien Tap; Thomas Brüls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; et al. (Nat., 2014)

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. - Marie Lisandra Zepeda Mendoza; Thomas Sicheritz-Pontén; M. Thomas P. Gilbert (Briefings Bioinform., 2015)

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)

Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data. - Kosai Al-Nakeeb; Thomas Nordahl Petersen; Thomas Sicheritz-Pontén (BMC Bioinform., 2017)

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)