VisRD–visual recombination detection. - Kristoffer Forslund; Daniel H. Huson; Vincent Moulton (Bioinform., 2004)

Constructing Phylogenetic Supernetworks from Quartets. - Stefan Grünewald; Andreas Spillner 001; Kristoffer Forslund; Vincent Moulton (WABI, 2008)

Predicting protein function from domain content. - Kristoffer Forslund; Erik L. L. Sonnhammer (Bioinform., 2008)

The Pfam protein families database. - Robert D. Finn; John G. Tate; Jaina Mistry; Penny C. Coggill; Stephen John Sammut; Hans-Rudolf Hotz; Goran Ceric; Kristoffer Forslund; Sean R. Eddy; Erik L. L. Sonnhammer; Alex Bateman (Nucleic Acids Res., 2008)

Benchmarking homology detection procedures with low complexity filters. - Kristoffer Forslund; Erik L. L. Sonnhammer (Bioinform., 2009)

The Pfam protein families database. - Robert D. Finn; Jaina Mistry; John G. Tate; Penny C. Coggill; Andreas Heger; Joanne E. Pollington; O. Luke Gavin; Prasad Gunasekaran; Goran Ceric; Kristoffer Forslund; Liisa Holm; Erik L. L. Sonnhammer; et al. (Nucleic Acids Res., 2010)

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. - Gabriel Östlund; Thomas Schmitt 003; Kristoffer Forslund; Tina Köstler; David N. Messina; Sanjit Roopra; Oliver Frings; Erik L. L. Sonnhammer (Nucleic Acids Res., 2010)

OrthoDisease: tracking disease gene orthologs across 100 species. - Kristoffer Forslund; Fabian Schreiber; Nattaphon Thanintorn; Erik L. L. Sonnhammer (Briefings Bioinform., 2011)

Domain architecture conservation in orthologs. - Kristoffer Forslund; Isabella Pekkari; Erik L. L. Sonnhammer (BMC Bioinform., 2011)

The Pfam protein families database. - Marco Punta; Penny C. Coggill; Ruth Y. Eberhardt; Jaina Mistry; John G. Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; et al. (Nucleic Acids Res., 2012)

eggNOG v4.0: nested orthology inference across 3686 organisms. - Sean Powell; Kristoffer Forslund; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth 001; Jaime Huerta-Cepas; Toni Gabaldón; Thomas Rattei; Christopher J. Creevey; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2014)

STRING v10: protein-protein interaction networks, integrated over the tree of life. - Damian Szklarczyk; Andrea Franceschini; Stefan Wyder; Kristoffer Forslund; Davide Heller; Jaime Huerta-Cepas; Milan Simonovic; Alexander Roth 001; Alberto Santos; Kalliopi Tsafou; Michael Kuhn 004; Peer Bork; et al. (Nucleic Acids Res., 2015)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. - Kristoffer Forslund; Falk Hildebrand; Trine Nielsen; Gwen Falony; Emmanuelle Le Chatelier; Shinichi Sunagawa; Edi Prifti; Sara Vieira-Silva; Valborg Gudmundsdottir; Helle Krogh Pedersen; Manimozhiyan Arumugam; Karsten Kristiansen; et al. (Nat., 2015)

MOCAT2: a metagenomic assembly, annotation and profiling framework. - Jens Roat Kultima; Luís Pedro Coelho; Kristoffer Forslund; Jaime Huerta-Cepas; Simone S. Li; Marja Driessen; Anita Yvonne Voigt; Georg Zeller; Shinichi Sunagawa; Peer Bork (Bioinform., 2016)

Benchmarking the next generation of homology inference tools. - Ganapathi Varma Saripella; Erik L. L. Sonnhammer; Kristoffer Forslund (Bioinform., 2016)

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. - Jaime Huerta-Cepas; Damian Szklarczyk; Kristoffer Forslund; Helen Cook; Davide Heller; Mathias C. Walter; Thomas Rattei; Daniel R. Mende; Shinichi Sunagawa; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2016)

RTK: efficient rarefaction analysis of large datasets. - Paul Saary; Kristoffer Forslund; Peer Bork; Falk Hildebrand (Bioinform., 2017)

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. - Daniel R. Mende; Ivica Letunic; Jaime Huerta-Cepas; Simone S. Li; Kristoffer Forslund; Shinichi Sunagawa; Peer Bork (Nucleic Acids Res., 2017)

A Semi-supervised Approach to Discover Bivariate Causality in Large Biological Data. - Nataliya Sokolovska; Olga Permiakova; Sofia K. Forslund; Jean-Daniel Zucker (MLDM (1), 2018)

Gearing up to handle the mosaic nature of life in the quest for orthologs. - Kristoffer Forslund; Cécile Pereira; Salvador Capella-Gutiérrez; Alan W. Sousa da Silva; Adrian M. Altenhoff; Jaime Huerta-Cepas; Matthieu Muffato; Mateus Patricio; Klaas Vandepoele; Ingo Ebersberger; Judith A. Blake; Jesualdo Tomás Fernández-Breis; et al. (Bioinform., 2018)

Domainoid: domain-oriented orthology inference. - Emma Persson; Mateusz Kaduk; Sofia K. Forslund; Erik L. L. Sonnhammer (BMC Bioinform., 2019)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. - Jaime Huerta-Cepas; Damian Szklarczyk; Davide Heller; Ana Hernández-Plaza; Sofia K. Forslund; Helen Cook; Daniel R. Mende; Ivica Letunic; Thomas Rattei; Lars Juhl Jensen; Christian von Mering; Peer Bork (Nucleic Acids Res., 2019)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. - Daniel R. Mende; Ivica Letunic; Oleksandr M. Maistrenko; Thomas S. B. Schmidt; Alessio Milanese; Lucas Paoli; Ana Hernández-Plaza; Askarbek N. Orakov; Sofia K. Forslund; Shinichi Sunagawa; Georg Zeller; Jaime Huerta-Cepas; et al. (Nucleic Acids Res., 2020)

Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines. - Nataliya Sokolovska; Olga Permiakova; Sofia K. Forslund; Jean-Daniel Zucker (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)