Sofia K. Forslund

According to our database, Sofia K. Forslund authored at least 24 papers between 2004 and 2020.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

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

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, Luís Pedro Coelho, Peer Bork

Nucleic Acids Res., 2020

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

Domainoid: domain-oriented orthology inference.

Emma Persson, Mateusz Kaduk, Sofia K. Forslund, Erik L. L. Sonnhammer

BMC Bioinform., 2019

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, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis

Bioinform., 2018

A Semi-supervised Approach to Discover Bivariate Causality in Large Biological Data.

Nataliya Sokolovska, Olga Permiakova, Sofia K. Forslund, Jean-Daniel Zucker

Proceedings of the Machine Learning and Data Mining in Pattern Recognition, 2018

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

RTK: efficient rarefaction analysis of large datasets.

Paul Saary, Kristoffer Forslund, Peer Bork, Falk Hildebrand

Bioinform., 2017

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, Lars Juhl Jensen, Christian von Mering, Peer Bork

Nucleic Acids Res., 2016

Benchmarking the next generation of homology inference tools.

Ganapathi Varma Saripella, Erik L. L. Sonnhammer, Kristoffer Forslund

Bioinform., 2016

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

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, Anita Yvonne Voigt, Henrik Vestergaard, Rajna Hercog, Paul I. Costea, Jens Roat Kultima, Junhua Li, Torben Jørgensen, Florence Levenez, Joël Dore, Henrik Bjørn Nielsen, Søren Brunak, Jeroen Raes, Torben Hansen, Jun Wang, S. Dusko Ehrlich, Peer Bork, Oluf Pedersen

Nat., 2015

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, Alberto Santos, Kalliopi Tsafou, Michael Kuhn, Peer Bork, Lars Juhl Jensen, Christian von Mering

Nucleic Acids Res., 2015

2014

eggNOG v4.0: nested orthology inference across 3686 organisms.

Sean Powell, Kristoffer Forslund, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Jaime Huerta-Cepas, Toni Gabaldón, Thomas Rattei, Christopher J. Creevey, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork

Nucleic Acids Res., 2014

2012

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, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn

Nucleic Acids Res., 2012

2011

Domain architecture conservation in orthologs.

Kristoffer Forslund, Isabella Pekkari, Erik L. L. Sonnhammer

BMC Bioinform., 2011

OrthoDisease: tracking disease gene orthologs across 100 species.

Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn, Erik L. L. Sonnhammer

Briefings Bioinform., 2011

2010

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, Erik L. L. Sonnhammer

Nucleic Acids Res., 2010

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, Sean R. Eddy, Alex Bateman

Nucleic Acids Res., 2010

2009

Benchmarking homology detection procedures with low complexity filters.

Kristoffer Forslund, Erik L. L. Sonnhammer

Bioinform., 2009

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

Predicting protein function from domain content.

Kristoffer Forslund, Erik L. L. Sonnhammer

Bioinform., 2008

Constructing Phylogenetic Supernetworks from Quartets.

Stefan Grünewald, Andreas Spillner, Kristoffer Forslund, Vincent Moulton

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

2004

VisRD--visual recombination detection.

Kristoffer Forslund, Daniel H. Huson, Vincent Moulton

Bioinform., 2004