Erik L. L. Sonnhammer

According to our database, Erik L. L. Sonnhammer authored at least 75 papers between 1992 and 2022.

Collaborative distances:

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

2022

GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.

Deniz Seçilmis, Thomas Hillerton, Erik L. L. Sonnhammer

Nucleic Acids Res., 2022

The Quest for Orthologs orthology benchmark service in 2022.

Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codó, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Adrian M. Altenhoff, Elspeth A. Bruford, Christophe Dessimoz, Ingo Ebersberger, David M. Emms, Toni Gabaldón, Natasha M. Glover, Yanhui Hu, Wataru Iwasaki, Odile Lecompte, Benjamin Linard, María J. Martín, David S. Roos, Erik Sonhammer, Paul D. Thomas, David Thybert, Klaas Vandepoele, Salvador Capella-Gutiérrez, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Dmitry Repchevsky, Vicky Sundesha, Erik L. L. Sonnhammer

Nucleic Acids Res., 2022

InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.

Emma Persson, Erik L. L. Sonnhammer

Bioinform., 2022

Fast and accurate gene regulatory network inference by normalized least squares regression.

Thomas Hillerton, Deniz Seçilmis, Sven Nelander, Erik L. L. Sonnhammer

Bioinform., 2022

2021

Pfam: The protein families database in 2021.

Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A. Salazar, Erik L. L. Sonnhammer, Silvio C. E. Tosatto, Lisanna Paladin, Shriya Raj, Lorna J. Richardson, Robert D. Finn, Alex Bateman

Nucleic Acids Res., 2021

Inferring the experimental design for accurate gene regulatory network inference.

Deniz Seçilmis, Thomas Hillerton, Sven Nelander, Erik L. L. Sonnhammer

Bioinform., 2021

2020

The Quest for Orthologs benchmark service and consensus calls in 2020.

Adrian M. Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M. Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José María Fernández, Laia Codó, The Quest for Orthologs Consortium, Josep Lluis Gelpí, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria Jesus Martin, Salvador Capella-Gutiérrez, Paul D. Thomas, Erik L. L. Sonnhammer, Christophe Dessimoz

Nucleic Acids Res., 2020

Genome-wide functional association networks: background, data & state-of-the-art resources.

Dimitri Guala, Christoph Ogris, Nikola Müller, Erik L. L. Sonnhammer

Briefings Bioinform., 2020

2019

The Pfam protein families database in 2019.

Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R. Eddy, Aurelien Luciani, Simon C. Potter, Matloob Qureshi, Lorna J. Richardson, Gustavo A. Salazar, Alfredo Smart, Erik L. L. Sonnhammer, Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto, Robert D. Finn

Nucleic Acids Res., 2019

Domainoid: domain-oriented orthology inference.

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

BMC Bioinform., 2019

A generalized framework for controlling FDR in gene regulatory network inference.

Daniel Morgan, Andreas Tjärnberg, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer

Bioinform., 2019

2018

FunCoup 4: new species, data, and visualization.

Christoph Ogris, Dimitri Guala, Mateusz Kaduk, Erik L. L. Sonnhammer

Nucleic Acids Res., 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

2017

HieranoiDB: a database of orthologs inferred by Hieranoid.

Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L. L. Sonnhammer

Nucleic Acids Res., 2017

Improved orthology inference with Hieranoid 2.

Mateusz Kaduk, Erik L. L. Sonnhammer

Bioinform., 2017

2016

PathwAX: a web server for network crosstalk based pathway annotation.

Christoph Ogris, Thomas Helleday, Erik L. L. Sonnhammer

Nucleic Acids Res., 2016

Benchmarking the next generation of homology inference tools.

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

Bioinform., 2016

TreeDom: a graphical web tool for analysing domain architecture evolution.

Christian Haider, Marina Kavic, Erik L. L. Sonnhammer

Bioinform., 2016

2015

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic.

Erik L. L. Sonnhammer, Gabriel Östlund

Nucleic Acids Res., 2015

2014

FunCoup 3.0: database of genome-wide functional coupling networks.

Thomas Schmitt, Christoph Ogris, Erik L. L. Sonnhammer

Nucleic Acids Res., 2014

Pfam: the protein families database.

Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta

Nucleic Acids Res., 2014

Functional association networks as priors for gene regulatory network inference.

Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer

Bioinform., 2014

Big data and other challenges in the quest for orthologs.

Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, The Quest for Orthologs Consortium

Bioinform., 2014

MaxLink: network-based prioritization of genes tightly linked to a disease seed set.

Dimitri Guala, Erik Sjölund, Erik L. L. Sonnhammer

Bioinform., 2014

2013

Optimal Sparsity Criteria for Network Inference.

Andreas Tjärnberg, Torbjörn E. M. Nordling, Matthew Studham, Erik L. L. Sonnhammer

J. Comput. Biol., 2013

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

Comparative interactomics with Funcoup 2.0.

Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dimitri Guala, Oliver Frings, Erik L. L. Sonnhammer

Nucleic Acids Res., 2012

Toward community standards in the quest for orthologs.

Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero

Bioinform., 2012

2011

Domain architecture conservation in orthologs.

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

BMC Bioinform., 2011

Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information.

Thomas Schmitt, David N. Messina, Fabian Schreiber, Erik L. L. Sonnhammer

Briefings 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

MetaTM - a consensus method for transmembrane protein topology prediction.

Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. L. Sonnhammer

BMC Bioinform., 2009

DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.

David N. Messina, Erik L. L. Sonnhammer

Bioinform., 2009

Benchmarking homology detection procedures with low complexity filters.

Kristoffer Forslund, Erik L. L. Sonnhammer

Bioinform., 2009

Comparative analysis and unification of domain-domain interaction networks.

Patrik Björkholm, 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

InParanoid 6: eukaryotic ortholog clusters with inparalogs.

Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer

Nucleic Acids Res., 2008

Employing conservation of co-expression to improve functional inference.

Carsten O. Daub, Erik L. L. Sonnhammer

BMC Syst. Biol., 2008

jSquid: a Java applet for graphical on-line network exploration.

Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer

Bioinform., 2008

Predicting protein function from domain content.

Kristoffer Forslund, Erik L. L. Sonnhammer

Bioinform., 2008

siRNA specificity searching incorporating mismatch tolerance data.

Alistair M. Chalk, Erik L. L. Sonnhammer

Bioinform., 2008

2007

Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server.

Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer

Nucleic Acids Res., 2007

Automatic extraction of reliable regions from multiple sequence alignments.

Timo Lassmann, Erik L. L. Sonnhammer

BMC Bioinform., 2007

PfamAlyzer: domain-centric homology search.

Volker Hollich, Erik L. L. Sonnhammer

Bioinform., 2007

2006

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.

Timo Lassmann, Erik L. L. Sonnhammer

Nucleic Acids Res., 2006

Pfam: clans, web tools and services.

Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman

Nucleic Acids Res., 2006

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

Andrey Alexeyenko, Ivica Tamas, Gang Liu, Erik L. L. Sonnhammer

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Inparanoid: a comprehensive database of eukaryotic orthologs.

Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer

Nucleic Acids Res., 2005

siRNAdb: a database of siRNA sequences.

Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer

Nucleic Acids Res., 2005

FunShift: a database of function shift analysis on protein subfamilies.

Saraswathi Abhiman, Erik L. L. Sonnhammer

Nucleic Acids Res., 2005

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.

Markus Wistrand, Erik L. L. Sonnhammer

BMC Bioinform., 2005

<i>Scoredist</i>: A simple and robust protein sequence distance estimator.

Erik L. L. Sonnhammer, Volker Hollich

BMC Bioinform., 2005

Kalign - an accurate and fast multiple sequence alignment algorithm.

Timo Lassmann, Erik L. L. Sonnhammer

BMC Bioinform., 2005

An HMM posterior decoder for sequence feature prediction that includes homology information.

Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004

The Pfam protein families database.

Alex Bateman, Lachlan James M. Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, Sean R. Eddy

Nucleic Acids Res., 2004

Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination.

Markus Wistrand, Erik L. L. Sonnhammer

J. Comput. Biol., 2004

Profiled support vector machines for antisense oligonucleotide efficacy prediction.

Gustavo Camps-Valls, Alistair M. Chalk, Antonio J. Serrano-López, José David Martín-Guerrero, Erik L. L. Sonnhammer

BMC Bioinform., 2004

ChromoWheel: a new spin on eukaryotic chromosome visualization.

Sven Ekdahl, Erik L. L. Sonnhammer

Bioinform., 2004

Sfixem - graphical sequence feature display in Java.

Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer

Bioinform., 2004

2002

The Pfam Protein Families Database.

Alex Bateman, Ewan Birney, Lorenzo Cerutti, Richard Durbin, Laurence Ettwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, Erik L. L. Sonnhammer

Nucleic Acids Res., 2002

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.

Christian E. V. Storm, Erik L. L. Sonnhammer

Bioinform., 2002

OrthoGUI: graphical presentation of Orthostrapper results.

Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer

Bioinform., 2002

Computational antisense oligo prediction with a neural network model.

Alistair M. Chalk, Erik L. L. Sonnhammer

Bioinform., 2002

2001

NIFAS: visual analysis of domain evolution in proteins.

Christian E. V. Storm, Erik L. L. Sonnhammer

Bioinform., 2001

MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.

Raf M. Podowski, Erik L. L. Sonnhammer

Bioinform., 2001

2000

The Pfam Protein Families Database.

Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer

Nucleic Acids Res., 2000

1999

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer

Nucleic Acids Res., 1999

A comparison of sequence and structure protein domain families as a basis for structural genomics.

Arne Elofsson, Erik L. L. Sonnhammer

Bioinform., 1999

1998

Pfam: multiple sequence alignments and HMM-profiles of protein domains.

Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin

Nucleic Acids Res., 1998

A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences.

Erik L. L. Sonnhammer, Gunnar von Heijne, Anders Krogh

Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

1994

A workbench for large-scale sequence homology analysis.

Erik L. L. Sonnhammer, Richard Durbin

Comput. Appl. Biosci., 1994

An Expert System for Processing Sequence Homology Data.

Erik L. L. Sonnhammer, Richard Durbin

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994

1992

METASIM: object-oriented modelling of cell regulation.

H. J. Stoffers, Erik L. L. Sonnhammer, G. J. Blommestijn, N. J. Raat, Hans V. Westerhoff

Comput. Appl. Biosci., 1992