Erik L. L. Sonnhammer

81 papers A 2Journal 77Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
BiGSM: Bayesian inference of gene regulatory network via sparse modelling.
Bioinform.
Hang Qin, Mateusz Garbulowski, Erik L. L. Sonnhammer, Saikat Chatterjee
2025 J jnl
The FunCoup Cytoscape App: multi-species network analysis and visualization.
Bioinform.
Davide Buzzao, Lukas Steininger, Dimitri Guala, Erik L. L. Sonnhammer
2025 J jnl
Topology-based metrics for finding the optimal sparsity in gene regulatory network inference.
Bioinform.
Nils Lundqvist, Mateusz Garbulowski, Thomas Hillerton, Erik L. L. Sonnhammer
2024 J jnl
Benchmarking enrichment analysis methods with the disease pathway network.
Briefings Bioinform.
Davide Buzzao, Miguel Castresana Aguirre, Dimitri Guala, Erik L. L. Sonnhammer
2022 J jnl
Fast and accurate gene regulatory network inference by normalized least squares regression.
Bioinform.
Thomas Hillerton, Deniz Seçilmis, Sven Nelander, Erik L. L. Sonnhammer
2022 J jnl
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.
Nucleic Acids Res.
Deniz Seçilmis, Thomas Hillerton, Erik L. L. Sonnhammer
2022 J jnl
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.
Bioinform.
Emma Persson, Erik L. L. Sonnhammer
2022 J jnl
PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk.
Bioinform.
Christoph Ogris, Miguel Castresana Aguirre, Erik L. L. Sonnhammer
2022 J jnl
The Quest for Orthologs orthology benchmark service in 2022.
Nucleic Acids Res.
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
2021 J jnl
Inferring the experimental design for accurate gene regulatory network inference.
Bioinform.
Deniz Seçilmis, Thomas Hillerton, Sven Nelander, Erik L. L. Sonnhammer
2021 J jnl
Pfam: The protein families database in 2021.
Nucleic Acids Res.
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
2020 J jnl
Genome-wide functional association networks: background, data & state-of-the-art resources.
Briefings Bioinform.
Dimitri Guala, Christoph Ogris, Nikola Müller, Erik L. L. Sonnhammer
2020 J jnl
The Quest for Orthologs benchmark service and consensus calls in 2020.
Nucleic Acids Res.
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, Quest for Orthologs Consortium, Josep Lluís 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
2019 J jnl
A generalized framework for controlling FDR in gene regulatory network inference.
Bioinform.
Daniel Morgan, Andreas Tjärnberg, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer
2019 J jnl
Domainoid: domain-oriented orthology inference.
BMC Bioinform.
Emma Persson, Mateusz Kaduk, Sofia K. Forslund, Erik L. L. Sonnhammer
2019 J jnl
The Pfam protein families database in 2019.
Nucleic Acids Res.
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
2018 J jnl
FunCoup 4: new species, data, and visualization.
Nucleic Acids Res.
Christoph Ogris, Dimitri Guala, Mateusz Kaduk, Erik L. L. Sonnhammer
2018 J jnl
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Bioinform.
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, Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis
2017 J jnl
HieranoiDB: a database of orthologs inferred by Hieranoid.
Nucleic Acids Res.
Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L. L. Sonnhammer
2017 J jnl
Improved orthology inference with Hieranoid 2.
Bioinform.
Mateusz Kaduk, Erik L. L. Sonnhammer
2016 J jnl
Benchmarking the next generation of homology inference tools.
Bioinform.
Ganapathi Varma Saripella, Erik L. L. Sonnhammer, Kristoffer Forslund
2016 J jnl
PathwAX: a web server for network crosstalk based pathway annotation.
Nucleic Acids Res.
Christoph Ogris, Thomas Helleday, Erik L. L. Sonnhammer
2016 J jnl
TreeDom: a graphical web tool for analysing domain architecture evolution.
Bioinform.
Christian Haider, Marina Kavic, Erik L. L. Sonnhammer
2015 J jnl
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic.
Nucleic Acids Res.
Erik L. L. Sonnhammer, Gabriel Östlund
2014 J jnl
Big data and other challenges in the quest for orthologs.
Bioinform.
Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, Quest for Orthologs Consortium
2014 J jnl
FunCoup 3.0: database of genome-wide functional coupling networks.
Nucleic Acids Res.
Thomas Schmitt, Christoph Ogris, Erik L. L. Sonnhammer
2014 J jnl
Functional association networks as priors for gene regulatory network inference.
Bioinform.
Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer
2014 J jnl
MaxLink: network-based prioritization of genes tightly linked to a disease seed set.
Bioinform.
Dimitri Guala, Erik Sjölund, Erik L. L. Sonnhammer
2014 J jnl
Pfam: the protein families database.
Nucleic Acids Res.
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
2013 J jnl
Optimal Sparsity Criteria for Network Inference.
J. Comput. Biol.
Andreas Tjärnberg, Torbjörn E. M. Nordling, Matthew Studham, Erik L. L. Sonnhammer
2012 J jnl
Comparative interactomics with Funcoup 2.0.
Nucleic Acids Res.
Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dimitri Guala, Oliver Frings, Erik L. L. Sonnhammer
2012 J jnl
The Pfam protein families database.
Nucleic Acids Res.
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
2012 J jnl
Toward community standards in the quest for orthologs.
Bioinform.
Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero
2011 J jnl
Domain architecture conservation in orthologs.
BMC Bioinform.
Kristoffer Forslund, Isabella Pekkari, Erik L. L. Sonnhammer
2011 J jnl
Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information.
Briefings Bioinform.
Thomas Schmitt, David N. Messina, Fabian Schreiber, Erik L. L. Sonnhammer
2011 J jnl
OrthoDisease: tracking disease gene orthologs across 100 species.
Briefings Bioinform.
Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn, Erik L. L. Sonnhammer
2010 J jnl
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
Nucleic Acids Res.
Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, Erik L. L. Sonnhammer
2010 J jnl
The Pfam protein families database.
Nucleic Acids Res.
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
2009 J jnl
Benchmarking homology detection procedures with low complexity filters.
Bioinform.
Kristoffer Forslund, Erik L. L. Sonnhammer
2009 J jnl
Comparative analysis and unification of domain-domain interaction networks.
Bioinform.
Patrik Björkholm, Erik L. L. Sonnhammer
2009 J jnl
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.
Bioinform.
David N. Messina, Erik L. L. Sonnhammer
2009 J jnl
MetaTM - a consensus method for transmembrane protein topology prediction.
BMC Bioinform.
Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. L. Sonnhammer
2009 J jnl
Predicting protein function from domain content.
Bioinform.
Kristoffer Forslund, Erik L. L. Sonnhammer
2008 J jnl
Employing conservation of co-expression to improve functional inference.
BMC Syst. Biol.
Carsten O. Daub, Erik L. L. Sonnhammer
2008 J jnl
InParanoid 6: eukaryotic ortholog clusters with inparalogs.
Nucleic Acids Res.
Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer
2008 J jnl
Predicting protein function from domain content.
Bioinform.
Kristoffer Forslund, Erik L. L. Sonnhammer
2008 J jnl
Predicting protein function from domain content.
Bioinform.
Kristoffer Forslund, Erik L. L. Sonnhammer
2008 J jnl
The Pfam protein families database.
Nucleic Acids Res.
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
2008 J jnl
jSquid: a Java applet for graphical on-line network exploration.
Bioinform.
Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer
2008 J jnl
siRNA specificity searching incorporating mismatch tolerance data.
Bioinform.
Alistair M. Chalk, Erik L. L. Sonnhammer
2007 J jnl
Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server.
Nucleic Acids Res.
Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer
2007 J jnl
Automatic extraction of reliable regions from multiple sequence alignments.
BMC Bioinform.
Timo Lassmann, Erik L. L. Sonnhammer
2007 J jnl
PfamAlyzer: domain-centric homology search.
Bioinform.
Volker Hollich, Erik L. L. Sonnhammer
2006 — conf
Automatic clustering of orthologs and inparalogs shared by multiple proteomes.
ISMB (Supplement of Bioinformatics)
Andrey Alexeyenko, Ivica Tamas, Gang Liu, Erik L. L. Sonnhammer
2006 J jnl
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
Nucleic Acids Res.
Timo Lassmann, Erik L. L. Sonnhammer
2006 J jnl
Pfam: clans, web tools and services.
Nucleic Acids Res.
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
2005 — conf
An HMM posterior decoder for sequence feature prediction that includes homology information.
ISMB (Supplement of Bioinformatics)
Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer
2005 J jnl
FunShift: a database of function shift analysis on protein subfamilies.
Nucleic Acids Res.
Saraswathi Abhiman, Erik L. L. Sonnhammer
2005 J jnl
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.
BMC Bioinform.
Markus Wistrand, Erik L. L. Sonnhammer
2005 J jnl
Inparanoid: a comprehensive database of eukaryotic orthologs.
Nucleic Acids Res.
Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer
2005 J jnl
Kalign - an accurate and fast multiple sequence alignment algorithm.
BMC Bioinform.
Timo Lassmann, Erik L. L. Sonnhammer
2005 J jnl
siRNAdb: a database of siRNA sequences.
Nucleic Acids Res.
Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer
2004 J jnl
ChromoWheel: a new spin on eukaryotic chromosome visualization.
Bioinform.
Sven Ekdahl, Erik L. L. Sonnhammer
2004 J jnl
Profiled support vector machines for antisense oligonucleotide efficacy prediction.
BMC Bioinform.
Gustavo Camps-Valls, Alistair M. Chalk, Antonio J. Serrano-López, José David Martín-Guerrero, Erik L. L. Sonnhammer
2004 J jnl
Sfixem - graphical sequence feature display in Java.
Bioinform.
Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer
2004 J jnl
The Pfam protein families database.
Nucleic Acids Res.
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
2004 J jnl
Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination.
J. Comput. Biol.
Markus Wistrand, Erik L. L. Sonnhammer
2002 J jnl
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
Bioinform.
Christian E. V. Storm, Erik L. L. Sonnhammer
2002 J jnl
Computational antisense oligo prediction with a neural network model.
Bioinform.
Alistair M. Chalk, Erik L. L. Sonnhammer
2002 J jnl
OrthoGUI: graphical presentation of Orthostrapper results.
Bioinform.
Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer
2002 J jnl
The Pfam Protein Families Database.
Nucleic Acids Res.
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
2001 J jnl
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
Bioinform.
Raf M. Podowski, Erik L. L. Sonnhammer
2001 J jnl
NIFAS: visual analysis of domain evolution in proteins.
Bioinform.
Christian E. V. Storm, Erik L. L. Sonnhammer
2000 J jnl
The Pfam Protein Families Database.
Nucleic Acids Res.
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer
1999 J jnl
A comparison of sequence and structure protein domain families as a basis for structural genomics.
Bioinform.
Arne Elofsson, Erik L. L. Sonnhammer
1999 J jnl
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
Nucleic Acids Res.
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer
1998 A conf
A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences.
ISMB
Erik L. L. Sonnhammer, Gunnar von Heijne, Anders Krogh
1998 J jnl
Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Nucleic Acids Res.
Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin
1994 J jnl
A workbench for large-scale sequence homology analysis.
Comput. Appl. Biosci.
Erik L. L. Sonnhammer, Richard Durbin
1994 A conf
An Expert System for Processing Sequence Homology Data.
ISMB
Erik L. L. Sonnhammer, Richard Durbin
1992 J jnl
METASIM: object-oriented modelling of cell regulation.
Comput. Appl. Biosci.
H. J. Stoffers, Erik L. L. Sonnhammer, G. J. Blommestijn, N. J. Raat, Hans V. Westerhoff