Erik L. L. Sonnhammer

Publication Activity (10 Years)

Years Active: 1992-2022
Publications (10 Years): 18

Top Topics

Protein Families

Probabilistic Inference

Metropolis Hastings Algorithm

Top Venues

Nucleic Acids Res.

J. Comput. Biol.

Publications

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 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
The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 50 (W1) (2022)
Emma Persson, Erik L. L. Sonnhammer
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. Bioinform. 38 (10) (2022)
Thomas Hillerton, Deniz Seçilmis, Sven Nelander, Erik L. L. Sonnhammer
Fast and accurate gene regulatory network inference by normalized least squares regression. Bioinform. 38 (8) (2022)
Deniz Seçilmis, Thomas Hillerton, Erik L. L. Sonnhammer
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods. Nucleic Acids Res. 50 (W1) (2022)
Deniz Seçilmis, Thomas Hillerton, Sven Nelander, Erik L. L. Sonnhammer
Inferring the experimental design for accurate gene regulatory network inference. Bioinform. 37 (20) (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
Pfam: The protein families database in 2021. Nucleic Acids Res. 49 (Database-Issue) (2021)
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
The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Dimitri Guala, Christoph Ogris, Nikola Müller, Erik L. L. Sonnhammer
Genome-wide functional association networks: background, data & state-of-the-art resources. Briefings Bioinform. 21 (4) (2020)
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
The Pfam protein families database in 2019. Nucleic Acids Res. 47 (Database-Issue) (2019)
Emma Persson, Mateusz Kaduk, Sofia K. Forslund, Erik L. L. Sonnhammer
Domainoid: domain-oriented orthology inference. BMC Bioinform. 20 (1) (2019)
Daniel Morgan, Andreas Tjärnberg, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer
A generalized framework for controlling FDR in gene regulatory network inference. Bioinform. 35 (6) (2019)
Christoph Ogris, Dimitri Guala, Mateusz Kaduk, Erik L. L. Sonnhammer
FunCoup 4: new species, data, and visualization. Nucleic Acids Res. 46 (Database-Issue) (2018)
Kristoffer Forslund, Cecile 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
Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinform. 34 (2) (2018)
Mateusz Kaduk, Erik L. L. Sonnhammer
Improved orthology inference with Hieranoid 2. Bioinform. 33 (8) (2017)
Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L. L. Sonnhammer
HieranoiDB: a database of orthologs inferred by Hieranoid. Nucleic Acids Res. 45 (Database-Issue) (2017)
Christoph Ogris, Thomas Helleday, Erik L. L. Sonnhammer
PathwAX: a web server for network crosstalk based pathway annotation. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Ganapathi Varma Saripella, Erik L. L. Sonnhammer, Kristoffer Forslund
Benchmarking the next generation of homology inference tools. Bioinform. 32 (17) (2016)
Christian Haider, Marina Kavic, Erik L. L. Sonnhammer
TreeDom: a graphical web tool for analysing domain architecture evolution. Bioinform. 32 (15) (2016)
Erik L. L. Sonnhammer, Gabriel Östlund
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 43 (Database-Issue) (2015)
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
Big data and other challenges in the quest for orthologs. Bioinform. 30 (21) (2014)
Thomas Schmitt, Christoph Ogris, Erik L. L. Sonnhammer
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res. 42 (Database-Issue) (2014)
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
Pfam: the protein families database. Nucleic Acids Res. 42 (Database-Issue) (2014)
Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer
Functional association networks as priors for gene regulatory network inference. Bioinform. 30 (12) (2014)
Dimitri Guala, Erik Sjölund, Erik L. L. Sonnhammer
MaxLink: network-based prioritization of genes tightly linked to a disease seed set. Bioinform. 30 (18) (2014)
Andreas Tjärnberg, Torbjörn E. M. Nordling, Matthew Studham, Erik L. L. Sonnhammer
Optimal Sparsity Criteria for Network Inference. J. Comput. Biol. 20 (5) (2013)
Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero
Toward community standards in the quest for orthologs. Bioinform. 28 (6) (2012)
Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dimitri Guala, Oliver Frings, Erik L. L. Sonnhammer
Comparative interactomics with Funcoup 2.0. Nucleic Acids Res. 40 (Database-Issue) (2012)
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
The Pfam protein families database. Nucleic Acids Res. 40 (Database-Issue) (2012)
Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn, Erik L. L. Sonnhammer
OrthoDisease: tracking disease gene orthologs across 100 species. Briefings Bioinform. 12 (5) (2011)
Kristoffer Forslund, Isabella Pekkari, Erik L. L. Sonnhammer
Domain architecture conservation in orthologs. BMC Bioinform. 12 (2011)
Thomas Schmitt, David N. Messina, Fabian Schreiber, Erik L. L. Sonnhammer
Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information. Briefings Bioinform. 12 (5) (2011)
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
The Pfam protein families database. Nucleic Acids Res. 38 (Database-Issue) (2010)
Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, Erik L. L. Sonnhammer
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38 (Database-Issue) (2010)
Kristoffer Forslund, Erik L. L. Sonnhammer
Predicting protein function from domain content. Bioinform. 25 (9) (2009)
Kristoffer Forslund, Erik L. L. Sonnhammer
Benchmarking homology detection procedures with low complexity filters. Bioinform. 25 (19) (2009)
Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. L. Sonnhammer
MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinform. 10 (2009)
Patrik Björkholm, Erik L. L. Sonnhammer
Comparative analysis and unification of domain-domain interaction networks. Bioinform. 25 (22) (2009)
David N. Messina, Erik L. L. Sonnhammer
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinform. 25 (10) (2009)
Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer
InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 36 (Database-Issue) (2008)
Kristoffer Forslund, Erik L. L. Sonnhammer
Predicting protein function from domain content. Bioinform. 24 (15) (2008)
Alistair M. Chalk, Erik L. L. Sonnhammer
siRNA specificity searching incorporating mismatch tolerance data. Bioinform. 24 (10) (2008)
Kristoffer Forslund, Erik L. L. Sonnhammer
Predicting protein function from domain content. Bioinform. 24 (19) (2008)
Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer
jSquid: a Java applet for graphical on-line network exploration. Bioinform. 24 (12) (2008)
Carsten O. Daub, Erik L. L. Sonnhammer
Employing conservation of co-expression to improve functional inference. BMC Syst. Biol. 2 (2008)
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
The Pfam protein families database. Nucleic Acids Res. 36 (Database-Issue) (2008)
Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer
Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Volker Hollich, Erik L. L. Sonnhammer
PfamAlyzer: domain-centric homology search. Bioinform. 23 (24) (2007)
Timo Lassmann, Erik L. L. Sonnhammer
Automatic extraction of reliable regions from multiple sequence alignments. BMC Bioinform. 8 (S-5) (2007)
Andrey Alexeyenko, Ivica Tamas, Gang Liu, Erik L. L. Sonnhammer
Automatic clustering of orthologs and inparalogs shared by multiple proteomes. ISMB (Supplement of Bioinformatics) (2006)
Timo Lassmann, Erik L. L. Sonnhammer
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
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
Pfam: clans, web tools and services. Nucleic Acids Res. 34 (Database-Issue) (2006)
Erik L. L. Sonnhammer, Volker Hollich
: A simple and robust protein sequence distance estimator. BMC Bioinform. 6 (2005)
Saraswathi Abhiman, Erik L. L. Sonnhammer
FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res. 33 (Database-Issue) (2005)
Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer
Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33 (Database-Issue) (2005)
Markus Wistrand, Erik L. L. Sonnhammer
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinform. 6 (2005)
Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer
siRNAdb: a database of siRNA sequences. Nucleic Acids Res. 33 (Database-Issue) (2005)
Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer
An HMM posterior decoder for sequence feature prediction that includes homology information. ISMB (Supplement of Bioinformatics) (2005)
Timo Lassmann, Erik L. L. Sonnhammer
Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinform. 6 (2005)
Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer
Sfixem - graphical sequence feature display in Java. Bioinform. 20 (15) (2004)
Sven Ekdahl, Erik L. L. Sonnhammer
ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinform. 20 (4) (2004)
Gustavo Camps-Valls, Alistair M. Chalk, Antonio J. Serrano-López, José David Martín-Guerrero, Erik L. L. Sonnhammer
Profiled support vector machines for antisense oligonucleotide efficacy prediction. BMC Bioinform. 5 (2004)
Markus Wistrand, Erik L. L. Sonnhammer
Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. J. Comput. Biol. 11 (1) (2004)
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
The Pfam protein families database. Nucleic Acids Res. 32 (Database-Issue) (2004)
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
The Pfam Protein Families Database. Nucleic Acids Res. 30 (1) (2002)
Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer
OrthoGUI: graphical presentation of Orthostrapper results. Bioinform. 18 (9) (2002)
Christian E. V. Storm, Erik L. L. Sonnhammer
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinform. 18 (1) (2002)
Alistair M. Chalk, Erik L. L. Sonnhammer
Computational antisense oligo prediction with a neural network model. Bioinform. 18 (12) (2002)
Raf M. Podowski, Erik L. L. Sonnhammer
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs. Bioinform. 17 (7) (2001)
Christian E. V. Storm, Erik L. L. Sonnhammer
NIFAS: visual analysis of domain evolution in proteins. Bioinform. 17 (4) (2001)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer
The Pfam Protein Families Database. Nucleic Acids Res. 28 (1) (2000)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27 (1) (1999)
Arne Elofsson, Erik L. L. Sonnhammer
A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinform. 15 (6) (1999)
Erik L. L. Sonnhammer, Gunnar von Heijne, Anders Krogh
A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences. ISMB (1998)
Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin
Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26 (1) (1998)
Erik L. L. Sonnhammer, Richard Durbin
An Expert System for Processing Sequence Homology Data. ISMB (1994)
Erik L. L. Sonnhammer, Richard Durbin
A workbench for large-scale sequence homology analysis. Comput. Appl. Biosci. 10 (3) (1994)
H. J. Stoffers, Erik L. L. Sonnhammer, G. J. Blommestijn, N. J. Raat, Hans V. Westerhoff
METASIM: object-oriented modelling of cell regulation. Comput. Appl. Biosci. 8 (5) (1992)