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)

An Expert System for Processing Sequence Homology Data. - Erik L. L. Sonnhammer; Richard Durbin (ISMB, 1994)

A workbench for large-scale sequence homology analysis. - Erik L. L. Sonnhammer; Richard Durbin (Comput. Appl. Biosci., 1994)

A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences. - Erik L. L. Sonnhammer; Gunnar von Heijne; Anders Krogh (ISMB, 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 comparison of sequence and structure protein domain families as a basis for structural genomics. - Arne Elofsson; Erik L. L. Sonnhammer (Bioinform., 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)

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)

MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs. - Raf M. Podowski; Erik L. L. Sonnhammer (Bioinform., 2001)

NIFAS: visual analysis of domain evolution in proteins. - Christian E. V. Storm; Erik L. L. Sonnhammer (Bioinform., 2001)

Computational antisense oligo prediction with a neural network model. - Alistair M. Chalk; Erik L. L. Sonnhammer (Bioinform., 2002)

OrthoGUI: graphical presentation of Orthostrapper results. - Volker Hollich; Christian E. V. Storm; Erik L. L. Sonnhammer (Bioinform., 2002)

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. - Christian E. V. Storm; Erik L. L. Sonnhammer (Bioinform., 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)

Sfixem - graphical sequence feature display in Java. - Alistair M. Chalk; Martin Wennerberg; Erik L. L. Sonnhammer (Bioinform., 2004)

ChromoWheel: a new spin on eukaryotic chromosome visualization. - Sven Ekdahl; Erik L. L. Sonnhammer (Bioinform., 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)

Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. - Markus Wistrand; Erik L. L. Sonnhammer (J. Comput. Biol., 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; et al. (Nucleic Acids Res., 2004)

An HMM posterior decoder for sequence feature prediction that includes homology information. - Lukas Käll; Anders Krogh; Erik L. L. Sonnhammer (ISMB (Supplement of Bioinformatics), 2005)

Kalign - an accurate and fast multiple sequence alignment algorithm. - Timo Lassmann; Erik L. L. Sonnhammer (BMC Bioinform., 2005)

Scoredist: A simple and robust protein sequence distance estimator. - Erik L. L. Sonnhammer; Volker Hollich (BMC Bioinform., 2005)

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. - Markus Wistrand; Erik L. L. Sonnhammer (BMC Bioinform., 2005)

FunShift: a database of function shift analysis on protein subfamilies. - Saraswathi Abhiman; 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)

Inparanoid: a comprehensive database of eukaryotic orthologs. - Kevin P. O'Brien; Maido Remm; Erik L. L. Sonnhammer (Nucleic Acids Res., 2005)

Automatic clustering of orthologs and inparalogs shared by multiple proteomes. - Andrey Alexeyenko; Ivica Tamas; Gang Liu; Erik L. L. Sonnhammer (ISMB (Supplement of Bioinformatics), 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; et al. (Nucleic Acids Res., 2006)

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. - Timo Lassmann; Erik L. L. Sonnhammer (Nucleic Acids Res., 2006)

PfamAlyzer: domain-centric homology search. - Volker Hollich; Erik L. L. Sonnhammer (Bioinform., 2007)

Automatic extraction of reliable regions from multiple sequence alignments. - Timo Lassmann; Erik L. L. Sonnhammer (BMC Bioinform., 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)

siRNA specificity searching incorporating mismatch tolerance data. - Alistair M. Chalk; Erik L. L. Sonnhammer (Bioinform., 2008)

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

jSquid: a Java applet for graphical on-line network exploration. - Martin Klammer; Sanjit Roopra; Erik L. L. Sonnhammer (Bioinform., 2008)

Employing conservation of co-expression to improve functional inference. - Carsten O. Daub; Erik L. L. Sonnhammer (BMC Syst. Biol., 2008)

InParanoid 6: eukaryotic ortholog clusters with inparalogs. - Ann-Charlotte Berglund; Erik Sjölund; Gabriel Östlund; Erik L. L. Sonnhammer (Nucleic Acids Res., 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)

Comparative analysis and unification of domain-domain interaction networks. - Patrik Björkholm; Erik L. L. Sonnhammer (Bioinform., 2009)

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

DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. - David N. Messina; Erik L. L. Sonnhammer (Bioinform., 2009)

MetaTM - a consensus method for transmembrane protein topology prediction. - Martin Klammer; David N. Messina; Thomas Schmitt 003; Erik L. L. Sonnhammer (BMC 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)

Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information. - Thomas Schmitt 003; David N. Messina; Fabian Schreiber; Erik L. L. Sonnhammer (Briefings Bioinform., 2011)

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

Toward community standards in the quest for orthologs. - Christophe Dessimoz; Toni Gabaldón; David S. Roos; Erik L. L. Sonnhammer; Javier Herrero (Bioinform., 2012)

Comparative interactomics with Funcoup 2.0. - Andrey Alexeyenko; Thomas Schmitt 003; Andreas Tjärnberg; Dimitri Guala; Oliver Frings; Erik L. L. Sonnhammer (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2012)

Optimal Sparsity Criteria for Network Inference. - Andreas Tjärnberg; Torbjörn E. M. Nordling; Matthew Studham; Erik L. L. Sonnhammer (J. Comput. Biol., 2013)

MaxLink: network-based prioritization of genes tightly linked to a disease seed set. - Dimitri Guala; Erik Sjölund; 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; Quest for Orthologs Consortium (Bioinform., 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)

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; et al. (Nucleic Acids Res., 2014)

FunCoup 3.0: database of genome-wide functional coupling networks. - Thomas Schmitt 003; Christoph Ogris; Erik L. L. Sonnhammer (Nucleic Acids Res., 2014)

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. - Erik L. L. Sonnhammer; Gabriel Östlund (Nucleic Acids Res., 2015)

TreeDom: a graphical web tool for analysing domain architecture evolution. - Christian Haider; Marina Kavic; Erik L. L. Sonnhammer (Bioinform., 2016)

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

PathwAX: a web server for network crosstalk based pathway annotation. - Christoph Ogris; Thomas Helleday; Erik L. L. Sonnhammer (Nucleic Acids Res., 2016)

Improved orthology inference with Hieranoid 2. - Mateusz Kaduk; Erik L. L. Sonnhammer (Bioinform., 2017)

HieranoiDB: a database of orthologs inferred by Hieranoid. - Mateusz Kaduk; Christian Riegler; Oliver Lemp; Erik L. L. Sonnhammer (Nucleic Acids Res., 2017)

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)

FunCoup 4: new species, data, and visualization. - Christoph Ogris; Dimitri Guala; Mateusz Kaduk; Erik L. L. Sonnhammer (Nucleic Acids Res., 2018)

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)

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

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)

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 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

Inferring the experimental design for accurate gene regulatory network inference. - Deniz Seçilmis; Thomas Hillerton; Sven Nelander; Erik L. L. Sonnhammer (Bioinform., 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)

Fast and accurate gene regulatory network inference by normalized least squares regression. - Thomas Hillerton; Deniz Seçilmis; Sven Nelander; Erik L. L. Sonnhammer (Bioinform., 2022)

PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk. - Christoph Ogris; Miguel Castresana Aguirre; Erik L. L. Sonnhammer (Bioinform., 2022)

InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. - Emma Persson; Erik L. L. Sonnhammer (Bioinform., 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; et al. (Nucleic Acids Res., 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)

Benchmarking enrichment analysis methods with the disease pathway network. - Davide Buzzao; Miguel Castresana Aguirre; Dimitri Guala; Erik L. L. Sonnhammer (Briefings Bioinform., 2024)