Erik L. L. Sonnhammer

Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero: Toward community standards in the quest for orthologs. Bioinformatics 28(6): 900-904 (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 Research 40(Database-Issue): 290-301 (2012)

Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dmitri Guala, Oliver Frings, Erik L. L. Sonnhammer: Comparative interactomics with Funcoup 2.0. Nucleic Acids Research 40(Database-Issue): 821-828 (2012)

Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn, Erik L. L. Sonnhammer: OrthoDisease: tracking disease gene orthologs across 100 species. Briefings in Bioinformatics 12(5): 463-473 (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 in Bioinformatics 12(5): 485-488 (2011)

Kristoffer Forslund, Isabella Pekkari, Erik L. L. Sonnhammer: Domain architecture conservation in orthologs. BMC Bioinformatics 12: 326 (2011)

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 Research 38(Database-Issue): 196-203 (2010)

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 Research 38(Database-Issue): 211-222 (2010)

Kristoffer Forslund, Erik L. L. Sonnhammer: Predicting protein function from domain content. Bioinformatics 25(9): 1214 (2009)

David N. Messina, Erik L. L. Sonnhammer: DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinformatics 25(10): 1333-1334 (2009)

Kristoffer Forslund, Erik L. L. Sonnhammer: Benchmarking homology detection procedures with low complexity filters. Bioinformatics 25(19): 2500-2505 (2009)

Patrik Björkholm, Erik L. L. Sonnhammer: Comparative analysis and unification of domain-domain interaction networks. Bioinformatics 25(22): 3020-3025 (2009)

Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. L. Sonnhammer: MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics 10: 314 (2009)

Alistair M. Chalk, Erik L. L. Sonnhammer: siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics 24(10): 1316-1317 (2008)

Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer: jSquid: a Java applet for graphical on-line network exploration. Bioinformatics 24(12): 1467-1468 (2008)

Kristoffer Forslund, Erik L. L. Sonnhammer: Predicting protein function from domain content. Bioinformatics 24(15): 1681-1687 (2008)

Kristoffer Forslund, Erik L. L. Sonnhammer: Predicting protein function from domain content. Bioinformatics 24(19): 2275 (2008)

Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer: InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Research 36(Database-Issue): 263-266 (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 Research 36(Database-Issue): 281-288 (2008)

Volker Hollich, Erik L. L. Sonnhammer: PfamAlyzer: domain-centric homology search. Bioinformatics 23(24): 3382-3383 (2007)

Timo Lassmann, Erik L. L. Sonnhammer: Automatic extraction of reliable regions from multiple sequence alignments. BMC Bioinformatics 8(S-5) (2007)

Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer: Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Research 35(Web-Server-Issue): 429-432 (2007)

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 Research 34(Database-Issue): 247-251 (2006)

Timo Lassmann, Erik L. L. Sonnhammer: Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Research 34(Web-Server-Issue): 596-599 (2006)

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: 9-15

Markus Wistrand, Erik L. L. Sonnhammer: Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics 6: 99 (2005)

Erik L. L. Sonnhammer, Volker Hollich: Scoredist: A simple and robust protein sequence distance estimator. BMC Bioinformatics 6: 108 (2005)

Timo Lassmann, Erik L. L. Sonnhammer: Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6: 298 (2005)

Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer: siRNAdb: a database of siRNA sequences. Nucleic Acids Research 33(Database-Issue): 131-134 (2005)

Saraswathi Abhiman, Erik L. L. Sonnhammer: FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Research 33(Database-Issue): 197-200 (2005)

Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer: Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Research 33(Database-Issue): 476-480 (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: 251-257

Sven Ekdahl, Erik L. L. Sonnhammer: ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics 20(4): 576-577 (2004)

Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer: Sfixem - graphical sequence feature display in Java. Bioinformatics 20(15): 2488-2490 (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 Bioinformatics 5: 135 (2004)

Markus Wistrand, Erik L. L. Sonnhammer: Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. Journal of Computational Biology 11(1): 181-193 (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 Research 32(Database-Issue): 138-141 (2004)

Christian E. V. Storm, Erik L. L. Sonnhammer: Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18(1): 92-99 (2002)

Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer: OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics 18(9): 1272-1273 (2002)

Alistair M. Chalk, Erik L. L. Sonnhammer: Computational antisense oligo prediction with a neural network model. Bioinformatics 18(12): 1567-1575 (2002)

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 Research 30(1): 276-280 (2002)

Christian E. V. Storm, Erik L. L. Sonnhammer: NIFAS: visual analysis of domain evolution in proteins. Bioinformatics 17(4): 343-348 (2001)

Raf M. Podowski, Erik L. L. Sonnhammer: MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs. Bioinformatics 17(7): 656-657 (2001)

Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer: The Pfam Protein Families Database. Nucleic Acids Research 28(1): 263-266 (2000)

Arne Elofsson, Erik L. L. Sonnhammer: A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics 15(6): 480-500 (1999)

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 Research 27(1): 260-262 (1999)

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 Research 26(1): 320-322 (1998)

Erik L. L. Sonnhammer, Gunnar von Heijne, Anders Krogh: A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences. ISMB 1998: 175-182

Erik L. L. Sonnhammer, Richard Durbin: A workbench for large-scale sequence homology analysis. Computer Applications in the Biosciences 10(3): 301-307 (1994)

Erik L. L. Sonnhammer, Richard Durbin: An Expert System for Processing Sequence Homology Data. ISMB 1994: 363-368

H. J. Stoffers, Erik L. L. Sonnhammer, G. J. Blommestijn, N. J. Raat, H. V. Westerhoff: METASIM: object-oriented modelling of cell regulation. Computer Applications in the Biosciences 8(5): 443-449 (1992)