FIND

researchers

DISCOVER

relevant articles

PROMOTE

your research

now for free

Erik Sonnhammer

Research Profile

Activities & Behaviors

Chemicals & Drugs

Proteins

Occupations

Procedures

Concepts & Ideas

Phenomena

Evolution, Molecular

Genes & Molecular Sequences

Co-author Network

Publications

TOP 3
Fabian Schreiber; Erik L L Sonnhammer
Hieranoid: hierarchical orthology inference.
Andreas Tjärnberg; Matthew Studham; Torbjörn E M Nordling; Erik L L Sonnhammer
Optimal sparsity criteria for network inference.
Theodore McCormack; Andrey Alexeyenko; Oliver Frings; Erik L L Sonnhammer
Statistical assessment of crosstalk enrichment between gene groups in biological networks.

Register for free to view:

Visualized networks:

See your personal network in
sophisticated graphical views

GeoTargeted Searches:

Locate experts around the world
and connect with global collaborators

Research Profiles:

See the research activity
of experts around the globe

Geonetwork of Erik Sonnhammer (preview)

Cities where this author has publications
Cities where co-authors of this author have publications

Flash Player Required

All Publications

2013: Fabian Schreiber; Erik L L Sonnhammer
Hieranoid: hierarchical orthology inference.
Journal of molecular biology 2013;425(11):2072-81.
2013: Andreas Tjärnberg; Matthew Studham; Torbjörn E M Nordling; Erik L L Sonnhammer
Optimal sparsity criteria for network inference.
Journal of computational biology : a journal of computational molecular cell biology 2013;20(5):398-408.
2013: Theodore McCormack; Andrey Alexeyenko; Oliver Frings; Erik L L Sonnhammer
Statistical assessment of crosstalk enrichment between gene groups in biological networks.
PloS one 2013;8(1):e54945.
2012: Gabriel Ostlund; Erik L L Sonnhammer
Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation.
Gene 2012;497(2):228-36.
2012: Christophe Dessimoz; Toni Gabaldón; Javier Herrero; David S Roos; Erik L L Sonnhammer
Toward community standards in the quest for orthologs.
Bioinformatics (Oxford, England) 2012;28(6):900-4.
2012: Oliver Frings; Judith E Mank; Andrey Alexeyenko; Erik L L Sonnhammer
Network analysis of functional genomics data: application to avian sex-biased gene expression.
TheScientificWorldJournal 2012;2012():130491.
2012: Kristoffer Forslund; Erik L L Sonnhammer
Evolution of protein domain architectures.
Methods in molecular biology (Clifton, N.J.) 2012;856():187-216.
2012: Marco Punta; Erik L L Sonnhammer; J Tate; Kristoffer Forslund; Andreas Heger; Liisa Holm; Jaina Mistry; Ningze Pang; Alex Bateman; Chris Boursnell; Goran Ceric; Jody Clements; Penny Coggill; Ruth Y Eberhardt; Sean R Eddy; Robert D Finn
The Pfam protein families database.
Nucleic acids research 2012;40(Database issue):D290-301.
2011: Thomas Schmitt; Fabian Schreiber; David N Messina; Erik L L Sonnhammer
Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information.
Briefings in bioinformatics 2011;12(5):485-8.
2011: Kristoffer Forslund; Fabian Schreiber; Nattaphon Thanintorn; Erik L L Sonnhammer
OrthoDisease: tracking disease gene orthologs across 100 species.
Briefings in bioinformatics 2011;12(5):463-73.
2010: Gabriel Ostlund; Mats Lindskog; Erik L L Sonnhammer
Network-based Identification of novel cancer genes.
Molecular & cellular proteomics : MCP 2010;9(4):648-55.
2010: Anna Henricson; Kristoffer Forslund; Erik L L Sonnhammer
Orthology confers intron position conservation.
BMC genomics 2010;11():412.
2010: Andrey Alexeyenko; Deena M Wassenberg; Edward K Lobenhofer; Jerry Yen; Elwood Linney; Erik L L Sonnhammer; Joel N Meyer
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity.
PloS one 2010;5(5):e10465.
2010: Robert D Finn; Jaina Mistry; J Tate; Penny 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 2010;38(Database issue):D211-22.
2010: Gabriel Ostlund; 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 2010;38(Database issue):D196-203.
2009: Patrik Björkholm; Erik L L Sonnhammer
Comparative analysis and unification of domain-domain interaction networks.
Bioinformatics (Oxford, England) 2009;25(22):3020-5.
2009: Kristoffer Forslund; Erik L L Sonnhammer
Benchmarking homology detection procedures with low complexity filters.
Bioinformatics (Oxford, England) 2009;25(19):2500-5.
2009: Andrey Alexeyenko; Erik L L Sonnhammer
Global networks of functional coupling in eukaryotes from comprehensive data integration.
Genome research 2009;19(6):1107-16.
2009: David N Messina; Erik L L Sonnhammer
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.
Bioinformatics (Oxford, England) 2009;25(10):1333-4.
2009: Timo Lassmann; Oliver Frings; Erik L L Sonnhammer
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.
Nucleic acids research 2009;37(3):858-65.
2009: Martin Klammer; David N Messina; Thomas Schmitt; Erik L L Sonnhammer
MetaTM - a consensus method for transmembrane protein topology prediction.
BMC bioinformatics 2009;10():314.
2008: Kristoffer Forslund; Erik L L Sonnhammer
Predicting protein function from domain content.
Bioinformatics (Oxford, England) 2008;24(15):1681-7.
2008: Martin Klammer; Sanjit Roopra; Erik L L Sonnhammer
jSquid: a Java applet for graphical on-line network exploration.
Bioinformatics (Oxford, England) 2008;24(12):1467-8.
2008: Alistair Chalk; Erik L L Sonnhammer
siRNA specificity searching incorporating mismatch tolerance data.
Bioinformatics (Oxford, England) 2008;24(10):1316-7.
2008: Junmei Hong; Na Wei; Alistair Chalk; Jue Wang; Yutong Song; Fan Yi; Ren-Ping Qiao; Erik L L Sonnhammer; Claes Wahlestedt; Zicai Liang; Quan Du
Focusing on RISC assembly in mammalian cells.
Biochemical and biophysical research communications 2008;368(3):703-8.
2008: Kristoffer Forslund; Anna Henricson; Volker Hollich; Erik L L Sonnhammer
Domain tree-based analysis of protein architecture evolution.
Molecular biology and evolution 2008;25(2):254-64.
2008: Nicolas Joannin; Abhiman Saraswathi; Erik L L Sonnhammer; Mats Wahlgren
Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family.
BMC genomics 2008;9():19.
2008: Ann-Charlotte Berglund; Erik Sjölund; Gabriel Ostlund; Erik L L Sonnhammer
InParanoid 6: eukaryotic ortholog clusters with inparalogs.
Nucleic acids research 2008;36(Database issue):D263-6.
2008: Robert D Finn; J 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 2008;36(Database issue):D281-8.
2007: Volker Hollich; Erik L L Sonnhammer
PfamAlyzer: domain-centric homology search.
Bioinformatics (Oxford, England) 2007;23(24):3382-3.
2007: Carolina Boekel Lundin; Lukas Käll; Scott Kreher; Katja Kapp; Erik L L Sonnhammer; John R Carlson; Gunnar von Heijne; IngMarie Nilsson
Membrane topology of the Drosophila OR83b odorant receptor.
FEBS letters 2007;581(29):5601-4.
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 2007;35(Web Server issue):W429-32.
2007: Timo Lassmann; Erik L L Sonnhammer
Automatic extraction of reliable regions from multiple sequence alignments.
BMC bioinformatics 2007;8 Suppl 5():S9.
2006: Andrey Alexeyenko; A Harvey Millar; James Whelan; Erik L L Sonnhammer
Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis.
Trends in genetics : TIG 2006;22(11):589-93.
2006: Andrey Alexeyenko; Ivica Tamas; Gang Liu; Erik L L Sonnhammer
Automatic clustering of orthologs and inparalogs shared by multiple proteomes.
Bioinformatics (Oxford, England) 2006;22(14):e9-15.
2006: Timo Lassmann; Erik L L Sonnhammer
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
Nucleic acids research 2006;34(Web Server issue):W596-9.
2006: Abhiman Saraswathi; Carsten O Daub; Erik L L Sonnhammer
Prediction of function divergence in protein families using the substitution rate variation parameter alpha.
Molecular biology and evolution 2006;23(7):1406-13.
2006: Markus Wistrand; Lukas Käll; Erik L L Sonnhammer
A general model of G protein-coupled receptor sequences and its application to detect remote homologs.
Protein science : a publication of the Protein Society 2006;15(3):509-21.
2006: Danielle Kemmer; Raf M Podowski; David Arenillas; Jonathan Lim; Emily Hodges; Peggy Roth; Erik L L Sonnhammer; Christer Höög; Wyeth W Wasserman
NovelFam3000--uncharacterized human protein domains conserved across model organisms.
BMC genomics 2006;7():48.
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 research 2006;34(Database issue):D247-51.
2005: Volker Hollich; Lena Milchert; Lars Arvestad; Erik L L Sonnhammer
Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction.
Molecular biology and evolution 2005;22(11):2257-64.
2005: Abhiman Saraswathi; Erik L L Sonnhammer
Large-scale prediction of function shift in protein families with a focus on enzymatic function.
Proteins 2005;60(4):758-68.
2005: Lukas Käll; Anders Krogh; Erik L L Sonnhammer
An HMM posterior decoder for sequence feature prediction that includes homology information.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i251-7.
2005: Anna Henricson; Lukas Käll; Erik L L Sonnhammer
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence.
The FEBS journal 2005;272(11):2727-33.
2005: Timo Lassmann; Erik L L Sonnhammer
Automatic assessment of alignment quality.
Nucleic acids research 2005;33(22):7120-8.
2005: Timo Lassmann; Erik L L Sonnhammer
Kalign--an accurate and fast multiple sequence alignment algorithm.
BMC bioinformatics 2005;6():298.
2005: Erik L L Sonnhammer; Volker Hollich
Scoredist: a simple and robust protein sequence distance estimator.
BMC bioinformatics 2005;6():108.
2005: Markus Wistrand; Erik L L Sonnhammer
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.
BMC bioinformatics 2005;6():99.
2005: Erik L L Sonnhammer
Genome informatics: taming the avalanche of genomic data.
Genome biology 2005;6(1):301.
2005: Kevin P O'Brien; Maido Remm; Erik L L Sonnhammer
Inparanoid: a comprehensive database of eukaryotic orthologs.
Nucleic acids research 2005;33(Database issue):D476-80.
2005: Abhiman Saraswathi; Erik L L Sonnhammer
FunShift: a database of function shift analysis on protein subfamilies.
Nucleic acids research 2005;33(Database issue):D197-200.
2005: Alistair Chalk; Richard E Warfinge; Patrick Georgii-Hemming; Erik L L Sonnhammer
siRNAdb: a database of siRNA sequences.
Nucleic acids research 2005;33(Database issue):D131-4.
2004: Anna Henricson; Erik L L Sonnhammer; David Baillie; Ana Vaz Gomes
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs.
BMC genomics 2004;5():85.
2004: Alistair Chalk; Martin Wennerberg; Erik L L Sonnhammer
Sfixem--graphical sequence feature display in Java.
Bioinformatics (Oxford, England) 2004;20(15):2488-90.
2004: Gustavo Camps-Valls; Alistair Chalk; Antonio José Serrano-López; José David Martín-Guerrero; Erik L L Sonnhammer
Profiled support vector machines for antisense oligonucleotide efficacy prediction.
BMC bioinformatics 2004;5():135.
2004: Kevin P O'Brien; Isabelle Westerlund; Erik L L Sonnhammer
OrthoDisease: a database of human disease orthologs.
Human mutation 2004;24(2):112-9.
2004: Alistair Chalk; Claes Wahlestedt; Erik L L Sonnhammer
Improved and automated prediction of effective siRNA.
Biochemical and biophysical research communications 2004;319(1):264-74.
2004: Lukas Käll; Anders Krogh; Erik L L Sonnhammer
A combined transmembrane topology and signal peptide prediction method.
Journal of molecular biology 2004;338(5):1027-36.
2004: Markus Wistrand; Erik L L Sonnhammer
Improving profile HMM discrimination by adapting transition probabilities.
Journal of molecular biology 2004;338(4):847-54.
2004: Sven Ekdahl; Erik L L Sonnhammer
ChromoWheel: a new spin on eukaryotic chromosome visualization.
Bioinformatics (Oxford, England) 2004;20(4):576-7.
2004: Danielle Kemmer; Margareta Faxén; Emily Hodges; Jonathan Lim; Elena Herzog; Elsebrit Ljungström; Anders Lundmark; Mary K Olsen; Raf Podowski; Erik L L Sonnhammer; Peter Nilsson; Mark Reimers; Boris Lenhard; Steven L Roberds; Claes Wahlestedt; Christer Höög; Pankaj Agarwal; Wyeth W Wasserman
Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies.
Comparative and functional genomics 2004;5(8):584-95.
2004: Markus Wistrand; Erik L L Sonnhammer
transition priors for protein hidden Markov models: an empirical study towards maximum discrimination.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(1):181-93.
2004: Alex Bateman; Lachlan 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 2004;32(Database issue):D138-41.
2003: Christian E V Storm; Erik L L Sonnhammer
Comprehensive analysis of orthologous protein domains using the HOPS database.
Genome research 2003;13(10):2353-62.
2003: Jennifer M Lee; Erik L L Sonnhammer
Genomic gene clustering analysis of pathways in eukaryotes.
Genome research 2003;13(5):875-82.
2002: Lukas Käll; Erik L L Sonnhammer
Reliability of transmembrane predictions in whole-genome data.
FEBS letters 2002;532(3):415-8.
2002: Alistair Chalk; Erik L L Sonnhammer
Computational antisense oligo prediction with a neural network model.
Bioinformatics (Oxford, England) 2002;18(12):1567-75.
2002: Erik L L Sonnhammer; Eugene V Koonin
Orthology, paralogy and proposed classification for paralog subtypes.
Trends in genetics : TIG 2002;18(12):619-20.
2002: Timo Lassmann; Erik L L Sonnhammer
Quality assessment of multiple alignment programs.
FEBS letters 2002;529(1):126-30.
2002: Volker Hollich; Christian E V Storm; Erik L L Sonnhammer
OrthoGUI: graphical presentation of Orthostrapper results.
Bioinformatics (Oxford, England) 2002;18(9):1272-3.
2002: Christian E V Storm; Erik L L Sonnhammer
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
Bioinformatics (Oxford, England) 2002;18(1):92-9.
2002: Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R Eddy; Sam Griffiths-Jones; Kevin L Howe; Mhairi Marshall; Erik L L Sonnhammer
The Pfam protein families database.
Nucleic acids research 2002;30(1):276-80.
2001: Maido Remm; Christian E V Storm; Erik L L Sonnhammer
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.
Journal of molecular biology 2001;314(5):1041-52.
2001: Erik L L Sonnhammer; J C Wootton
Integrated graphical analysis of protein sequence features predicted from sequence composition.
Proteins 2001;45(3):262-73.
2001: Raf M Podowski; Erik L L Sonnhammer
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
Bioinformatics (Oxford, England) 2001;17(7):656-7.
2001: Christian E V Storm; Erik L L Sonnhammer
NIFAS: visual analysis of domain evolution in proteins.
Bioinformatics (Oxford, England) 2001;17(4):343-8.
2001: Anders Krogh; B Larsson; Gunnar von Heijne; Erik L L Sonnhammer
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Journal of molecular biology 2001;305(3):567-80.
2000: Maido Remm; Erik L L Sonnhammer
Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs.
Genome research 2000;10(11):1679-89.
2000: Alex Bateman; Ewan Birney; Richard Durbin; Sean R Eddy; Kevin L Howe; Erik L L Sonnhammer
The Pfam protein families database.
Nucleic acids research 2000;28(1):263-6.
1999: Arne Elofsson; Erik L L Sonnhammer
A comparison of sequence and structure protein domain families as a basis for structural genomics.
Bioinformatics (Oxford, England) 1999;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 1999;27(1):260-2.
1998: Erik L L Sonnhammer; Sean R Eddy; Ewan Birney; A Bateman; Richard Durbin
Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Nucleic acids research 1998;26(1):320-2.
1997: Erik L L Sonnhammer; R Durbin
Analysis of protein domain families in Caenorhabditis elegans.
Genomics 1997;46(2):200-16.
1997: Erik L L Sonnhammer; Sean R Eddy; Richard Durbin
Pfam: a comprehensive database of protein domain families based on seed alignments.
Proteins 1997;28(3):405-20.
1996: Ian A Hope; D G Albertson; S D Martinelli; A S Lynch; Erik L L Sonnhammer; R Durbin
The C. elegans expression pattern database: a beginning.
Trends in genetics : TIG 1996;12(9):370-1.
1995: Erik L L Sonnhammer; Richard Durbin
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
Gene 1995;167(1-2):GC1-10.
1994: Erik L L Sonnhammer; Richard Durbin
A workbench for large-scale sequence homology analysis.
Computer applications in the biosciences : CABIOS 1994;10(3):301-7.
1994: Erik L L Sonnhammer; Richard Durbin
An expert system for processing sequence homology data.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():363-8.