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Erik Sonnhammer
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Research Profile (preview)
Activities & Behaviors
Chemicals & Drugs
Procedures
Occupations
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Phenomena
Genes & Molecular Sequences
Living Beings
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Network (preview)
10
Durbin, Richard
8
Eddy, Sean
7
Hollich, Volker
7
Lassmann, Timo
7
Käll, Lukas
6
Chalk, Alistair
6
Bateman, Alex
5
Storm, Christian
4
Birney, Ewan
4
Finn, Robert
4
Krogh, Anders
4
Forslund, Kristoffer
4
Wistrand, Markus
4
Saraswathi, Abhiman
3
Remm, Maido
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All Publications
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2009: Björkholm Patrik; Sonnhammer Erik L L
Comparative analysis and unification of domain-domain interaction networks.
Bioinformatics (Oxford, England) 2009;25(22):3020-5.
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2009: Forslund Kristoffer; Sonnhammer Erik L L
Benchmarking homology detection procedures with low complexity filters.
Bioinformatics (Oxford, England) 2009;25(19):2500-5.
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2009: Alexeyenko Andrey; Sonnhammer Erik L L
Global networks of functional coupling in eukaryotes from comprehensive data integration.
Genome research 2009;19(6):1107-16.
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2009: Messina David N; Sonnhammer Erik L L
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.
Bioinformatics (Oxford, England) 2009;25(10):1333-4.
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2009: Lassmann Timo; Frings Oliver; Sonnhammer Erik L L
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.
Nucleic acids research 2009;37(3):858-65.
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2009: Klammer Martin; Messina David N; Schmitt Thomas; Sonnhammer Erik L L
MetaTM - a consensus method for transmembrane protein topology prediction.
BMC bioinformatics 2009;10():314.
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2008: Forslund Kristoffer; Sonnhammer Erik L L
Predicting protein function from domain content.
Bioinformatics (Oxford, England) 2008;24(15):1681-7.
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2008: Klammer Martin; Roopra Sanjit; Sonnhammer Erik L L
jSquid: a Java applet for graphical on-line network exploration.
Bioinformatics (Oxford, England) 2008;24(12):1467-8.
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2008: Chalk Alistair M; Sonnhammer Erik L L
siRNA specificity searching incorporating mismatch tolerance data.
Bioinformatics (Oxford, England) 2008;24(10):1316-7.
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2008: Hong Junmei; Wei Na; Chalk Alistair; Wang Jue; Song Yutong; Yi Fan; Qiao Ren-Ping; Sonnhammer Erik L L; Wahlestedt Claes; Liang Zicai; Du Quan
Focusing on RISC assembly in mammalian cells.
Biochemical and biophysical research communications 2008;368(3):703-8.
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2008: Forslund Kristoffer; Henricson Anna; Hollich Volker; Sonnhammer Erik L L
Domain tree-based analysis of protein architecture evolution.
Molecular biology and evolution 2008;25(2):254-64.
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2008: Berglund Ann-Charlotte; Sjölund Erik; Ostlund Gabriel; Sonnhammer Erik L L
InParanoid 6: eukaryotic ortholog clusters with inparalogs.
Nucleic acids research 2008;36(Database issue):D263-6.
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2008: Finn Robert D; Tate John; Mistry Jaina; Coggill Penny C; Sammut Stephen John; Hotz Hans-Rudolf; Ceric Goran; Forslund Kristoffer; Eddy Sean R; Sonnhammer Erik L L; Bateman Alex
The Pfam protein families database.
Nucleic acids research 2008;36(Database issue):D281-8.
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2008: Joannin Nicolas; Abhiman Saraswathi; Sonnhammer Erik L; Wahlgren Mats
Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family.
BMC genomics 2008;9():19.
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2007: Lundin Carolina; Käll Lukas; Kreher Scott A; Kapp Katja; Sonnhammer Erik L; Carlson John R; Heijne Gunnar von; Nilsson IngMarie
Membrane topology of the Drosophila OR83b odorant receptor.
FEBS letters 2007;581(29):5601-4.
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2007: Hollich Volker; Sonnhammer Erik L L
PfamAlyzer: domain-centric homology search.
Bioinformatics (Oxford, England) 2007;23(24):3382-3.
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2007: Käll Lukas; Krogh Anders; Sonnhammer Erik L L
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.
Nucleic acids research 2007;35(Web Server issue):W429-32.
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2007: Lassmann Timo; Sonnhammer Erik Ll
Automatic extraction of reliable regions from multiple sequence alignments.
BMC bioinformatics 2007;8 Suppl 5():S9.
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2006: Alexeyenko Andrey; Millar A Harvey; Whelan James; Sonnhammer Erik L L
Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis.
Trends in genetics : TIG 2006;22(11):589-93.
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2006: Alexeyenko Andrey; Tamas Ivica; Liu Gang; Sonnhammer Erik L L
Automatic clustering of orthologs and inparalogs shared by multiple proteomes.
Bioinformatics (Oxford, England) 2006;22(14):e9-15.
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2006: Lassmann Timo; Sonnhammer Erik L L
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
Nucleic acids research 2006;34(Web Server issue):W596-9.
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2006: Abhiman Saraswathi; Daub Carsten O; Sonnhammer Erik L L
Prediction of function divergence in protein families using the substitution rate variation parameter alpha.
Molecular biology and evolution 2006;23(7):1406-13.
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2006: Wistrand Markus; Käll Lukas; Sonnhammer Erik L L
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.
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2006: Finn Robert D; Mistry Jaina; Schuster-Böckler Benjamin; Griffiths-Jones Sam; Hollich Volker; Lassmann Timo; Moxon Simon; Marshall Mhairi; Khanna Ajay; Durbin Richard; Eddy Sean R; Sonnhammer Erik L L; Bateman Alex
Pfam: clans, web tools and services.
Nucleic acids research 2006;34(Database issue):D247-51.
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2006: Kemmer Danielle; Podowski Raf M; Arenillas David; Lim Jonathan; Hodges Emily; Roth Peggy; Sonnhammer Erik L L; Höög Christer; Wasserman Wyeth W
NovelFam3000--uncharacterized human protein domains conserved across model organisms.
BMC genomics 2006;7():48.
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2005: Hollich Volker; Milchert Lena; Arvestad Lars; Sonnhammer Erik L L
Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction.
Molecular biology and evolution 2005;22(11):2257-64.
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2005: Abhiman Saraswathi; Sonnhammer Erik L L
Large-scale prediction of function shift in protein families with a focus on enzymatic function.
Proteins 2005;60(4):758-68.
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2005: Käll Lukas; Krogh Anders; Sonnhammer Erik L L
An HMM posterior decoder for sequence feature prediction that includes homology information.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i251-7.
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2005: Henricson Anna; Käll Lukas; Sonnhammer Erik L L
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence.
The FEBS journal 2005;272(11):2727-33.
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2005: O'Brien Kevin P; Remm Maido; Sonnhammer Erik L L
Inparanoid: a comprehensive database of eukaryotic orthologs.
Nucleic acids research 2005;33(Database issue):D476-80.
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2005: Abhiman Saraswathi; Sonnhammer Erik L L
FunShift: a database of function shift analysis on protein subfamilies.
Nucleic acids research 2005;33(Database issue):D197-200.
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2005: Chalk Alistair M; Warfinge Richard E; Georgii-Hemming Patrick; Sonnhammer Erik L L
siRNAdb: a database of siRNA sequences.
Nucleic acids research 2005;33(Database issue):D131-4.
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2005: Lassmann Timo; Sonnhammer Erik L L
Automatic assessment of alignment quality.
Nucleic acids research 2005;33(22):7120-8.
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2005: Lassmann Timo; Sonnhammer Erik L L
Kalign--an accurate and fast multiple sequence alignment algorithm.
BMC bioinformatics 2005;6():298.
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2005: Sonnhammer Erik L L; Hollich Volker
Scoredist: a simple and robust protein sequence distance estimator.
BMC bioinformatics 2005;6():108.
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2005: Wistrand Markus; Sonnhammer Erik L L
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.
BMC bioinformatics 2005;6():99.
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2005: Sonnhammer Erik L L
Genome informatics: taming the avalanche of genomic data.
Genome biology 2005;6(1):301.
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2004: Henricson Anna; Sonnhammer Erik L L; Baillie David L; Gomes Ana Vaz
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs.
BMC genomics 2004;5(1):85.
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2004: Chalk Alistair M; Wennerberg Martin; Sonnhammer Erik L L
Sfixem--graphical sequence feature display in Java.
Bioinformatics (Oxford, England) 2004;20(15):2488-90.
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2004: Camps-Valls Gustavo; Chalk Alistair M; Serrano-López Antonio J; Martín-Guerrero José D; Sonnhammer Erik L L
Profiled support vector machines for antisense oligonucleotide efficacy prediction.
BMC bioinformatics 2004;5():135.
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2004: O'Brien Kevin P; Westerlund Isabelle; Sonnhammer Erik L L
OrthoDisease: a database of human disease orthologs.
Human mutation 2004;24(2):112-9.
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2004: Chalk Alistair M; Wahlestedt Claes; Sonnhammer Erik L L
Improved and automated prediction of effective siRNA.
Biochemical and biophysical research communications 2004;319(1):264-74.
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2004: Käll Lukas; Krogh Anders; Sonnhammer Erik L L
A combined transmembrane topology and signal peptide prediction method.
Journal of molecular biology 2004;338(5):1027-36.
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2004: Wistrand Markus; Sonnhammer Erik L L
Improving profile HMM discrimination by adapting transition probabilities.
Journal of molecular biology 2004;338(4):847-54.
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2004: Ekdahl Sven; Sonnhammer Erik L L
ChromoWheel: a new spin on eukaryotic chromosome visualization.
Bioinformatics (Oxford, England) 2004;20(4):576-7.
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2004: Bateman Alex; Coin Lachlan; Durbin Richard; Finn Robert D; Hollich Volker; Griffiths-Jones Sam; Khanna Ajay; Marshall Mhairi; Moxon Simon; Sonnhammer Erik L L; Studholme David J; Yeats Corin; Eddy Sean R
The Pfam protein families database.
Nucleic acids research 2004;32(Database issue):D138-41.
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2004: Kemmer Danielle; Faxén Margareta; Hodges Emily; Lim Jonathan; Herzog Elena; Ljungström Elsebrit; Lundmark Anders; Olsen Mary K; Podowski Raf; Sonnhammer Erik L L; Nilsson Peter; Reimers Mark; Lenhard Boris; Roberds Steven L; Wahlestedt Claes; Höög Christer; Agarwal Pankaj; Wasserman Wyeth W
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.
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2004: Wistrand Markus; Sonnhammer Erik L L
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.
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2003: Storm Christian E V; Sonnhammer Erik L L
Comprehensive analysis of orthologous protein domains using the HOPS database.
Genome research 2003;13(10):2353-62.
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2003: Lee Jennifer M; Sonnhammer Erik L L
Genomic gene clustering analysis of pathways in eukaryotes.
Genome research 2003;13(5):875-82.
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2002: Chalk Alistair M; Sonnhammer Erik L L
Computational antisense oligo prediction with a neural network model.
Bioinformatics (Oxford, England) 2002;18(12):1567-75.
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2002: Käll Lukas; Sonnhammer Erik L L
Reliability of transmembrane predictions in whole-genome data.
FEBS letters 2002;532(3):415-8.
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2002: Sonnhammer Erik L L; Koonin Eugene V
Orthology, paralogy and proposed classification for paralog subtypes.
Trends in genetics : TIG 2002;18(12):619-20.
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2002: Lassmann Timo; Sonnhammer Erik L L
Quality assessment of multiple alignment programs.
FEBS letters 2002;529(1):126-30.
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2002: Hollich Volker; Storm Christian E V; Sonnhammer Erik L L
OrthoGUI: graphical presentation of Orthostrapper results.
Bioinformatics (Oxford, England) 2002;18(9):1272-3.
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2002: Storm Christian E V; Sonnhammer Erik L L
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
Bioinformatics (Oxford, England) 2002;18(1):92-9.
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2002: Bateman Alex; Birney Ewan; Cerruti Lorenzo; Durbin Richard; Etwiller Laurence; Eddy Sean R; Griffiths-Jones Sam; Howe Kevin L; Marshall Mhairi; Sonnhammer Erik L L
The Pfam protein families database.
Nucleic acids research 2002;30(1):276-80.
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2001: Remm M; Storm C E; Sonnhammer E L
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.
Journal of molecular biology 2001;314(5):1041-52.
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2001: Sonnhammer E L; Wootton J C
Integrated graphical analysis of protein sequence features predicted from sequence composition.
Proteins 2001;45(3):262-73.
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2001: Podowski R M; Sonnhammer E L
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
Bioinformatics (Oxford, England) 2001;17(7):656-7.
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2001: Storm C E; Sonnhammer E L
NIFAS: visual analysis of domain evolution in proteins.
Bioinformatics (Oxford, England) 2001;17(4):343-8.
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2001: Krogh A; Larsson B; von Heijne G; Sonnhammer E L
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Journal of molecular biology 2001;305(3):567-80.
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2000: Remm M; Sonnhammer E
Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs.
Genome research 2000;10(11):1679-89.
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2000: Bateman A; Birney E; Durbin R; Eddy S R; Howe K L; Sonnhammer E L
The Pfam protein families database.
Nucleic acids research 2000;28(1):263-6.
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1999: Elofsson A; Sonnhammer E L
A comparison of sequence and structure protein domain families as a basis for structural genomics.
Bioinformatics (Oxford, England) 1999;15(6):480-500.
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1999: Bateman A; Birney E; Durbin R; Eddy S R; Finn R D; Sonnhammer E L
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
Nucleic acids research 1999;27(1):260-2.
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1998: Sonnhammer E L; Eddy S R; Birney E; Bateman A; Durbin R
Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Nucleic acids research 1998;26(1):320-2.
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1997: Sonnhammer E L; Durbin R
Analysis of protein domain families in Caenorhabditis elegans.
Genomics 1997;46(2):200-16.
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1997: Sonnhammer E L; Eddy S R; Durbin R
Pfam: a comprehensive database of protein domain families based on seed alignments.
Proteins 1997;28(3):405-20.
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1996: Hope I A; Albertson D G; Martinelli S D; Lynch A S; Sonnhammer E; Durbin R
The C. elegans expression pattern database: a beginning.
Trends in genetics : TIG 1996;12(9):370-1.
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1995: Sonnhammer E L; Durbin R
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
Gene 1995;167(1-2):GC1-10.
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1994: Sonnhammer E L; Durbin R
A workbench for large-scale sequence homology analysis.
Computer applications in the biosciences : CABIOS 1994;10(3):301-7.
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1994: Sonnhammer E L; Durbin R
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.
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