Published in Bioinformatics on April 15, 2004
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 15.77
Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res (2005) 9.90
Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25
Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics (2005) 7.01
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res (2009) 5.90
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29
InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res (2007) 4.15
Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics (2006) 3.98
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics (2002) 3.79
Quality assessment of multiple alignment programs. FEBS Lett (2002) 3.28
An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics (2005) 3.05
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res (2008) 2.97
Genomic gene clustering analysis of pathways in eukaryotes. Genome Res (2003) 2.89
OrthoDisease: a database of human disease orthologs. Hum Mutat (2004) 2.52
jSquid: a Java applet for graphical on-line network exploration. Bioinformatics (2008) 2.46
Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res (2009) 2.43
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
PfamAlyzer: domain-centric homology search. Bioinformatics (2007) 1.90
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res (2006) 1.89
ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics (2004) 1.78
A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci (2006) 1.67
Improved and automated prediction of effective siRNA. Biochem Biophys Res Commun (2004) 1.58
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res (2013) 1.56
Predicting protein function from domain content. Bioinformatics (2008) 1.47
Domain tree-based analysis of protein architecture evolution. Mol Biol Evol (2007) 1.46
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence. FEBS J (2005) 1.42
Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res (2003) 1.39
Toward community standards in the quest for orthologs. Bioinformatics (2012) 1.36
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics (2005) 1.33
Reliability of transmembrane predictions in whole-genome data. FEBS Lett (2002) 1.31
Comparative interactomics with Funcoup 2.0. Nucleic Acids Res (2011) 1.29
Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Mol Biol Evol (2005) 1.28
Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. Brief Bioinform (2011) 1.20
FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res (2005) 1.12
Network-based Identification of novel cancer genes. Mol Cell Proteomics (2009) 1.12
OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics (2002) 1.10
Domain architecture conservation in orthologs. BMC Bioinformatics (2011) 1.06
Hieranoid: hierarchical orthology inference. J Mol Biol (2013) 1.05
Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol (2004) 1.04
Benchmarking homology detection procedures with low complexity filters. Bioinformatics (2009) 1.01
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinformatics (2009) 0.98
Orthology confers intron position conservation. BMC Genomics (2010) 0.97
Evolution of protein domain architectures. Methods Mol Biol (2012) 0.96
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. PLoS One (2010) 0.96
Profiled support vector machines for antisense oligonucleotide efficacy prediction. BMC Bioinformatics (2004) 0.96
Statistical assessment of crosstalk enrichment between gene groups in biological networks. PLoS One (2013) 0.94
Comparative analysis and unification of domain-domain interaction networks. Bioinformatics (2009) 0.92
Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins (2005) 0.92
Computational antisense oligo prediction with a neural network model. Bioinformatics (2002) 0.92
Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling. Am J Pathol (2013) 0.92
siRNAdb: a database of siRNA sequences. Nucleic Acids Res (2005) 0.91
MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics (2009) 0.87
siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics (2008) 0.86
transition priors for protein hidden Markov models: an empirical study towards maximum discrimination. J Comput Biol (2004) 0.83
Focusing on RISC assembly in mammalian cells. Biochem Biophys Res Commun (2008) 0.83
Prediction of function divergence in protein families using the substitution rate variation parameter alpha. Mol Biol Evol (2006) 0.83
Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis. Trends Genet (2006) 0.82
OrthoDisease: tracking disease gene orthologs across 100 species. Brief Bioinform (2011) 0.81
Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation. Gene (2012) 0.80
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs. BMC Genomics (2004) 0.78
NovelFam3000--uncharacterized human protein domains conserved across model organisms. BMC Genomics (2006) 0.78
MGclus: network clustering employing shared neighbors. Mol Biosyst (2013) 0.77
Avoiding pitfalls in L1-regularised inference of gene networks. Mol Biosyst (2014) 0.76
Optimal sparsity criteria for network inference. J Comput Biol (2013) 0.76
Network analysis of functional genomics data: application to avian sex-biased gene expression. ScientificWorldJournal (2012) 0.76
Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies. Comp Funct Genomics (2004) 0.75
GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties. Mol Biosyst (2017) 0.75