Published in J Mol Biol on July 16, 2004
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
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AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res (2006) 10.39
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res (2006) 7.93
Purified Wnt5a protein activates or inhibits beta-catenin-TCF signaling depending on receptor context. PLoS Biol (2006) 7.36
PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res (2008) 6.73
Variant ionotropic glutamate receptors as chemosensory receptors in Drosophila. Cell (2009) 6.16
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
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Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics (2009) 4.67
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A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc Natl Acad Sci U S A (2007) 4.04
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
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Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56
Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res (2006) 3.47
Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol (2006) 3.45
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol (2007) 3.43
Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J Bacteriol (2006) 3.40
Widespread protein aggregation as an inherent part of aging in C. elegans. PLoS Biol (2010) 3.36
Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci U S A (2006) 3.35
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Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog (2007) 3.27
Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A (2009) 3.16
Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells. Nat Med (2006) 3.09
Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03
Odorant-binding proteins OBP57d and OBP57e affect taste perception and host-plant preference in Drosophila sechellia. PLoS Biol (2007) 3.03
Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. PLoS Genet (2010) 3.03
The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature (2008) 3.02
Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol (2012) 2.95
The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol (2006) 2.93
Whole-genome sequence of Schistosoma haematobium. Nat Genet (2012) 2.91
Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins. Proc Natl Acad Sci U S A (2004) 2.90
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res (2005) 2.89
Strain-specific activation of the NF-kappaB pathway by GRA15, a novel Toxoplasma gondii dense granule protein. J Exp Med (2011) 2.87
Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proc Natl Acad Sci U S A (2008) 2.85
A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics (2009) 2.85
OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res (2005) 2.82
Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet (2010) 2.80
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet (2010) 2.77
The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res (2010) 2.74
Vaccine assembly from surface proteins of Staphylococcus aureus. Proc Natl Acad Sci U S A (2006) 2.71
Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors. Plant Cell (2005) 2.70
CryptoDB: a Cryptosporidium bioinformatics resource update. Nucleic Acids Res (2006) 2.68
Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains. Genome Biol (2007) 2.68
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res (2007) 2.67
Erythrocyte binding protein PfRH5 polymorphisms determine species-specific pathways of Plasmodium falciparum invasion. Cell Host Microbe (2008) 2.66
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog (2012) 2.66
A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics (2010) 2.63
Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol (2005) 2.54
Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines. Plant Cell (2005) 2.53
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol (2006) 2.43
Metagenomics - a guide from sampling to data analysis. Microb Inform Exp (2012) 2.42
Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol (2004) 2.39
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol (2010) 2.36
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biol (2006) 2.35
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. BMC Bioinformatics (2008) 2.32
SIMAP: the similarity matrix of proteins. Nucleic Acids Res (2006) 2.26
Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Mol Microbiol (2010) 2.24
NetB, a new toxin that is associated with avian necrotic enteritis caused by Clostridium perfringens. PLoS Pathog (2008) 2.23
Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One (2007) 2.22
Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci U S A (2011) 2.22
A versatile class of cell surface directional motors gives rise to gliding motility and sporulation in Myxococcus xanthus. PLoS Biol (2013) 2.22
Integrating protein annotation resources through the Distributed Annotation System. Nucleic Acids Res (2005) 2.21
The role of p58IPK in protecting the stressed endoplasmic reticulum. Mol Biol Cell (2007) 2.20
Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc Natl Acad Sci U S A (2007) 2.18
A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS One (2008) 2.17
The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. Proc Natl Acad Sci U S A (2007) 2.17
Gel-forming mucins appeared early in metazoan evolution. Proc Natl Acad Sci U S A (2007) 2.16
The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog (2010) 2.15
Improved expression of halorhodopsin for light-induced silencing of neuronal activity. Brain Cell Biol (2008) 2.12
Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature (2013) 2.11
Probing metagenomics by rapid cluster analysis of very large datasets. PLoS One (2008) 2.11
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics (2007) 2.10
Proteomics analysis of A33 immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature. Mol Cell Proteomics (2009) 2.08
Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol (2007) 2.07
Modulation of the Surface Proteome through Multiple Ubiquitylation Pathways in African Trypanosomes. PLoS Pathog (2015) 2.07
Stage- and gender-specific proteomic analysis of Brugia malayi excretory-secretory products. PLoS Negl Trop Dis (2008) 2.06
Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci U S A (2007) 2.06
Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J Bacteriol (2006) 2.02
The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan. Proc Natl Acad Sci U S A (2008) 2.00
Delivering proteins for export from the cytosol. Nat Rev Mol Cell Biol (2009) 2.00
AlgK is a TPR-containing protein and the periplasmic component of a novel exopolysaccharide secretin. Structure (2010) 1.97
Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathog (2009) 1.97
The nicotinic acetylcholine receptor Dalpha7 is required for an escape behavior in Drosophila. PLoS Biol (2006) 1.97
The abundance of short proteins in the mammalian proteome. PLoS Genet (2006) 1.96
The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet (2012) 1.95
Mapping the pathways to staphylococcal pathogenesis by comparative secretomics. Microbiol Mol Biol Rev (2006) 1.93
Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera). Genome Res (2006) 1.92
An aspartyl protease directs malaria effector proteins to the host cell. Nature (2010) 1.92
Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms. BMC Genomics (2006) 1.91
Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. BMC Genomics (2010) 1.90
Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci (2012) 1.90
CASP9 assessment of free modeling target predictions. Proteins (2011) 1.90
The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PLoS One (2011) 1.90
Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol (2006) 1.89
Transcellular delivery of vesicular SOCS proteins from macrophages to epithelial cells blunts inflammatory signaling. J Exp Med (2015) 1.88
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature (2005) 7.72
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Preoperative staging of lung cancer with combined PET-CT. N Engl J Med (2009) 7.38
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel (2004) 5.15
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature (2007) 4.60
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
Global topology analysis of the Escherichia coli inner membrane proteome. Science (2005) 4.11
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J Virol (2002) 3.38
Membrane insertion of a potassium-channel voltage sensor. Science (2005) 3.30
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17
Reliability measures for membrane protein topology prediction algorithms. J Mol Biol (2003) 3.13
Identification and evolution of dual-topology membrane proteins. Nat Struct Mol Biol (2006) 3.12
Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel (2004) 3.05
Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03
Emulating membrane protein evolution by rational design. Science (2007) 2.96
Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci U S A (2005) 2.92
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res (2005) 2.89
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J (2013) 2.58
Increased short- and long-term risk of inflammatory bowel disease after salmonella or campylobacter gastroenteritis. Gastroenterology (2009) 2.57
Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A (2008) 2.55
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell (2002) 2.48
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol (2006) 2.43
Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics (2004) 2.39
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Risk for myocardial infarction and stroke after community-acquired bacteremia: a 20-year population-based cohort study. Circulation (2014) 2.29
Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput (2002) 2.29
Control of membrane protein topology by a single C-terminal residue. Science (2010) 2.28
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell (2013) 2.28
Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics (2008) 2.24
Membrane protein structure: prediction versus reality. Annu Rev Biochem (2007) 2.21
NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res (2003) 2.21
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol (2005) 2.19
Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc Natl Acad Sci U S A (2002) 2.17
High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2007) 2.15
Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS Comput Biol (2011) 2.14
Macrophage serum markers in pneumococcal bacteremia: Prediction of survival by soluble CD163. Crit Care Med (2006) 2.06
GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae. Nat Protoc (2008) 2.06
How translocons select transmembrane helices. Annu Rev Biophys (2008) 2.03
Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. Hum Reprod (2010) 1.97
Modeling the adaptive immune system: predictions and simulations. Bioinformatics (2007) 1.95
Impact of hepatitis C virus coinfection on response to highly active antiretroviral therapy and outcome in HIV-infected individuals: a nationwide cohort study. Clin Infect Dis (2006) 1.87
Human gut microbes impact host serum metabolome and insulin sensitivity. Nature (2016) 1.85
Prediction of the human membrane proteome. Proteomics (2010) 1.85
Prediction of proteasome cleavage motifs by neural networks. Protein Eng (2002) 1.81
Protein complexes of the Escherichia coli cell envelope. J Biol Chem (2005) 1.69
A study of the membrane-water interface region of membrane proteins. J Mol Biol (2004) 1.68
Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. Nat Cell Biol (2005) 1.66
Transmembrane helices before, during, and after insertion. Curr Opin Struct Biol (2005) 1.64
Continuum secondary structure captures protein flexibility. Structure (2002) 1.63
Biogenesis of inner membrane proteins in Escherichia coli. Annu Rev Microbiol (2005) 1.61
Somatic acquisition and signaling of TGFBR1*6A in cancer. JAMA (2005) 1.59
Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments. J Membr Biol (2010) 1.58
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics (2004) 1.57
Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins (2005) 1.57
Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J Proteome Res (2004) 1.57
Photocross-linking of nascent chains to the STT3 subunit of the oligosaccharyltransferase complex. J Cell Biol (2003) 1.54
Protein interaction-based genome-wide analysis of incident coronary heart disease. Circ Cardiovasc Genet (2011) 1.54
A nine-transmembrane domain topology for presenilin 1. J Biol Chem (2005) 1.52
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50
New weakly expressed cell cycle-regulated genes in yeast. Yeast (2005) 1.49
Membrane topology of the human seipin protein. FEBS Lett (2006) 1.48
Clarithromycin for 2 weeks for stable coronary heart disease: 6-year follow-up of the CLARICOR randomized trial and updated meta-analysis of antibiotics for coronary heart disease. Cardiology (2008) 1.47
A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci U S A (2006) 1.45
Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. Am J Hum Genet (2013) 1.43
Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature (2012) 1.42
K65R with and without S68: a new resistance profile in vivo detected in most patients failing abacavir, didanosine and stavudine. Antivir Ther (2003) 1.42
Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem (2003) 1.40
A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing. J Biol Chem (2011) 1.40
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol (2007) 1.39
Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol (2010) 1.35