Published in Bioinformatics on June 01, 2005
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29
Integrating sequence and structural biology with DAS. BMC Bioinformatics (2007) 5.12
Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics (2009) 4.67
Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56
Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res (2007) 3.16
Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A (2008) 2.55
PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res (2014) 2.00
Identification of a novel coronavirus from a beluga whale by using a panviral microarray. J Virol (2008) 1.81
Hepatitis C virus NS2 protein contributes to virus particle assembly via opposing epistatic interactions with the E1-E2 glycoprotein and NS3-NS4A enzyme complexes. J Virol (2009) 1.76
Genome-defence small RNAs exapted for epigenetic mating-type inheritance. Nature (2014) 1.72
LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics (2008) 1.64
A novel pathway of intercellular signalling in Bacillus subtilis involves a protein with similarity to a component of type III secretion channels. Mol Microbiol (2008) 1.58
Evolution of the gene lineage encoding the carbon dioxide receptor in insects. J Insect Sci (2009) 1.51
Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions. Mol Biol Cell (2010) 1.51
A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Nucleic Acids Res (2011) 1.41
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res (2015) 1.35
Nyamanini and midway viruses define a novel taxon of RNA viruses in the order Mononegavirales. J Virol (2009) 1.33
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins. BMC Genomics (2011) 1.18
Polar positioning of a conjugation protein from the integrative and conjugative element ICEBs1 of Bacillus subtilis. J Bacteriol (2010) 1.11
LocTree2 predicts localization for all domains of life. Bioinformatics (2012) 1.11
The obesity gene, TMEM18, is of ancient origin, found in majority of neuronal cells in all major brain regions and associated with obesity in severely obese children. BMC Med Genet (2010) 1.09
Transmembrane segment 3 of Drosophila melanogaster odorant receptor subunit 85b contributes to ligand-receptor interactions. J Biol Chem (2010) 1.08
A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes. PLoS One (2012) 1.08
Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res (2010) 1.06
Identification of contractile vacuole proteins in Trypanosoma cruzi. PLoS One (2011) 1.05
Localization and function of the membrane-bound riboflavin in the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. J Biol Chem (2010) 1.02
CandidaDB: a multi-genome database for Candida species and related Saccharomycotina. Nucleic Acids Res (2007) 1.01
Ion and nutrient uptake by malaria parasite-infected erythrocytes. Cell Microbiol (2012) 1.01
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics (2006) 1.01
Structural genomics plucks high-hanging membrane proteins. Curr Opin Struct Biol (2012) 0.98
An automatic method for identifying surface proteins in bacteria: SLEP. BMC Bioinformatics (2010) 0.96
A novel approach to dissect the abscission process in Arabidopsis. Plant Physiol (2012) 0.96
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors. Nat Commun (2015) 0.95
Cystinosin, MPDU1, SWEETs and KDELR belong to a well-defined protein family with putative function of cargo receptors involved in vesicle trafficking. PLoS One (2012) 0.92
HID-1, a new component of the peptidergic signaling pathway. Genetics (2010) 0.91
Proteomic analysis of the acidocalcisome, an organelle conserved from bacteria to human cells. PLoS Pathog (2014) 0.91
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics (2010) 0.90
Candida albicans VMA3 is necessary for V-ATPase assembly and function and contributes to secretion and filamentation. Eukaryot Cell (2013) 0.90
Purification and functional characterisation of rhiminopeptidase A, a novel aminopeptidase from the venom of Bitis gabonica rhinoceros. PLoS Negl Trop Dis (2010) 0.90
Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR. PLoS One (2011) 0.89
Computational studies of membrane proteins: models and predictions for biological understanding. Biochim Biophys Acta (2011) 0.88
GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic enzymes in the Golgi apparatus of living tissues. PLoS One (2012) 0.87
MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics (2009) 0.87
Analysis of an optimal hidden Markov model for secondary structure prediction. BMC Struct Biol (2006) 0.86
Characterization of SNAREs determines the absence of a typical Golgi apparatus in the ancient eukaryote Giardia lamblia. J Biol Chem (2008) 0.86
Two Golgi-resident 3'-Phosphoadenosine 5'-phosphosulfate transporters play distinct roles in heparan sulfate modifications and embryonic and larval development in Caenorhabditis elegans. J Biol Chem (2010) 0.85
A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA). J Comput Biol (2012) 0.85
Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci (2007) 0.85
DOR - a Database of Olfactory Receptors - Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes. Bioinform Biol Insights (2014) 0.85
Validating subcellular localization prediction tools with mycobacterial proteins. BMC Bioinformatics (2009) 0.84
Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus 'Robusta 5' accessions. BMC Genet (2012) 0.84
Generalized centroid estimators in bioinformatics. PLoS One (2011) 0.84
Carbohydrate-active enzymes in pythium and their role in plant cell wall and storage polysaccharide degradation. PLoS One (2013) 0.83
Hyperdiversity of genes encoding integral light-harvesting proteins in the dinoflagellate Symbiodinium sp. PLoS One (2012) 0.83
Fertilization in C. elegans requires an intact C-terminal RING finger in sperm protein SPE-42. BMC Dev Biol (2011) 0.82
Decoding HMMs using the k best paths: algorithms and applications. BMC Bioinformatics (2010) 0.82
Burkholderia cenocepacia and Salmonella enterica ArnT proteins that transfer 4-amino-4-deoxy-l-arabinose to lipopolysaccharide share membrane topology and functional amino acids. Sci Rep (2015) 0.82
Homology modeling, molecular dynamic simulation, and docking based binding site analysis of human dopamine (D4) receptor. J Mol Model (2015) 0.82
Structural and Functional Evidence for Testosterone Activation of GPRC6A in Peripheral Tissues. Mol Endocrinol (2015) 0.81
Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation. BMC Genomics (2014) 0.81
Domain organization of long signal peptides of single-pass integral membrane proteins reveals multiple functional capacity. PLoS One (2008) 0.81
Comparative analysis of mitochondrial genomes in Bombina (Anura; Bombinatoridae). J Mol Evol (2008) 0.81
Sul1 and Sul2 sulfate transceptors signal to protein kinase A upon exit of sulfur starvation. J Biol Chem (2015) 0.81
The NfeD protein family and its conserved gene neighbours throughout prokaryotes: functional implications for stomatin-like proteins. J Mol Evol (2009) 0.81
A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun (2015) 0.81
A CLAG3 mutation in an amphipathic transmembrane domain alters malaria parasite nutrient channels and confers leupeptin resistance. Infect Immun (2015) 0.80
Rhodopsin 7-The unusual Rhodopsin in Drosophila. PeerJ (2016) 0.80
The YARHG domain: an extracellular domain in search of a function. PLoS One (2012) 0.79
Evidence for Osteocalcin Binding and Activation of GPRC6A in β-Cells. Endocrinology (2016) 0.79
Cross-complementation study of the flagellar type III export apparatus membrane protein FlhB. PLoS One (2012) 0.79
Topology of the yeast Ras converting enzyme as inferred from cysteine accessibility studies. Biochemistry (2013) 0.79
A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation. Mol Cell Proteomics (2015) 0.79
New decoding algorithms for Hidden Markov Models using distance measures on labellings. BMC Bioinformatics (2010) 0.79
Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol (2015) 0.78
High-throughput cloning and expression of integral membrane proteins in Escherichia coli. Curr Protoc Protein Sci (2013) 0.78
Identification of Plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden Markov models. PLoS One (2011) 0.78
Annotation and characterization of the Plasmodium vivax rhoptry neck protein 4 (PvRON4). Malar J (2013) 0.77
Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology. Proc Natl Acad Sci U S A (2016) 0.76
TagDust2: a generic method to extract reads from sequencing data. BMC Bioinformatics (2015) 0.76
Critical Components of the Conjugation Machinery of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis. J Bacteriol (2015) 0.76
TMSEG: Novel prediction of transmembrane helices. Proteins (2016) 0.75
In silico evaluation of the influence of the translocon on partitioning of membrane segments. BMC Bioinformatics (2014) 0.75
An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom. BMC Bioinformatics (2016) 0.75
Regulation by the quorum sensor from Vibrio indicates a receptor function for the membrane anchors of adenylate cyclases. Elife (2016) 0.75
The Plasmodium vivax rhoptry neck protein 5 is expressed in the apical pole of Plasmodium vivax VCG-1 strain schizonts and binds to human reticulocytes. Malar J (2015) 0.75
Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies. J Mol Model (2016) 0.75
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
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res (2007) 8.79
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J Biol Chem (2007) 7.46
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
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinformatics (2003) 6.63
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
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
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics (2005) 4.25
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
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Quality assessment of multiple alignment programs. FEBS Lett (2002) 3.28
Reliability measures for membrane protein topology prediction algorithms. J Mol Biol (2003) 3.13
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
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res (2008) 2.60
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
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23
microRNA-101 is a potent inhibitor of autophagy. EMBO J (2011) 2.00
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci U S A (2014) 1.91
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
Molecular composition of IMP1 ribonucleoprotein granules. Mol Cell Proteomics (2007) 1.80
ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics (2004) 1.78
Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res (2010) 1.75
The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res (2011) 1.70
A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci (2006) 1.67
MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One (2010) 1.64
Improving ancient DNA read mapping against modern reference genomes. BMC Genomics (2012) 1.59
Improved and automated prediction of effective siRNA. Biochem Biophys Res Commun (2004) 1.58
Sampling realistic protein conformations using local structural bias. PLoS Comput Biol (2006) 1.56
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res (2013) 1.56
A generative, probabilistic model of local protein structure. Proc Natl Acad Sci U S A (2008) 1.50
Predicting protein function from domain content. Bioinformatics (2008) 1.47
miR-449 inhibits cell proliferation and is down-regulated in gastric cancer. Mol Cancer (2011) 1.46
Asap: a framework for over-representation statistics for transcription factor binding sites. PLoS One (2008) 1.46
Domain tree-based analysis of protein architecture evolution. Mol Biol Evol (2007) 1.46
Computational evidence for hundreds of non-conserved plant microRNAs. BMC Genomics (2005) 1.43
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence. FEBS J (2005) 1.42
A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics (2006) 1.40
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
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns. Genome Biol (2012) 1.34
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics (2005) 1.33
Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun (2013) 1.31
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
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29
Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Mol Biol Evol (2005) 1.28
MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA (2011) 1.26
RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. J Mol Biol (2003) 1.25
Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. Brief Bioinform (2011) 1.20
miRMaid: a unified programming interface for microRNA data resources. BMC Bioinformatics (2010) 1.20
MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells. BMC Cancer (2012) 1.16
Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol (2007) 1.16
FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res (2005) 1.12
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res (2013) 1.12
Network-based Identification of novel cancer genes. Mol Cell Proteomics (2009) 1.12
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing. BMC Med Genomics (2009) 1.10
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics (2007) 1.10
OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics (2002) 1.10
Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients. Blood (2013) 1.09
Domain architecture conservation in orthologs. BMC Bioinformatics (2011) 1.06
Bias of purine stretches in sequenced chromosomes. Comput Chem (2002) 1.05
Hieranoid: hierarchical orthology inference. J Mol Biol (2013) 1.05
Discovery of regulatory elements is improved by a discriminatory approach. PLoS Comput Biol (2009) 1.04
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
An evolutionary method for learning HMM structure: prediction of protein secondary structure. BMC Bioinformatics (2007) 0.95
Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat Commun (2013) 0.95
microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer. Mol Cancer (2012) 0.95
Statistical assessment of crosstalk enrichment between gene groups in biological networks. PLoS One (2013) 0.94
Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs. Microb Ecol (2015) 0.93
Comparative analysis and unification of domain-domain interaction networks. Bioinformatics (2009) 0.92
Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling. Am J Pathol (2013) 0.92