Published in BMC Bioinformatics on September 23, 2008
Vertebrate protein glycosylation: diversity, synthesis and function. Nat Rev Mol Cell Biol (2012) 2.83
Modulation of the Surface Proteome through Multiple Ubiquitylation Pathways in African Trypanosomes. PLoS Pathog (2015) 2.07
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
Approaches to Fungal Genome Annotation. Mycology (2011) 1.47
Chilling of dormant buds hyperinduces FLOWERING LOCUS T and recruits GA-inducible 1,3-beta-glucanases to reopen signal conduits and release dormancy in Populus. Plant Cell (2011) 1.46
Sugarcane giant borer transcriptome analysis and identification of genes related to digestion. PLoS One (2015) 1.42
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PLoS Genet (2011) 1.20
Global profiling of protein lipidation using chemical proteomic technologies. Curr Opin Chem Biol (2014) 1.10
Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii. Mol Cell Proteomics (2010) 1.00
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res (2010) 0.99
Semi-rolled leaf1 encodes a putative glycosylphosphatidylinositol-anchored protein and modulates rice leaf rolling by regulating the formation of bulliform cells. Plant Physiol (2012) 0.99
Recruitment of EB1, a master regulator of microtubule dynamics, to the surface of the Theileria annulata schizont. PLoS Pathog (2013) 0.95
WallProtDB, a database resource for plant cell wall proteomics. Plant Methods (2015) 0.94
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data. BMC Genomics (2010) 0.94
Larval midgut modifications associated with Bti resistance in the yellow fever mosquito using proteomic and transcriptomic approaches. BMC Genomics (2012) 0.93
Insight into the salivary transcriptome and proteome of Dipetalogaster maxima. J Proteome Res (2011) 0.93
Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin. BMC Genomics (2012) 0.93
Field-Evolved Mode 1 Resistance of the Fall Armyworm to Transgenic Cry1Fa-Expressing Corn Associated with Reduced Cry1Fa Toxin Binding and Midgut Alkaline Phosphatase Expression. Appl Environ Microbiol (2015) 0.90
Architecture of a Host-Parasite Interface: Complex Targeting Mechanisms Revealed Through Proteomics. Mol Cell Proteomics (2015) 0.89
Toxoplasma gondii proteomics. Expert Rev Proteomics (2009) 0.89
Calcium currents are enhanced by α2δ-1 lacking its membrane anchor. J Biol Chem (2012) 0.88
Residues surrounding the glycosylphosphatidylinositol anchor attachment site of PrP modulate prion infection: insight from the resistance of rabbits to prion disease. J Virol (2010) 0.88
Computational studies of membrane proteins: models and predictions for biological understanding. Biochim Biophys Acta (2011) 0.88
Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome. BMC Genomics (2014) 0.88
PvRON2, a new Plasmodium vivax rhoptry neck antigen. Malar J (2011) 0.87
Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane. PLoS One (2015) 0.87
MemPype: a pipeline for the annotation of eukaryotic membrane proteins. Nucleic Acids Res (2011) 0.87
Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts. PLoS Negl Trop Dis (2012) 0.86
Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a novel nucleotide phosphodiesterase regulated by cholesterol in human macrophages. J Biol Chem (2014) 0.85
Male gametophyte development and function in angiosperms: a general concept. Plant Reprod (2016) 0.84
The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp. BMC Genomics (2016) 0.84
Targeting of voltage-gated calcium channel α2δ-1 subunit to lipid rafts is independent from a GPI-anchoring motif. PLoS One (2011) 0.84
High sequence variability, diverse subcellular localizations, and ecological implications of alkaline phosphatase in dinoflagellates and other eukaryotic phytoplankton. Front Microbiol (2012) 0.84
Characterization of major surface protease homologues of Trypanosoma congolense. J Biomed Biotechnol (2010) 0.82
Voltage-gated calcium channels and their auxiliary subunits: physiology and pathophysiology and pharmacology. J Physiol (2016) 0.82
GPI-anchor synthesis is indispensable for the germline development of the nematode Caenorhabditis elegans. Mol Biol Cell (2012) 0.82
Non-specific lipid transfer proteins in maize. BMC Plant Biol (2014) 0.81
Transcriptomic characterization of the enzymatic antioxidants FeSOD, MnSOD, APX and KatG in the dinoflagellate genus Symbiodinium. BMC Evol Biol (2015) 0.81
An insight into the sialotranscriptome of Triatoma rubida (Hemiptera: Heteroptera). J Med Entomol (2012) 0.81
Heparin-binding motifs and biofilm formation by Candida albicans. J Infect Dis (2013) 0.81
Efficient glycosylphosphatidylinositol (GPI) modification of membrane proteins requires a C-terminal anchoring signal of marginal hydrophobicity. J Biol Chem (2012) 0.80
Frequent loss and alteration of the MOXD2 gene in catarrhines and whales: a possible connection with the evolution of olfaction. PLoS One (2014) 0.80
Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins. BMC Genomics (2014) 0.80
Identification of a novel aminopeptidase P-like gene (OnAPP) possibly involved in Bt toxicity and resistance in a major corn pest (Ostrinia nubilalis). PLoS One (2011) 0.80
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics (2015) 0.80
A phylogenetic approach to study the origin and evolution of plasmodesmata-localized glycosyl hydrolases family 17. Front Plant Sci (2014) 0.80
Organization, evolution and functions of the human and mouse Ly6/uPAR family genes. Hum Genomics (2016) 0.79
Secretome of the biocontrol agent metarhizium anisopliae induced by the cuticle of the cotton pest Dysdercus peruvianus reveals new insights into infection. J Proteome Res (2014) 0.79
Cholinergic Targets in Lung Cancer. Curr Pharm Des (2016) 0.79
TbGT8 is a bifunctional glycosyltransferase that elaborates N-linked glycans on a protein phosphatase AcP115 and a GPI-anchor modifying glycan in Trypanosoma brucei. Parasitol Int (2014) 0.79
Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometry. BMC Genomics (2014) 0.79
Proteomic identification of mammalian cell surface derived glycosylphosphatidylinositol-anchored proteins through selective glycan enrichment. Proteomics (2014) 0.78
Global analysis of proline-rich tandem repeat proteins reveals broad phylogenetic diversity in plant secretomes. PLoS One (2011) 0.78
Inactivation of ca10a and ca10b Genes Leads to Abnormal Embryonic Development and Alters Movement Pattern in Zebrafish. PLoS One (2015) 0.78
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. Elife (2015) 0.77
Genome-wide analysis of excretory/secretory proteins in Echinococcus multilocularis: insights into functional characteristics of the tapeworm secretome. Parasit Vectors (2015) 0.77
Examining marginal sequence similarities between bacterial type III secretion system components and Trypanosoma cruzi surface proteins: horizontal gene transfer or convergent evolution? Front Genet (2013) 0.77
Annotation and characterization of the Plasmodium vivax rhoptry neck protein 4 (PvRON4). Malar J (2013) 0.77
The Trypanosome Exocyst: A Conserved Structure Revealing a New Role in Endocytosis. PLoS Pathog (2017) 0.76
Function of a p24 Heterodimer in Morphogenesis and Protein Transport in Penicillium oxalicum. Sci Rep (2015) 0.76
A targeted immunomic approach identifies diagnostic antigens in the human pathogen Babesia microti. Transfusion (2016) 0.76
Origins and Evolution of tetherin, an Orphan Antiviral Gene. Cell Host Microbe (2016) 0.76
Multiplex assay detection of immunoglobulin G antibodies that recognize Babesia microti antigens. Clin Vaccine Immunol (2012) 0.76
Evolution of acetylcholinesterase and butyrylcholinesterase in the vertebrates: an atypical butyrylcholinesterase from the Medaka Oryzias latipes. PLoS One (2011) 0.76
Cold acclimation is accompanied by complex responses of glycosylphosphatidylinositol (GPI)-anchored proteins in Arabidopsis. J Exp Bot (2016) 0.76
Proteomic analysis of apoplastic fluid of Coffea arabica leaves highlights novel biomarkers for resistance against Hemileia vastatrix. Front Plant Sci (2015) 0.76
Localization and proteomic characterization of cholesterol-rich membrane microdomains in the inner ear. J Proteomics (2014) 0.76
Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements. PLoS One (2016) 0.76
A new role for Hedgehogs in juxtacrine signaling. Mech Dev (2013) 0.76
Characterization of the highly variable immune response gene family, He185/333, in the sea urchin, Heliocidaris erythrogramma. PLoS One (2014) 0.76
Rapidly diverging evolution of an atypical alkaline phosphatase (PhoA(aty)) in marine phytoplankton: insights from dinoflagellate alkaline phosphatases. Front Microbiol (2015) 0.76
Genome Sequencing of the Pyruvate-producing Strain Candida glabrata CCTCC M202019 and Genomic Comparison with Strain CBS138. Sci Rep (2016) 0.75
Both Drosophila matrix metalloproteinases have released and membrane-tethered forms but have different substrates. Sci Rep (2017) 0.75
An ancient autoproteolytic domain found in GAIN, ZU5 and Nucleoporin98. J Mol Biol (2014) 0.75
Molecular evolution and in vitro characterization of Botryllus histocompatibility factor. Immunogenetics (2015) 0.75
Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle-Associated Genes. Sci Rep (2017) 0.75
A theoretical estimate for nucleotide sugar demand towards Chinese Hamster Ovary cellular glycosylation. Sci Rep (2016) 0.75
Proteomic Analysis to Identify Tightly-Bound Cell Wall Protein in Rice Calli. Mol Cells (2015) 0.75
Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates. Database (Oxford) (2016) 0.75
Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi. PeerJ (2017) 0.75
RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection. mSystems (2016) 0.75
Promoter-Specific Expression and Genomic Structure of IgLON Family Genes in Mouse. Front Neurosci (2017) 0.75
Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi. PLoS One (2016) 0.75
Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Mol Biol Cell (2016) 0.75
Glycosylation Quality Control by the Golgi Structure. J Mol Biol (2016) 0.75
Soluble and membrane-bound β-glucosidases are involved in trimming the xyloglucan backbone. Plant Physiol (2016) 0.75
MOXD2, a Gene Possibly Associated with Olfaction, Is Frequently Inactivated in Birds. PLoS One (2016) 0.75
Genomic Identification and Comparative Expansion Analysis of the Non-Specific Lipid Transfer Protein Gene Family in Gossypium. Sci Rep (2016) 0.75
Gene identification and comparative molecular modeling of a Trypanosoma rangeli major surface protease. J Mol Model (2013) 0.75
Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization. BMC Genomics (2017) 0.75
A Glycosylphosphatidylinositol-Anchored Carbonic Anhydrase-Related Protein of Toxoplasma gondii Is Important for Rhoptry Biogenesis and Virulence. mSphere (2017) 0.75
A simple method for displaying the hydropathic character of a protein. J Mol Biol (1982) 150.65
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (2000) 11.75
Bst-2/HM1.24 is a raft-associated apical membrane protein with an unusual topology. Traffic (2003) 5.32
Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol (1999) 2.95
Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol (2003) 2.44
Thematic review series: lipid posttranslational modifications. GPI anchoring of protein in yeast and mammalian cells, or: how we learned to stop worrying and love glycophospholipids. J Lipid Res (2007) 2.35
Functional biology of the alpha(2)delta subunits of voltage-gated calcium channels. Trends Pharmacol Sci (2007) 2.13
Identification of GPI anchor attachment signals by a Kohonen self-organizing map. Bioinformatics (2005) 1.99
Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiol (2003) 1.72
Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment. J Proteome Res (2006) 1.71
The GPI-anchor and protein sorting. Cell Mol Life Sci (2001) 1.69
Proteomic analysis of glycosylphosphatidylinositol-anchored membrane proteins. Mol Cell Proteomics (2003) 1.65
FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring. Genomics Proteomics Bioinformatics (2007) 1.49
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics (2005) 1.49
MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem Biophys Res Commun (2007) 1.41
Requirements for glycosylphosphatidylinositol attachment are similar but not identical in mammalian cells and parasitic protozoa. J Cell Biol (1994) 1.35
Most pathogenic mutations do not alter the membrane topology of the prion protein. J Biol Chem (2000) 1.19
Multiple sequence signals determine the distribution of glycosylphosphatidylinositol proteins between the plasma membrane and cell wall in Saccharomyces cerevisiae. Microbiology (2004) 1.05
GPI-anchored proteins and lipid rafts. Ital J Biochem (2004) 0.95
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res (2005) 4.32
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics (2004) 3.50
Transglutaminases: nature's biological glues. Biochem J (2002) 3.42
Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat (2009) 3.14
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics (2003) 3.10
Prediction of coordination number and relative solvent accessibility in proteins. Proteins (2002) 2.66
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23
A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics (2004) 2.16
BaCelLo: a balanced subcellular localization predictor. Bioinformatics (2006) 2.14
Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem (2002) 1.74
A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics (2008) 1.73
SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. J Natl Cancer Inst (2011) 1.53
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics (2005) 1.49
Predicting protein stability changes from sequences using support vector machines. Bioinformatics (2005) 1.46
Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform (2009) 1.44
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics (2003) 1.44
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29
CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype. Blood (2013) 1.28
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network. Proteomics (2004) 1.20
An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics (2010) 1.18
WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics (2013) 1.14
In silico prediction of the structure of membrane proteins: is it feasible? Brief Bioinform (2003) 1.13
Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans. Hum Mutat (2008) 1.11
eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res (2006) 1.10
Reconstruction of 3D structures from protein contact maps. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.10
The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation. Brief Funct Genomic Proteomic (2008) 1.10
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinformatics (2005) 1.09
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. Protein Eng (2002) 1.09
Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria. Protein Sci (2003) 1.08
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. Bioinformatics (2008) 1.08
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinformatics (2003) 1.07
EX-HOM (EXome HOMozygosity): a proof of principle. Hum Hered (2011) 1.06
A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes. BMC Genomics (2012) 1.05
New Escherichia coli outer membrane proteins identified through prediction and experimental verification. Protein Sci (2006) 1.00
Preprotein translocase of the outer mitochondrial membrane: reconstituted Tom40 forms a characteristic TOM pore. J Mol Biol (2005) 1.00
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res (2011) 0.99
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res (2010) 0.99
Substitution in the murine nectin1 receptor of a single conserved amino acid at a position distal from the herpes simplex virus gD binding site confers high-affinity binding to gD. J Virol (2002) 0.98
The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis. J Proteome Res (2009) 0.96
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. Bioinformatics (2011) 0.94
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinformatics (2009) 0.91
Hierarchical mechanochemical switches in angiostatin. Chembiochem (2006) 0.90
Predicting protein thermostability changes from sequence upon multiple mutations. Bioinformatics (2008) 0.89
Expression of IGF-1 receptor in KIT/PDGF receptor-α wild-type gastrointestinal stromal tumors with succinate dehydrogenase complex dysfunction. Future Oncol (2013) 0.88
Retracted Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy. Protein Sci (2002) 0.87
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. BMC Genomics (2012) 0.87
The pros and cons of predicting protein contact maps. Methods Mol Biol (2008) 0.87
MemPype: a pipeline for the annotation of eukaryotic membrane proteins. Nucleic Acids Res (2011) 0.87
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. Bioinformatics (2011) 0.86
New functions of an old protein: the eukaryotic porin or voltage dependent anion selective channel (VDAC). Ital J Biochem (2003) 0.86
Role of the C-terminus of Pleurotus eryngii Ery4 laccase in determining enzyme structure, catalytic properties and stability. Protein Eng Des Sel (2012) 0.86
The WWWH of remote homolog detection: the state of the art. Brief Bioinform (2006) 0.85
MIMO: an efficient tool for molecular interaction maps overlap. BMC Bioinformatics (2013) 0.83
A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues. Proteins (2004) 0.83
Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy. Protein Sci (2003) 0.82
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. BMC Bioinformatics (2013) 0.82
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. BMC Genomics (2015) 0.81
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines. Bioinformatics (2011) 0.81
Effect of molecular confinement on internal enzyme dynamics: frequency domain fluorometry and molecular dynamics simulation studies. Biopolymers (2002) 0.81
Predicting cancer-associated germline variations in proteins. BMC Genomics (2012) 0.81
A low-resolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus. Protein Eng (2002) 0.80
How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinformatics (2013) 0.80
Frataxin mRNA isoforms in FRDA patients and normal subjects: effect of tocotrienol supplementation. Biomed Res Int (2013) 0.80
Functional characterization of a second porin isoform in Drosophila melanogaster. DmPorin2 forms voltage-independent cation-selective pores. J Biol Chem (2004) 0.80
Substrate-induced conformational changes of the mitochondrial oxoglutarate carrier: a spectroscopic and molecular modelling study. Mol Membr Biol (2005) 0.80
3D structure of Sulfolobus solfataricus carboxypeptidase developed by molecular modeling is confirmed by site-directed mutagenesis and small angle X-ray scattering. Biophys J (2003) 0.80
Fast overlapping of protein contact maps by alignment of eigenvectors. Bioinformatics (2010) 0.80
Pressure and temperature as tools for investigating the role of individual non-covalent interactions in enzymatic reactions Sulfolobus solfataricus carboxypeptidase as a model enzyme. Biochim Biophys Acta (2006) 0.80