Published in Nucleic Acids Res on May 05, 2010
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. Nucleic Acids Res (2011) 1.07
NeuroPID: a classifier of neuropeptide precursors. Nucleic Acids Res (2014) 0.78
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. BMC Bioinformatics (2013) 0.76
ProtoBug: functional families from the complete proteomes of insects. Database (Oxford) (2015) 0.76
miRror-Suite: decoding coordinated regulation by microRNAs. Database (Oxford) (2014) 0.75
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics (2004) 11.23
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71
Protein function annotation by homology-based inference. Genome Biol (2009) 2.20
ProtoNet 4.0: a hierarchical classification of one million protein sequences. Nucleic Acids Res (2005) 1.74
Mining sequence annotation databanks for association patterns. Bioinformatics (2005) 1.62
PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res (2003) 1.31
Functional annotation prediction: all for one and one for all. Protein Sci (2006) 1.17
A proteomic survey of rat cerebral cortical synaptosomes. Proteomics (2005) 1.16
Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet (2013) 7.44
Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N Engl J Med (2014) 6.89
Synaptic, transcriptional and chromatin genes disrupted in autism. Nature (2014) 5.30
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron (2013) 2.45
Protein function annotation by homology-based inference. Genome Biol (2009) 2.20
ProtoNet: hierarchical classification of the protein space. Nucleic Acids Res (2003) 1.88
zCall: a rare variant caller for array-based genotyping: genetics and population analysis. Bioinformatics (2012) 1.87
ProtoNet 4.0: a hierarchical classification of one million protein sequences. Nucleic Acids Res (2005) 1.74
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Bioinformatics (2008) 1.72
Novel unsupervised feature filtering of biological data. Bioinformatics (2006) 1.64
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. Mol Syst Biol (2009) 1.48
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Am J Hum Genet (2013) 1.39
Unsupervised feature selection under perturbations: meeting the challenges of biological data. Bioinformatics (2007) 1.32
PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res (2003) 1.31
A functional hierarchical organization of the protein sequence space. BMC Bioinformatics (2004) 1.28
The metric space of proteins-comparative study of clustering algorithms. Bioinformatics (2002) 1.25
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. Biol Direct (2010) 1.19
Functional annotation prediction: all for one and one for all. Protein Sci (2006) 1.17
Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics (2012) 1.15
A robust method to detect structural and functional remote homologues. Proteins (2004) 1.09
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. Nucleic Acids Res (2011) 1.07
MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets. Bioinformatics (2010) 1.06
Apoptotic cell thrombospondin-1 and heparin-binding domain lead to dendritic-cell phagocytic and tolerizing states. Blood (2006) 1.03
The complete peptide dictionary--a meta-proteomics resource. Proteomics (2010) 1.01
EVEREST: automatic identification and classification of protein domains in all protein sequences. BMC Bioinformatics (2006) 0.99
Codon usage is associated with the evolutionary age of genes in metazoan genomes. BMC Evol Biol (2009) 0.98
Direct interaction of target SNAREs with the Kv2.1 channel. Modal regulation of channel activation and inactivation gating. J Biol Chem (2003) 0.98
Is GAS1 a co-receptor for the GDNF family of ligands? Trends Pharmacol Sci (2006) 0.98
Protection of pancreatic beta-cells from various stress conditions is mediated by DJ-1. J Biol Chem (2010) 0.97
Global considerations in hierarchical clustering reveal meaningful patterns in data. PLoS One (2008) 0.95
Polysaccharide-oligoamine based conjugates for gene delivery. J Med Chem (2002) 0.94
ClanTox: a classifier of short animal toxins. Nucleic Acids Res (2009) 0.94
Selecting targets for structural determination by navigating in a graph of protein families. Bioinformatics (2002) 0.91
Novel families of toxin-like peptides in insects and mammals: a computational approach. J Mol Biol (2007) 0.91
Working together: combinatorial regulation by microRNAs. Adv Exp Med Biol (2013) 0.90
Toward a combinatorial nature of microRNA regulation in human cells. Nucleic Acids Res (2012) 0.90
Dead-end elimination for multistate protein design. J Comput Chem (2007) 0.89
Predicting fold novelty based on ProtoNet hierarchical classification. Bioinformatics (2004) 0.88
Cellular processes underlying maturation of P19 neurons: Changes in protein folding regimen and cytoskeleton organization. Proteomics (2007) 0.87
ProtoBee: hierarchical classification and annotation of the honey bee proteome. Genome Res (2006) 0.87
Conservation of the relative tRNA composition in healthy and cancerous tissues. RNA (2012) 0.87
ProtoNet: charting the expanding universe of protein sequences. Nat Biotechnol (2013) 0.86
Viral proteins acquired from a host converge to simplified domain architectures. PLoS Comput Biol (2012) 0.86
Design of multispecific protein sequences using probabilistic graphical modeling. Proteins (2010) 0.86
Connect the dots: exposing hidden protein family connections from the entire sequence tree. Bioinformatics (2008) 0.86
The advantage of functional prediction based on clustering of yeast genes and its correlation with non-sequence based classifications. J Comput Biol (2002) 0.86
Prenatal stress diminishes gender differences in behavior and in expression of hippocampal synaptic genes and proteins in rats. Hippocampus (2010) 0.85
The leader peptide of MMTV Env precursor localizes to the nucleoli in MMTV-derived T cell lymphomas and interacts with nucleolar protein B23. Virology (2003) 0.85
ProTeus: identifying signatures in protein termini. Nucleic Acids Res (2005) 0.84
EVEREST: a collection of evolutionary conserved protein domains. Nucleic Acids Res (2006) 0.84
Hydrophobized dextran-spermine conjugate as potential vector for in vitro gene transfection. J Control Release (2004) 0.84
NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes. Bioinformatics (2013) 0.83
Synaptic proteins as multi-sensor devices of neurotransmission. BMC Neurosci (2006) 0.82
Automatic detection of false annotations via binary property clustering. BMC Bioinformatics (2005) 0.82
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry. Nucleic Acids Res (2011) 0.82
Generative probabilistic models for protein-protein interaction networks--the biclique perspective. Bioinformatics (2011) 0.81
Functional grouping based on signatures in protein termini. Proteins (2006) 0.80
PROCEED: A proteomic method for analysing plasma membrane proteins in living mammalian cells. Brief Funct Genomic Proteomic (2003) 0.80
Short toxin-like proteins attack the defense line of innate immunity. Toxins (Basel) (2013) 0.79
Quaternary ammonium polysaccharides for gene delivery. Bioconjug Chem (2005) 0.79
Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle. Genome Biol (2008) 0.79
Coordinated expression of cytoskeleton regulating genes in the accelerated neurite outgrowth of P19 embryonic carcinoma cells. Exp Cell Res (2007) 0.79
Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains. Bioinformatics (2005) 0.78
UFFizi: a generic platform for ranking informative features. BMC Bioinformatics (2010) 0.78
SPRINT: side-chain prediction inference toolbox for multistate protein design. Bioinformatics (2010) 0.78
A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes. Bioinformatics (2010) 0.78
Recovering key biological constituents through sparse representation of gene expression. Bioinformatics (2011) 0.78
Gene expression in women conceiving spontaneously over the age of 45 years. Fertil Steril (2007) 0.77
miRror2.0: a platform for assessing the joint action of microRNAs in cell regulation. J Bioinform Comput Biol (2013) 0.77
Pardaxin stimulation of phospholipases A2 and their involvement in exocytosis in PC-12 cells. J Pharmacol Exp Ther (2002) 0.77
Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty? BMC Genomics (2009) 0.77
Evolutional insights on uncharacterized SARS coronavirus genes. FEBS Lett (2004) 0.77
Exposing the co-adaptive potential of protein-protein interfaces through computational sequence design. Bioinformatics (2010) 0.76
Susceptibility of the human pathways graphs to fragmentation by small sets of microRNAs. Bioinformatics (2012) 0.76
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. BMC Bioinformatics (2013) 0.76
ProTarget: automatic prediction of protein structure novelty. Nucleic Acids Res (2005) 0.75
Short toxin-like proteins abound in Cnidaria genomes. Toxins (Basel) (2012) 0.75
Implicit biology in peptide spectral libraries. Anal Chem (2012) 0.75
Paving the future: finding suitable ISMB venues. Bioinformatics (2012) 0.75