Published in Nucleic Acids Res on April 14, 2008
Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors. Genes (Basel) (2011) 1.56
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. Nucleic Acids Res (2008) 0.97
Protein comparison at the domain architecture level. BMC Bioinformatics (2009) 0.96
FACT: functional annotation transfer between proteins with similar feature architectures. BMC Bioinformatics (2010) 0.87
d-Omix: a mixer of generic protein domain analysis tools. Nucleic Acids Res (2009) 0.78
From local structure to a global framework: recognition of protein folds. J R Soc Interface (2014) 0.76
An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins. Bioinformation (2013) 0.76
Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. Proteins (2016) 0.75
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
Detecting protein function and protein-protein interactions from genome sequences. Science (1999) 18.69
Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol (1990) 17.64
GenBank. Nucleic Acids Res (2007) 16.92
CDART: protein homology by domain architecture. Genome Res (2002) 12.95
BLAST: improvements for better sequence analysis. Nucleic Acids Res (2006) 9.77
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol (1998) 9.09
Evolution of the protein repertoire. Science (2003) 4.24
Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol (2007) 3.37
Genome evolution and the evolution of exon-shuffling--a review. Gene (1999) 2.72
An insight into domain combinations. Bioinformatics (2001) 2.14
Domain rearrangements in protein evolution. J Mol Biol (2005) 2.12
Supra-domains: evolutionary units larger than single protein domains. J Mol Biol (2004) 1.82
TXTGate: profiling gene groups with text-based information. Genome Biol (2004) 1.72
An evolutionarily structured universe of protein architecture. Genome Res (2003) 1.61
A tree of life based on protein domain organizations. Mol Biol Evol (2007) 1.42
SIMAP--structuring the network of protein similarities. Nucleic Acids Res (2007) 1.37
Domain architecture comparison for multidomain homology identification. J Comput Biol (2007) 1.21
An initial strategy for comparing proteins at the domain architecture level. Bioinformatics (2006) 1.14
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. Nucleic Acids Res (2005) 0.82
The Goodman-Kruskal coefficient and its applications in genetic diagnosis of cancer. IEEE Trans Biomed Eng (2004) 0.82
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
Inferring pathway activity toward precise disease classification. PLoS Comput Biol (2008) 3.48
Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors. Proc Natl Acad Sci U S A (2009) 2.61
Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell (2009) 2.44
A feature-based approach to modeling protein-protein interaction hot spots. Nucleic Acids Res (2009) 1.41
Modularized learning of genetic interaction networks from biological annotations and mRNA expression data. Bioinformatics (2005) 1.33
Optogenetic mimicry of the transient activation of dopamine neurons by natural reward is sufficient for operant reinforcement. PLoS One (2012) 1.32
A protein interaction network associated with asthma. J Theor Biol (2008) 1.14
SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. Nucleic Acids Res (2006) 1.14
Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage. Hum Mol Genet (2013) 1.08
Regression trees for regulatory element identification. Bioinformatics (2004) 1.07
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst Biol (2010) 1.04
RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics (2010) 1.03
Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification. Bioinformatics (2009) 1.03
Detecting clusters of different geometrical shapes in microarray gene expression data. Bioinformatics (2005) 1.03
Building the process-drug-side effect network to discover the relationship between biological processes and side effects. BMC Bioinformatics (2011) 1.00
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. Nucleic Acids Res (2006) 0.98
Protein comparison at the domain architecture level. BMC Bioinformatics (2009) 0.96
Analysis of AML genes in dysregulated molecular networks. BMC Bioinformatics (2009) 0.93
Specificity of molecular interactions in transient protein-protein interaction interfaces. Proteins (2006) 0.93
Multivariate classification of urine metabolome profiles for breast cancer diagnosis. BMC Bioinformatics (2010) 0.93
Density-induced support vector data description. IEEE Trans Neural Netw (2007) 0.91
PLPD: reliable protein localization prediction from imbalanced and overlapped datasets. Nucleic Acids Res (2006) 0.90
Architecture of basic building blocks in protein and domain structural interaction networks. Bioinformatics (2004) 0.89
Speed estimation from a tri-axial accelerometer using neural networks. Conf Proc IEEE Eng Med Biol Soc (2007) 0.89
The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions. BMC Genomics (2004) 0.86
Identification of temporal association rules from time-series microarray data sets. BMC Bioinformatics (2009) 0.85
A method to improve protein subcellular localization prediction by integrating various biological data sources. BMC Bioinformatics (2009) 0.85
bZIPDB: a database of regulatory information for human bZIP transcription factors. BMC Genomics (2007) 0.84
AsiDesigner: exon-based siRNA design server considering alternative splicing. Nucleic Acids Res (2008) 0.83
Discovering context-specific relationships from biological literature by using multi-level context terms. BMC Med Inform Decis Mak (2012) 0.82
Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics. J Comput Biol (2010) 0.82
Social deficits in the AY-9944 mouse model of atypical absence epilepsy. Behav Brain Res (2012) 0.82
Rule-based multi-scale simulation for drug effect pathway analysis. BMC Med Inform Decis Mak (2013) 0.82
H-CORE: enabling genome-scale Bayesian analysis of biological systems without prior knowledge. Biosystems (2006) 0.82
Generation and application of drug indication inference models using typed network motif comparison analysis. BMC Med Inform Decis Mak (2013) 0.81
CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics. Genomics Inform (2012) 0.81
MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge. BMC Bioinformatics (2010) 0.81
Mathematical modeling of humoral immune response suppression by passively administered antibodies in mice. J Theor Biol (2006) 0.80
Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer. BMC Syst Biol (2011) 0.79
SigCS base: an integrated genetic information resource for human cerebral stroke. BMC Syst Biol (2011) 0.79
Predicting disease phenotypes based on the molecular networks with condition-responsive correlation. Int J Data Min Bioinform (2011) 0.79
Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets. Bioinformatics (2010) 0.79
Prediction of cancer prognosis with the genetic basis of transcriptional variations. Genomics (2011) 0.78
Computational identification of combinatorial regulation and transcription factor binding sites. Biotechnol Bioeng (2007) 0.77
Towards clustering of incomplete microarray data without the use of imputation. Bioinformatics (2006) 0.77
Context-dependent transcriptional regulations between signal transduction pathways. BMC Bioinformatics (2011) 0.77
An Approach to Reducing Information Loss and Achieving Diversity of Sensitive Attributes in k-anonymity Methods. Interact J Med Res (2012) 0.76
Genome-wide DNA-binding specificity of PIL5, an Arabidopsis basic Helix-Loop-Helix (bHLH) transcription factor. Int J Data Min Bioinform (2010) 0.76
Relationships between genetic polymorphisms and transcriptional profiles for outcome prediction in anticancer agent treatment. BMB Rep (2010) 0.76
Synthetic inter-species cooperation of host and virus for targeted genetic evolution. J Biotechnol (2011) 0.76
Computational identification of altered metabolism using gene expression and metabolic pathways. Biotechnol Bioeng (2009) 0.76
Inference of combinatorial neuronal synchrony with Bayesian networks. J Neurosci Methods (2009) 0.76
Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation, gene expression, and trait variation. Mol Cells (2012) 0.76
Context-based resolution of semantic conflicts in biological pathways. BMC Med Inform Decis Mak (2015) 0.76
Analysis of AML Genes in Dysregulated Molecular Networks. Summit on Translat Bioinforma (2009) 0.75
Comparative analysis of the JAK/STAT signaling through erythropoietin receptor and thrombopoietin receptor using a systems approach. BMC Bioinformatics (2009) 0.75
PSExplorer: whole parameter space exploration for molecular signaling pathway dynamics. Bioinformatics (2010) 0.75
Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases. BMC Bioinformatics (2009) 0.75
Inferring disease association using clinical factors in a combinatorial manner and their use in drug repositioning. Bioinformatics (2013) 0.75
Inference of brain pathway activities for Alzheimer's disease classification. BMC Med Inform Decis Mak (2015) 0.75
Predicting the Absorption Potential of Chemical Compounds through a Deep Learning Approach. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75
Normalization of Tumor Vessels by Tie2 Activation and Ang2 Inhibition Enhances Drug Delivery and Produces a Favorable Tumor Microenvironment. Cancer Cell (2017) 0.75
A Bayesian ensemble approach with a disease gene network predicts damaging effects of missense variants of human cancers. Hum Genet (2012) 0.75
CONVIRT: a web-based tool for transcriptional regulatory site identification using a conserved virtual chromosome. BMB Rep (2009) 0.75
Computational identification of significantly regulated metabolic reactions by integration of data on enzyme activity and gene expression. BMB Rep (2008) 0.75
Predicting tissue-specific expressions based on sequence characteristics. BMB Rep (2011) 0.75
Fuzzy branching temporal logic. IEEE Trans Syst Man Cybern B Cybern (2004) 0.75