Published in Nucleic Acids Res on July 01, 2004
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2005) 22.98
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.85
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res (2006) 16.26
NCBI BLAST: a better web interface. Nucleic Acids Res (2008) 15.14
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
BLAST: improvements for better sequence analysis. Nucleic Acids Res (2006) 9.77
Computational solutions to large-scale data management and analysis. Nat Rev Genet (2010) 6.58
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res (2006) 5.60
AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics (2006) 5.50
OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res (2007) 4.96
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res (2007) 3.02
BLAST: a more efficient report with usability improvements. Nucleic Acids Res (2013) 2.77
Evolutionary dynamics of GII.4 noroviruses over a 34-year period. J Virol (2009) 2.74
LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics (2008) 2.73
REBASE--restriction enzymes and DNA methyltransferases. Nucleic Acids Res (2005) 2.70
Classification and nomenclature of all human homeobox genes. BMC Biol (2007) 2.61
iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One (2008) 2.18
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res (2011) 2.03
The tmRDB and SRPDB resources. Nucleic Acids Res (2006) 2.01
Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol (2005) 1.98
Novel plasmid and its variant harboring both a bla(NDM-1) gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii. Antimicrob Agents Chemother (2012) 1.97
Differential repression of alternative transcripts: a screen for miRNA targets. PLoS Comput Biol (2006) 1.82
Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet (2006) 1.81
Persistence and availability of Web services in computational biology. PLoS One (2011) 1.80
The Nfs1 interacting protein Isd11 has an essential role in Fe/S cluster biogenesis in mitochondria. EMBO J (2005) 1.79
Conservation of alternative polyadenylation patterns in mammalian genes. BMC Genomics (2006) 1.75
Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. PLoS Comput Biol (2006) 1.73
Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res (2005) 1.68
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics (2008) 1.68
Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet (2007) 1.67
YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. J Bacteriol (2006) 1.58
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Res (2012) 1.57
A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A (2008) 1.56
SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. Nucleic Acids Res (2007) 1.55
A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. BMC Evol Biol (2008) 1.54
Heteroplasmy in the mitochondrial genomes of human lice and ticks revealed by high throughput sequencing. PLoS One (2013) 1.49
A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. J Virol (2015) 1.48
Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol (2008) 1.47
Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. Methods Enzymol (2007) 1.46
Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res (2009) 1.40
CFGP: a web-based, comparative fungal genomics platform. Nucleic Acids Res (2007) 1.39
Evidence for recombination in Mycobacterium tuberculosis. J Bacteriol (2006) 1.37
Loss-of-function mutations of ILDR1 cause autosomal-recessive hearing impairment DFNB42. Am J Hum Genet (2011) 1.37
The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genet (2010) 1.36
Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast- and formula-fed infants. Appl Environ Microbiol (2009) 1.35
In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites. BMC Bioinformatics (2008) 1.32
Dynamics of Recognition between tRNA and elongation factor Tu. J Mol Biol (2008) 1.32
The bZIP transcription factor MoAP1 mediates the oxidative stress response and is critical for pathogenicity of the rice blast fungus Magnaporthe oryzae. PLoS Pathog (2011) 1.32
Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice. Appl Environ Microbiol (2006) 1.31
An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res (2015) 1.30
Knockdown of Nurr1 in the rat hippocampus: implications to spatial discrimination learning and memory. Learn Mem (2006) 1.30
Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: t-elements contribute to 5' and 3' end formation. Nucleic Acids Res (2007) 1.29
Comparative evolution of GII.3 and GII.4 norovirus over a 31-year period. J Virol (2011) 1.28
A novel pathogenicity gene is required in the rice blast fungus to suppress the basal defenses of the host. PLoS Pathog (2009) 1.27
Bordetella petrii clinical isolate. Emerg Infect Dis (2005) 1.27
RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res (2006) 1.25
Large-scale identification of odorant-binding proteins and chemosensory proteins from expressed sequence tags in insects. BMC Genomics (2009) 1.24
Structural and functional differences in isoforms of mouse major urinary proteins: a male-specific protein that preferentially binds a male pheromone. Biochem J (2005) 1.24
Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis (2008) 1.23
Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305phi8-36. Virology (2007) 1.21
A genetic map of Xenopus tropicalis. Dev Biol (2011) 1.20
Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor. Appl Environ Microbiol (2008) 1.19
Fungi and animals may share a common ancestor to nuclear receptors. Proc Natl Acad Sci U S A (2006) 1.18
Functional annotation prediction: all for one and one for all. Protein Sci (2006) 1.17
Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data. PLoS One (2012) 1.17
Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120. J Biol Chem (2009) 1.17
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. Genome Res (2008) 1.16
Identification and characterization of a novel human methyltransferase modulating Hsp70 protein function through lysine methylation. J Biol Chem (2013) 1.16
Respiratory nitrate ammonification by Shewanella oneidensis MR-1. J Bacteriol (2006) 1.15
Single nucleotide polymorphisms and linkage disequilibrium in sunflower. Genetics (2007) 1.14
Whole-genome sequencing reveals a link between β-lactam resistance and synthetases of the alarmone (p)ppGpp in Staphylococcus aureus. Microb Drug Resist (2013) 1.14
Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions. J Proteome Res (2008) 1.13
Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics (2011) 1.13
Localization of polyketide synthase encoding genes to the toxic dinoflagellate Karenia brevis. Phytochemistry (2005) 1.12
Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinformatics (2009) 1.12
Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. Genome Biol (2014) 1.12
Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proc Biol Sci (2016) 1.11
Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals. BMC Genomics (2006) 1.11
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PLoS One (2009) 1.10
Identification of alternatively spliced transcripts using a proteomic informatics approach. Methods Mol Biol (2011) 1.10
Comparative genome analysis of Enterobacter cloacae. PLoS One (2013) 1.10
De novo sequencing and transcriptome analysis of the central nervous system of mollusc Lymnaea stagnalis by deep RNA sequencing. PLoS One (2012) 1.07
Roots of angiosperm formins: the evolutionary history of plant FH2 domain-containing proteins. BMC Evol Biol (2008) 1.07
The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability. Mol Genet Genomics (2006) 1.06
A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4. Genetics (2008) 1.05
In search of an uncultured human-associated TM7 bacterium in the environment. PLoS One (2011) 1.04
Development and application of a novel peptide nucleic acid probe for the specific detection of Helicobacter pylori in gastric biopsy specimens. J Clin Microbiol (2007) 1.04
Evolution of the land plant exocyst complexes. Front Plant Sci (2012) 1.04
Tracembler--software for in-silico chromosome walking in unassembled genomes. BMC Bioinformatics (2007) 1.04
Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics (2011) 1.02
Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin. J Bacteriol (2011) 1.02
The disparate nature of "intergenic" polyadenylation sites. RNA (2006) 1.02
T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. BMC Bioinformatics (2010) 1.02
Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach. Int J Legal Med (2009) 1.02
An isoform of ZBP-89 predisposes the colon to colitis. Nucleic Acids Res (2006) 1.02
Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3. ISME J (2010) 1.02
Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio. Appl Microbiol Biotechnol (2008) 1.01
Role of Salmonella enterica serovar Typhimurium two-component system PreA/PreB in modulating PmrA-regulated gene transcription. J Bacteriol (2006) 1.01
PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species. BMC Microbiol (2010) 1.01
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
A greedy algorithm for aligning DNA sequences. J Comput Biol (2000) 47.89
PatternHunter: faster and more sensitive homology search. Bioinformatics (2002) 35.65
Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res (1998) 23.87
Amino acid substitution matrices from an information theoretic perspective. J Mol Biol (1991) 23.38
CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res (2002) 18.54
Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science (1997) 7.95
Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics (2001) 7.12
Analysis of expressed sequence tags (EST) obtained from common carp, Cyprinus carpio L., head kidney cells after stimulation by two mitogens, lipopolysaccharide and concanavalin-A. Comp Biochem Physiol B Biochem Mol Biol (2002) 2.01
Human choroideremia protein contains a FAD-binding domain. Nat Genet (1996) 1.96
BLAST+: architecture and applications. BMC Bioinformatics (2009) 36.53
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2005) 22.98
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2007) 22.53
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2008) 21.36
Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res (2002) 19.40
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.85
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.84
Database resources of the National Center for Biotechnology. Nucleic Acids Res (2003) 18.26
NCBI BLAST: a better web interface. Nucleic Acids Res (2008) 15.14
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2009) 12.51
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2010) 10.97
Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res (2004) 9.85
BLAST: improvements for better sequence analysis. Nucleic Acids Res (2006) 9.77
Database indexing for production MegaBLAST searches. Bioinformatics (2008) 8.73
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics (2012) 8.61
IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res (2013) 3.33
Domain enhanced lookup time accelerated BLAST. Biol Direct (2012) 2.87
BLAST: a more efficient report with usability improvements. Nucleic Acids Res (2013) 2.77
New finite-size correction for local alignment score distributions. BMC Res Notes (2012) 0.84