Published in Biol Direct on January 15, 2010
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc Natl Acad Sci U S A (2011) 3.41
Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One (2010) 2.92
Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA. PLoS One (2012) 1.31
Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One (2011) 1.26
Secondary structure improves OTU assignments of 16S rRNA gene sequences. ISME J (2012) 1.24
The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS. Biomed Res Int (2013) 1.14
The ITS2 Database. J Vis Exp (2012) 0.96
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front Zool (2014) 0.92
Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa. BMC Evol Biol (2011) 0.92
Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept. PLoS One (2013) 0.91
A close-up view on ITS2 evolution and speciation - a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evol Biol (2011) 0.90
Identification of commercial Ganoderma (Lingzhi) species by ITS2 sequences. Chin Med (2015) 0.86
The changing epitome of species identification - DNA barcoding. Saudi J Biol Sci (2014) 0.84
ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding. PLoS One (2015) 0.84
Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota). PLoS One (2014) 0.83
Molecular taxonomy of Dunaliella (Chlorophyceae), with a special focus on D. salina: ITS2 sequences revisited with an extensive geographical sampling. Aquat Biosyst (2012) 0.82
Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae). BMC Evol Biol (2013) 0.82
Secondary structure analysis of ITS2 in the rDNA of three Indian paramphistomid species found in local livestock. Parasitol Res (2010) 0.82
Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree. PLoS One (2014) 0.79
An ITS-based phylogenetic framework for the genus Vorticella: finding the molecular and morphological gaps in a taxonomically difficult group. Proc Biol Sci (2013) 0.78
A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data. BMC Res Notes (2010) 0.78
Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2. Ann Bot (2011) 0.77
Considerations For Optimizing Microbiome Analysis Using a Marker Gene. Front Nutr (2016) 0.77
Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment. BMC Evol Biol (2015) 0.77
Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum. PLoS One (2017) 0.75
Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market. Sci Rep (2017) 0.75
Secondary structure of nrDNA Internal Transcribed Spacers as a useful tool to align highly divergent species in phylogenetic studies. Genet Mol Biol (2017) 0.75
ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae). Genetica (2016) 0.75
PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. Front Microbiol (2017) 0.75
Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure. Genetica (2017) 0.75
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
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Modeling amino acid replacement. J Comput Biol (2000) 3.40
Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet (2001) 3.39
ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet (2003) 3.31
The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol (2002) 3.11
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol (2003) 2.55
5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene (2008) 2.51
Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst Biol (2003) 2.27
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics (2006) 2.24
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol (2005) 2.16
A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol (1994) 2.15
Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res (2007) 2.14
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA (2005) 1.94
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res (2006) 1.92
The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence? Mol Biol Evol (2001) 1.84
On the best evolutionary rate for phylogenetic analysis. Syst Biol (1998) 1.77
More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae). Syst Biol (1999) 1.68
ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol Phylogenet Evol (2009) 1.55
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res Notes (2008) 1.54
The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res (2007) 1.41
The advantages of the ITS2 region of the nuclear rDNA cistron for analysis of phylogenetic relationships of insects: a Drosophila example. Mol Phylogenet Evol (2004) 1.38
High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA. Genetics (1998) 1.33
Nuclear and mitochondrial data reveal different evolutionary processes in the Lake Tanganyika cichlid genus Tropheus. BMC Evol Biol (2007) 1.31
Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol Biol Evol (2002) 1.27
Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals. BMC Evol Biol (2007) 1.26
ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments. Bioinformatics (2008) 1.25
QDist--quartet distance between evolutionary trees. Bioinformatics (2004) 1.23
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics (2005) 1.13
Snake phylogeny: evidence from nuclear and mitochondrial genes. Mol Phylogenet Evol (2002) 1.13
In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics (2005) 1.05
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evol Biol (2008) 1.00
Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae. Mol Phylogenet Evol (2006) 0.94
Identifying site-specific substitution rates. Mol Biol Evol (2003) 0.88
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nat Genet (2009) 13.03
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet (2006) 6.74
HMM Logos for visualization of protein families. BMC Bioinformatics (2004) 5.69
Systematic identification of novel protein domain families associated with nuclear functions. Genome Res (2002) 3.50
Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics (2008) 3.00
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA (2005) 2.75
Genome expression analysis of Anopheles gambiae: responses to injury, bacterial challenge, and malaria infection. Proc Natl Acad Sci U S A (2002) 2.59
On the power of profiles for transcription factor binding site detection. Stat Appl Genet Mol Biol (2003) 2.52
5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene (2008) 2.51
Inactive enzyme-homologues find new function in regulatory processes. J Mol Biol (2004) 2.47
Combined effects of different interleukin-28B gene variants on the outcome of dual combination therapy in chronic hepatitis C virus type 1 infection. Hepatology (2012) 2.42
A Variegated Squirrel Bornavirus Associated with Fatal Human Encephalitis. N Engl J Med (2015) 2.34
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics (2006) 2.24
Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol Mol Biol Rev (2004) 2.19
Mitochondrial changes in skeletal muscle in amyotrophic lateral sclerosis and other neurogenic atrophies. Brain (2005) 2.18
Graft-versus-host disease is enhanced by extracellular ATP activating P2X7R. Nat Med (2010) 2.17
Evaluation of liver disease progression in the German hepatitis C virus (1b)-contaminated anti-D cohort at 35 years after infection. Hepatology (2013) 2.13
Polymorphisms in melanoma differentiation-associated gene 5 link protein function to clearance of hepatitis C virus. Hepatology (2015) 2.11
Importance of IL28B gene polymorphisms in hepatitis C virus genotype 2 and 3 infected patients. J Hepatol (2010) 2.09
Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. Proc Natl Acad Sci U S A (2008) 2.06
Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nat Rev Microbiol (2010) 2.04
The ITS2 Database III--sequences and structures for phylogeny. Nucleic Acids Res (2009) 2.04
Predicting protein cellular localization using a domain projection method. Genome Res (2002) 1.98
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA (2005) 1.94
BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics (2010) 1.93
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res (2006) 1.92
Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat Genet (2013) 1.83
Distinguishing species. RNA (2007) 1.74
Platelet protein interactions: map, signaling components, and phosphorylation groundstate. Arterioscler Thromb Vasc Biol (2008) 1.71
Local application of FTY720 to the lung abrogates experimental asthma by altering dendritic cell function. J Clin Invest (2006) 1.67
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J (2010) 1.66
L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res (2005) 1.57
ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol Phylogenet Evol (2009) 1.55
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res Notes (2008) 1.54
Distinct, alcohol-modulated effects of PNPLA3 genotype on progression of chronic hepatitis C. J Hepatol (2011) 1.52
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evol Biol (2004) 1.51
Metabolites: a helping hand for pathway evolution? Trends Biochem Sci (2003) 1.50
Production of serotonin by tryptophan hydroxylase 1 and release via platelets contribute to allergic airway inflammation. Am J Respir Crit Care Med (2013) 1.49
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol (2006) 1.48
Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res (2004) 1.47
The serotoninergic receptors of human dendritic cells: identification and coupling to cytokine release. J Immunol (2004) 1.44
The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'. BMC Genomics (2008) 1.42
The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res (2007) 1.41
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In Silico Biol (2005) 1.39
Time-efficient CT colonography interpretation using an advanced image-gallery-based, computer-aided "first-reader" workflow for the detection of colorectal adenomas. Eur Radiol (2012) 1.38
An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach. Plant Cell (2006) 1.37
IL28B, HLA-C, and KIR variants additively predict response to therapy in chronic hepatitis C virus infection in a European Cohort: a cross-sectional study. PLoS Med (2011) 1.36
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics (2007) 1.32
5-Hydroxytryptamine modulates cytokine and chemokine production in LPS-primed human monocytes via stimulation of different 5-HTR subtypes. Int Immunol (2005) 1.30
Extracellular adenosine triphosphate and chronic obstructive pulmonary disease. Am J Respir Crit Care Med (2010) 1.30
ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus ). BMC Evol Biol (2009) 1.30
Interactions of methylene blue with human disulfide reductases and their orthologues from Plasmodium falciparum. Antimicrob Agents Chemother (2007) 1.28
ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies. Mol Phylogenet Evol (2012) 1.28
Genome-wide mapping of foamy virus vector integrations into a human cell line. J Gen Virol (2006) 1.28
P2X7 receptor signaling in the pathogenesis of smoke-induced lung inflammation and emphysema. Am J Respir Cell Mol Biol (2010) 1.27
Toward computer-based cleavage site prediction of cysteine endopeptidases. Biol Chem (2003) 1.27
Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One (2011) 1.26
ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments. Bioinformatics (2008) 1.25
Lack of the purinergic receptor P2X(7) results in resistance to contact hypersensitivity. J Exp Med (2010) 1.25
Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy. J Biol Chem (2006) 1.25
Metabolic programming of MEST DNA methylation by intrauterine exposure to gestational diabetes mellitus. Diabetes (2012) 1.25
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics (2005) 1.24