Published in J Exp Zool B Mol Dev Evol on July 15, 2008
Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Proc Natl Acad Sci U S A (2013) 1.36
Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes. Proc Natl Acad Sci U S A (2009) 1.33
Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci U S A (2010) 1.20
Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard. Genome Res (2009) 1.06
How Hox genes can shed light on the place of echinoderms among the deuterostomes. Evodevo (2014) 1.02
Evolution of coding and non-coding genes in HOX clusters of a marsupial. BMC Genomics (2012) 0.95
Evolution of Hox gene clusters in deuterostomes. BMC Dev Biol (2013) 0.91
A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution. BMC Evol Biol (2010) 0.89
Evolution of developmental regulation in the vertebrate FgfD subfamily. J Exp Zool B Mol Dev Evol (2010) 0.85
Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis. J Mol Evol (2010) 0.84
Evolution of anterior Hox regulatory elements among chordates. BMC Evol Biol (2011) 0.83
Broken colinearity of the amphioxus Hox cluster. Evodevo (2012) 0.81
Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster. Dev Genes Evol (2008) 0.80
Ambulacrarian prototypical Hox and ParaHox gene complements of the indirect-developing hemichordate Balanoglossus simodensis. Dev Genes Evol (2009) 0.79
Conservation of gene linkage in dispersed vertebrate NK homeobox clusters. Dev Genes Evol (2009) 0.76
Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome. BMC Genomics (2015) 0.75
The Hox8 of the hemichordate Balanoglossus misakiensis. Dev Genes Evol (2009) 0.75
Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution. Zoological Lett (2017) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality. N Engl J Med (2005) 16.59
Prepublication data sharing. Nature (2009) 12.24
ViennaRNA Package 2.0. Algorithms Mol Biol (2011) 9.43
Secondary structure prediction for aligned RNA sequences. J Mol Biol (2002) 8.80
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
The primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
Molecular evolution of a microRNA cluster. J Mol Biol (2004) 5.94
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood (2007) 5.14
tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res (2008) 4.88
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet (2009) 4.72
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol (2005) 4.68
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics (2011) 4.15
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res (2006) 3.59
The reality of pervasive transcription. PLoS Biol (2011) 3.41
MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol (2012) 3.41
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria. Cell (2007) 3.12
Thermodynamics of RNA-RNA binding. Bioinformatics (2006) 3.10
Targeted screening of cis-regulatory variation in human haplotypes. Genome Res (2008) 3.10
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78
Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics (2006) 2.77
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol (2006) 2.74
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Am J Hum Genet (2009) 2.56
A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res (2009) 2.55
Alignment of RNA base pairing probability matrices. Bioinformatics (2004) 2.42
Evolution. Transitions from nonliving to living matter. Science (2004) 2.26
Local RNA base pairing probabilities in large sequences. Bioinformatics (2005) 2.17
Rfx6 directs islet formation and insulin production in mice and humans. Nature (2010) 2.15
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics (2006) 2.13
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res (2008) 2.10
Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet (2012) 2.07
A defect in a novel Nek-family kinase causes cystic kidney disease in the mouse and in zebrafish. Development (2002) 2.00
Variations on RNA folding and alignment: lessons from Benasque. J Math Biol (2007) 1.91
DNA sequence and analysis of human chromosome 8. Nature (2006) 1.91
RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput (2010) 1.87
A survey of nematode SmY RNAs. RNA Biol (2009) 1.85
Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol (2004) 1.81
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature (2006) 1.81
Evolution of microRNAs located within Hox gene clusters. J Exp Zool B Mol Dev Evol (2005) 1.77
Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biol (2008) 1.75
Centers of complex networks. J Theor Biol (2003) 1.74
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs. Genome Res (2002) 1.70
The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. Am J Hum Genet (2003) 1.70
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
An X-to-autosome retrogene is required for spermatogenesis in mice. Nat Genet (2004) 1.63
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics (2009) 1.55
The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol (2005) 1.54
SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics (2007) 1.51
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA (2012) 1.51
Analysis of the DNA sequence and duplication history of human chromosome 15. Nature (2006) 1.50
Evolutionary patterns of non-coding RNAs. Theory Biosci (2005) 1.49
Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet (2013) 1.48
Independent Hox-cluster duplications in lampreys. J Exp Zool B Mol Dev Evol (2003) 1.48
Visualization of barrier tree sequences. IEEE Trans Vis Comput Graph (2006) 1.45
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA (2011) 1.42
Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Curr Biol (2012) 1.40
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 1.38
Structure and function of the smallest vertebrate telomerase RNA from teleost fish. J Biol Chem (2007) 1.38
Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance. Genome Res (2009) 1.37
Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zool B Mol Dev Evol (2006) 1.34
Evolution of vault RNAs. Mol Biol Evol (2009) 1.31
Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc Natl Acad Sci U S A (2002) 1.29
Insights into spawning behavior and development of the European amphioxus (Branchiostoma lanceolatum). J Exp Zool B Mol Dev Evol (2007) 1.29
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res (2012) 1.27
Counterexamples in chemical ring perception. J Chem Inf Comput Sci (2004) 1.27
Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection. Microbiome (2013) 1.26
The development of the larval nervous system, musculature and ciliary bands of Pomatoceros lamarckii (Annelida): heterochrony in polychaetes. Front Zool (2006) 1.26
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res (2011) 1.25
Evolution of spliceosomal snRNA genes in metazoan animals. J Mol Evol (2008) 1.25
RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res (2011) 1.25
Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol (2009) 1.24
Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res (2011) 1.22
Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology (2008) 1.21
Non-coding RNAs in Ciona intestinalis. Bioinformatics (2005) 1.21