Published in Theory Biosci on May 10, 2007
Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci (2009) 5.08
Tentaculate fossils from the Cambrian of Canada (British Columbia) and China (Yunnan) interpreted as primitive deuterostomes. PLoS One (2010) 1.24
The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes. BMC Evol Biol (2009) 1.03
Evolution of centralized nervous systems: two schools of evolutionary thought. Proc Natl Acad Sci U S A (2012) 1.00
Back in time: a new systematic proposal for the Bilateria. Philos Trans R Soc Lond B Biol Sci (2008) 0.96
The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis. BMC Evol Biol (2010) 0.87
What is Xenoturbella? Zoological Lett (2015) 0.83
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. BMC Evol Biol (2011) 0.81
The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae. Sci Rep (2017) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
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 primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70
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
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
MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol (2012) 3.41
The reality of pervasive transcription. PLoS Biol (2011) 3.41
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
Thermodynamics of RNA-RNA binding. Bioinformatics (2006) 3.10
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
Cytoglobin: a novel globin type ubiquitously expressed in vertebrate tissues. Mol Biol Evol (2002) 2.53
Neuroglobin and cytoglobin. Fresh blood for the vertebrate globin family. EMBO Rep (2002) 2.50
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
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
Variations on RNA folding and alignment: lessons from Benasque. J Math Biol (2007) 1.91
RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput (2010) 1.87
How does the eye breathe? Evidence for neuroglobin-mediated oxygen supply in the mammalian retina. J Biol Chem (2002) 1.85
A survey of nematode SmY RNAs. RNA Biol (2009) 1.85
Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol (2004) 1.81
Evolution of microRNAs located within Hox gene clusters. J Exp Zool B Mol Dev Evol (2005) 1.77
Human brain neuroglobin structure reveals a distinct mode of controlling oxygen affinity. Structure (2003) 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
Risk of coronary artery disease associated with polymorphism of the cytochrome P450 epoxygenase CYP2J2. Circulation (2004) 1.73
Neuroglobin and cytoglobin in search of their role in the vertebrate globin family. J Inorg Biochem (2005) 1.71
What is the function of neuroglobin? J Exp Biol (2009) 1.65
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60
ESTAnnotator: A tool for high throughput EST annotation. Nucleic Acids Res (2003) 1.56
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics (2009) 1.55
Cytoglobin is a respiratory protein in connective tissue and neurons, which is up-regulated by hypoxia. J Biol Chem (2003) 1.54
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
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
The redox state of the cell regulates the ligand binding affinity of human neuroglobin and cytoglobin. J Biol Chem (2003) 1.47
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
Structure and function of the smallest vertebrate telomerase RNA from teleost fish. J Biol Chem (2007) 1.38
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 1.38
Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta. Mol Biol Evol (2007) 1.35
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
New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evol Biol (2013) 1.32
A globin gene of ancient evolutionary origin in lower vertebrates: evidence for two distinct globin families in animals. Mol Biol Evol (2004) 1.28
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
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
Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) reconstructed with nuclear small subunit rRNA gene sequences: discrepancies and accordances with morphological data. J Eukaryot Microbiol (2007) 1.24
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
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
Multiple sequence alignment with user-defined anchor points. Algorithms Mol Biol (2006) 1.20
CREx: inferring genomic rearrangements based on common intervals. Bioinformatics (2007) 1.19
Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res (2009) 1.19
The common ancestral core of vertebrate and fungal telomerase RNAs. Nucleic Acids Res (2012) 1.18
Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res (2009) 1.18
A novel family of plasmid-transferred anti-sense ncRNAs. RNA Biol (2010) 1.18
Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res (2013) 1.18
Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol (2012) 1.18
A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogenet Evol (2013) 1.17
The tedious task of finding homologous noncoding RNA genes. RNA (2009) 1.17
The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene (2005) 1.17
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res (2011) 1.16
Neuroglobin: a respiratory protein of the nervous system. News Physiol Sci (2004) 1.16
Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol (2008) 1.16