Published in Bioinformatics on December 15, 2005
Mammalian mirtron genes. Mol Cell (2007) 5.75
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res (2006) 5.23
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells (2008) 3.14
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res (2010) 2.56
RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinformatics (2008) 2.39
Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One (2009) 2.37
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol (2009) 2.02
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc Natl Acad Sci U S A (2010) 1.99
Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res (2009) 1.64
Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea. PLoS Genet (2007) 1.63
Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Res (2012) 1.63
miROrtho: computational survey of microRNA genes. Nucleic Acids Res (2008) 1.60
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics (2008) 1.43
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biol (2007) 1.38
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33
RNA stem-loops: to be or not to be cleaved by RNAse III. RNA (2007) 1.28
Complete probabilistic analysis of RNA shapes. BMC Biol (2006) 1.27
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. BMC Genomics (2009) 1.21
Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics (2008) 1.21
Small RNA expression and strain specificity in the rat. BMC Genomics (2010) 1.16
GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol (2014) 1.12
Automated and fast building of three-dimensional RNA structures. Sci Rep (2012) 1.10
Computational methods in noncoding RNA research. J Math Biol (2007) 1.08
A deep sequencing approach to uncover the miRNOME in the human heart. PLoS One (2013) 1.04
TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinformatics (2011) 1.03
Naturally occurring mitochondrial DNA heteroplasmy in the MRL mouse. Mitochondrion (2008) 1.01
RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evol Biol (2007) 1.01
Structural analysis of aligned RNAs. Nucleic Acids Res (2006) 1.00
A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA (2007) 1.00
Identification of Schistosoma mansoni microRNAs. BMC Genomics (2011) 1.00
Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA (2013) 0.99
Secondary structure is required for 3' splice site recognition in yeast. Nucleic Acids Res (2011) 0.98
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res (2013) 0.97
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One (2009) 0.96
Abstract folding space analysis based on helices. RNA (2012) 0.96
Computational generation and screening of RNA motifs in large nucleotide sequence pools. Nucleic Acids Res (2010) 0.95
Large-scale identification of mirtrons in Arabidopsis and rice. PLoS One (2012) 0.95
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales. Genes (Basel) (2011) 0.94
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinformatics (2010) 0.94
RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res (2007) 0.93
Stochastic sampling of the RNA structural alignment space. Nucleic Acids Res (2009) 0.93
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics (2012) 0.93
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis. Bioinformatics (2013) 0.91
Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Res (2011) 0.91
Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei). BMC Evol Biol (2013) 0.91
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules. BMC Bioinformatics (2007) 0.89
Faster computation of exact RNA shape probabilities. Bioinformatics (2010) 0.88
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics (2013) 0.88
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinformatics (2012) 0.88
Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method. J Math Biol (2007) 0.88
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA (2011) 0.87
The complete nucleotide sequence of the mitochondrial genome of Bactrocera minax (Diptera: Tephritidae). PLoS One (2014) 0.86
RNA localization signals: deciphering the message with bioinformatics. Semin Cell Dev Biol (2007) 0.86
RNA structure prediction from evolutionary patterns of nucleotide composition. Nucleic Acids Res (2009) 0.86
Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition. J Math Biol (2007) 0.85
A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA). J Comput Biol (2012) 0.85
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions. BMC Bioinformatics (2008) 0.85
Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinformatics (2012) 0.84
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure. BMC Bioinformatics (2008) 0.84
NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. J Nucleic Acids (2010) 0.83
RNA Movies 2: sequential animation of RNA secondary structures. Nucleic Acids Res (2007) 0.82
Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa. Eukaryot Cell (2010) 0.82
Transcriptional regulation of translocator protein (Tspo) via a SINE B2-mediated natural antisense transcript in MA-10 Leydig cells. Biol Reprod (2012) 0.81
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. PLoS One (2015) 0.81
Unrooted unordered homeomorphic subtree alignment of RNA trees. Algorithms Mol Biol (2013) 0.80
Informatic resources for identifying and annotating structural RNA motifs. Mol Biotechnol (2008) 0.80
Comparing RNA secondary structures using a relaxed base-pair score. RNA (2010) 0.80
A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Res (2015) 0.80
RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. Bioinformatics (2011) 0.79
Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools. Nucleic Acids Res (2015) 0.79
Secondary structural entropy in RNA switch (Riboswitch) identification. BMC Bioinformatics (2015) 0.79
The tRNA-Derived Small RNAs Regulate Gene Expression through Triggering Sequence-Specific Degradation of Target Transcripts in the Oomycete Pathogen Phytophthora sojae. Front Plant Sci (2016) 0.79
Identification and profiling of miRNAs during herbivory reveals jasmonate-dependent and -independent patterns of accumulation in Nicotiana attenuata. BMC Plant Biol (2012) 0.78
Combinatorics of locally optimal RNA secondary structures. J Math Biol (2012) 0.78
Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin a-chain. Biochemistry (2007) 0.78
Long non-coding RNAs: a novel endogenous source for the generation of Dicer-like 1-dependent small RNAs in Arabidopsis thaliana. RNA Biol (2014) 0.77
NoFold: RNA structure clustering without folding or alignment. RNA (2014) 0.77
Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble. Nucleic Acids Res (2014) 0.77
Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci (2016) 0.77
Genome-wide identification of reverse complementary microRNA genes in plants. PLoS One (2012) 0.76
Virus versus host plant microRNAs: who determines the outcome of the interaction? PLoS One (2014) 0.75
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. J Comput Biol (2015) 0.75
Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic. PLoS One (2016) 0.75
New insights from cluster analysis methods for RNA secondary structure prediction. Wiley Interdiscip Rev RNA (2016) 0.75
Role of RNA secondary structure in emergence of compartment specific hepatitis B virus immune escape variants. World J Virol (2016) 0.75
Conserved and highly expressed tRNA derived fragments in zebrafish. BMC Mol Biol (2015) 0.75
Computing the probability of RNA hairpin and multiloop formation. J Comput Biol (2014) 0.75
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinformatics (2016) 0.75
Accurate Classification of RNA Structures Using Topological Fingerprints. PLoS One (2016) 0.75
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. Genes (Basel) (2016) 0.75
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM. BMC Bioinformatics (2013) 0.75
Optimizing RNA structures by sequence extensions using RNAcop. Nucleic Acids Res (2015) 0.75
New tools to analyze overlapping coding regions. BMC Bioinformatics (2016) 0.75
An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin. PLoS One (2015) 0.75
Bioinformatic tools for analysis of CLIP ribonucleoprotein data. Wiley Interdiscip Rev RNA (2016) 0.75
Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. Rice (N Y) (2017) 0.75
Introduction to special issue on RNA. J Math Biol (2008) 0.75
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J (2017) 0.75
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 18.88
Fast and effective prediction of microRNA/target duplexes. RNA (2004) 18.10
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18
RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res (2006) 7.39
Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol (2007) 4.66
Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61
A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nat Cell Biol (2009) 3.44
A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics (2004) 3.20
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A (2011) 2.84
Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster. Dev Cell (2003) 2.75
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics (2004) 2.73
Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics (2006) 2.66
PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics (2002) 2.43
Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf (2003) 2.33
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res (2010) 2.21
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol (2009) 2.02
Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 1.91
Abstract shapes of RNA. Nucleic Acids Res (2004) 1.90
GenAlyzer: interactive visualization of sequence similarities between entire genomes. Bioinformatics (2004) 1.85
Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.79
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics (2005) 1.74
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. Nucleic Acids Res (2007) 1.74
High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm. PLoS Genet (2011) 1.53
A novel approach to remote homology detection: jumping alignments. J Comput Biol (2002) 1.45
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics (2008) 1.43
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Res (2009) 1.39
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biol (2007) 1.38
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biol (2011) 1.33
Evaluating the predictability of conformational switching in RNA. Bioinformatics (2004) 1.30
Complete probabilistic analysis of RNA shapes. BMC Biol (2006) 1.27
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics (2010) 1.24
Beyond Mfold: recent advances in RNA bioinformatics. J Biotechnol (2006) 1.23
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021. BMC Genomics (2013) 1.21
Microevolution in cyanobacteria: re-sequencing a motile substrain of Synechocystis sp. PCC 6803. DNA Res (2012) 1.14
Locomotif: from graphical motif description to RNA motif search. Bioinformatics (2007) 1.10
Effective ambiguity checking in biosequence analysis. BMC Bioinformatics (2005) 1.06
jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Res (2006) 1.05
Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics (2011) 1.04
The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria. RNA Biol (2009) 1.03
Two distinct types of 6S RNA in Prochlorococcus. Gene (2007) 1.02
KnotInFrame: prediction of -1 ribosomal frameshift events. Nucleic Acids Res (2008) 1.02
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics (2011) 1.01
RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Res (2003) 1.00
Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein. Mol Microbiol (2011) 1.00
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. Nucleic Acids Res (2004) 0.99
Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics (2005) 0.97
A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris. ISME J (2010) 0.97
Heterocyst-specific transcription of NsiR1, a non-coding RNA encoded in a tandem array of direct repeats in cyanobacteria. J Mol Biol (2010) 0.97
Shape based indexing for faster search of RNA family databases. BMC Bioinformatics (2008) 0.96
mkESA: enhanced suffix array construction tool. Bioinformatics (2009) 0.94
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics (2012) 0.93
Response to Wang and Luo. BMC Biol (2012) 0.93
GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics (2006) 0.93
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown. PLoS One (2011) 0.92
Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species. PLoS Biol (2008) 0.92
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis. Bioinformatics (2013) 0.91
Alignment of minisatellite maps based on run-length encoding scheme. J Bioinform Comput Biol (2009) 0.91
Faster computation of exact RNA shape probabilities. Bioinformatics (2010) 0.88
Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions. ISME J (2012) 0.88
Small RNAs of the halophilic archaeon Haloferax volcanii. Biochem Soc Trans (2009) 0.87
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. Bioinformatics (2009) 0.86
RNA secondary structure analysis using the RNAshapes package. Curr Protoc Bioinformatics (2009) 0.86
Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeon Haloferax volcanii. RNA Biol (2011) 0.86
Comparative homology agreement search: an effective combination of homology-search methods. Proc Natl Acad Sci U S A (2004) 0.85
Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server. Brief Bioinform (2008) 0.82
Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics (2010) 0.81
Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biol (2012) 0.81
XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics (2005) 0.81
Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biol (2015) 0.79
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA. RNA (2010) 0.78
The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. BMC Genomics (2014) 0.78
Abstract shape analysis of RNA. Methods Mol Biol (2014) 0.78
WAMI: a web server for the analysis of minisatellite maps. BMC Evol Biol (2010) 0.77
A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis. PLoS One (2013) 0.77
Introduction to RNA secondary structure comparison. Methods Mol Biol (2014) 0.76
The BRaliBase dent-a tale of benchmark design and interpretation. Brief Bioinform (2017) 0.75
Surprises in approximating Levenshtein distances. J Theor Biol (2006) 0.75
A strategy for identifying fluorescence intensity profiles of single rod-shaped cells. J Bioinform Comput Biol (2012) 0.75