Published in BMC Bioinformatics on November 03, 2011
Abstract folding space analysis based on helices. RNA (2012) 0.96
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis. Bioinformatics (2013) 0.91
The RNA shapes studio. Bioinformatics (2014) 0.91
Computational methods for ab initio detection of microRNAs. Front Genet (2012) 0.86
Analysing RNA-kinetics based on folding space abstraction. BMC Bioinformatics (2014) 0.84
Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biol (2015) 0.79
Direct updating of an RNA base-pairing probability matrix with marginal probability constraints. J Comput Biol (2012) 0.78
A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis. PLoS One (2013) 0.77
Pareto optimization in algebraic dynamic programming. Algorithms Mol Biol (2015) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
Stability of ribonucleic acid double-stranded helices. J Mol Biol (1974) 16.35
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry (1998) 9.75
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06
Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers (1999) 7.80
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol (2008) 6.83
RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics (2010) 5.71
CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics (2006) 4.31
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60
Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol (2001) 3.39
A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics (2004) 3.20
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol (2007) 2.81
Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics (2008) 2.48
RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinformatics (2008) 2.39
Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J Am Chem Soc (2008) 2.26
Abstract shapes of RNA. Nucleic Acids Res (2004) 1.90
Frequency and isostericity of RNA base pairs. Nucleic Acids Res (2009) 1.88
Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33
Complete probabilistic analysis of RNA shapes. BMC Biol (2006) 1.27
Analysis and classification of RNA tertiary structures. RNA (2008) 1.20
Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. J Mol Biol (1999) 1.20
Long RNA dangling end has large energetic contribution to duplex stability. J Am Chem Soc (2002) 1.03
The dynamic structural basis of differential enhancement of conformational stability by 5'- and 3'-dangling ends in RNA. Biochemistry (2008) 1.02
Shape based indexing for faster search of RNA family databases. BMC Bioinformatics (2008) 0.96
On quantitative effects of RNA shape abstraction. Theory Biosci (2009) 0.89
Faster computation of exact RNA shape probabilities. Bioinformatics (2010) 0.88
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
RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics (2005) 3.20
A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics (2004) 3.20
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
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf (2003) 2.33
Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 1.91
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
STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics (2006) 1.46
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics (2008) 1.43
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
Evaluating the predictability of conformational switching in RNA. Bioinformatics (2004) 1.30
Viroid-specific small RNA in plant disease. RNA Biol (2012) 1.28
Complete probabilistic analysis of RNA shapes. BMC Biol (2006) 1.27
The RNA structure alignment ontology. RNA (2009) 1.26
Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana. Plant Cell (2005) 1.26
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
Locomotif: from graphical motif description to RNA motif search. Bioinformatics (2007) 1.10
From alpaca to zebrafish: hammerhead ribozymes wherever you look. RNA (2010) 1.07
Effective ambiguity checking in biosequence analysis. BMC Bioinformatics (2005) 1.06
Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics (2011) 1.04
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. BMC Bioinformatics (2009) 1.02
KnotInFrame: prediction of -1 ribosomal frameshift events. Nucleic Acids Res (2008) 1.02
ConStruct: Improved construction of RNA consensus structures. BMC Bioinformatics (2008) 1.00
RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Res (2003) 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
Shape based indexing for faster search of RNA family databases. BMC Bioinformatics (2008) 0.96
Accumulation of viroid-specific small RNAs and increase in nucleolytic activities linked to viroid-caused pathogenesis. Biol Chem (2007) 0.95
mkESA: enhanced suffix array construction tool. Bioinformatics (2009) 0.94
Cracking the elusive alignment hypothesis: the microtubule-cellulose synthase nexus unraveled. Trends Plant Sci (2012) 0.94
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics (2012) 0.93
GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics (2006) 0.93
Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA. Genome Res (2009) 0.92
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis. Bioinformatics (2013) 0.91
Structural characterization of the 69 nucleotide potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis. J Mol Biol (2003) 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
Analysis of thermal stress-mediated PSTVd variation and biolistic inoculation of progeny of viroid "thermomutants" to tomato and Brassica species. Virology (2004) 0.88
Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato. Biol Chem (2010) 0.87
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. Bioinformatics (2009) 0.86
Transcription of potato spindle tuber viroid by RNA polymerase II starts in the left terminal loop. Virology (2006) 0.86
RNA secondary structure analysis using the RNAshapes package. Curr Protoc Bioinformatics (2009) 0.86
Alternative splicing of platelet cyclooxygenase-2 mRNA in patients after coronary artery bypass grafting. Thromb Haemost (2007) 0.84
NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. J Nucleic Acids (2010) 0.83
Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server. Brief Bioinform (2008) 0.82
Elimination of hop latent viroid upon developmental activation of pollen nucleases. Biol Chem (2008) 0.82
Thermostable RNase P RNAs lacking P18 identified in the Aquificales. RNA (2006) 0.82
Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics (2010) 0.81
Give It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone. Front Plant Sci (2012) 0.81
XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics (2005) 0.81
Biological and molecular analysis of the pathogenic variant C3 of potato spindle tuber viroid (PSTVd) evolved during adaptation to chamomile (Matricaria chamomilla). Biol Chem (2012) 0.79
Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biol (2015) 0.79
A database search for double-strand containing RNAs in Dictyostelium discoideum. Biol Chem (2004) 0.79
Abstract shape analysis of RNA. Methods Mol Biol (2014) 0.78
Use of TILLING and robotised enzyme assays to generate an allelic series of Arabidopsis thaliana mutants with altered ADP-glucose pyrophosphorylase activity. J Plant Physiol (2011) 0.78
WAMI: a web server for the analysis of minisatellite maps. BMC Evol Biol (2010) 0.77
Complete sequence of a cryptic virus from hemp (Cannabis sativa). Arch Virol (2011) 0.77
A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis. PLoS One (2013) 0.77
Expression and translation of the COX-1b gene in human cells--no evidence of generation of COX-1b protein. Biol Chem (2013) 0.77
Introduction to RNA secondary structure comparison. Methods Mol Biol (2014) 0.76
Plant 7SL RNA and tRNA(Tyr) genes with inserted antisense sequences are efficiently expressed in an in vitro transcription system from Nicotiana tabacum cells. Plant Mol Biol (2002) 0.76
Sequence elements outside the catalytic core of natural hairpin ribozymes modulate the reactions differentially. Biol Chem (2011) 0.75
The BRaliBase dent-a tale of benchmark design and interpretation. Brief Bioinform (2017) 0.75
Corrigendum: Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nat Plants (2016) 0.75
Surprises in approximating Levenshtein distances. J Theor Biol (2006) 0.75
It's a loop world - single strands in RNA as structural and functional elements. Biomol Concepts (2011) 0.75