Published in Bioinformatics on January 16, 2009
Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA. Nucleic Acids Res (2010) 1.84
An effective hybrid of hill climbing and genetic algorithm for 2D triangular protein structure prediction. Proteome Sci (2011) 0.87
Producing high-accuracy lattice models from protein atomic coordinates including side chains. Adv Bioinformatics (2012) 0.85
An effective evolutionary algorithm for protein folding on 3D FCC HP model by lattice rotation and generalized move sets. Proteome Sci (2013) 0.83
On the characterization and software implementation of general protein lattice models. PLoS One (2013) 0.80
A versatile method for systematic conformational searches: application to CheY. J Comput Chem (2011) 0.77
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. BMC Bioinformatics (2010) 0.75
A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction. Adv Bioinformatics (2014) 0.75
A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences. Int J Mol Sci (2015) 0.75
Theory for the folding and stability of globular proteins. Biochemistry (1985) 5.92
Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ (2006) 3.76
The complexity and accuracy of discrete state models of protein structure. J Mol Biol (1995) 1.86
Side-chain entropy and packing in proteins. Protein Sci (1994) 1.75
Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. J Comput Biol (1998) 1.45
CPSP-tools--exact and complete algorithms for high-throughput 3D lattice protein studies. BMC Bioinformatics (2008) 1.20
Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study. Bioinformatics (2007) 1.05
Modelling sequential protein folding under kinetic control. Bioinformatics (2006) 0.98
Classifying proteinlike sequences in arbitrary lattice protein models using LatPack. HFSP J (2008) 0.92
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics (2008) 2.88
Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat Genet (2004) 2.41
The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal. Mol Microbiol (2011) 2.00
Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell (2013) 1.99
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics (2005) 1.98
Pre-mRNA secondary structures influence exon recognition. PLoS Genet (2007) 1.92
Variations on RNA folding and alignment: lessons from Benasque. J Math Biol (2007) 1.91
Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA. Nucleic Acids Res (2010) 1.84
INFO-RNA--a fast approach to inverse RNA folding. Bioinformatics (2006) 1.73
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res (2006) 1.55
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA (2012) 1.51
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res (2008) 1.47
Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Nucleic Acids Res (2012) 1.41
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 1.38
Global or local? Predicting secondary structure and accessibility in mRNAs. Nucleic Acids Res (2012) 1.36
Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A (2013) 1.29
Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing. Am J Hum Genet (2005) 1.29
Structator: fast index-based search for RNA sequence-structure patterns. BMC Bioinformatics (2011) 1.24
CPSP-tools--exact and complete algorithms for high-throughput 3D lattice protein studies. BMC Bioinformatics (2008) 1.20
A partition function algorithm for interacting nucleic acid strands. Bioinformatics (2009) 1.18
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics (2009) 1.17
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res (2013) 1.16
Mir-148a improves response to chemotherapy in sensitive and resistant oesophageal adenocarcinoma and squamous cell carcinoma cells. J Gastrointest Surg (2011) 1.14
CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein. PLoS One (2013) 1.13
A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Proc Natl Acad Sci U S A (2012) 1.12
GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol (2014) 1.12
A multiple-feature framework for modelling and predicting transcription factor binding sites. Bioinformatics (2005) 1.09
Phylogenetically widespread alternative splicing at unusual GYNGYN donors. Genome Biol (2006) 1.09
Accurate prediction of NAGNAG alternative splicing. Nucleic Acids Res (2009) 1.08
Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinformatics (2009) 1.07
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics (2010) 1.07
Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics (2008) 1.04
Fast prediction of RNA-RNA interaction. Algorithms Mol Biol (2010) 1.04
Local sequence-structure motifs in RNA. J Bioinform Comput Biol (2004) 1.04
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? RNA Biol (2012) 1.04
A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii. J Biol Chem (2014) 1.02
Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology. PLoS One (2010) 1.02
Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns. Genome Biol (2007) 1.01
Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res (2009) 1.01
Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B. RNA Biol (2013) 1.01
Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA (2012) 1.01
INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints. Nucleic Acids Res (2007) 1.00
Non-EST based prediction of exon skipping and intron retention events using Pfam information. Nucleic Acids Res (2005) 0.97
TassDB: a database of alternative tandem splice sites. Nucleic Acids Res (2006) 0.97
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data. Nucleic Acids Res (2007) 0.96
Abstract folding space analysis based on helices. RNA (2012) 0.96
Assessing the fraction of short-distance tandem splice sites under purifying selection. RNA (2008) 0.95
TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinformatics (2010) 0.93
An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res (2012) 0.93
Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression. J Clin Invest (2014) 0.93
Classifying proteinlike sequences in arbitrary lattice protein models using LatPack. HFSP J (2008) 0.92
Two CRISPR-Cas systems in Methanosarcina mazei strain Gö1 display common processing features despite belonging to different types I and III. RNA Biol (2013) 0.90
Fungal virulence in a lepidopteran model is an emergent property with deterministic features. MBio (2013) 0.90
Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies. Cell Host Microbe (2013) 0.90
Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function. Genome Biol (2005) 0.89
Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PLoS One (2013) 0.89
GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics (2012) 0.88
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. Nucleic Acids Res (2011) 0.88
Selection against tandem splice sites affecting structured protein regions. BMC Evol Biol (2008) 0.88
Alternative splicing at NAGNAG acceptors: simply noise or noise and more? PLoS Genet (2006) 0.87
Sequencing errors or SNPs at splice-acceptor guanines in dbSNP? Nat Biotechnol (2006) 0.87
CARNA--alignment of RNA structure ensembles. Nucleic Acids Res (2012) 0.86
Producing high-accuracy lattice models from protein atomic coordinates including side chains. Adv Bioinformatics (2012) 0.85
Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system. Biochem Soc Trans (2013) 0.85
Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinformatics (2011) 0.85
Efficient prediction of alternative splice forms using protein domain homology. In Silico Biol (2004) 0.85
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J Biomed Semantics (2013) 0.85
SECISDesign: a server to design SECIS-elements within the coding sequence. Bioinformatics (2005) 0.84
A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. Bioinformatics (2013) 0.84
Lifting prediction to alignment of RNA pseudoknots. J Comput Biol (2010) 0.84
Anomalous expansion of attractively interacting fermionic atoms in an optical lattice. Science (2010) 0.83
Comparative analysis ofCas6b processing and CRISPR RNA stability. RNA Biol (2013) 0.83
Cluster based prediction of PDZ-peptide interactions. BMC Genomics (2014) 0.80
Regulatory RNAs in archaea: first target identification in Methanoarchaea. Biochem Soc Trans (2013) 0.80
Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens. BMC Plant Biol (2010) 0.80
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PLoS One (2013) 0.79
Ultracold fermionic Feshbach molecules of 23Na40K. Phys Rev Lett (2012) 0.78
Local Exact Pattern Matching for Non-Fixed RNA Structures. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.78
Improved identification of conserved cassette exons using Bayesian networks. BMC Bioinformatics (2008) 0.76
Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA. Methods Mol Biol (2007) 0.76
The SH2-domain of SHIP1 interacts with the SHIP1 C-terminus: impact on SHIP1/Ig-α interaction. Biochim Biophys Acta (2011) 0.76
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. Bioinformatics (2012) 0.75
An efficient procedure for the preparation of natural products bearing the 2-(2-phenylethyl)chromone skeleton. Tetrahedron Lett (2013) 0.75
Simultaneous alignment and folding of protein sequences. J Comput Biol (2014) 0.75