RNAshapes: an integrated RNA analysis package based on abstract shapes

Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R (2006)
Bioinformatics 22(4): 500-503.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Abstract / Bemerkung
We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.
Page URI


Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 2006;22(4):500-503.
Steffen, P., Voss, B., Rehmsmeier, M., Reeder, J., & Giegerich, R. (2006). RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22(4), 500-503. https://doi.org/10.1093/bioinformatics/btk010
Steffen, Peter, Voss, Björn, Rehmsmeier, Marc, Reeder, Jens, and Giegerich, Robert. 2006. “RNAshapes: an integrated RNA analysis package based on abstract shapes”. Bioinformatics 22 (4): 500-503.
Steffen, P., Voss, B., Rehmsmeier, M., Reeder, J., and Giegerich, R. (2006). RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics 22, 500-503.
Steffen, P., et al., 2006. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22(4), p 500-503.
P. Steffen, et al., “RNAshapes: an integrated RNA analysis package based on abstract shapes”, Bioinformatics, vol. 22, 2006, pp. 500-503.
Steffen, P., Voss, B., Rehmsmeier, M., Reeder, J., Giegerich, R.: RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 22, 500-503 (2006).
Steffen, Peter, Voss, Björn, Rehmsmeier, Marc, Reeder, Jens, and Giegerich, Robert. “RNAshapes: an integrated RNA analysis package based on abstract shapes”. Bioinformatics 22.4 (2006): 500-503.

157 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Structural prediction of RNA switches using conditional base-pair probabilities.
Manzourolajdad A, Spouge JL., PLoS One 14(6), 2019
PMID: 31188853
ENTRNA: a framework to predict RNA foldability.
Su C, Weir JD, Zhang F, Yan H, Wu T., BMC Bioinformatics 20(1), 2019
PMID: 31269893
Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection.
Chen L, Zhang YH, Huang G, Pan X, Wang S, Huang T, Cai YD., Mol Genet Genomics 293(1), 2018
PMID: 28913654
Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.
Lin L, McKerrow WH, Richards B, Phonsom C, Lawrence CE., BMC Bioinformatics 19(1), 2018
PMID: 29506466
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.
Polishchuk M, Paz I, Yakhini Z, Mandel-Gutfreund Y., Nucleic Acids Res 46(w1), 2018
PMID: 29800452
Characterization and comparative analysis of microRNAs in the rice pest Sogatella furcifera.
Chang ZX, Akinyemi IA, Guo DY, Wu Q., PLoS One 13(9), 2018
PMID: 30248141
Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis.
Yu D, Xu M, Ito H, Shao W, Ma X, Wang H, Meng Y., Front Genet 9(), 2018
PMID: 30487815
Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures.
Sabarinathan R, Anthon C, Gorodkin J, Seemann SE., Genes (Basel) 9(12), 2018
PMID: 30518121
Bioinformatic tools for analysis of CLIP ribonucleoprotein data.
De S, Gorospe M., Wiley Interdiscip Rev RNA 8(4), 2017
PMID: 28008714
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.
Woods CT, Lackey L, Williams B, Dokholyan NV, Gotz D, Laederach A., Biophys J 113(2), 2017
PMID: 28625696
Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs.
Yu D, Ma X, Zuo Z, Shao W, Wang H, Meng Y., Rice (N Y) 10(1), 2017
PMID: 28786034
An efficient graph kernel method for non-coding RNA functional prediction.
Navarin N, Costa F., Bioinformatics 33(17), 2017
PMID: 28475710
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
Heller D, Krestel R, Ohler U, Vingron M, Marsico A., Nucleic Acids Res 45(19), 2017
PMID: 28977546
Conserved RNA structures in the intergenic regions of ambisense viruses.
Kiening M, Weber F, Frishman D., Sci Rep 7(1), 2017
PMID: 29192224
Toward a next-generation atlas of RNA secondary structure.
Bai Y, Dai X, Harrison A, Johnston C, Chen M., Brief Bioinform 17(1), 2016
PMID: 25922372
A deep learning framework for modeling structural features of RNA-binding protein targets.
Zhang S, Zhou J, Hu H, Gong H, Chen L, Cheng C, Zeng J., Nucleic Acids Res 44(4), 2016
PMID: 26467480
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers.
Orenstein Y, Berger B., J Comput Biol 23(2), 2016
PMID: 26713687
Structure Prediction: New Insights into Decrypting Long Noncoding RNAs.
Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A., Int J Mol Sci 17(1), 2016
PMID: 26805815
New insights from cluster analysis methods for RNA secondary structure prediction.
Rogers E, Heitsch C., Wiley Interdiscip Rev RNA 7(3), 2016
PMID: 26971529
Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic.
Manzourolajdad A, Gonzalez M, Spouge JL., PLoS One 11(9), 2016
PMID: 27685447
Accurate Classification of RNA Structures Using Topological Fingerprints.
Huang J, Li K, Gribskov M., PLoS One 11(10), 2016
PMID: 27755571
New tools to analyze overlapping coding regions.
Bayegan AH, Garcia-Martin JA, Clote P., BMC Bioinformatics 17(1), 2016
PMID: 27964762
The tRNA-Derived Small RNAs Regulate Gene Expression through Triggering Sequence-Specific Degradation of Target Transcripts in the Oomycete Pathogen Phytophthora sojae.
Wang Q, Li T, Xu K, Zhang W, Wang X, Quan J, Jin W, Zhang M, Fan G, Wang MB, Shan W., Front Plant Sci 7(), 2016
PMID: 28066490
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools.
Kunz M, Wolf B, Schulze H, Atlan D, Walles T, Walles H, Dandekar T., Genes (Basel) 8(1), 2016
PMID: 28035947
Chaining sequence/structure seeds for computing RNA similarity.
Bourgeade L, Chauve C, Allali J., J Comput Biol 22(3), 2015
PMID: 25768236
Tissue-type plasminogen activator-binding RNA aptamers inhibiting low-density lipoprotein receptor family-mediated internalisation.
Bjerregaard N, Bøtkjær KA, Helsen N, Andreasen PA, Dupont DM., Thromb Haemost 114(1), 2015
PMID: 25855589
Secondary structural entropy in RNA switch (Riboswitch) identification.
Manzourolajdad A, Arnold J., BMC Bioinformatics 16(), 2015
PMID: 25928324
An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin.
Bratanov D, Balandin T, Round E, Shevchenko V, Gushchin I, Polovinkin V, Borshchevskiy V, Gordeliy V., PLoS One 10(6), 2015
PMID: 26046789
Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools.
Dupont DM, Larsen N, Jensen JK, Andreasen PA, Kjems J., Nucleic Acids Res 43(21), 2015
PMID: 26163061
Optimizing RNA structures by sequence extensions using RNAcop.
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J., Nucleic Acids Res 43(17), 2015
PMID: 26283181
Improving tRNAscan-SE Annotation Results via Ensemble Classifiers.
Zou Q, Guo J, Ju Y, Wu M, Zeng X, Hong Z., Mol Inform 34(11-12), 2015
PMID: 27491037
Conserved and highly expressed tRNA derived fragments in zebrafish.
Soares AR, Fernandes N, Reverendo M, Araújo HR, Oliveira JL, Moura GM, Santos MA., BMC Mol Biol 16(), 2015
PMID: 26694924
Combinatorics of locally optimal RNA secondary structures.
Fusy E, Clote P., J Math Biol 68(1-2), 2014
PMID: 23263300
Finding the target sites of RNA-binding proteins.
Li X, Kazan H, Lipshitz HD, Morris QD., Wiley Interdiscip Rev RNA 5(1), 2014
PMID: 24217996
GraphProt: modeling binding preferences of RNA-binding proteins.
Maticzka D, Lange SJ, Costa F, Backofen R., Genome Biol 15(1), 2014
PMID: 24451197
Computing the probability of RNA hairpin and multiloop formation.
Ding Y, Lorenz WA, Dotu I, Senter E, Clote P., J Comput Biol 21(3), 2014
PMID: 24559086
Virus versus host plant microRNAs: who determines the outcome of the interaction?
Maghuly F, Ramkat RC, Laimer M., PLoS One 9(6), 2014
PMID: 24896088
The complete nucleotide sequence of the mitochondrial genome of Bactrocera minax (Diptera: Tephritidae).
Zhang B, Nardi F, Hull-Sanders H, Wan X, Liu Y., PLoS One 9(6), 2014
PMID: 24964138
sRNA-seq analysis of human embryonic stem cells and definitive endoderm reveals differentially expressed microRNAs and novel IsomiRs with distinct targets.
Hinton A, Hunter SE, Afrikanova I, Jones GA, Lopez AD, Fogel GB, Hayek A, King CC., Stem Cells 32(9), 2014
PMID: 24805944
NoFold: RNA structure clustering without folding or alignment.
Middleton SA, Kim J., RNA 20(11), 2014
PMID: 25234928
Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble.
Rogers E, Heitsch CE., Nucleic Acids Res 42(22), 2014
PMID: 25392423
A reversed framework for the identification of microRNA-target pairs in plants.
Shao C, Chen M, Meng Y., Brief Bioinform 14(3), 2013
PMID: 22811545
Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues.
Kusakabe R, Tani S, Nishitsuji K, Shindo M, Okamura K, Miyamoto Y, Nakai K, Suzuki Y, Kusakabe TG, Inoue K., Gene Expr Patterns 13(1-2), 2013
PMID: 23159539
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.
Achawanantakun R, Sun Y., BMC Bioinformatics 14 Suppl 2(), 2013
PMID: 23369147
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.
Sauthoff G, Möhl M, Janssen S, Giegerich R., Bioinformatics 29(5), 2013
PMID: 23355290
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.
Puton T, Kozlowski LP, Rother KM, Bujnicki JM., Nucleic Acids Res 41(7), 2013
PMID: 23435231
A deep sequencing approach to uncover the miRNOME in the human heart.
Leptidis S, El Azzouzi H, Lok SI, de Weger R, Olieslagers S, Kisters N, Silva GJ, Heymans S, Cuppen E, Berezikov E, De Windt LJ, da Costa Martins P., PLoS One 8(2), 2013
PMID: 23460909
Unrooted unordered homeomorphic subtree alignment of RNA trees.
Milo N, Zakov S, Katzenelson E, Bachmat E, Dinitz Y, Ziv-Ukelson M., Algorithms Mol Biol 8(1), 2013
PMID: 23590940
Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei).
Poulsen JY, Byrkjedal I, Willassen E, Rees D, Takeshima H, Satoh TP, Shinohara G, Nishida M, Miya M., BMC Evol Biol 13(), 2013
PMID: 23731841
Developmental expression and evolution of muscle-specific microRNAs conserved in vertebrates.
Tani S, Kuraku S, Sakamoto H, Inoue K, Kusakabe R., Evol Dev 15(4), 2013
PMID: 23809703
Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis.
Shao C, Wu Q, Qiu J, Jin S, Zhang B, Qian J, Chen M, Meng Y., Gene 527(2), 2013
PMID: 23850578
Large-scale study of long non-coding RNA functions based on structure and expression features.
Zhao Y, Wang J, Chen X, Luo H, Zhao Y, Xiao Y, Chen R., Sci China Life Sci 56(10), 2013
PMID: 24091687
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032.
Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24138339
Statistical evaluation of improvement in RNA secondary structure prediction.
Xu Z, Almudevar A, Mathews DH., Nucleic Acids Res 40(4), 2012
PMID: 22139940
Maximum expected accuracy structural neighbors of an RNA secondary structure.
Clote P, Lou F, Lorenz WA., BMC Bioinformatics 13 Suppl 5(), 2012
PMID: 22537010
Discovery of hundreds of mirtrons in mouse and human small RNA data.
Ladewig E, Okamura K, Flynt AS, Westholm JO, Lai EC., Genome Res 22(9), 2012
PMID: 22955976
Computational prediction and experimental verification of miRNAs in Panicum miliaceum L.
Wu Y, Du J, Wang X, Fang X, Shan W, Liang Z., Sci China Life Sci 55(9), 2012
PMID: 23015130
RNA locally optimal secondary structures.
Saffarian A, Giraud M, de Monte A, Touzet H., J Comput Biol 19(10), 2012
PMID: 23057822
Automated and fast building of three-dimensional RNA structures.
Zhao Y, Huang Y, Gong Z, Wang Y, Man J, Xiao Y., Sci Rep 2(), 2012
PMID: 23071898
Genome-wide identification of reverse complementary microRNA genes in plants.
Shao C, Ma X, Xu X, Wang H, Meng Y., PLoS One 7(10), 2012
PMID: 23110057
Abstract folding space analysis based on helices.
Huang J, Backofen R, Voß B., RNA 18(12), 2012
PMID: 23104999
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.
El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P., BMC Bioinformatics 13 Suppl 17(), 2012
PMID: 23281941
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.
Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC., Genome Res 21(2), 2011
PMID: 21177969
Identification of Schistosoma mansoni microRNAs.
Simões MC, Lee J, Djikeng A, Cerqueira GC, Zerlotini A, da Silva-Pereira RA, Dalby AR, LoVerde P, El-Sayed NM, Oliveira G., BMC Genomics 12(), 2011
PMID: 21247453
Improvements of the hierarchical approach for predicting RNA tertiary structure.
Zhao Y, Gong Z, Xiao Y., J Biomol Struct Dyn 28(5), 2011
PMID: 21294592
TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.
Harmanci AO, Sharma G, Mathews DH., BMC Bioinformatics 12(), 2011
PMID: 21507242
RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences.
Wei D, Alpert LV, Lawrence CE., Bioinformatics 27(18), 2011
PMID: 21788211
Secondary structure is required for 3' splice site recognition in yeast.
Gahura O, Hammann C, Valentová A, Půta F, Folk P., Nucleic Acids Res 39(22), 2011
PMID: 21893588
Finding stable local optimal RNA secondary structures.
Li Y, Zhang S., Bioinformatics 27(21), 2011
PMID: 21903624
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.
Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C., RNA 17(11), 2011
PMID: 21947200
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schlüter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
Evolution of an X-linked primate-specific micro RNA cluster.
Li J, Liu Y, Dong D, Zhang Z., Mol Biol Evol 27(3), 2010
PMID: 19933172
Faster computation of exact RNA shape probabilities.
Janssen S, Giegerich R., Bioinformatics 26(5), 2010
PMID: 20080511
Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa.
Bullerwell CE, Burger G, Gott JM, Kourennaia O, Schnare MN, Gray MW., Eukaryot Cell 9(5), 2010
PMID: 20304999
Comparing RNA secondary structures using a relaxed base-pair score.
Agius P, Bennett KP, Zuker M., RNA 16(5), 2010
PMID: 20360393
Small RNA expression and strain specificity in the rat.
Linsen SE, de Wit E, de Bruijn E, Cuppen E., BMC Genomics 11(), 2010
PMID: 20403161
Computational generation and screening of RNA motifs in large nucleotide sequence pools.
Kim N, Izzo JA, Elmetwaly S, Gan HH, Schlick T., Nucleic Acids Res 38(13), 2010
PMID: 20448026
NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome.
Teune JH, Steger G., J Nucleic Acids 2010(), 2010
PMID: 20871826
Computational approaches for RNA energy parameter estimation.
Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP., RNA 16(12), 2010
PMID: 20940338
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, Söding J, Westhof E, Wilson DN, Beckmann R., Proc Natl Acad Sci U S A 107(46), 2010
PMID: 20980660
miROrtho: computational survey of microRNA genes.
Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM., Nucleic Acids Res 37(database issue), 2009
PMID: 18927110
Informatic resources for identifying and annotating structural RNA motifs.
George AD, Tenenbaum SA., Mol Biotechnol 41(2), 2009
PMID: 18979204
RNA structure prediction from evolutionary patterns of nucleotide composition.
Smit S, Knight R, Heringa J., Nucleic Acids Res 37(5), 2009
PMID: 19129237
Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries.
Wyman SK, Parkin RK, Mitchell PS, Fritz BR, O'Briant K, Godwin AK, Urban N, Drescher CW, Knudsen BS, Tewari M., PLoS One 4(4), 2009
PMID: 19390579
Stochastic sampling of the RNA structural alignment space.
Harmanci AO, Sharma G, Mathews DH., Nucleic Acids Res 37(12), 2009
PMID: 19429694
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.
Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR., BMC Genomics 10(), 2009
PMID: 19531245
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR., Nat Biotechnol 27(7), 2009
PMID: 19561594
Sequence and structural analysis of the 5' noncoding region of hepatitis C virus in patients with chronic infection.
Araújo FM, Machado-Lima A, Durham AM, Teixeira R, Oliveira G., J Med Virol 81(7), 2009
PMID: 19475610
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.
Zhang H, Yang JH, Zheng YS, Zhang P, Chen X, Wu J, Xu L, Luo XQ, Ke ZY, Zhou H, Qu LH, Chen YQ., PLoS One 4(9), 2009
PMID: 19724645
Repertoire and evolution of miRNA genes in four divergent nematode species.
de Wit E, Linsen SE, Cuppen E, Berezikov E., Genome Res 19(11), 2009
PMID: 19755563
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation.
Georg J, Voss B, Scholz I, Mitschke J, Wilde A, Hess WR., Mol Syst Biol 5(), 2009
PMID: 19756044
On quantitative effects of RNA shape abstraction.
Nebel ME, Scheid A., Theory Biosci 128(4), 2009
PMID: 19756808
Computational methods in noncoding RNA research.
Machado-Lima A, del Portillo HA, Durham AM., J Math Biol 56(1-2), 2008
PMID: 17786447
Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition.
Zhao J, Malmberg RL, Cai L., J Math Biol 56(1-2), 2008
PMID: 17906862
Introduction to special issue on RNA.
Clote P., J Math Biol 56(1-2), 2008
PMID: 17938928
Asymptotics of RNA shapes.
Lorenz WA, Ponty Y, Clote P., J Comput Biol 15(1), 2008
PMID: 18257676
The birth and death of microRNA genes in Drosophila.
Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI., Nat Genet 40(3), 2008
PMID: 18278047
Strategies for measuring evolutionary conservation of RNA secondary structures.
Gruber AR, Bernhart SH, Hofacker IL, Washietl S., BMC Bioinformatics 9(), 2008
PMID: 18302738
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.
Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X., BMC Bioinformatics 9(), 2008
PMID: 18373878
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI.
Lamprecht AL, Margaria T, Steffen B, Sczyrba A, Hartmeier S, Giegerich R., BMC Bioinformatics 9 Suppl 4(), 2008
PMID: 18460174
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M., Stem Cells 26(10), 2008
PMID: 18583537
Naturally occurring mitochondrial DNA heteroplasmy in the MRL mouse.
Sachadyn P, Zhang XM, Clark LD, Naviaux RK, Heber-Katz E., Mitochondrion 8(5-6), 2008
PMID: 18761428
RNA STRAND: the RNA secondary structure and statistical analysis database.
Andronescu M, Bereg V, Hoos HH, Condon A., BMC Bioinformatics 9(), 2008
PMID: 18700982
RNase MRP and the RNA processing cascade in the eukaryotic ancestor.
Woodhams MD, Stadler PF, Penny D, Collins LJ., BMC Evol Biol 7 Suppl 1(), 2007
PMID: 17288571
RNA localization signals: deciphering the message with bioinformatics.
Hamilton RS, Davis I., Semin Cell Dev Biol 18(2), 2007
PMID: 17452113
RNA stem-loops: to be or not to be cleaved by RNAse III.
Ritchie W, Legendre M, Gautheret D., RNA 13(4), 2007
PMID: 17299129
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution.
Fattash I, Voss B, Reski R, Hess WR, Frank W., BMC Plant Biol 7(), 2007
PMID: 17359535
Bridging the gap in RNA structure prediction.
Shapiro BA, Yingling YG, Kasprzak W, Bindewald E., Curr Opin Struct Biol 17(2), 2007
PMID: 17383172
Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin a-chain.
Roday S, Saen-oon S, Schramm VL., Biochemistry 46(21), 2007
PMID: 17477546
RNAbor: a web server for RNA structural neighbors.
Freyhult E, Moulton V, Clote P., Nucleic Acids Res 35(web server issue), 2007
PMID: 17526527
RNA structure: bioinformatic analysis.
Jossinet F, Ludwig TE, Westhof E., Curr Opin Microbiol 10(3), 2007
PMID: 17548241
RNA Movies 2: sequential animation of RNA secondary structures.
Kaiser A, Krüger J, Evers DJ., Nucleic Acids Res 35(web server issue), 2007
PMID: 17567618
Boltzmann probability of RNA structural neighbors and riboswitch detection.
Freyhult E, Moulton V, Clote P., Bioinformatics 23(16), 2007
PMID: 17573364
A structure-based flexible search method for motifs in RNA.
Veksler-Lublinsky I, Ziv-Ukelson M, Barash D, Kedem K., J Comput Biol 14(7), 2007
PMID: 17803370
MicroRNA expression is required for pancreatic islet cell genesis in the mouse.
Lynn FC, Skewes-Cox P, Kosaka Y, McManus MT, Harfe BD, German MS., Diabetes 56(12), 2007
PMID: 17804764
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules.
Horesh Y, Doniger T, Michaeli S, Unger R., BMC Bioinformatics 8(), 2007
PMID: 17908318
Mammalian mirtron genes.
Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC., Mol Cell 28(2), 2007
PMID: 17964270
Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation.
Schöning JC, Streitner C, Page DR, Hennig S, Uchida K, Wolf E, Furuya M, Staiger D., Plant J 52(6), 2007
PMID: 17924945
Complete probabilistic analysis of RNA shapes.
Voss B, Giegerich R, Rehmsmeier M., BMC Biol 4(), 2006
PMID: 16480488
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis.
Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano H, Plasterk R, Cuppen E., Genome Res 16(10), 2006
PMID: 16954537
Structural analysis of aligned RNAs.
Voss B., Nucleic Acids Res 34(19), 2006
PMID: 17020924
XML schemas for common bioinformatic data types and their application in workflow systems.
Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R., BMC Bioinformatics 7(), 2006
PMID: 17087823

11 References

Daten bereitgestellt von Europe PubMed Central.

A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
A comprehensive comparison of comparative RNA structure prediction approaches.
Gardner PP, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15458580
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J., Bioinformatics 21(9), 2005
PMID: 15657094



Shapiro, Bioinformatics 4(3), 1988
Complete suboptimal folding of RNA and the stability of secondary structures.
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 16357029
PubMed | Europe PMC

Suchen in

Google Scholar