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
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Einrichtung
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.
Erscheinungsjahr
2006
Zeitschriftentitel
Bioinformatics
Band
22
Ausgabe
4
Seite(n)
500-503
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1600421
Zitieren
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.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
157 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL., F1000Res 8(), 2019
PMID: 31069053
Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL., F1000Res 8(), 2019
PMID: 31069053
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL., 2019
PMID: PPR76998
Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL., 2019
PMID: PPR76998
Prediction of binding property of RNA-binding proteins using multi-sized filters and multi-modal deep convolutional neural network.
Chung T, Kim D., PLoS One 14(4), 2019
PMID: 31026297
Chung T, Kim D., PLoS One 14(4), 2019
PMID: 31026297
Structural prediction of RNA switches using conditional base-pair probabilities.
Manzourolajdad A, Spouge JL., PLoS One 14(6), 2019
PMID: 31188853
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
Su C, Weir JD, Zhang F, Yan H, Wu T., BMC Bioinformatics 20(1), 2019
PMID: 31269893
Effective enhancement of resistance to Phytophthora infestans by overexpression of miR172a and b in Solanum lycopersicum.
Luan Y, Cui J, Li J, Jiang N, Liu P, Meng J., Planta 247(1), 2018
PMID: 28884358
Luan Y, Cui J, Li J, Jiang N, Liu P, Meng J., Planta 247(1), 2018
PMID: 28884358
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
Chen L, Zhang YH, Huang G, Pan X, Wang S, Huang T, Cai YD., Mol Genet Genomics 293(1), 2018
PMID: 28913654
ITS2 sequence-structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars.
Yan DH, Gao Q, Sun X, Song X, Li H., Genetica 146(2), 2018
PMID: 29397500
Yan DH, Gao Q, Sun X, Song X, Li H., Genetica 146(2), 2018
PMID: 29397500
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
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
Polishchuk M, Paz I, Yakhini Z, Mandel-Gutfreund Y., Nucleic Acids Res 46(w1), 2018
PMID: 29800452
Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks.
Pan X, Rijnbeek P, Yan J, Shen HB., BMC Genomics 19(1), 2018
PMID: 29970003
Pan X, Rijnbeek P, Yan J, Shen HB., BMC Genomics 19(1), 2018
PMID: 29970003
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Rogers E, Heitsch C., Wiley Interdiscip Rev RNA 7(3), 2016
PMID: 26971529
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.
Orenstein Y, Wang Y, Berger B., Bioinformatics 32(12), 2016
PMID: 27307637
Orenstein Y, Wang Y, Berger B., Bioinformatics 32(12), 2016
PMID: 27307637
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
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
Huang J, Li K, Gribskov M., PLoS One 11(10), 2016
PMID: 27755571
Role of RNA secondary structure in emergence of compartment specific hepatitis B virus immune escape variants.
Datta S, Chakravarty R., World J Virol 5(4), 2016
PMID: 27878103
Datta S, Chakravarty R., World J Virol 5(4), 2016
PMID: 27878103
New tools to analyze overlapping coding regions.
Bayegan AH, Garcia-Martin JA, Clote P., BMC Bioinformatics 17(1), 2016
PMID: 27964762
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
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
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
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
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
Manzourolajdad A, Arnold J., BMC Bioinformatics 16(), 2015
PMID: 25928324
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs.
Chiang K, Shu J, Zempleni J, Cui J., PLoS One 10(6), 2015
PMID: 26030752
Chiang K, Shu J, Zempleni J, Cui J., PLoS One 10(6), 2015
PMID: 26030752
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
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
Dupont DM, Larsen N, Jensen JK, Andreasen PA, Kjems J., Nucleic Acids Res 43(21), 2015
PMID: 26163061
PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features.
Pan X, Xiong K., Mol Biosyst 11(8), 2015
PMID: 26028480
Pan X, Xiong K., Mol Biosyst 11(8), 2015
PMID: 26028480
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
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
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
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
Fusy E, Clote P., J Math Biol 68(1-2), 2014
PMID: 23263300
Fighting against uncertainty: an essential issue in bioinformatics.
Hamada M., Brief Bioinform 15(5), 2014
PMID: 23803300
Hamada M., Brief Bioinform 15(5), 2014
PMID: 23803300
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
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
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
Ding Y, Lorenz WA, Dotu I, Senter E, Clote P., J Comput Biol 21(3), 2014
PMID: 24559086
A tricistronic heat shock operon is important for stress tolerance of Pseudomonas putida and conserved in many environmental bacteria.
Krajewski SS, Joswig M, Nagel M, Narberhaus F., Environ Microbiol 16(6), 2014
PMID: 24612349
Krajewski SS, Joswig M, Nagel M, Narberhaus F., Environ Microbiol 16(6), 2014
PMID: 24612349
Long non-coding RNAs: a novel endogenous source for the generation of Dicer-like 1-dependent small RNAs in Arabidopsis thaliana.
Ma X, Shao C, Jin Y, Wang H, Meng Y., RNA Biol 11(4), 2014
PMID: 24717238
Ma X, Shao C, Jin Y, Wang H, Meng Y., RNA Biol 11(4), 2014
PMID: 24717238
Transcriptional co-regulation of evolutionarily conserved microRNA/cone opsin gene pairs: implications for photoreceptor subtype specification.
Daido Y, Hamanishi S, Kusakabe TG., Dev Biol 392(1), 2014
PMID: 24797636
Daido Y, Hamanishi S, Kusakabe TG., Dev Biol 392(1), 2014
PMID: 24797636
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
Maghuly F, Ramkat RC, Laimer M., PLoS One 9(6), 2014
PMID: 24896088
Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.
Neshat A, Mentz A, Rückert C, Kalinowski J., J Biotechnol 190(), 2014
PMID: 24910972
Neshat A, Mentz A, Rückert C, Kalinowski J., J Biotechnol 190(), 2014
PMID: 24910972
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Xu Z, Almudevar A, Mathews DH., Nucleic Acids Res 40(4), 2012
PMID: 22139940
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.
Seetin MG, Mathews DH., Bioinformatics 28(6), 2012
PMID: 22285566
Seetin MG, Mathews DH., Bioinformatics 28(6), 2012
PMID: 22285566
A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).
Hamada M, Asai K., J Comput Biol 19(5), 2012
PMID: 22313125
Hamada M, Asai K., J Comput Biol 19(5), 2012
PMID: 22313125
Large-scale identification of mirtrons in Arabidopsis and rice.
Meng Y, Shao C., PLoS One 7(2), 2012
PMID: 22348048
Meng Y, Shao C., PLoS One 7(2), 2012
PMID: 22348048
Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants.
Meng Y, Shao C, Wang H, Chen M., RNA Biol 9(3), 2012
PMID: 22336711
Meng Y, Shao C, Wang H, Chen M., RNA Biol 9(3), 2012
PMID: 22336711
Maximum expected accuracy structural neighbors of an RNA secondary structure.
Clote P, Lou F, Lorenz WA., BMC Bioinformatics 13 Suppl 5(), 2012
PMID: 22537010
Clote P, Lou F, Lorenz WA., BMC Bioinformatics 13 Suppl 5(), 2012
PMID: 22537010
Transcriptional regulation of translocator protein (Tspo) via a SINE B2-mediated natural antisense transcript in MA-10 Leydig cells.
Fan J, Papadopoulos V., Biol Reprod 86(5), 2012
PMID: 22378763
Fan J, Papadopoulos V., Biol Reprod 86(5), 2012
PMID: 22378763
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
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
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
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
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
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
Huang J, Backofen R, Voß B., RNA 18(12), 2012
PMID: 23104999
Identification and profiling of miRNAs during herbivory reveals jasmonate-dependent and -independent patterns of accumulation in Nicotiana attenuata.
Bozorov TA, Baldwin IT, Kim SG., BMC Plant Biol 12(), 2012
PMID: 23134682
Bozorov TA, Baldwin IT, Kim SG., BMC Plant Biol 12(), 2012
PMID: 23134682
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
El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P., BMC Bioinformatics 13 Suppl 17(), 2012
PMID: 23281941
Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction.
Barash D, Churkin A., Brief Bioinform 12(2), 2011
PMID: 21422070
Barash D, Churkin A., Brief Bioinform 12(2), 2011
PMID: 21422070
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
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
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.
Xu Z, Mathews DH., Bioinformatics 27(5), 2011
PMID: 21193521
Xu Z, Mathews DH., Bioinformatics 27(5), 2011
PMID: 21193521
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
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
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
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
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
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
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
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
Reinkensmeier J, Schlüter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
Genomic organization and embryonic expression of miR-430 in medaka (Oryzias latipes): insights into the post-transcriptional gene regulation in early development.
Tani S, Kusakabe R, Naruse K, Sakamoto H, Inoue K., Gene 449(1-2), 2010
PMID: 19770025
Tani S, Kusakabe R, Naruse K, Sakamoto H, Inoue K., Gene 449(1-2), 2010
PMID: 19770025
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
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
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
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
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
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
Kim N, Izzo JA, Elmetwaly S, Gan HH, Schlick T., Nucleic Acids Res 38(13), 2010
PMID: 20448026
Phylogenetic utility of five genes for dipteran phylogeny: a test case in the Chironomidae leads to generic synonymies.
Ekrem T, Willassen E, Stur E., Mol Phylogenet Evol 57(2), 2010
PMID: 20601017
Ekrem T, Willassen E, Stur E., Mol Phylogenet Evol 57(2), 2010
PMID: 20601017
NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome.
Teune JH, Steger G., J Nucleic Acids 2010(), 2010
PMID: 20871826
Teune JH, Steger G., J Nucleic Acids 2010(), 2010
PMID: 20871826
A complexity-based method to compare RNA secondary structures and its application.
Zhang S, Wang T., J Biomol Struct Dyn 28(2), 2010
PMID: 20645657
Zhang S, Wang T., J Biomol Struct Dyn 28(2), 2010
PMID: 20645657
Computational approaches for RNA energy parameter estimation.
Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP., RNA 16(12), 2010
PMID: 20940338
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Zhao J, Malmberg RL, Cai L., J Math Biol 56(1-2), 2008
PMID: 17906862
Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method.
Ponty Y., J Math Biol 56(1-2), 2008
PMID: 17932676
Ponty Y., J Math Biol 56(1-2), 2008
PMID: 17932676
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
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
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
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
Lamprecht AL, Margaria T, Steffen B, Sczyrba A, Hartmeier S, Giegerich R., BMC Bioinformatics 9 Suppl 4(), 2008
PMID: 18460174
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.
Churkin A, Barash D., BMC Bioinformatics 9(), 2008
PMID: 18445289
Churkin A, Barash D., BMC Bioinformatics 9(), 2008
PMID: 18445289
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
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
Reconstruction of natural RNA sequences from RNA shape, thermodynamic stability, mutational robustness, and linguistic complexity by evolutionary computation.
Dromi N, Avihoo A, Barash D., J Biomol Struct Dyn 26(1), 2008
PMID: 18533734
Dromi N, Avihoo A, Barash D., J Biomol Struct Dyn 26(1), 2008
PMID: 18533734
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
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
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
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
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
Ritchie W, Legendre M, Gautheret D., RNA 13(4), 2007
PMID: 17299129
A computational proposal for designing structured RNA pools for in vitro selection of RNAs.
Kim N, Gan HH, Schlick T., RNA 13(4), 2007
PMID: 17322501
Kim N, Gan HH, Schlick T., RNA 13(4), 2007
PMID: 17322501
Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model.
Waldispühl J, Clote P., J Comput Biol 14(2), 2007
PMID: 17456015
Waldispühl J, Clote P., J Comput Biol 14(2), 2007
PMID: 17456015
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
Fattash I, Voss B, Reski R, Hess WR, Frank W., BMC Plant Biol 7(), 2007
PMID: 17359535
Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea.
Burbano HA, Andrade E., Gene 396(1), 2007
PMID: 17433860
Burbano HA, Andrade E., Gene 396(1), 2007
PMID: 17433860
Bridging the gap in RNA structure prediction.
Shapiro BA, Yingling YG, Kasprzak W, Bindewald E., Curr Opin Struct Biol 17(2), 2007
PMID: 17383172
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
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
Freyhult E, Moulton V, Clote P., Nucleic Acids Res 35(web server issue), 2007
PMID: 17526527
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment.
Xu X, Ji Y, Stormo GD., Bioinformatics 23(15), 2007
PMID: 17537756
Xu X, Ji Y, Stormo GD., Bioinformatics 23(15), 2007
PMID: 17537756
RNA structure: bioinformatic analysis.
Jossinet F, Ludwig TE, Westhof E., Curr Opin Microbiol 10(3), 2007
PMID: 17548241
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
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
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
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
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
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
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
Schöning JC, Streitner C, Page DR, Hennig S, Uchida K, Wolf E, Furuya M, Staiger D., Plant J 52(6), 2007
PMID: 17924945
Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea.
Brenneis M, Hering O, Lange C, Soppa J., PLoS Genet 3(12), 2007
PMID: 18159946
Brenneis M, Hering O, Lange C, Soppa J., PLoS Genet 3(12), 2007
PMID: 18159946
Complete probabilistic analysis of RNA shapes.
Voss B, Giegerich R, Rehmsmeier M., BMC Biol 4(), 2006
PMID: 16480488
Voss B, Giegerich R, Rehmsmeier M., BMC Biol 4(), 2006
PMID: 16480488
Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm.
Shapiro BA, Kasprzak W, Grunewald C, Aman J., J Mol Graph Model 25(4), 2006
PMID: 16725358
Shapiro BA, Kasprzak W, Grunewald C, Aman J., J Mol Graph Model 25(4), 2006
PMID: 16725358
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
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
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
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
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
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
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
Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J., Bioinformatics 21(9), 2005
PMID: 15657094
AUTHOR UNKNOWN, MONATSHEFTE F CHEMIE 125(), 1994
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
Mathews DH, Turner DH., J. Mol. Biol. 317(2), 2002
PMID: 11902836
Mathews DH, Turner DH., J. Mol. Biol. 317(2), 2002
PMID: 11902836
The equilibrium partition function and base pair binding probabilities for RNA secondary structure.
McCaskill JS., Biopolymers 29(6-7), 1990
PMID: 1695107
McCaskill JS., Biopolymers 29(6-7), 1990
PMID: 1695107
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction.
Reeder J, Giegerich R., Bioinformatics 21(17), 2005
PMID: 16020472
Reeder J, Giegerich R., Bioinformatics 21(17), 2005
PMID: 16020472
AUTHOR UNKNOWN, SIAM J APPL MATH 45(), 1985
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
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 16357029
PubMed | Europe PMC
Suchen in
Google Scholar