Works matching DE "MOLECULAR structure of RNA"

Results: 316

Micro-terminator: 'Hasta la vista, lncRNA!'.

Published in:

Nature Structural & Molecular Biology, 2015, v. 22, n. 4, p. 279, doi. 10.1038/nsmb.3001

By:

Diederichs, Sven

Publication type:

Article

Toll-like receptor 8 senses degradation products of single-stranded RNA.

Published in:

Nature Structural & Molecular Biology, 2015, v. 22, n. 2, p. 109, doi. 10.1038/nsmb.2943

By:

Tanji, Hiromi;
Ohto, Umeharu;
Shibata, Takuma;
Taoka, Masato;
Yamauchi, Yoshio;
Isobe, Toshiaki;
Miyake, Kensuke;
Shimizu, Toshiyuki

Publication type:

Article

Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 8, p. 721, doi. 10.1038/nsmb.2859

By:

Yamamoto, Hiroshi;
Unbehaun, Anett;
Loerke, Justus;
Behrmann, Elmar;
Collier, Marianne;
Bürger, Jörg;
Mielke, Thorsten;
Spahn, Christian M T

Publication type:

Article

Structural basis for RNA recognition by a dimeric PPR-protein complex.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 12, p. 1377, doi. 10.1038/nsmb.2710

By:

Ke, Jiyuan;
Chen, Run-Ze;
Ban, Ting;
Zhou, X Edward;
Gu, Xin;
Tan, M H Eileen;
Chen, Chen;
Kang, Yanyong;
Brunzelle, Joseph S;
Zhu, Jian-Kang;
Melcher, Karsten;
Xu, H Eric

Publication type:

Article

Structural requirements for RNA degradation by HIV-1 reverse transcriptase.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 12, p. 1341, doi. 10.1038/nsmb.2725

By:

Das, Kalyan;
Sarafianos, Stefan G;
Arnold, Eddy

Publication type:

Article

Reply to 'Structural requirements for RNA degradation by HIV-1 reverse transcriptase'.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 12, p. 1342, doi. 10.1038/nsmb.2726

By:

Lapkouski, Mikalai;
Tian, Lan;
Miller, Jennifer T;
Le Grice, Stuart F J;
Yang, Wei

Publication type:

Article

Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 2, p. 230, doi. 10.1038/nsmb.2485

By:

Lapkouski, Mikalai;
Tian, Lan;
Miller, Jennifer T;
Le Grice, Stuart F J;
Yang, Wei

Publication type:

Article

The molecular architecture of human Dicer.

Published in:

Nature Structural & Molecular Biology, 2012, v. 19, n. 4, p. 436, doi. 10.1038/nsmb.2268

By:

Lau, Pick-Wei;
Guiley, Keelan Z;
De, Nabanita;
Potter, Clinton S;
Carragher, Bridget;
MacRae, Ian J

Publication type:

Article

A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair.

Published in:

Angewandte Chemie, 2015, v. 127, n. 34, p. 9991, doi. 10.1002/ange.201504731

By:

Hernandez, Armando R.;
Shao, Yaming;
Hoshika, Shuichi;
Yang, Zunyi;
Shelke, Sandip A.;
Herrou, Julien;
Kim, Hyo ‐ Joong;
Kim, Myong ‐ Jung;
Piccirilli, Joseph A.;
Benner, Steven A.

Publication type:

Article

The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites.

Published in:

Journal of Biological Physics, 2013, v. 39, n. 2, p. 163, doi. 10.1007/s10867-013-9312-1

By:

Harvey, Stephen;
Zeng, Yingying;
Heitsch, Christine

Publication type:

Article

Highly conserved nucleotide motifs present in the 5′UTR of the heme-receptor gene shmR are required for HmuP-dependent expression of shmR in Ensifer meliloti.

Published in:

BioMetals, 2019, v. 32, n. 2, p. 273, doi. 10.1007/s10534-019-00184-6

By:

Amarelle, Vanesa;
Koziol, Uriel;
Fabiano, Elena

Publication type:

Article

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra “Soils” of the Puna de Atacama Volcanic Zone.

Published in:

Microbial Ecology, 2018, v. 76, n. 2, p. 340, doi. 10.1007/s00248-017-1129-1

By:

Solon, Adam J.;
Vimercati, Lara;
Darcy, J. L.;
Arán, Pablo;
Porazinska, Dorota;
Dorador, C.;
Farías, M. E.;
Schmidt, S. K.

Publication type:

Article

Uneven Distribution of Halobacillus trueperi Species in Arid Natural Saline Systems of Southern Tunisian Sahara.

Published in:

Microbial Ecology, 2013, v. 66, n. 4, p. 831, doi. 10.1007/s00248-013-0274-4

By:

Guesmi, Amel;
Ettoumi, Besma;
Hidri, Darine;
Essanaa, Jihene;
Cherif, Hanene;
Mapelli, Francesca;
Marasco, Ramona;
Rolli, Eleonora;
Boudabous, Abdellatif;
Cherif, Ameur

Publication type:

Article

RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup.

Published in:

Journal of Mathematical Biology, 2016, v. 72, n. 3, p. 527, doi. 10.1007/s00285-015-0894-z

By:

Jin, Emma;
Nebel, Markus

Publication type:

Article

Combinatorics of locally optimal RNA secondary structures.

Published in:

Journal of Mathematical Biology, 2014, v. 68, n. 1/2, p. 341, doi. 10.1007/s00285-012-0631-9

By:

Fusy, Éric;
Clote, Peter

Publication type:

Article

Molecular analysis of different classes of RNA molecules from formalin-fixed paraffin-embedded autoptic tissues: a pilot study.

Published in:

International Journal of Legal Medicine, 2015, v. 129, n. 1, p. 11, doi. 10.1007/s00414-014-1066-1

By:

Muciaccia, Barbara;
Vico, Carmen;
Aromatario, Mariarosaria;
Fazi, Francesco;
Cecchi, Rossana

Publication type:

Article

Phylogenetic utility of the trnH- psbA IGR and stem-loop diversity of the 3′ UTR in Cactaceae (Caryophyllales).

Published in:

Plant Systematics & Evolution, 2017, v. 303, n. 3, p. 299, doi. 10.1007/s00606-016-1372-9

By:

Hernández-Ledesma, Patricia;
Bárcenas, Rolando

Publication type:

Article

Classification of RNA structure change by ‘gazing’ at experimental data.

Published in:

Bioinformatics, 2017, v. 33, n. 11, p. 1647, doi. 10.1093/bioinformatics/btx041

By:

Woods, Chanin Tolson;
Laederach, Alain

Publication type:

Article

A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 988, doi. 10.1093/bioinformatics/btw728

By:

Umu, Sinan Uğur;
Gardner, Paul P.

Publication type:

Article

SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 441, doi. 10.1093/bioinformatics/btw627

By:

Choudhary, Krishna;
Luyao Ruan;
Fei Deng;
Shih, Nathan;
Aviran, Sharon

Publication type:

Article

FoldAtlas: a repository for genome-wide RNA structure probing data.

Published in:

Bioinformatics, 2017, v. 33, n. 2, p. 306, doi. 10.1093/bioinformatics/btw611

By:

Norris, Matthew;
Chun Kit Kwok;
Cheema, Jitender;
Hartley, Matthew;
Morris, Richard J.;
Aviran, Sharon;
Yiliang Ding

Publication type:

Article

ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. 2626, doi. 10.1093/bioinformatics/btw175

By:

Sahoo, Sudhakar;
Świtnicki, Michał P.;
Pedersen, Jakob Skou

Publication type:

Article

AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1033, doi. 10.1093/bioinformatics/btv682

By:

DiChiacchio, Laura;
Sloma, Michael F.;
Mathews, David H.

Publication type:

Article

CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules.

Published in:

Bioinformatics, 2016, v. 32, n. 5, p. 697, doi. 10.1093/bioinformatics/btv635

By:

Cestarelli, Valerio;
Fiscon, Giulia;
Felici, Giovanni;
Bertolazzi, Paola;
Weitschek, Emanuel

Publication type:

Article

catRAPID signature: identification of ribonucleoproteins and RNA-binding regions.

Published in:

Bioinformatics, 2016, v. 32, n. 5, p. 773, doi. 10.1093/bioinformatics/btv629

By:

Livi, Carmen Maria;
Klus, Petr;
Delli Ponti, Riccardo;
Gaetano Tartaglia, Gian

Publication type:

Article

RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.

Published in:

Bioinformatics, 2016, v. 32, n. 3, p. 459, doi. 10.1093/bioinformatics/btv571

By:

Incarnato, Danny;
Neri, Francesco;
Anselmi, Francesca;
Oliviero, Salvatore

Publication type:

Article

Pairwise RNA secondary structure alignment with conserved stem pattern.

Published in:

Bioinformatics, 2015, v. 31, n. 24, p. 3914, doi. 10.1093/bioinformatics/btv471

By:

Jimmy Ka Ho Chiu;
Yi-Ping Phoebe Chen

Publication type:

Article

BackCLIP: a tool to identify common background presence in PAR-CLIP datasets.

Published in:

Bioinformatics, 2015, v. 31, n. 22, p. 3703, doi. 10.1093/bioinformatics/btv442

By:

Reyes-Herrera, P. H.;
Speck-Hernandez, C. A.;
Sierra, C. A.;
Herrera, S.

Publication type:

Article

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation.

Published in:

Bioinformatics, 2015, v. 31, n. 22, p. 3676, doi. 10.1093/bioinformatics/btv423

By:

Honglei Liu;
Zheng Wei;
Dominguez, Antonia;
Yanda Li;
Xiaowo Wang;
Qi, Lei S.

Publication type:

Article

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3377, doi. 10.1093/bioinformatics/btv372

By:

Kerpedjiev, Peter;
Hammer, Stefan;
Hofacker, Ivo L.

Publication type:

Article

Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.

Published in:

Bioinformatics, 2015, v. 31, n. 17, p. 2808, doi. 10.1093/bioinformatics/btv282

By:

Seungmyung Lee;
Hanjoo Kim;
Siqi Tian;
Taehoon Lee;
Sungroh Yoon;
Rhiju Das

Publication type:

Article

iFoldRNA v2: folding RNA with constraints.

Published in:

Bioinformatics, 2015, v. 31, n. 17, p. 2891, doi. 10.1093/bioinformatics/btv221

By:

Krokhotin, Andrey;
Houlihan, Kevin;
Dokholyan, Nikolay V.

Publication type:

Article

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

Published in:

2015

By:

Yin Tang;
Bouvier, Emil;
Chun Kit Kwok;
Yiliang Ding;
Nekrutenko, Anton;
Bevilacqua, Philip C.;
Assmann, Sarah M.

Publication type:

Product Review

The RNA shapes studio.

Published in:

Bioinformatics, 2015, v. 31, n. 3, p. 423, doi. 10.1093/bioinformatics/btu649

By:

Janssen, Stefan;
Giegerich, Robert

Publication type:

Article

Memory-efficient RNA energy landscape exploration.

Published in:

Bioinformatics, 2014, v. 30, n. 18, p. 2584, doi. 10.1093/bioinformatics/btu337

By:

Mann, Martin;
Kucharík, Marcel;
Flamm, Christoph;
Wolfinger, Michael T.

Publication type:

Article

Evolutionary solution for the RNA design problem.

Published in:

Bioinformatics, 2014, v. 30, n. 9, p. 1250, doi. 10.1093/bioinformatics/btu001

By:

Esmaili-Taheri, Ali;
Ganjtabesh, Mohammad;
Mohammad-Noori, Morteza

Publication type:

Article

Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.

Published in:

Bioinformatics, 2014, v. 30, n. 8, p. 1049, doi. 10.1093/bioinformatics/btt757

By:

Hu, Xihao;
Wong, Thomas K. F.;
Lu, Zhi John;
Chan, Ting Fung;
Lau, Terrence Chi Kong;
Yiu, Siu Ming;
Yip, Kevin Y.

Publication type:

Article

Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs.

Published in:

Bioinformatics, 2014, v. 30, n. 3, p. 343, doi. 10.1093/bioinformatics/btt695

By:

Day, Luke;
Abdelhadi Ep Souki, Ouala;
Albrecht, Andreas A.;
Steinhöfel, Kathleen

Publication type:

Article

RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.

Published in:

Bioinformatics, 2013, v. 29, n. 23, p. 3102, doi. 10.1093/bioinformatics/btt536

By:

Schnattinger, Thomas;
Schöning, Uwe;
Marchfelder, Anita;
Kestler, Hans A.

Publication type:

Article

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.

Published in:

Bioinformatics, 2013, v. 29, n. 22, p. 2938, doi. 10.1093/bioinformatics/btt494

By:

Weinbrand, Lina;
Avihoo, Assaf;
Barash, Danny

Publication type:

Article

Infernal 1.1: 100-fold faster RNA homology searches.

Published in:

Bioinformatics, 2013, v. 29, n. 22, p. 2933, doi. 10.1093/bioinformatics/btt509

By:

Nawrocki, Eric P.;
Eddy, Sean R.

Publication type:

Article

RNA secondary structure diagrams for very large molecules: RNAfdl.

Published in:

Bioinformatics, 2013, v. 29, n. 22, p. 2941, doi. 10.1093/bioinformatics/btt496

By:

Hecker, Nikolai;
Wiegels, Tim;
Torda, Andrew E.

Publication type:

Article

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.

Published in:

Bioinformatics, 2013, v. 29, n. 9, p. 1112, doi. 10.1093/bioinformatics/btt096

By:

Kemena, Carsten;
Bussotti, Giovanni;
Capriotti, Emidio;
Marti-Renom, Marc A.;
Notredame, Cedric

Publication type:

Article

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.

Published in:

Bioinformatics, 2013, v. 29, n. 6, p. 704, doi. 10.1093/bioinformatics/btt050

By:

Anderson, James W. J.;
Haas, Pierre A.;
Mathieson, Leigh-Anne;
Volynkin, Vladimir;
Lyngsø, Rune;
Tataru, Paula;
Hein, Jotun

Publication type:

Article

Fast alignment and comparison of RNA structures.

Published in:

Bioinformatics, 2013, v. 29, n. 5, p. 588, doi. 10.1093/bioinformatics/btt006

By:

Wiegels, Tim;
Bienert, Stefan;
Torda, Andrew E.

Publication type:

Article

StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction.

Published in:

Bioinformatics, 2013, v. 29, n. 5, p. 654, doi. 10.1093/bioinformatics/btt025

By:

Arunapuram, Preeti;
Edvardsson, Ingolfur;
Golden, Michael;
Anderson, James W. J.;
Novák, Ádám;
Sükösd, Zsuzsanna;
Hein, Jotun

Publication type:

Article

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.

Published in:

Bioinformatics, 2012, v. 28, n. 24, p. 3218, doi. 10.1093/bioinformatics/bts612

By:

Sato, Kengo;
Kato, Yuki;
Akutsu, Tatsuya;
Asai, Kiyoshi;
Sakakibara, Yasubumi

Publication type:

Article

Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.

Published in:

Bioinformatics, 2012, v. 28, n. 17, p. 2242, doi. 10.1093/bioinformatics/bts369

By:

Doose, Gero;
Metzler, Dirk

Publication type:

Article

Efficient RNA pairwise structure comparison by SETTER method.

Published in:

Bioinformatics, 2012, v. 28, n. 14, p. 1858, doi. 10.1093/bioinformatics/bts301

By:

Hoksza, David;
Svozil, Daniel

Publication type:

Article

GraphClust: alignment-free structural clustering of local RNA secondary structures.

Published in:

Bioinformatics, 2012, v. 28, n. 12, p. i224, doi. 10.1093/bioinformatics/bts224

By:

Heyne, Steffen;
Costa, Fabrizio;
Rose, Dominic;
Backofen, Rolf

Publication type:

Article