Works matching DE "RNA folding"

Results: 71

The Paradox of Dual Roles in the RNA World: Resolving the Conflict Between Stable Folding and Templating Ability.

Published in:

2013

By:

Ivica, Nikola;
Obermayer, Benedikt;
Campbell, Gregory;
Rajamani, Sudha;
Gerland, Ulrich;
Chen, Irene

Publication type:

Letter

Modeling key pathological features of frontotemporal dementia with C9ORF72 repeat expansion in iPSC-derived human neurons.

Published in:

Acta Neuropathologica, 2013, v. 126, n. 3, p. 385, doi. 10.1007/s00401-013-1149-y

By:

Almeida, Sandra;
Gascon, Eduardo;
Tran, Hélène;
Chou, Hsin;
Gendron, Tania;
DeGroot, Steven;
Tapper, Andrew;
Sellier, Chantal;
Charlet-Berguerand, Nicolas;
Karydas, Anna;
Seeley, William;
Boxer, Adam;
Petrucelli, Leonard;
Miller, Bruce;
Gao, Fen-Biao

Publication type:

Article

The structure of the box C/D enzyme reveals regulation of RNA methylation.

Published in:

Nature, 2013, v. 502, n. 7472, p. 519, doi. 10.1038/nature12581

By:

Lapinaite, Audrone;
Simon, Bernd;
Skjaerven, Lars;
Rakwalska-Bange, Magdalena;
Gabel, Frank;
Carlomagno, Teresa

Publication type:

Article

rClone Red facilitates bacterial gene expression research by undergraduates in the teaching laboratory.

Published in:

Synthetic Biology (23977000), 2018, v. 3, n. 1, p. 1, doi. 10.1093/synbio/ysy013

By:

Campbell, A Malcolm;
Eckdahl, Todd T

Publication type:

Article

Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.

Published in:

Genes, 2018, v. 9, n. 8, p. 371, doi. 10.3390/genes9080371

By:

Jain, Swati;
Bayrak, Cigdem S.;
Schlick, Tamar;
Petingi, Louis

Publication type:

Article

Predicting Model and Algorithm in RNA Folding Structure Including Pseudoknots.

Published in:

International Journal of Pattern Recognition & Artificial Intelligence, 2018, v. 32, n. 10, p. N.PAG, doi. 10.1142/S0218001418510059

By:

Liu, Zhendong;
Zhu, Daming;
Dai, Qionghai

Publication type:

Article

GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops.

Published in:

BMC Research Notes, 2012, v. 5, n. 1, p. 1, doi. 10.1186/1756-0500-5-341

By:

Shel Swenson, M.;
Anderson, Joshua;
Ash, Andrew;
Gaurav, Prashant;
Sükösd, Zsuzsanna;
Bader, David A.;
Harvey, Stephen C.;
Heitsch, Christine E.

Publication type:

Article

Characteristics of equipartition for RNA structure.

Published in:

2014

By:

Hengwu Li;
Daming Zhu;
Caiming Zhang;
Huijian Han;
Crandall, Keith A.

Publication type:

Conference Paper/Materials

Unzippers, Resolvers and Sensors: A Structural and Functional Biochemistry Tale of RNA Helicases.

Published in:

International Journal of Molecular Sciences, 2015, v. 16, n. 2, p. 2269, doi. 10.3390/ijms16022269

By:

Leitão, Ana Lúcia;
Costa, Marina C.;
Enguita, Francisco J.

Publication type:

Article

RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN.

Published in:

Journal of Bioinformatics & Computational Biology, 2013, v. 11, n. 2, p. 1, doi. 10.1142/S0219720013500017

By:

GARCIA-MARTIN, JUAN ANTONIO;
CLOTE, PETER;
DOTU, IVAN

Publication type:

Article

PRACTICALITY AND TIME COMPLEXITY OF A SPARSIFIED RNA FOLDING ALGORITHM.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 2, p. 1241007-1, doi. 10.1142/S0219720012410077

By:

DIMITRIEVA, SLAVICA;
BUCHER, PHILIPP

Publication type:

Article

Role of a Conserved J8/7 X P4 Base-Triple in the Tetrahymena Ribozyme1.

Published in:

Journal of Biochemistry, 2002, v. 132, n. 5, p. 713, doi. 10.1093/oxfordjournals.jbchem.a003278

By:

Ohki, Yasushi;
Ikawa, Yoshiya;
Shiraishi, Hideaki;
Inoue, Tan

Publication type:

Article

Pseudoknots in RNA folding landscapes.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 187, doi. 10.1093/bioinformatics/btv572

By:

Kucharík, Marcel;
Hofacker, Ivo L.;
Stadler, Peter F.;
Jing Qin

Publication type:

Article

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

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.

Published in:

Bioinformatics, 2014, v. 30, n. 14, p. 2009

By:

Kucharík, Marcel;
Hofacker, Ivo L.;
Stadler, Peter F.;
Qin, Jing

Publication type:

Article

eSBMTools 1.0: enhanced native structure-based modeling tools.

Published in:

Bioinformatics, 2013, v. 29, n. 21, p. 2795, doi. 10.1093/bioinformatics/btt478

By:

Lutz, Benjamin;
Sinner, Claude;
Heuermann, Geertje;
Verma, Abhinav;
Schug, Alexander

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

Folding RNA/DNA hybrid duplexes.

Published in:

Bioinformatics, 2012, v. 28, n. 19, p. 2530, doi. 10.1093/bioinformatics/bts466

By:

Lorenz, Ronny;
Hofacker, Ivo L.;
Bernhart, Stephan H.

Publication type:

Article

Approximating the set of local minima in partial RNA folding landscapes.

Published in:

Bioinformatics, 2012, v. 28, n. 4, p. 523, doi. 10.1093/bioinformatics/btr715

By:

Sahoo, S.;
Albrecht, A.A.

Publication type:

Article

抑制RANKL诱导破骨细胞分化的DNA适配子的筛选.

Published in:

Progress in Modern Biomedicine, 2017, v. 17, n. 17, p. 3220, doi. 10.13241/j.cnki.pmb.2017.17.005

By:

吴太林;
沙鑫;
李锋;
张波波;
马文瑞;
陶惠人

Publication type:

Article

Nanopore electric snapshots of an RNA tertiary folding pathway.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01588-z

By:

Ruicheng Shi;
Xiao Du;
Burcke, Andrew J.;
Jing Wang;
Xinyue Zhang;
Kai Tian;
Li-Qun Gu;
Dong Zhang;
Chenhan Zhao;
Shi-Jie Chen

Publication type:

Article

Formation of RNA spatial structures.

Published in:

Molecular Biology, 2012, v. 46, n. 1, p. 34, doi. 10.1134/S0026893312010104

By:

Leonova, E.;
Baranov, M.;
Galzitskaya, O.

Publication type:

Article

A U⋅U Pair-to-U⋅C Pair Mutation-Induced RNA Native Structure Destabilisation and Stretching-Force-Induced RNA Misfolding.

Published in:

ChemPlusChem, 2015, v. 80, n. 8, p. 1267, doi. 10.1002/cplu.201500144

By:

Zhong, Zhensheng;
Soh, Lai Huat;
Lim, Ming Hui;
Chen, Gang

Publication type:

Article

Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution.

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0180827

By:

Szostak, Natalia;
Synak, Jaroslaw;
Borowski, Marcin;
Wasik, Szymon;
Blazewicz, Jacek

Publication type:

Article

Tiling Nussinov's RNA folding loop nest with a space-time approach.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2785-6

By:

Palkowski, Marek;
Bielecki, Wlodzimierz

Publication type:

Article

PSRna: Prediction of small RNA secondary structures based on reverse complementary folding method.

Published in:

Journal of Bioinformatics & Computational Biology, 2016, v. 14, n. 4, p. -1, doi. 10.1142/S0219720016430010

By:

Li, Jin;
Xu, Chengzhen;
Wang, Lei;
Liang, Hong;
Feng, Weixing;
Cai, Zhongxi;
Wang, Ying;
Cong, Wang;
Liu, Yunlong

Publication type:

Article

INTERACTIONS BETWEEN EVOLUTIONARY PROCESSES AT HIGH MUTATION RATES.

Published in:

Evolution, 2012, v. 66, n. 7, p. 2303, doi. 10.1111/j.1558-5646.2012.01596.x

By:

Keller, Thomas E.;
Wilke, Claus O.;
Bull, James J.

Publication type:

Article

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

Published in:

PLoS ONE, 2018, v. 13, n. 4, p. 1, doi. 10.1371/journal.pone.0194583

By:

Jabbari, Hosna;
Wark, Ian;
Montemagno, Carlo

Publication type:

Article

Folding of 16S rRNA in a Signal-Producing Structure for the Detection of Bacteria.

Published in:

Angewandte Chemie International Edition, 2013, v. 52, n. 40, p. 10586, doi. 10.1002/anie.201303919

By:

Gerasimova, Yulia V.;
Kolpashchikov, Dmitry M.

Publication type:

Article

Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET.

Published in:

Biochemical Society Transactions, 2015, v. 43, n. 2, p. 172, doi. 10.1042/BST20140268

By:

Bisaria, Namita;
Herschlag, Daniel

Publication type:

Article

An RNA folding motif: GNRA tetraloop–receptor interactions.

Published in:

Quarterly Reviews of Biophysics, 2013, v. 46, n. 3, p. 223, doi. 10.1017/S0033583513000048

By:

Fiore, Julie L.;
Nesbitt, David J.

Publication type:

Article

Rendering RNA in 3D.

Published in:

Nature Methods, 2012, v. 9, n. 6, p. 552, doi. 10.1038/nmeth.2045

By:

Behrouzi, Reza;
Woodson, Sarah A

Publication type:

Article

Analysis of the use of codon pairs in the HE gene of the ISA virus shows a correlation between bias in HPR codon-pair use and mortality rates caused by the virus.

Published in:

Virology Journal, 2013, v. 10, n. 1, p. 1, doi. 10.1186/1743-422X-10-180

By:

Tello, Mario;
Saavedra, José Miguel;
Spencer, Eugenio

Publication type:

Article

An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding.

Published in:

Algorithms for Molecular Biology, 2016, p. 1, doi. 10.1186/s13015-016-0081-9

By:

Frid, Yelena;
Gusfield, Dan

Publication type:

Article

Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.

Published in:

Algorithms for Molecular Biology, 2016, v. 11, p. 1, doi. 10.1186/s13015-016-0071-y

By:

Will, Sebastian;
Jabbari, Hosna

Publication type:

Article

RNA folding with hard and soft constraints.

Published in:

Algorithms for Molecular Biology, 2016, v. 11, p. 1, doi. 10.1186/s13015-016-0070-z

By:

Lorenz, Ronny;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

Faster algorithms for RNA-folding using the Four-Russians method.

Published in:

Algorithms for Molecular Biology, 2014, v. 9, n. 1, p. 1, doi. 10.1186/1748-7188-9-5

By:

Balaji Venkatachalam;
Gusfield, Dan;
Frid, Yelena

Publication type:

Article

Efficient edit distance with duplications and contractions.

Published in:

Algorithms for Molecular Biology, 2013, v. 8, n. 1, p. 2, doi. 10.1186/1748-7188-8-27

By:

Pinhas, Tamar;
Zakov, Shay;
Tsur, Dekel;
Ziv-Ukelson, Michal

Publication type:

Article

Asymptotic structural properties of quasi-random saturated structures of RNA.

Published in:

Algorithms for Molecular Biology, 2013, v. 8, n. 1, p. 2, doi. 10.1186/1748-7188-8-24

By:

Clote, Peter;
Kranakis, Evangelos;
Krizanc, Danny

Publication type:

Article

Efficient procedures for the numerical simulation of mid-size RNA kinetics.

Published in:

Algorithms for Molecular Biology, 2012, v. 7, n. 1, p. 24, doi. 10.1186/1748-7188-7-24

By:

Aviram, Iddo;
Veltman, Ilia;
Churkin, Alexander;
Barash, Danny

Publication type:

Article

Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

Published in:

BMC Bioinformatics, 2018, v. 19, p. 1, doi. 10.1186/s12859-018-2008-6

By:

Palkowski, Marek;
Bielecki, Wlodzimierz

Publication type:

Article

Cache and energy efficient algorithms for Nussinov's RNA Folding.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1917-0

By:

Chunchun Zhao;
Sahni, Sartaj

Publication type:

Article

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1707-8

By:

Palkowski, Marek;
Bielecki, Wlodzimierz

Publication type:

Article

Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus.

Published in:

PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0148281

By:

Lenartowicz, Elzbieta;
Kesy, Julita;
Ruszkowska, Agnieszka;
Soszynska-Jozwiak, Marta;
Michalak, Paula;
Moss, Walter N.;
Turner, Douglas H.;
Kierzek, Ryszard;
Kierzek, Elzbieta

Publication type:

Article

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

Published in:

PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0136444

By:

Boudard, Mélanie;
Bernauer, Julie;
Barth, Dominique;
Cohen, Johanne;
Denise, Alain

Publication type:

Article

An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.

Published in:

PLoS ONE, 2015, v. 10, n. 7, p. 1, doi. 10.1371/journal.pone.0134262

By:

Drory Retwitzer, Matan;
Kifer, Ilona;
Sengupta, Supratim;
Yakhini, Zohar;
Barash, Danny

Publication type:

Article

On the Normalization of the Minimum Free Energy of RNAs by Sequence Length.

Published in:

PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0113380

By:

Trotta, Edoardo

Publication type:

Article

Viral RNAs Are Unusually Compact.

Published in:

PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0105875

By:

Gopal, Ajaykumar;
Egecioglu, Defne E.;
Yoffe, Aron M.;
Ben-Shaul, Avinoam;
Rao, Ayala L. N.;
Knobler, Charles M.;
Gelbart, William M.

Publication type:

Article

Helix Capping in RNA Structure.

Published in:

PLoS ONE, 2014, v. 9, n. 4, p. 1, doi. 10.1371/journal.pone.0093664

By:

Lee, Jung C.;
Gutell, Robin R.

Publication type:

Article

Predicting Helical Topologies in RNA Junctions as Tree Graphs.

Published in:

PLoS ONE, 2013, v. 8, n. 8, p. 1, doi. 10.1371/journal.pone.0071947

By:

Laing, Christian;
Jung, Segun;
Kim, Namhee;
Elmetwaly, Shereef;
Zahran, Mai;
Schlick, Tamar

Publication type:

Article