Works matching IS 03051048 AND DT 2015 AND VI 43 AND IP 21

Results: 49

Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10560, doi. 10.1093/nar/gkv1071

By:

Hui Zhou;
Vonk, Brenda;
Roubos, Johannes A.;
Bovenberg, Roel A. L.;
Voigt, Christopher A.

Publication type:

Article

A SnoRNA-derived piRNA interacts with human interleukin-4 pre-mRNA and induces its decay in nuclear exosomes.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10474, doi. 10.1093/nar/gkv954

By:

Fudi Zhong;
Nan Zhou;
Kang Wu;
Yubiao Guo;
Weiping Tan;
Hong Zhang;
Xue Zhang;
Guannan Geng;
Ting Pan;
Haihua Luo;
Yijun Zhang;
Zhibin Xu;
Jun Liu;
Bingfeng Liu;
Wenchao Gao;
Chao Liu;
Liangliang Ren;
Jun Li;
Jie Zhou;
Hui Zhang

Publication type:

Article

New insights into the enzymatic role of EF-G in ribosome recycling.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10525, doi. 10.1093/nar/gkv995

By:

Dejiu Zhang;
Kaige Yan;
Yiwei Zhang;
Guangqiao Liu;
Xintao Cao;
Guangtao Song;
Qiang Xie;
Ning Gao;
Yan Qin

Publication type:

Article

Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv738

By:

Miao Yu;
Lexiang Ji;
Neumann, Drexel A.;
Dae-hwan Chung;
Groom, Joseph;
Westpheling, Janet;
Chuan He;
Schmitz, Robert J.

Publication type:

Article

Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10264, doi. 10.1093/nar/gkv894

By:

Ying Yuan;
Britton, Sébastien;
Delteil1, Christine;
Coates, Julia;
Jackson, Stephen P.;
Barboule, Nadia;
Frit, Philippe;
Calsou, Patrick

Publication type:

Article

Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10251, doi. 10.1093/nar/gkv883

By:

Yang, Darren;
Boyer, Benjamin;
Prévost, Chantal;
Danilowicz, Claudia;
Prentiss, Mara

Publication type:

Article

An endogenous protein inhibitor, YjhX (TopAI), for topoisomerase I from Escherichia coli.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10387, doi. 10.1093/nar/gkv1197

By:

Yoshihiro Yamaguchi;
Masayori Inouye

Publication type:

Article

Knockout of Drosophila RNase ZL impairs mitochondrial transcript processing, respiration and cell cycle progression.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10364, doi. 10.1093/nar/gkv1149

By:

Xie Xie;
Dubrovsky, Edward B.

Publication type:

Article

A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10411, doi. 10.1093/nar/gkv1095

By:

Yakunina, Maria;
Artamonova, Tatyana;
Borukhov, Sergei;
Makarova, Kira S.;
Severinov, Konstantin;
Minakhin, Leonid

Publication type:

Article

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv715

By:

Hao Wu;
Tianlei Xu;
Hao Feng;
Li Chen;
Ben Li;
Bing Yao;
Zhaohui Qin;
Peng Jin;
Conneely, Karen N.

Publication type:

Article

Computational learning on specificity-determining residue-nucleotide interactions.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10180, doi. 10.1093/nar/gkv1134

By:

Ka-Chun Wong;
Yue Li;
Chengbin Peng;
Moses, Alan M.;
Zhaolei Zhang

Publication type:

Article

Discovery and characterization of Alu repeat sequences via precise local read assembly.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10292, doi. 10.1093/nar/gkv1089

By:

Wildschutte, Julia H.;
Baron, Alayna;
Diroff, Nicolette M.;
Kidd, Jeffrey M.

Publication type:

Article

BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv733

By:

Junbai Wang;
Batmanov, Kirill

Publication type:

Article

SerRS-tRNASec complex structures reveal mechanism of the first step in selenocysteine biosynthesis.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10534, doi. 10.1093/nar/gkv996

By:

Caiyan Wang;
Yu Guo;
Qingnan Tian;
Qian Jia;
Yuanzhu Gao;
Qinfen Zhang;
Chun Zhou;
Wei Xie

Publication type:

Article

Identification of bacterial sRNA regulatory targets using ribosome profiling.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10308, doi. 10.1093/nar/gkv1158

By:

Jing Wang;
Rennie, William;
Chaochun Liu;
Carmack, Charles S.;
Prévost, Karine;
Caron, Marie-Pier;
Massé, Eric;
Ye Ding;
Wade, Joseph T.

Publication type:

Article

Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10168, doi. 10.1093/nar/gkv1039

By:

Sükösd, Zsuzsanna;
Andersen, Ebbe S.;
Seemann, Stefan E.;
Jensen, Mads Krogh;
Hansen, Mathias;
Gorodkin, Jan;
Kjems, Jørgen

Publication type:

Article

Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10430, doi. 10.1093/nar/gkv1129

By:

van Aelst, Kara;
Saikrishnan, Kayarat;
Szczelkun, Mark D.

Publication type:

Article

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv711

By:

Tarazona, Sonia;
Furió-Tarí, Pedro;
Turrà, David;
Di Pietro, Antonio;
Nueda, María José;
Ferrer, Alberto;
Conesa, Ana

Publication type:

Article

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10492, doi. 10.1093/nar/gkv956

By:

Tajnik, Mojca;
Vigilante, Alessandra;
Braun, Simon;
Hänel, Heike;
Luscombe, Nicholas M.;
Ule, Jernej;
Zarnack, Kathi;
König, Julian

Publication type:

Article

Dynamical features of the Plasmodium falciparum ribosome during translation.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10515, doi. 10.1093/nar/gkv991

By:

Ming Sun;
Wen Li;
Blomqvist, Karin;
Das, Sanchaita;
Hashem, Yaser;
Dvorin, Jeffrey D.;
Frank, Joachim

Publication type:

Article

Histone variant H3.3 provides the heterochromatic H3 lysine 9 tri-methylation mark at telomeres.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10227, doi. 10.1093/nar/gkv847

By:

Udugama, Maheshi;
Chang, Fiona T. M.;
Chan, F. Lyn;
Tang, Michelle C.;
Pickett, Hilda A.;
McGhie, James D. R.;
Mayne, Lynne;
Collas, Philippe;
Mann, Jeffrey R.;
Lee H. Wong

Publication type:

Article

DksA involvement in transcription fidelity buffers stochastic epigenetic change.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10190, doi. 10.1093/nar/gkv839

By:

Satory, Dominik;
Gordon, Alasdair J. E.;
Mengyu Wang;
Halliday, Jennifer A.;
Golding, Ido;
Herman, Christophe

Publication type:

Article

Collaborator of alternative reading frame protein (CARF) regulates early processing of pre-ribosomal RNA by retaining XRN2 (5'-3' exoribonuclease) in the nucleoplasm.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10397, doi. 10.1093/nar/gkv1069

By:

Shigeko Sato;
Hideaki Ishikawa;
Harunori Yoshikawa;
Keiichi Izumikawa;
Simpson, Richard J.;
Nobuhiro Takahashi

Publication type:

Article

Corrigendum.

Published in:: Nucleic Acids Research, 2015, v. 43, n. 21, p. 10571, doi. 10.1093/nar/gkv1000
Publication type:: Article

Blocking of targeted microRNAs from next-generation sequencing libraries.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv724

By:

Roberts, Brian S.;
Hardigan, Andrew A.;
Kirby, Marie K.;
Fitz-Gerald, Meredith B.;
Wilcox, C. Mel;
Kimberly, Robert P.;
Myers, Richard M.

Publication type:

Article

Zebrafish lacking functional DNA polymerase gamma survive to juvenile stage, despite rapid and sustained mitochondrial DNA depletion, altered energetics and growth.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10338, doi. 10.1093/nar/gkv1139

By:

Rahn, Jennifer J.;
Bestman, Jennifer E.;
Stackley, Krista D.;
Chan, Sherine S. L.

Publication type:

Article

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10114, doi. 10.1093/nar/gkv1133

By:

Miki Nakano;
Hisae Tateishi-Karimata;
Shigenori Tanaka;
Tama, Florence;
Osamu Miyashita;
Shu-ichi Nakano;
Naoki Sugimoto

Publication type:

Article

Nucleosome compaction facilitates HP1γ binding to methylated H3K9.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10200, doi. 10.1093/nar/gkv841

By:

Yuichi Mishima;
Jayasinghe, Chanika D.;
Kai Lu;
Junji Otani;
Masahiro Shirakawa;
Toru Kawakami;
Hironobu Kimura;
Hironobu Hojo;
Carlton, Peter;
Shoji Tajima;
Isao Suetake

Publication type:

Article

Sources of PCR-induced distortions in high-throughput sequencing data sets.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv717

By:

Kebschull, Justus M.;
Zador, Anthony M.

Publication type:

Article

A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10157, doi. 10.1093/nar/gkv1033

By:

Junyan Lu;
Chenxiao Jiang;
Xiaojing Li;
Lizhi Jiang;
Zengxia Li;
Schneider-Poetsch, Tilman;
Jianwei Liu;
Kunqian Yu;
Jun O. Liu;
Hualiang Jiang;
Cheng Luo;
Yongjun Dang

Publication type:

Article

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10143, doi. 10.1093/nar/gkv1028

By:

Liebl, Korbinian;
Drsata, Tomas;
Lankas, Filip;
Lipfert, Jan;
Zacharias, Martin

Publication type:

Article

Sumoylation of Sir2 differentially regulates transcriptional silencing in yeast.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10213, doi. 10.1093/nar/gkv842

By:

Hannan, Abdul;
Abraham, Neethu Maria;
Goyal, Siddharth;
Jamir, Imlitoshi;
Priyakumar, U. Deva;
Mishra, Krishnaveni

Publication type:

Article

Direct evidence of mitochondrial G-quadruplex DNA by using fluorescent anti-cancer agents.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10102, doi. 10.1093/nar/gkv1061

By:

Wei-Chun Huang;
Ting-Yuan Tseng;
Ying-Ting Chen;
Cheng-Chung Chang;
Zi-Fu Wang;
Chiung-Lin Wang;
Tsu-Ning Hsu;
Pei-Tzu Li;
Chin-Tin Chen;
Jing-Jer Lin;
Pei-Jen Lou;
Ta-Chau Chang

Publication type:

Article

DSSR: an integrated software tool for dissecting the spatial structure of RNA.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv716

By:

Xiang-Jun Lu;
Bussemaker, Harmen J.;
Olson, Wilma K.

Publication type:

Article

Intrastrand triplex DNA repeats in bacteria: a source of genomic instability.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10126, doi. 10.1093/nar/gkv1017

By:

Holder, Isabelle T.;
Wagner, Stefanie;
Peiwen Xiong;
Sinn, Malte;
Frickey, Tancred;
Meyer, Axel;
Hartig, Jörg S.

Publication type:

Article

A reconstituted system reveals how activating and inhibitory interactions control DDK dependent assembly of the eukaryotic replicative helicase.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10238, doi. 10.1093/nar/gkv881

By:

Herrera, M. Carmen;
Tognetti, Silvia;
Riera, Alberto;
Zech, Juergen;
Clarke, Pippa;
Fernández-Cid, Alejandra;
Speck, Christian

Publication type:

Article

Robust expression of vault RNAs induced by influenza A virus plays a critical role in suppression of PKR-mediated innate immunity.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10321, doi. 10.1093/nar/gkv1078

By:

Fang Li;
Yuhai Chen;
Zhaoyuan Zhang;
Jing Ouyang;
Yi Wang;
Ruoxiang Yan;
Shile Huang;
Fu Gao, George;
Guijie Guo;
Ji-Long Chen

Publication type:

Article

DNA targeting by the type I-G and type I-A CRISPR-Cas systems of Pyrococcus furiosus.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10353, doi. 10.1093/nar/gkv1140

By:

Elmore, Joshua;
Deighan, Trace;
Westpheling, Jan;
Terns, Rebecca M.;
Terns, Michael P.

Publication type:

Article

Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv700

By:

Dupont, Daniel M.;
Larsen, Niels;
Jensen, Jan. K.;
Andreasen, Peter A.;
Kjems, Jørgen

Publication type:

Article

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10421, doi. 10.1093/nar/gkv1098

By:

Dulin, David;
Vilfan, Igor D.;
Berghuis, Bojk A.;
Poranen, Minna M.;
Depken, Martin;
Dekker, Nynke H.

Publication type:

Article

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10444, doi. 10.1093/nar/gkv932

By:

De Leonardis, Eleonora;
Lutz, Benjamin;
Ratz, Sebastian;
Cocco, Simona;
Monasson, Rémi;
Schug, Alexander;
Weigt, Martin

Publication type:

Article

Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10456, doi. 10.1093/nar/gkv952

By:

Crisci, Angela;
Raleff, Flore;
Bagdiul, Ivona;
Raabe, Monika;
Urlaub, Henning;
Rain, Jean-Christophe;
Krämer, Angela

Publication type:

Article

Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G⋅G⋅X⋅O tetrad.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10506, doi. 10.1093/nar/gkv826

By:

Vee Vee Cheong;
Heddi, Brahim;
Lech, Christopher Jacques;
Anh Tuân Phan

Publication type:

Article

A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10546, doi. 10.1093/nar/gkv1005

By:

Changsoo Chang;
Tesar, Christine;
Xiaoqing Li;
Youngchang Kim;
Rodionov, Dmitry A.;
Joachimiak, Andrzej

Publication type:

Article

Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10376, doi. 10.1093/nar/gkv1167

By:

Bončina, Matjaž;
Podlipnik, Črtomir;
Piantanida, Ivo;
Eilmes, Julita;
Teulade-Fichou, Marie-Paule;
Vesnaver, Gorazd;
Lah, Jurij

Publication type:

Article

Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv718

By:

Arora, Ankita;
Sunbul, Murat;
Jäschke, Andres

Publication type:

Article

The current state of eukaryotic DNA base damage and repair.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10083, doi. 10.1093/nar/gkv1136

By:

Bauer, Nicholas C.;
Corbett, Anita H.;
Doetsch, Paul W.

Publication type:

Article

Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv727

By:

Andergassen, Daniel;
Dotter, Christoph P.;
Kulinski, Tomasz M.;
Guenzl, Philipp M.;
Bammer, Philipp C.;
Barlow, Denise P.;
Pauler, Florian M.;
Hudson, Quanah J.

Publication type:

Article

Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 21, p. 10277, doi. 10.1093/nar/gkv896

By:

Achar, Yathish Jagadheesh;
Balogh, David;
Neculai, Dante;
Juhasz, Szilvia;
Morocz, Monika;
Gali, Himabindu;
Dhe-Paganon, Sirano;
Venclovas, Česlovas;
Haracska, Lajos

Publication type:

Article