Works matching IS 03051048 AND DT 2016 AND VI 44 AND IP 11

Results: 52

mRNA secondary structure optimization using a correlated stem–loop prediction.

Published in:: Nucleic Acids Research, 2016, v. 44, n. 11, p. 5490, doi. 10.1093/nar/gkw127
Publication type:: Article

A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5083, doi. 10.1093/nar/gkw106

By:

Kuo Zhang;
Yuan Gao;
Jingjing Li;
Burgess, Rebecca;
Junhong Han;
Huanhuan Liang;
Zhiguo Zhang;
Yingfang Liu

Publication type:

Article

Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5105, doi. 10.1093/nar/gkw113

By:

Naoki Yamamoto;
Kiyokazu Agata;
Kinichi Nakashima;
Takuya Imamura

Publication type:

Article

Involvement of budding yeast Rad5 in translesion DNA synthesis through physical interaction with Rev1.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5231, doi. 10.1093/nar/gkw183

By:

Xin Xu;
Aiyang Lin;
Cuiyan Zhou;
Blackwell, Susan R.;
Yiran Zhang;
Zihao Wang;
Qianqian Feng;
Ruifang Guan;
Hanna, Michelle D.;
Zhucheng Chen;
Wei Xiao

Publication type:

Article

The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5399, doi. 10.1093/nar/gkw213

By:

Wells, Graeme R.;
Weichmann, Franziska;
Colvin, David;
Sloan, Katherine E.;
Kudla, Grzegorz;
Tollervey, David;
Watkins, Nicholas J.;
Schneider, Claudia

Publication type:

Article

Nascent RNA length dictates opposing effects of NusA on antitermination.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5378, doi. 10.1093/nar/gkw198

By:

Wells, Christopher D.;
Deighan, Padraig;
Brigham, MacKenzie;
Hochschild, Ann

Publication type:

Article

Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5204, doi. 10.1093/nar/gkw179

By:

Vriend, Lianne E. M.;
Prakash, Rohit;
Chun-Chin Chen;
Vanoli, Fabio;
Cavallo, Francesca;
Yu Zhang;
Jasin, Maria;
Krawczyk, Przemek M.

Publication type:

Article

Local potentiation of stress-responsive genes by upstream noncoding transcription.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5174, doi. 10.1093/nar/gkw142

By:

Naomichi Takemata;
Arisa Oda;
Takatomi Yamada;
Galipon, Josephine;
Tomoichiro Miyoshi;
Yutaka Suzuki;
Sumio Sugano;
Hoffman, Charles S.;
Kouji Hirota;
Kunihiro Ohta

Publication type:

Article

Editorial: CRISPR in Nucleic Acids Research.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 4989, doi. 10.1093/nar/gkw451

By:

Stoddard, Barry L.;
Fox, Keith

Publication type:

Article

Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw224

By:

Ståhlberg, Anders;
Krzyzanowski, Paul M.;
Jackson, Jennifer B.;
Egyud, Matthew;
Stein, Lincoln;
Godfrey, Tony E.

Publication type:

Article

iGEMS: an integrated model for identification of alternative exon usage events.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw263

By:

Sood, Sanjana;
Szkop, Krzysztof J.;
Nakhuda, Asif;
Gallagher, Iain J.;
Murie, Carl;
Brogan, Robert J.;
Kaprio, Jaakko;
Kainulainen, Heikki;
Atherton, Philip J.;
Kujala, Urho M.;
Gustafsson, Thomas;
Larsson, Ola;
Timmons, James A.

Publication type:

Article

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw210

By:

Sharma, Virag;
Elghafari, Anas;
Hiller, Michael

Publication type:

Article

Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5438, doi. 10.1093/nar/gkw248

By:

Schumacher, Maria A.;
Lee, Jeehyun;
Wenjie Zeng

Publication type:

Article

A new molecular signature method for prediction of driver cancer pathways from transcriptional data.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw269

By:

Rykunov, Dmitry;
Beckmann, Noam D.;
Hui Li;
Uzilov, Andrew;
Schadt, Eric E.;
Reva, Boris

Publication type:

Article

Complex mitochondrial DNA rearrangements in individual cells from patients with sporadic inclusion body myositis.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5313, doi. 10.1093/nar/gkw382

By:

Rygiel, Karolina A.;
Tuppen, Helen A.;
Grady, John P.;
Vincent, Amy;
Blakely, Emma L.;
Reeve, Amy K.;
Taylor, Robert W.;
Picard, Martin;
Miller, James;
Turnbull, Doug M.

Publication type:

Article

Exploring the modular nature of riboswitches and RNA thermometers.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5410, doi. 10.1093/nar/gkw232

By:

Roßmanith, Johanna;
Narberhaus, Franz

Publication type:

Article

Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw217

By:

Reinharz, Vladimir;
Ponty, Yann;
Waldispühl, Jérôme

Publication type:

Article

A ubiquitylation site in Cockayne syndrome B required for repair of oxidative DNA damage, but not for transcription-coupled nucleotide excision repair.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5246, doi. 10.1093/nar/gkw216

By:

Ranes, Michael;
Boeing, Stefan;
Yuming Wang;
Wienholz, Franziska;
Menoni, Hervé;
Walker, Jane;
Encheva, Vesela;
Chakravarty, Probir;
Mari, Pierre-Olivier;
Stewart, Aengus;
Giglia-Mari, Giuseppina;
Snijders, Ambrosius P.;
Vermeulen, Wim;
Svejstrup, Jesper Q.

Publication type:

Article

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw226

By:

Quang, Daniel;
Xiaohui Xie

Publication type:

Article

Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5450, doi. 10.1093/nar/gkw293

By:

Pasi, Marco;
Lavery, Richard

Publication type:

Article

Structural basis for recruiting and shuttling of the spliceosomal deubiquitinase USP4 by SART3.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5424, doi. 10.1093/nar/gkw218

By:

Joon Kyu Park;
Das, Tanuza;
Eun Joo Song;
Kim, Eunice EunKyeong

Publication type:

Article

Cre-dependent DNA recombination activates a STING-dependent innate immune response.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5356, doi. 10.1093/nar/gkw405

By:

Pépin, Geneviève;
Ferrand, Jonathan;
Höning, Klara;
Jayasekara, W. Samantha N.;
Cain, Jason E.;
Behlke, Mark A.;
Gough, Daniel J.;
Williams, Bryan R. G.;
Hornung, Veit;
Gantier, Michael P.

Publication type:

Article

Folding complex DNA nanostructures from limited sets of reusable sequences.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw208

By:

Niekamp, Stefan;
Blumer, Katy;
Nafisi, Parsa M.;
Tsui, Kathy;
Garbutt, John;
Douglas, Shawn M.

Publication type:

Article

Another look at the mechanism involving trimeric dUTPases in Staphylococcus aureus pathogenicity island induction involves novel players in the party.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5457, doi. 10.1093/nar/gkw317

By:

Maiques, Elisa;
Quiles-Puchalt, Nuria;
Donderis, Jorge;
Ciges-Tomas, J. Rafael;
Alite, Christian;
Bowring, Janine Z.;
Humphrey, Suzanne;
Penadés, José R.;
Marina, Alberto

Publication type:

Article

Chromosome intermingling--the physical basis of chromosome organization in differentiated cells.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5148, doi. 10.1093/nar/gkw131

By:

Maharana, Shovamayee;
Iyer, K. Venkatesan;
Jain, Nikhil;
Nagarajan, Mallika;
Yejun Wang;
Shivashankar, G. V.

Publication type:

Article

Alternative splicing affects the subcellular localization of Drosha.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5330, doi. 10.1093/nar/gkw400

By:

Link, Steffen;
Grund, Stefanie E.;
Diederichs, Sven

Publication type:

Article

Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5299, doi. 10.1093/nar/gkw350

By:

Lima, Walt F.;
Murray, Heather M.;
Damle, Sagar S.;
Hart, Christopher E.;
Gene Hung;
De Hoyos, Cheryl Li;
Xue-Hai Liang;
Crooke, Stanley T.

Publication type:

Article

Promoter-enhancer looping at the PPARγ2 locus during adipogenic differentiation requires the Prmt5 methyltransferase.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5133, doi. 10.1093/nar/gkw129

By:

LeBlanc, Scott E.;
Qiong Wu;
Lamba, Pallavi;
Sif, Saïd;
Imbalzano, Anthony N.

Publication type:

Article

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw227

By:

Zhongwu Lai;
Markovets, Aleksandra;
Ahdesmaki, Miika;
Chapman, Brad;
Hofmann, Oliver;
McEwen, Robert;
Johnson, Justin;
Dougherty, Brian;
Barrett, J. Carl;
Dry, Jonathan R.

Publication type:

Article

DNA methylation in human epigenomes depends on local topology of CpG sites.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5123, doi. 10.1093/nar/gkw124

By:

Lövkvist, Cecilia;
Dodd, Ian B.;
Sneppen, Kim;
Haerter, Jan O.

Publication type:

Article

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5022, doi. 10.1093/nar/gkw396

By:

Kozlov, Alexey M.;
Jiajie Zhang;
Yilmaz, Pelin;
Glöckner, Frank Oliver;
Stamatakis, Alexandros

Publication type:

Article

Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5010, doi. 10.1093/nar/gkw355

By:

Eiryo Kawakami;
Shinji Nakaoka;
Tazro Ohta;
Hiroaki Kitano

Publication type:

Article

An updated human snoRNAome.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5068, doi. 10.1093/nar/gkw386

By:

Jorjani, Hadi;
Kehr, Stephanie;
Jedlinski, Dominik J.;
Gumienny, Rafal;
Hertel, Jana;
Stadler, Peter F.;
Zavolan, Mihaela;
Gruber, Andreas R.

Publication type:

Article

Nonsense-mediated decay regulates key components of homologous recombination.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5218, doi. 10.1093/nar/gkw182

By:

Janke, Ryan;
Kong, Jeremy;
Braberg, Hannes;
Cantin, Greg;
Yates III, John R.;
Krogan, Nevan J.;
Heyer, Wolf-Dietrich

Publication type:

Article

LDSS-P: an advanced algorithm to extract functional short motifs associated with coordinated gene expression.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5045, doi. 10.1093/nar/gkw435

By:

Hiroyuki Ichida;
Long, Sharon R.

Publication type:

Article

A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5390, doi. 10.1093/nar/gkw201

By:

Lin Huang;
Jia Wang;
Lilley, David M. J.

Publication type:

Article

The Borrelia burgdorferi telomere resolvase, ResT, anneals ssDNA complexed with its cognate ssDNA-binding protein.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5288, doi. 10.1093/nar/gkw344

By:

Shu Hui Huang;
Kobryn, Kerri

Publication type:

Article

RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5054, doi. 10.1093/nar/gkw448

By:

Germain, Pierre-Luc;
Vitriolo, Alessandro;
Adamo, Antonio;
Laise, Pasquale;
Das, Vivek;
Testa, Giuseppe

Publication type:

Article

Corrigendum.

Published in:: Nucleic Acids Research, 2016, v. 44, n. 11, p. 5490, doi. 10.1093/nar/gkw127
Publication type:: Article

Distinct patterns of Cas9 mismatch tolerance in vitro and in vivo.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5365, doi. 10.1093/nar/gkw417

By:

Fu, Becky X. H.;
Onge, Robert P. St.;
Fire, Andrew Z.;
Smith, Justin D.

Publication type:

Article

Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw114

By:

Dumat, Blaise;
Larsen, Anders Foller;
Wilhelmsson, L. Marcus

Publication type:

Article

Staufen1 promotes HCV replication by inhibiting protein kinase R and transporting viral RNA to the site of translation and replication in the cells.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5271, doi. 10.1093/nar/gkw312

By:

Dixit, Updesh;
Pandey, Ashutosh K.;
Mishra, Priya;
Sengupta, Amitabha;
Pandey, Virendra N.

Publication type:

Article

Oxidized dNTPs and the OGG1 and MUTYH DNA glycosylases combine to induce CAG/CTG repeat instability.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5190, doi. 10.1093/nar/gkw170

By:

Cilli, Piera;
Ventura, Ilenia;
Minoprio, Anna;
Meccia, Ettore;
Martire, Alberto;
Wilson, Samuel H.;
Bignami, Margherita;
Mazzei, Filomena

Publication type:

Article

Reversal of epigenetic promoter silencing in Friedreich ataxia by a class I histone deacetylase inhibitor.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5095, doi. 10.1093/nar/gkw107

By:

Chutake, Yogesh K.;
Lam, Christina C.;
Costello, Whitney N.;
Anderson, Michael P.;
Bidichandani, Sanjay I.

Publication type:

Article

DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5161, doi. 10.1093/nar/gkw141

By:

Si Ho Choi;
Gearhart, Micah D.;
Ziyou Cui;
Bosnakovski, Darko;
Minjee Kim;
Schennum, Natalie;
Kyba, Michael

Publication type:

Article

De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 1, doi. 10.1093/nar/gkw225

By:

Yong Chen;
Yunfei Wang;
Zhenyu Xuan;
Min Chen;
Zhang, Michael Q.

Publication type:

Article

Use of chemical modification and mass spectrometry to identify substrate-contacting sites in proteinaceous RNase P, a tRNA processing enzyme.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5344, doi. 10.1093/nar/gkw391

By:

Tien-Hao Chen;
Akiko Tanimoto;
Shkriabai, Nikoloz;
Mamuka Kvaratskhelia;
Wysocki, Vicki;
Gopalan, Venkat

Publication type:

Article

Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5256, doi. 10.1093/nar/gkw242

By:

Chatterjee, Gouri;
Jimenez-Sainz, Judit;
Presti, Thomas;
Nguyen, Tiffany;
Jensen, Ryan B.

Publication type:

Article

Structure-Specific nuclease activities of Artemis and the Artemis: DNA-PKcs complex.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 4991, doi. 10.1093/nar/gkw456

By:

Chang, Howard H.Y.;
Lieber, Michael R.

Publication type:

Article

Deciphering the molecular mechanisms underlying the binding of the TWIST1/E12 complex to regulatory E-box sequences.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 11, p. 5470, doi. 10.1093/nar/gkw334

By:

Bouard, Charlotte;
Terreux, Raphael;
Honorat, Mylène;
Manship, Brigitte;
Ansieau, Stéphane;
Vigneron, Arnaud M.;
Puisieux, Alain;
Payen, Léa

Publication type:

Article