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Volume 43; Issue 3
Main
Nucleic Acids Research
Volume 43; Issue 3
Nucleic Acids Research
Volume 43; Issue 3
1
Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines
Ho, T.-T.
,
Zhou, N.
,
Huang, J.
,
Koirala, P.
,
Xu, M.
,
Fung, R.
,
Wu, F.
,
Mo, Y.-Y.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.85 MB
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english, 2015
2
Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells
Byrne, S. M.
,
Ortiz, L.
,
Mali, P.
,
Aach, J.
,
Church, G. M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.22 MB
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english, 2015
3
Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14
Ning, Y.-Q.
,
Ma, Z.-Y.
,
Huang, H.-W.
,
Mo, H.
,
Zhao, T.-t.
,
Li, L.
,
Cai, T.
,
Chen, S.
,
Ma, L.
,
He, X.-J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.67 MB
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english, 2015
4
Multilayered genetic safeguards limit growth of microorganisms to defined environments
Gallagher, R. R.
,
Patel, J. R.
,
Interiano, A. L.
,
Rovner, A. J.
,
Isaacs, F. J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.58 MB
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english, 2015
5
Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities
Wang, B.
,
Barahona, M.
,
Buck, M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.94 MB
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english, 2015
6
DICER-dependent biogenesis of let-7 miRNAs affects human cell response to DNA damage via targeting p21/p27
Liu, B.
,
Liu, M.
,
Wang, J.
,
Zhang, X.
,
Wang, X.
,
Wang, P.
,
Wang, H.
,
Li, W.
,
Wang, Y.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.97 MB
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english, 2015
7
53BP1 promotes microhomology-mediated end-joining in G1-phase cells
Xiong, X.
,
Du, Z.
,
Wang, Y.
,
Feng, Z.
,
Fan, P.
,
Yan, C.
,
Willers, H.
,
Zhang, J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 3.11 MB
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english, 2015
8
Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus
Wei, Y.
,
Chesne, M. T.
,
Terns, R. M.
,
Terns, M. P.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.03 MB
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english, 2015
9
Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner
Ebina, I.
,
Takemoto-Tsutsumi, M.
,
Watanabe, S.
,
Koyama, H.
,
Endo, Y.
,
Kimata, K.
,
Igarashi, T.
,
Murakami, K.
,
Kudo, R.
,
Ohsumi, A.
,
Noh, A. L.
,
Takahashi, H.
,
Naito, S.
,
Onouchi, H.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.46 MB
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10
Protein mistranslation protects bacteria against oxidative stress
Fan, Y.
,
Wu, J.
,
Ung, M. H.
,
De Lay, N.
,
Cheng, C.
,
Ling, J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.77 MB
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english, 2015
11
The Kruppel-associated box repressor domain induces reversible and irreversible regulation of endogenous mouse genes by mediating different chromatin states
Ying, Y.
,
Yang, X.
,
Zhao, K.
,
Mao, J.
,
Kuang, Y.
,
Wang, Z.
,
Sun, R.
,
Fei, J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 15.04 MB
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english, 2015
12
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq
Linde, J.
,
Duggan, S.
,
Weber, M.
,
Horn, F.
,
Sieber, P.
,
Hellwig, D.
,
Riege, K.
,
Marz, M.
,
Martin, R.
,
Guthke, R.
,
Kurzai, O.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.91 MB
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english, 2015
13
Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer
Sebestyen, E.
,
Zawisza, M.
,
Eyras, E.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.30 MB
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english, 2015
14
RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information
Suresh, V.
,
Liu, L.
,
Adjeroh, D.
,
Zhou, X.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.30 MB
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english, 2015
15
Bacterial global regulators DksA/ppGpp increase fidelity of transcription
Roghanian, M.
,
Zenkin, N.
,
Yuzenkova, Y.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 5.26 MB
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english, 2015
16
Sparse expression bases in cancer reveal tumor drivers
Logsdon, B. A.
,
Gentles, A. J.
,
Miller, C. P.
,
Blau, C. A.
,
Becker, P. S.
,
Lee, S.-I.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.88 MB
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english, 2015
17
Recombinase and translesion DNA polymerase decrease the speed of replication fork progression during the DNA damage response in Escherichia coli cells
Tan, K. W.
,
Pham, T. M.
,
Furukohri, A.
,
Maki, H.
,
Akiyama, M. T.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 541 KB
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english, 2015
18
A minimal ubiquitous chromatin opening element (UCOE) effectively prevents silencing of juxtaposed heterologous promoters by epigenetic remodeling in multipotent and pluripotent stem cells
Muller-Kuller, U.
,
Ackermann, M.
,
Kolodziej, S.
,
Brendel, C.
,
Fritsch, J.
,
Lachmann, N.
,
Kunkel, H.
,
Lausen, J.
,
Schambach, A.
,
Moritz, T.
,
Grez, M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.14 MB
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19
ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites
Carissimi, C.
,
Laudadio, I.
,
Cipolletta, E.
,
Gioiosa, S.
,
Mihailovich, M.
,
Bonaldi, T.
,
Macino, G.
,
Fulci, V.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 3.37 MB
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english, 2015
20
Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark
Corley, M.
,
Solem, A.
,
Qu, K.
,
Chang, H. Y.
,
Laederach, A.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.27 MB
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english, 2015
21
A basal level of DNA damage and telomere deprotection increases the sensitivity of cancer cells to G-quadruplex interactive compounds
Salvati, E.
,
Rizzo, A.
,
Iachettini, S.
,
Zizza, P.
,
Cingolani, C.
,
D'Angelo, C.
,
Porru, M.
,
Mondello, C.
,
Aiello, A.
,
Farsetti, A.
,
Gilson, E.
,
Leonetti, C.
,
Biroccio, A.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 11.60 MB
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english, 2015
22
Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein
Matsumoto, S.
,
Fischer, E. S.
,
Yasuda, T.
,
Dohmae, N.
,
Iwai, S.
,
Mori, T.
,
Nishi, R.
,
Yoshino, K.-i.
,
Sakai, W.
,
Hanaoka, F.
,
Thoma, N. H.
,
Sugasawa, K.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.12 MB
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english, 2015
23
A systematic survey of the Cys2His2 zinc finger DNA-binding landscape
Persikov, A. V.
,
Wetzel, J. L.
,
Rowland, E. F.
,
Oakes, B. L.
,
Xu, D. J.
,
Singh, M.
,
Noyes, M. B.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 11.96 MB
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english, 2015
24
Arrangements of human telomere DNA quadruplex in physiologically relevant K+ solutions
Ren iuk, D.
,
Kejnovska, I.
,
kolakova, P.
,
Bedna ova, K.
,
Motlova, J.
,
Vorli kova, M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 27 KB
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english, 2015
25
Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions
Mauger, O.
,
Klinck, R.
,
Chabot, B.
,
Muchardt, C.
,
Allemand, E.
,
Batsche, E.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 5.79 MB
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english, 2015
26
Repressor activity of the RpoS/ S-dependent RNA polymerase requires DNA binding
Levi-Meyrueis, C.
,
Monteil, V.
,
Sismeiro, O.
,
Dillies, M.-A.
,
Kolb, A.
,
Monot, M.
,
Dupuy, B.
,
Duarte, S. S.
,
Jagla, B.
,
Coppee, J.-Y.
,
Beraud, M.
,
Norel, F.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 3.67 MB
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english, 2015
27
Evaluating the potential for undesired genomic effects of the piggyBac transposon system in human cells
Saha, S.
,
Woodard, L. E.
,
Charron, E. M.
,
Welch, R. C.
,
Rooney, C. M.
,
Wilson, M. H.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.69 MB
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english, 2015
28
GRASP: Guided Reference-based Assembly of Short Peptides
Zhong, C.
,
Yang, Y.
,
Yooseph, S.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 860 KB
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english, 2015
29
Function of the N-terminal segment of the RecA-dependent nuclease Ref
Gruber, A. J.
,
Olsen, T. M.
,
Dvorak, R. H.
,
Cox, M. M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 3.97 MB
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english, 2015
30
A KALA-modified lipid nanoparticle containing CpG-free plasmid DNA as a potential DNA vaccine carrier for antigen presentation and as an immune-stimulative adjuvant
Miura, N.
,
Shaheen, S. M.
,
Akita, H.
,
Nakamura, T.
,
Harashima, H.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.55 MB
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31
Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure--a FRET study
Gansen, A.
,
Toth, K.
,
Schwarz, N.
,
Langowski, J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 529 KB
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english, 2015
32
ModuleBlast: identifying activated sub-networks within and across species
Zinman, G. E.
,
Naiman, S.
,
O'Dee, D. M.
,
Kumar, N.
,
Nau, G. J.
,
Cohen, H. Y.
,
Bar-Joseph, Z.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.07 MB
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33
The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences
Ren, J.
,
Briones, V.
,
Barbour, S.
,
Yu, W.
,
Han, Y.
,
Terashima, M.
,
Muegge, K.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 3.27 MB
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34
Nucleic Acids Research: Editorial Board
Journal:
Nucleic Acids Research
Year:
2015
File:
PDF, 1.04 MB
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2015
35
The POLD3 subunit of DNA polymerase can promote translesion synthesis independently of DNA polymerase
Hirota, K.
,
Yoshikiyo, K.
,
Guilbaud, G.
,
Tsurimoto, T.
,
Murai, J.
,
Tsuda, M.
,
Phillips, L. G.
,
Narita, T.
,
Nishihara, K.
,
Kobayashi, K.
,
Yamada, K.
,
Nakamura, J.
,
Pommier, Y.
,
Lehmann, A.
,
Sale, J. E.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.34 MB
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english, 2015
36
Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork
Richet, N.
,
Liu, D.
,
Legrand, P.
,
Velours, C.
,
Corpet, A.
,
Gaubert, A.
,
Bakail, M.
,
Moal-Raisin, G.
,
Guerois, R.
,
Compper, C.
,
Besle, A.
,
Guichard, B.
,
Almouzni, G.
,
Ochsenbein, F.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.21 MB
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37
A defense-offense multi-layered regulatory switch in a pathogenic bacterium
Nitzan, M.
,
Fechter, P.
,
Peer, A.
,
Altuvia, Y.
,
Bronesky, D.
,
Vandenesch, F.
,
Romby, P.
,
Biham, O.
,
Margalit, H.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.73 MB
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english, 2015
38
Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia
Carradec, Q.
,
Gotz, U.
,
Arnaiz, O.
,
Pouch, J.
,
Simon, M.
,
Meyer, E.
,
Marker, S.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 3.19 MB
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english, 2015
39
DNA lesion identity drives choice of damage tolerance pathway in murine cell chromosomes
Cohen, I. S.
,
Bar, C.
,
Paz-Elizur, T.
,
Ainbinder, E.
,
Leopold, K.
,
de Wind, N.
,
Geacintov, N.
,
Livneh, Z.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.93 MB
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english, 2015
40
DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors
Narasimhan, K.
,
Pillay, S.
,
Huang, Y.-H.
,
Jayabal, S.
,
Udayasuryan, B.
,
Veerapandian, V.
,
Kolatkar, P.
,
Cojocaru, V.
,
Pervushin, K.
,
Jauch, R.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 9.64 MB
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41
Transient DNMT1 suppression reveals hidden heritable marks in the genome
McGraw, S.
,
Zhang, J. X.
,
Farag, M.
,
Chan, D.
,
Caron, M.
,
Konermann, C.
,
Oakes, C. C.
,
Mohan, K. N.
,
Plass, C.
,
Pastinen, T.
,
Bourque, G.
,
Chaillet, J. R.
,
Trasler, J. M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 7.07 MB
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42
BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers
Abo, R. P.
,
Ducar, M.
,
Garcia, E. P.
,
Thorner, A. R.
,
Rojas-Rudilla, V.
,
Lin, L.
,
Sholl, L. M.
,
Hahn, W. C.
,
Meyerson, M.
,
Lindeman, N. I.
,
Van Hummelen, P.
,
MacConaill, L. E.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 814 KB
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43
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Croucher, N. J.
,
Page, A. J.
,
Connor, T. R.
,
Delaney, A. J.
,
Keane, J. A.
,
Bentley, S. D.
,
Parkhill, J.
,
Harris, S. R.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 740 KB
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44
Subscriptions
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 412 KB
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45
HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis
Diaz, A. A.
,
Qin, H.
,
Ramalho-Santos, M.
,
Song, J. S.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.67 MB
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46
Nucleic Acids Research: VOLUME 43 ISSUE 3 2015
Journal:
Nucleic Acids Research
Year:
2015
File:
PDF, 5.11 MB
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2015
47
Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies
Mukherjee, D.
,
Pal, A.
,
Chakravarty, D.
,
Chakrabarti, P.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.12 MB
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english, 2015
48
Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila
Busser, B. W.
,
Haimovich, J.
,
Huang, D.
,
Ovcharenko, I.
,
Michelson, A. M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 12.76 MB
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english, 2015
49
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G
Gumienny, R.
,
Zavolan, M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.77 MB
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english, 2015
50
The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA
Gully, B. S.
,
Cowieson, N.
,
Stanley, W. A.
,
Shearston, K.
,
Small, I. D.
,
Barkan, A.
,
Bond, C. S.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 6.19 MB
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english, 2015
51
Human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-U2 RNA
Schertzer, M.
,
Jouravleva, K.
,
Perderiset, M.
,
Dingli, F.
,
Loew, D.
,
Le Guen, T.
,
Bardoni, B.
,
de Villartay, J.-P.
,
Revy, P.
,
Londono-Vallejo, A.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 8.68 MB
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english, 2015
52
The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli
Zhang, W.
,
Collinet, B.
,
Perrochia, L.
,
Durand, D.
,
van Tilbeurgh, H.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.12 MB
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english, 2015
53
Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing
Losh, J. S.
,
King, A. K.
,
Bakelar, J.
,
Taylor, L.
,
Loomis, J.
,
Rosenzweig, J. A.
,
Johnson, S. J.
,
van Hoof, A.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 1.00 MB
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english, 2015
54
Development of a unique epigenetic signature during in vivo Th17 differentiation
Yang, B.-H.
,
Floess, S.
,
Hagemann, S.
,
Deyneko, I. V.
,
Groebe, L.
,
Pezoldt, J.
,
Sparwasser, T.
,
Lochner, M.
,
Huehn, J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 861 KB
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55
An intercalation-locked parallel-stranded DNA tetraplex
Tripathi, S.
,
Zhang, D.
,
Paukstelis, P. J.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.58 MB
Your tags:
english, 2015
56
The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA
Aibara, S.
,
Katahira, J.
,
Valkov, E.
,
Stewart, M.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 4.85 MB
Your tags:
english, 2015
57
NTF2-like domain of Tap plays a critical role in cargo mRNA recognition and export
Katahira, J.
,
Dimitrova, L.
,
Imai, Y.
,
Hurt, E.
Journal:
Nucleic Acids Research
Year:
2015
Language:
english
File:
PDF, 2.74 MB
Your tags:
english, 2015
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