Volume 43; Issue 5

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Nucleic Acids Research
Volume 43; Issue 5

Nucleic Acids Research

Volume 43; Issue 5

1

SwiftLib: rapid degenerate-codon-library optimization through dynamic programming

Jacobs, T. M., Yumerefendi, H., Kuhlman, B., Leaver-Fay, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 152 KB

english, 2015

2

Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2

Dubiez, E., Aleksandrov, A., Lazennec-Schurdevin, C., Mechulam, Y., Schmitt, E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.11 MB

english, 2015

3

Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures

Lee, S.-T., Muench, M. O., Fomin, M. E., Xiao, J., Zhou, M., de Smith, A., Martin-Subero, J. I., Heath, S., Houseman, E. A., Roy, R., Wrensch, M., Wiencke, J., Metayer, C., Wiemels, J. L.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.09 MB

english, 2015

4

Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins

Baranauske, S., Mickute, M., Plotnikova, A., Finke, A., Venclovas, eslovas, Klima auskas, S., Vilkaitis, G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.13 MB

english, 2015

5

In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

Martinez de Alba, A. E., Moreno, A. B., Gabriel, M., Mallory, A. C., Christ, A., Bounon, R., Balzergue, S., Aubourg, S., Gautheret, D., Crespi, M. D., Vaucheret, H., Maizel, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.86 MB

english, 2015

6

The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs

Nicklas, S., Okawa, S., Hillje, A.-L., Gonzalez-Cano, L., del Sol, A., Schwamborn, J. C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.51 MB

english, 2015

7

High-throughput data integration of RNA-miRNA-circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity

Caiment, F., Gaj, S., Claessen, S., Kleinjans, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

8

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

Esling, P., Lejzerowicz, F., Pawlowski, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.59 MB

english, 2015

9

Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities

Fukuyo, M., Nakano, T., Zhang, Y., Furuta, Y., Ishikawa, K., Watanabe-Matsui, M., Yano, H., Hamakawa, T., Ide, H., Kobayashi, I.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.29 MB

english, 2015

10

Structural basis for recognition of G-1-containing tRNA by histidyl-tRNA synthetase

Tian, Q., Wang, C., Liu, Y., Xie, W.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 7.43 MB

english, 2015

11

bHLH proteins involved in Drosophila neurogenesis are mutually regulated at the level of stability

Kiparaki, M., Zarifi, I., Delidakis, C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.46 MB

english, 2015

12

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

Crappe, J., Ndah, E., Koch, A., Steyaert, S., Gawron, D., De Keulenaer, S., De Meester, E., De Meyer, T., Van Criekinge, W., Van Damme, P., Menschaert, G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.38 MB

english, 2015

13

Synergistic effects of ATP and RNA binding to human DEAD-box protein DDX1

Kellner, J. N., Reinstein, J., Meinhart, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.41 MB

english, 2015

14

Structural plasticity of Cid1 provides a basis for its distributive RNA terminal uridylyl transferase activity

Yates, L. A., Durrant, B. P., Fleurdepine, S., Harlos, K., Norbury, C. J., Gilbert, R. J. C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 8.51 MB

english, 2015

15

Multiple facets of histone variant H2AX: a DNA double-strand-break marker with several biological functions

Turinetto, V., Giachino, C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 763 KB

english, 2015

16

Human Rap1 modulates TRF2 attraction to telomeric DNA

Janou kova, E., Ne asova, I., Pavlou kova, J., Zimmermann, M., Hluchy, M., Marini, V., Novakova, M., Hofr, C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.60 MB

english, 2015

17

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides

Hia, F., Chionh, Y. H., Pang, Y. L. J., DeMott, M. S., McBee, M. E., Dedon, P. C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.37 MB

english, 2015

18

Single molecule analysis of Trypanosoma brucei DNA replication dynamics

Calderano, S. G., Drosopoulos, W. C., Quaresma, M. M., Marques, C. A., Kosiyatrakul, S., McCulloch, R., Schildkraut, C. L., Elias, M. C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.42 MB

english, 2015

19

Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline

Camunas-Soler, J., Manosas, M., Frutos, S., Tulla-Puche, J., Albericio, F., Ritort, F.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 5.46 MB

english, 2015

20

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks

Zhang, X., Zhao, J., Hao, J.-K., Zhao, X.-M., Chen, L.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

21

microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes

Yoon, J.-K., Ahn, J., Kim, H. S., Han, S. M., Jang, H., Lee, M. G., Lee, J. H., Bang, D.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

22

Replication fork integrity and intra-S phase checkpoint suppress gene amplification

Kondratova, A., Watanabe, T., Marotta, M., Cannon, M., Segall, A. M., Serre, D., Tanaka, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.60 MB

english, 2015

23

Computational and molecular tools for scalable rAAV-mediated genome editing

Stoimenov, I., Ali, M. A., Pandzic, T., Sjoblom, T.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.30 MB

english, 2015

24

EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization

Rackham, O. J. L., Shihab, H. A., Johnson, M. R., Petretto, E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.43 MB

english, 2015

25

Concerted and differential actions of two enzymatic domains underlie Rad5 contributions to DNA damage tolerance

Choi, K., Batke, S., Szakal, B., Lowther, J., Hao, F., Sarangi, P., Branzei, D., Ulrich, H. D., Zhao, X.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.13 MB

english, 2015

26

H3K4me3 demethylation by the histone demethylase KDM5C/JARID1C promotes DNA replication origin firing

Rondinelli, B., Schwerer, H., Antonini, E., Gaviraghi, M., Lupi, A., Frenquelli, M., Cittaro, D., Segalla, S., Lemaitre, J.-M., Tonon, G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.64 MB

english, 2015

27

Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex

Ekumi, K. M., Paculova, H., Lenasi, T., Pospichalova, V., Bosken, C. A., Rybarikova, J., Bryja, V., Geyer, M., Blazek, D., Barboric, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.67 MB

english, 2015

28

RNA polymerase-induced remodelling of NusA produces a pause enhancement complex

Ma, C., Mobli, M., Yang, X., Keller, A. N., King, G. F., Lewis, P. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.41 MB

english, 2015

29

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

Sochacka, E., Szczepanowski, R. H., Cypryk, M., Sobczak, M., Janicka, M., Kraszewska, K., Bartos, P., Chwialkowska, A., Nawrot, B.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.64 MB

english, 2015

30

The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function

Bhat, P., Shwetha, S., Sharma, D. K., Joseph, A. P., Srinivasan, N., Das, S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.78 MB

english, 2015

31

Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster

Simoni, A., Siniscalchi, C., Chan, Y. S., Huen, D. S., Russell, S., Windbichler, N., Crisanti, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 84 KB

english, 2015

32

Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex

Wiedemann, C., Szambowska, A., Hafner, S., Ohlenschlager, O., Guhrs, K.-H., Gorlach, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

33

A novel endonuclease that may be responsible for damaged DNA base repair in Pyrococcus furiosus

Shiraishi, M., Ishino, S., Yamagami, T., Egashira, Y., Kiyonari, S., Ishino, Y.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.48 MB

english, 2015

34

EWS-FLI1 employs an E2F switch to drive target gene expression

Schwentner, R., Papamarkou, T., Kauer, M. O., Stathopoulos, V., Yang, F., Bilke, S., Meltzer, P. S., Girolami, M., Kovar, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.56 MB

english, 2015

35

Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1

Park, J., Kang, M., Kim, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.66 MB

english, 2015

36

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

Olarerin-George, A. O., Hogenesch, J. B.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 493 KB

english, 2015

37

Lesion search and recognition by thymine DNA glycosylase revealed by single molecule imaging

Buechner, C. N., Maiti, A., Drohat, A. C., Tessmer, I.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.67 MB

english, 2015

38

Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3' X-tail

Tuplin, A., Struthers, M., Cook, J., Bentley, K., Evans, D. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 854 KB

english, 2015

39

Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages

Liang, X.-h., Sun, H., Shen, W., Crooke, S. T.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 6.02 MB

english, 2015

40

Dynamic Escherichia coli SeqA complexes organize the newly replicated DNA at a considerable distance from the replisome

Helgesen, E., Fossum-Raunehaug, S., Saetre, F., Schink, K. O., Skarstad, K.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.47 MB

english, 2015

41

Alu RNA regulates the cellular pool of active ribosomes by targeted delivery of SRP9/14 to 40S subunits

Ivanova, E., Berger, A., Scherrer, A., Alkalaeva, E., Strub, K.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

42

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 1.04 MB

2015

43

Subscriptions

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 60 KB

english, 2015

44

Nucleic Acids Research: VOLUME 43 ISSUE 5 2015

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 4.04 MB

2015

45

Sequence-specific cleavage of dsRNA by Mini-III RNase

G ow, D., Pianka, D., Sulej, A. A., Koz owski, ukasz P., Czarnecka, J., Chojnowski, G., Skowronek, K. J., Bujnicki, J. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

46

CHK1-driven histone H3.3 serine 31 phosphorylation is important for chromatin maintenance and cell survival in human ALT cancer cells

Chang, F. T. M., Chan, F. L., R. McGhie, J. D., Udugama, M., Mayne, L., Collas, P., Mann, J. R., Wong, L. H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.73 MB

english, 2015

47

TEFM is a potent stimulator of mitochondrial transcription elongation in vitro

Posse, V., Shahzad, S., Falkenberg, M., Hallberg, B. M., Gustafsson, C. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1016 KB

english, 2015

48

Roles of Rad51 paralogs for promoting homologous recombination in Leishmania infantum

Genois, M.-M., Plourde, M., Ethier, C., Roy, G., Poirier, G. G., Ouellette, M., Masson, J.-Y.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.05 MB

english, 2015

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