Volume 42; Issue 15

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Nucleic Acids Research
Volume 42; Issue 15

Nucleic Acids Research

Volume 42; Issue 15

1

High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase

Gajula, K. S., Huwe, P. J., Mo, C. Y., Crawford, D. J., Stivers, J. T., Radhakrishnan, R., Kohli, R. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 890 KB

english, 2014

2

Characterizing RNA ensembles from NMR data with kinematic models

Fonseca, R., Pachov, D. V., Bernauer, J., van den Bedem, H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.78 MB

english, 2014

3

Double-strand break repair deficiency in NONO knockout murine embryonic fibroblasts and compensation by spontaneous upregulation of the PSPC1 paralog

Li, S., Li, Z., Shu, F.-J., Xiong, H., Phillips, A. C., Dynan, W. S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.40 MB

english, 2014

4

Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome

Thevenin, A., Ein-Dor, L., Ozery-Flato, M., Shamir, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 947 KB

english, 2014

5

Human fetal globin gene expression is regulated by LYAR

Ju, J., Wang, Y., Liu, R., Zhang, Y., Xu, Z., Wang, Y., Wu, Y., Liu, M., Cerruti, L., Zou, F., Ma, C., Fang, M., Tan, R., Jane, S. M., Zhao, Q.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

6

Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network

Kaboli, S., Yamakawa, T., Sunada, K., Takagaki, T., Sasano, Y., Sugiyama, M., Kaneko, Y., Harashima, S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.49 MB

english, 2014

7

The iron-sensing aconitase B binds its own mRNA to prevent sRNA-induced mRNA cleavage

Benjamin, J.-A. M., Masse, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.78 MB

english, 2014

8

ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK-RSK pathway

Adachi, S., Homoto, M., Tanaka, R., Hioki, Y., Murakami, H., Suga, H., Matsumoto, M., Nakayama, K. I., Hatta, T., Iemura, S.-i., Natsume, T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.41 MB

english, 2014

9

Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2)

Bhukya, H., Bhujbalrao, R., Bitra, A., Anand, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.60 MB

english, 2014

10

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2014

File:

PDF, 421 KB

2014

11

Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats

Malgowska, M., Gudanis, D., Kierzek, R., Wyszko, E., Gabelica, V., Gdaniec, Z.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.51 MB

english, 2014

12

Quantifying sequence and structural features of protein-RNA interactions

Li, S., Yamashita, K., Amada, K. M., Standley, D. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.53 MB

english, 2014

13

Eukaryotic translation initiation factor eIF5 promotes the accuracy of start codon recognition by regulating Pi release and conformational transitions of the preinitiation complex

Saini, A. K., Nanda, J. S., Martin-Marcos, P., Dong, J., Zhang, F., Bhardwaj, M., Lorsch, J. R., Hinnebusch, A. G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.87 MB

english, 2014

14

Homodimerization of RBPMS2 through a new RRM-interaction motif is necessary to control smooth muscle plasticity

Sagnol, S., Yang, Y., Bessin, Y., Allemand, F., Hapkova, I., Notarnicola, C., Guichou, J.-F., Faure, S., Labesse, G., Santa Barbara, P. d.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.88 MB

english, 2014

15

Chimeric bifunctional oligonucleotides as a novel tool to invade telomerase assembly

Azhibek, D., Zvereva, M., Zatsepin, T., Rubtsova, M., Dontsova, O.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.66 MB

english, 2014

16

Repair of O6-methylguanine adducts in human telomeric G-quadruplex DNA by O6-alkylguanine-DNA alkyltransferase

Hellman, L. M., Spear, T. J., Koontz, C. J., Melikishvili, M., Fried, M. G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.71 MB

english, 2014

17

Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles

Khisamutdinov, E. F., Li, H., Jasinski, D. L., Chen, J., Fu, J., Guo, P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.03 MB

english, 2014

18

Improved artificial origins for phage 29 terminal protein-primed replication. Insights into early replication events

Gella, P., Salas, M., Mencia, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 9.03 MB

english, 2014

19

The telomeric protein Pot1 from Schizosaccharomyces pombe binds ssDNA in two modes with differing 3' end availability

Dickey, T. H., Wuttke, D. S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.97 MB

english, 2014

20

Exquisite allele discrimination by toehold hairpin primers

Byrom, M., Bhadra, S., Jiang, Y. S., Ellington, A. D.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.60 MB

english, 2014

21

New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae

Blanchet, S., Cornu, D., Argentini, M., Namy, O.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.31 MB

english, 2014

22

The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription

Miron-Garcia, M. C., Garrido-Godino, A. I., Martinez-Fernandez, V., Fernandez-Pevida, A., Cuevas-Bermudez, A., Martin-Exposito, M., Chavez, S., de la Cruz, J., Navarro, F.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.86 MB

english, 2014

23

Negative feedback regulation of calcineurin-dependent Prz1 transcription factor by the CaMKK-CaMK1 axis in fission yeast

Cisneros-Barroso, E., Yance-Chavez, T., Kito, A., Sugiura, R., Gomez-Hierro, A., Gimenez-Zaragoza, D., Aligue, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.99 MB

english, 2014

24

Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity

Yadav, V. K., Thakur, R. K., Eckloff, B., Baral, A., Singh, A., Halder, R., Kumar, A., Alam, M. P., Kundu, T. K., Pandita, R., Pandita, T. K., Wieben, E. D., Chowdhury, S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.35 MB

english, 2014

25

A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies

Sun, J., Li, W., Sun, Y., Yu, D., Wen, X., Wang, H., Cui, J., Wang, G., Hoffman, A. R., Hu, J.-F.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.89 MB

english, 2014

26

Quantitative models for accelerated protein dissociation from nucleosomal DNA

Chen, C., Bundschuh, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 829 KB

english, 2014

27

Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs

Salinas, T., El Farouk-Ameqrane, S., Ubrig, E., Sauter, C., Duchene, A.-M., Marechal-Drouard, L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.55 MB

english, 2014

28

SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

Yalamanchili, H. K., Li, Z., Wang, P., Wong, M. P., Yao, J., Wang, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.07 MB

english, 2014

29

Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus

Gosalia, N., Neems, D., Kerschner, J. L., Kosak, S. T., Harris, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 757 KB

english, 2014

30

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

Lomsadze, A., Burns, P. D., Borodovsky, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 622 KB

english, 2014

31

Nucleic Acids Research: VOLUME 42 ISSUE 15 2014

Journal:

Nucleic Acids Research

Year:

2014

File:

PDF, 7.00 MB

2014

32

Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes

Nam, G.-M., Arya, G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.71 MB

english, 2014

33

Rrd1p, an RNA polymerase II-specific prolyl isomerase and activator of phosphoprotein phosphatase, promotes transcription independently of rapamycin response

Sen, R., Malik, S., Frankland-Searby, S., Uprety, B., Lahudkar, S., Bhaumik, S. R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 8.59 MB

english, 2014

34

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

Smits, A. H., Lindeboom, R. G. H., Perino, M., van Heeringen, S. J., Veenstra, G. J. C., Vermeulen, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 872 KB

english, 2014

35

Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development

Singer, R., Atar, S., Atias, O., Oron, E., Segal, D., Hirsch, J. A., Tuller, T., Orian, A., Chamovitz, D. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1021 KB

english, 2014

36

Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency

Deschamps-Francoeur, G., Garneau, D., Dupuis-Sandoval, F., Roy, A., Frappier, M., Catala, M., Couture, S., Barbe-Marcoux, M., Abou-Elela, S., Scott, M. S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.09 MB

english, 2014

37

Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase

Gaur, V., Vyas, R., Fowler, J. D., Efthimiopoulos, G., Feng, J. Y., Suo, Z.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.28 MB

english, 2014

38

Engineering the elongation factor Tu for efficient selenoprotein synthesis

Haruna, K.-i., Alkazemi, M. H., Liu, Y., Soll, D., Englert, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.01 MB

english, 2014

39

Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain

Prusa, J., Missak, J., Kittrell, J., Evans, J. J., Tapprich, W. E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 12.66 MB

english, 2014

40

Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli

Nilsson, A. N., Emilsson, G., Nyberg, L. K., Noble, C., Stadler, L. S., Fritzsche, J., Moore, E. R. B., Tegenfeldt, J. O., Ambjornsson, T., Westerlund, F.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.20 MB

english, 2014

41

Epstein-Barr virus nuclear antigen 3A protein regulates CDKN2B transcription via interaction with MIZ-1

Bazot, Q., Deschamps, T., Tafforeau, L., Siouda, M., Leblanc, P., Harth-Hertle, M. L., Rabourdin-Combe, C., Lotteau, V., Kempkes, B., Tommasino, M., Gruffat, H., Manet, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.85 MB

english, 2014

42

7SL RNA represses p53 translation by competing with HuR

Abdelmohsen, K., Panda, A. C., Kang, M.-J., Guo, R., Kim, J., Grammatikakis, I., Yoon, J.-H., Dudekula, D. B., Noh, J. H., Yang, X., Martindale, J. L., Gorospe, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.84 MB

english, 2014

43

Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing

Seguin-Estevez, Q., Dunand-Sauthier, I., Lemeille, S., Iseli, C., Ibberson, M., Ioannidis, V., Schmid, C. D., Rousseau, P., Barras, E., Geinoz, A., Xenarios, I., Acha-Orbea, H., Reith, W.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.80 MB

english, 2014

44

The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence

Wen, Y., Behiels, E., Felix, J., Elegheert, J., Vergauwen, B., Devreese, B., Savvides, S. N.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 9.98 MB

english, 2014

45

A fully enzymatic method for site-directed spin labeling of long RNA

Lebars, I., Vileno, B., Bourbigot, S., Turek, P., Wolff, P., Kieffer, B.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.41 MB

english, 2014

46

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

Jost, D., Carrivain, P., Cavalli, G., Vaillant, C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.23 MB

english, 2014

47

Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei

Reynolds, D., Cliffe, L., Forstner, K. U., Hon, C.-C., Siegel, T. N., Sabatini, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.31 MB

english, 2014

48

Fanconi anemia signaling and Mus81 cooperate to safeguard development and crosslink repair

Larin, M., Gallo, D., Tamblyn, L., Yang, J., Liao, H., Sabat, N., Brown, G. W., McPherson, J. P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 12.24 MB

english, 2014

49

Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering

Srivastava, A. K., Chopra, R., Ali, S., Aggarwal, S., Vig, L., Koul Bamezai, R. N.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.86 MB

english, 2014

50

ATP insertion opposite 8-oxo-deoxyguanosine by Pol4 mediates error-free tolerance in Schizosaccharomyces pombe

Sastre-Moreno, G., Sanchez, A., Esteban, V., Blanco, L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 8.22 MB

english, 2014

51

Drosophila Brahma complex remodels nucleosome organizations in multiple aspects

Shi, J., Zheng, M., Ye, Y., Li, M., Chen, X., Hu, X., Sun, J., Zhang, X., Jiang, C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.18 MB

english, 2014

52

Hydration of protein-RNA recognition sites

Barik, A., Bahadur, R. P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.85 MB

english, 2014

53

Effects of genetic variations on microRNA: target interactions

Liu, C., Rennie, W. A., Carmack, C. S., Kanoria, S., Cheng, J., Lu, J., Ding, Y.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.54 MB

english, 2014

54

Crucial role of the Rcl1p-Bms1p interaction for yeast pre-ribosomal RNA processing

Delprato, A., Kadri, Y. A., Perebaskine, N., Monfoulet, C., Henry, Y., Henras, A. K., Fribourg, S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.69 MB

english, 2014

55

Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis

Koster, T., Meyer, K., Weinholdt, C., Smith, L. M., Lummer, M., Speth, C., Grosse, I., Weigel, D., Staiger, D.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.99 MB

english, 2014

56

An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion synthesis polymerases within the B family

Jozwiakowski, S. K., Keith, B. J., Gilroy, L., Doherty, A. J., Connolly, B. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 8.93 MB

english, 2014

57

RNA recognition and self-association of CPEB4 is mediated by its tandem RRM domains

Schelhorn, C., Gordon, J. M. B., Ruiz, L., Alguacil, J., Pedroso, E., Macias, M. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.62 MB

english, 2014

58

The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus

Senissar, M., Saux, A. L., Belgareh-Touze, N., Adam, C., Banroques, J., Tanner, N. K.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 8.14 MB

english, 2014

59

Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho

Shashni, R., Qayyum, M. Z., Vishalini, V., Dey, D., Sen, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.96 MB

english, 2014

60

HIV-1 Nef and KSHV oncogene K1 synergistically promote angiogenesis by inducing cellular miR-718 to regulate the PTEN/AKT/mTOR signaling pathway

Xue, M., Yao, S., Hu, M., Li, W., Hao, T., Zhou, F., Zhu, X., Lu, H., Qin, D., Yan, Q., Zhu, J., Gao, S.-J., Lu, C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 26.48 MB

english, 2014

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