Volume 42; Issue 14

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Nucleic Acids Research
Volume 42; Issue 14

Nucleic Acids Research

Volume 42; Issue 14

1

Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks

Wang, B., Barahona, M., Buck, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

2

Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study

Afonina, Z. A., Myasnikov, A. G., Shirokov, V. A., Klaholz, B. P., Spirin, A. S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 614 KB

english, 2014

3

G-quadruplexes within prion mRNA: the missing link in prion disease?

Olsthoorn, R. C. L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.99 MB

english, 2014

4

Structure, stability and behaviour of nucleic acids in ionic liquids

Tateishi-Karimata, H., Sugimoto, N.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.17 MB

english, 2014

5

Discovery of the -barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs

Kimura, S., Miyauchi, K., Ikeuchi, Y., Thiaville, P. C., Crecy-Lagard, V. d., Suzuki, T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.33 MB

english, 2014

6

G-quadruplexes are specifically recognized and distinguished by selected designed ankyrin repeat proteins

Scholz, O., Hansen, S., Pluckthun, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.73 MB

english, 2014

7

Single-cell RNA-seq: advances and future challenges

Saliba, A.-E., Westermann, A. J., Gorski, S. A., Vogel, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.40 MB

english, 2014

8

CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages

Martel, B., Moineau, S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 841 KB

english, 2014

9

Evidence of efficient stop codon readthrough in four mammalian genes

Loughran, G., Chou, M.-Y., Ivanov, I. P., Jungreis, I., Kellis, M., Kiran, A. M., Baranov, P. V., Atkins, J. F.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.39 MB

english, 2014

10

In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner

Sachdeva, G., Garg, A., Godding, D., Way, J. C., Silver, P. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.68 MB

english, 2014

11

Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5-SMG7 and SMG6

Chakrabarti, S., Bonneau, F., Schussler, S., Eppinger, E., Conti, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.14 MB

english, 2014

12

The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells

Keam, S. P., Young, P. E., McCorkindale, A. L., Dang, T. H. Y., Clancy, J. L., Humphreys, D. T., Preiss, T., Hutvagner, G., Martin, D. I. K., Cropley, J. E., Suter, C. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.06 MB

english, 2014

13

Engineering self-contained DNA circuit for proximity recognition and localized signal amplification of target biomolecules

Ang, Y. S., Yung, L.-Y. L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.91 MB

english, 2014

14

Road rules for traffic on DNA--systematic analysis of transcriptional roadblocking in vivo

Hao, N., Krishna, S., Ahlgren-Berg, A., Cutts, E. E., Shearwin, K. E., Dodd, I. B.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1006 KB

english, 2014

15

Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons

Szafranski, K., Fritsch, C., Schumann, F., Siebel, L., Sinha, R., Hampe, J., Hiller, M., Englert, C., Huse, K., Platzer, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.46 MB

english, 2014

16

Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases

Krishnakumar, R., Grose, C., Haft, D. H., Zaveri, J., Alperovich, N., Gibson, D. G., Merryman, C., Glass, J. I.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 932 KB

english, 2014

17

Molecular basis of nucleotide-dependent substrate engagement and remodeling by an AAA+ activator

Darbari, V. C., Lawton, E., Lu, D., Burrows, P. C., Wiesler, S., Joly, N., Zhang, N., Zhang, X., Buck, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.77 MB

english, 2014

18

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation

Tomaru, Y., Hasegawa, R., Suzuki, T., Sato, T., Kubosaki, A., Suzuki, M., Kawaji, H., Forrest, A. R. R., Hayashizaki, Y., Shin, J. W., Suzuki, H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.43 MB

english, 2014

19

A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB

Sievers, S., Sternkopf Lillebaek, E. M., Jacobsen, K., Lund, A., Mollerup, M. S., Nielsen, P. K., Kallipolitis, B. H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.75 MB

english, 2014

20

Design and characterization of a dual-mode promoter with activation and repression capability for tuning gene expression in yeast

Mazumder, M., McMillen, D. R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 695 KB

english, 2014

21

Subscriptions

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 58 KB

english, 2014

22

Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay

Larman, H. B., Scott, E. R., Wogan, M., Oliveira, G., Torkamani, A., Schultz, P. G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.98 MB

english, 2014

23

Inhibition of RNA binding to hepatitis C virus RNA-dependent RNA polymerase: a new mechanism for antiviral intervention

Ahmed-Belkacem, A., Guichou, J.-F., Brillet, R., Ahnou, N., Hernandez, E., Pallier, C., Pawlotsky, J.-M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.56 MB

english, 2014

24

Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition

Figiel, M., Nowotny, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.68 MB

english, 2014

25

The structural code of cyanobacterial genomes

Lehmann, R., Machne, R., Herzel, H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.20 MB

english, 2014

26

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes

Melnikov, A., Rogov, P., Wang, L., Gnirke, A., Mikkelsen, T. S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.87 MB

english, 2014

27

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

Gruber, A. J., Grandy, W. A., Balwierz, P. J., Dimitrova, Y. A., Pachkov, M., Ciaudo, C., Nimwegen, E. v., Zavolan, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 897 KB

english, 2014

28

Structural determinants of an internal ribosome entry site that direct translational reading frame selection

Ren, Q., Au, H. H. T., Wang, Q. S., Lee, S., Jan, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.34 MB

english, 2014

29

A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD

Nicholson, P., Josi, C., Kurosawa, H., Yamashita, A., Muhlemann, O.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 9.71 MB

english, 2014

30

Slow repair of lipid peroxidation-induced DNA damage at p53 mutation hotspots in human cells caused by low turnover of a DNA glycosylase

Woodrick, J., Gupta, S., Khatkar, P., Sarangi, S., Narasimhan, G., Trehan, A., Adhikari, S., Roy, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.51 MB

english, 2014

31

Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion

Swart, E. C., Wilkes, C. D., Sandoval, P. Y., Arambasic, M., Sperling, L., Nowacki, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.59 MB

english, 2014

32

Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site

D'Annessa, I., Coletta, A., Sutthibutpong, T., Mitchell, J., Chillemi, G., Harris, S., Desideri, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.78 MB

english, 2014

33

The RNA-mediated, asymmetric ring regulatory mechanism of the transcription termination Rho helicase decrypted by time-resolved Nucleotide Analog Interference Probing (trNAIP)

Soares, E., Schwartz, A., Nollmann, M., Margeat, E., Boudvillain, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.94 MB

english, 2014

34

ARH-seq: identification of differential splicing in RNA-seq data

Rasche, A., Lienhard, M., Yaspo, M.-L., Lehrach, H., Herwig, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.60 MB

english, 2014

35

Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses

Schnettler, E., Tykalova, H., Watson, M., Sharma, M., Sterken, M. G., Obbard, D. J., Lewis, S. H., McFarlane, M., Bell-Sakyi, L., Barry, G., Weisheit, S., Best, S. M., Kuhn, R. J., Pijlman, G. P., Cha

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.67 MB

english, 2014

36

Acute hypoxia affects P-TEFb through HDAC3 and HEXIM1-dependent mechanism to promote gene-specific transcriptional repression

Safronova, O. S., Nakahama, K.-I., Morita, I.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 14.06 MB

english, 2014

37

Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer

L'Abbate, A., Macchia, G., D'Addabbo, P., Lonoce, A., Tolomeo, D., Trombetta, D., Kok, K., Bartenhagen, C., Whelan, C. W., Palumbo, O., Severgnini, M., Cifola, I., Dugas, M., Carella, M., De Bellis, G

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.30 MB

english, 2014

38

DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal

Britton, S., Dernoncourt, E., Delteil, C., Froment, C., Schiltz, O., Salles, B., Frit, P., Calsou, P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.48 MB

english, 2014

39

The mRNP remodeling mediated by UPF1 promotes rapid degradation of replication-dependent histone mRNA

Choe, J., Ahn, S. H., Kim, Y. K.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.86 MB

english, 2014

40

Psip1/Ledgf p75 restrains Hox gene expression by recruiting both trithorax and polycomb group proteins

Pradeepa, M. M., Grimes, G. R., Taylor, G. C. A., Sutherland, H. G., Bickmore, W. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.76 MB

english, 2014

41

Nuclear dynamics of topoisomerase II reflects its catalytic activity that is regulated by binding of RNA to the C-terminal domain

Onoda, A., Hosoya, O., Sano, K., Kiyama, K., Kimura, H., Kawano, S., Furuta, R., Miyaji, M., Tsutsui, K., Tsutsui, K. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.94 MB

english, 2014

42

Microscopic mechanism of DNA damage searching by hOGG1

Rowland, M. M., Schonhoft, J. D., McKibbin, P. L., David, S. S., Stivers, J. T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.29 MB

english, 2014

43

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2014

File:

PDF, 421 KB

2014

44

VNTRseek--a computational tool to detect tandem repeat variants in high-throughput sequencing data

Gelfand, Y., Hernandez, Y., Loving, J., Benson, G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 657 KB

english, 2014

45

The PARP inhibitor Olaparib disrupts base excision repair of 5-aza-2'-deoxycytidine lesions

Orta, M. L., Hoglund, A., Calderon-Montano, J. M., Dominguez, I., Burgos-Moron, E., Visnes, T., Pastor, N., Strom, C., Lopez-lazaro, M., Helleday, T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.15 MB

english, 2014

46

A dimeric state for PRC2

Davidovich, C., Goodrich, K. J., Gooding, A. R., Cech, T. R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.90 MB

english, 2014

47

Spacing requirements for Class I transcription activation in bacteria are set by promoter elements

Zhou, Y., Kolb, A., Busby, S. J. W., Wang, Y.-P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.63 MB

english, 2014

48

Engineered TAL Effector modulators for the large-scale gain-of-function screening

Zhang, H., Li, J., Hou, S., Wang, G., Jiang, M., Sun, C., Hu, X., Zhuang, F., Dai, Z., Dai, J., Xi, J. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.74 MB

english, 2014

49

SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples

Kimes, P. K., Cabanski, C. R., Wilkerson, M. D., Zhao, N., Johnson, A. R., Perou, C. M., Makowski, L., Maher, C. A., Liu, Y., Marron, J. S., Hayes, D. N.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.64 MB

english, 2014

50

metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA

Dale, R. K., Matzat, L. H., Lei, E. P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 8.19 MB

english, 2014

51

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

Giallonardo, F. D., Topfer, A., Rey, M., Prabhakaran, S., Duport, Y., Leemann, C., Schmutz, S., Campbell, N. K., Joos, B., Lecca, M. R., Patrignani, A., Daumer, M., Beisel, C., Rusert, P., Trkola, A.,

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.19 MB

english, 2014

52

5' isomiR variation is of functional and evolutionary importance

Tan, G. C., Chan, E., Molnar, A., Sarkar, R., Alexieva, D., Isa, I. M., Robinson, S., Zhang, S., Ellis, P., Langford, C. F., Guillot, P. V., Chandrashekran, A., Fisk, N. M., Castellano, L., Meister, G

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.30 MB

english, 2014

53

The effect of tRNA levels on decoding times of mRNA codons

Dana, A., Tuller, T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.03 MB

english, 2014

54

The effect of Pot1 binding on the repair of thymine analogs in a telomeric DNA sequence

Theruvathu, J. A., Darwanto, A., Hsu, C. W., Sowers, L. C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 736 KB

english, 2014

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