Volume 40; Issue 19

Main
Nucleic Acids Research
Volume 40; Issue 19

Nucleic Acids Research

Volume 40; Issue 19

1

GFam: a platform for automatic annotation of gene families

Sasidharan, R., Nepusz, T., Swarbreck, D., Huala, E., Paccanaro, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

2

microRNAs associated with the different human Argonaute proteins

Dueck, A., Ziegler, C., Eichner, A., Berezikov, E., Meister, G.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.74 MB

english, 2012

3

Toward a combinatorial nature of microRNA regulation in human cells

Balaga, O., Friedman, Y., Linial, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.83 MB

english, 2012

4

A distant cis acting intronic element induces site-selective RNA editing

Daniel, C., Veno, M. T., Ekdahl, Y., Kjems, J., Ohman, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.00 MB

english, 2012

5

Transferring isolated mitochondria into tissue culture cells

Yang, Y.-W., Koob, M. D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.90 MB

english, 2012

6

2'-Deoxyriboguanylurea, the primary breakdown product of 5-aza-2'-deoxyribocytidine, is a mutagen, an epimutagen, an inhibitor of DNA methyltransferases and an inducer of 5-azacytidine-type fragile sites

Lamparska, K., Clark, J., Babilonia, G., Bedell, V., Yip, W., Smith, S. S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.47 MB

english, 2012

7

p53-Independent regulation of p21Waf1/Cip1 expression and senescence by PRMT6

Phalke, S., Mzoughi, S., Bezzi, M., Jennifer, N., Mok, W. C., Low, D. H. P., Thike, A. A., Kuznetsov, V. A., Tan, P. H., Voorhoeve, P. M., Guccione, E.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.29 MB

english, 2012

8

The role of Ca2+ in the activity of Mycobacterium tuberculosis DNA gyrase

Karkare, S., Yousafzai, F., Mitchenall, L. A., Maxwell, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.62 MB

english, 2012

9

Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis

Rochat, T., Nicolas, P., Delumeau, O., Rabatinova, A., Korelusova, J., Leduc, A., Bessieres, P., Dervyn, E., Krasny, L., Noirot, P.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.25 MB

english, 2012

10

Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease

Horton, J. R., Mabuchi, M. Y., Cohen-Karni, D., Zhang, X., Griggs, R. M., Samaranayake, M., Roberts, R. J., Zheng, Y., Cheng, X.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 18.65 MB

english, 2012

11

3D chromatin conformation correlates with replication timing and is conserved in resting cells

Moindrot, B., Audit, B., Klous, P., Baker, A., Thermes, C., de Laat, W., Bouvet, P., Mongelard, F., Arneodo, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 10.55 MB

english, 2012

12

Cockayne Syndrome group B protein interacts with TRF2 and regulates telomere length and stability

Batenburg, N. L., Mitchell, T. R. H., Leach, D. M., Rainbow, A. J., Zhu, X.-D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 10.74 MB

english, 2012

13

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

Zhang, S., Liu, C.-C., Li, W., Shen, H., Laird, P. W., Zhou, X. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.51 MB

english, 2012

14

Co-clustering phenome-genome for phenotype classification and disease gene discovery

Hwang, T., Atluri, G., Xie, M., Dey, S., Hong, C., Kumar, V., Kuang, R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.36 MB

english, 2012

15

Motif effects in Affymetrix GeneChips seriously affect probe intensities

Upton, G. J. G., Harrison, A. P.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 816 KB

english, 2012

16

Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets

Allenby, N. E. E., Laing, E., Bucca, G., Kierzek, A. M., Smith, C. P.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.42 MB

english, 2012

17

Winding single-molecule double-stranded DNA on a nanometer-sized reel

You, H., Iino, R., Watanabe, R., Noji, H.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.40 MB

english, 2012

18

Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription

Cong, R., Das, S., Ugrinova, I., Kumar, S., Mongelard, F., Wong, J., Bouvet, P.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.53 MB

english, 2012

19

Detection of dispersed short tandem repeats using reversible jump Markov chain Monte Carlo

Liang, T., Fan, X., Li, Q., Li, S.-y. R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 274 KB

english, 2012

20

Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis

Richter, H., Zoephel, J., Schermuly, J., Maticzka, D., Backofen, R., Randau, L.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.34 MB

english, 2012

21

Helicobacter pylori oriC--the first bipartite origin of chromosome replication in Gram-negative bacteria

Donczew, R., Weigel, C., Lurz, R., Zakrzewska-Czerwinska, J., Zawilak-Pawlik, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 12.00 MB

english, 2012

22

Recurrent transcriptional clusters in the genome of mouse pluripotent stem cells

Skylaki, S., Tomlinson, S. R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 13.88 MB

english, 2012

23

Cell type-specific genomics of Drosophila neurons

Henry, G. L., Davis, F. P., Picard, S., Eddy, S. R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 13.45 MB

english, 2012

24

PDGF enhances IRES-mediated translation of Laminin B1 by cytoplasmic accumulation of La during epithelial to mesenchymal transition

Petz, M., Them, N. C. C., Huber, H., Mikulits, W.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.62 MB

english, 2012

25

Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA

Morera, S., Grin, I., Vigouroux, A., Couve, S., Henriot, V., Saparbaev, M., Ishchenko, A. A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.38 MB

english, 2012

26

Intrinsic properties of Tcf1 and Tcf4 splice variants determine cell-type-specific Wnt/ -catenin target gene expression

Wallmen, B., Schrempp, M., Hecht, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.87 MB

english, 2012

27

DNA stabilization at the Bacillus subtilis PolX core--a binding model to coordinate polymerase, AP-endonuclease and 3'-5' exonuclease activities

Banos, B., Villar, L., Salas, M., de Vega, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 11.35 MB

english, 2012

28

dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes

Lloret-Llinares, M., Perez-Lluch, S., Rossell, D., Moran, T., Ponsa-Cobas, J., Auer, H., Corominas, M., Azorin, F.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.73 MB

english, 2012

29

p32/gC1qR is indispensable for fetal development and mitochondrial translation: importance of its RNA-binding ability

Yagi, M., Uchiumi, T., Takazaki, S., Okuno, B., Nomura, M., Yoshida, S.-i., Kanki, T., Kang, D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.01 MB

english, 2012

30

The ATPase activity of Fml1 is essential for its roles in homologous recombination and DNA repair

Nandi, S., Whitby, M. C.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.30 MB

english, 2012

31

A small RNA response at DNA ends in Drosophila

Michalik, K. M., Bottcher, R., Forstemann, K.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 337 KB

english, 2012

32

Nucleotide excision repair of 2-acetylaminofluorene- and 2-aminofluorene-(C8)-guanine adducts: molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair efficiencies

Mu, H., Kropachev, K., Wang, L., Zhang, L., Kolbanovskiy, A., Kolbanovskiy, M., E. Geacintov, N., Broyde, S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 10.43 MB

english, 2012

33

Subscriptions

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 49 KB

english, 2012

34

Nucleoside analog studies indicate mechanistic differences between RNA-editing adenosine deaminases

Mizrahi, R. A., Phelps, K. J., Ching, A. Y., Beal, P. A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 2.67 MB

english, 2012

35

Histone dosage regulates DNA damage sensitivity in a checkpoint-independent manner by the homologous recombination pathway

Liang, D., Burkhart, S. L., Singh, R. K., Kabbaj, M.-H. M., Gunjan, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.61 MB

english, 2012

36

Targeting a pre-mRNA structure with bipartite antisense molecules modulates tau alternative splicing

Peacey, E., Rodriguez, L., Liu, Y., Wolfe, M. S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.83 MB

english, 2012

37

Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA

Wojtas, M. N., Mogni, M., Millet, O., Bell, S. D., Abrescia, N. G. A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 15.28 MB

english, 2012

38

Ablation of PRMT6 reveals a role as a negative transcriptional regulator of the p53 tumor suppressor

Neault, M., Mallette, F. A., Vogel, G., Michaud-Levesque, J., Richard, S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.09 MB

english, 2012

39

Deoxycytidine kinase regulates the G2/M checkpoint through interaction with cyclin-dependent kinase 1 in response to DNA damage

Yang, C., Lee, M., Hao, J., Cui, X., Guo, X., Smal, C., Bontemps, F., Ma, S., Liu, X., Engler, D., Parker, W. B., Xu, B.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.99 MB

english, 2012

40

Meiotic DNA joint molecule resolution depends on Nse5-Nse6 of the Smc5-Smc6 holocomplex

Wehrkamp-Richter, S., Hyppa, R. W., Prudden, J., Smith, G. R., Boddy, M. N.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 11.30 MB

english, 2012

41

Structure of the RNA claw of the DNA packaging motor of bacteriophage 29

Harjes, E., Kitamura, A., Zhao, W., Morais, M. C., Jardine, P. J., Grimes, S., Matsuo, H.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.35 MB

english, 2012

42

Nucleic Acids Research - Editorial Board

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 58 KB

english, 2012

43

Towards the classification of DYT6 dystonia mutants in the DNA-binding domain of THAP1

Campagne, S., Muller, I., Milon, A., Gervais, V.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.69 MB

english, 2012

44

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

Scheibe, M., Butter, F., Hafner, M., Tuschl, T., Mann, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 441 KB

english, 2012

45

Rhythmic binding of Topoisomerase I impacts on the transcription of Bmal1 and circadian period

Onishi, Y., Kawano, Y.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.99 MB

english, 2012

46

Translation termination efficiency modulates ATF4 response by regulating ATF4 mRNA translation at 5' short ORFs

Ait Ghezala, H., Jolles, B., Salhi, S., Castrillo, K., Carpentier, W., Cagnard, N., Bruhat, A., Fafournoux, P., Jean-Jean, O.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.18 MB

english, 2012

47

The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease

Messing, S. A. J., Ton-Hoang, B., Hickman, A. B., McCubbin, A. J., Peaslee, G. F., Ghirlando, R., Chandler, M., Dyda, F.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 13.02 MB

english, 2012

48

Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns

Chan, T.-M., Leung, K.-S., Lee, K.-H., Wong, M.-H., Lau, T. C.-K., Tsui, S. K.-W.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.36 MB

english, 2012

49

DNA of a circular minichromosome linearized by restriction enzymes or other reagents is resistant to further cleavage: an influence of chromatin topology on the accessibility of DNA

Kumala, S., Hadj-Sahraoui, Y., Rzeszowska-Wolny, J., Hancock, R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.02 MB

english, 2012

50

Nucleosomes affect local transformation efficiency

Aslankoohi, E., Voordeckers, K., Sun, H., Sanchez-Rodriguez, A., van der Zande, E., Marchal, K., Verstrepen, K. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.59 MB

english, 2012

51

A novel Plasmodium falciparum SR protein is an alternative splicing factor required for the parasites' proliferation in human erythrocytes

Eshar, S., Allemand, E., Sebag, A., Glaser, F., Muchardt, C., Mandel-Gutfreund, Y., Karni, R., Dzikowski, R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.71 MB

english, 2012

52

Silencing of Parkinson's disease-associated genes with artificial mirtron mimics of miR-1224

Sibley, C. R., Seow, Y., Curtis, H., Weinberg, M. S., Wood, M. J. A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.42 MB

english, 2012

53

Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation

Skreka, K., Schafferer, S., Nat, I.-R., Zywicki, M., Salti, A., Apostolova, G., Griehl, M., Rederstorff, M., Dechant, G., Huttenhofer, A.

Journal:

Nucleic Acids Research

Year:

2012

File:

PDF, 31 KB

2012

54

Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation

Skreka, K., Schafferer, S., Nat, I.-R., Zywicki, M., Salti, A., Apostolova, G., Griehl, M., Rederstorff, M., Dechant, G., Huttenhofer, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 31 KB

english, 2012

55

A single amino acid change in histone H4 enhances UV survival and DNA repair in yeast

Nag, R., Gong, F., Fahy, D., Smerdon, M. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 340 KB

english, 2012