Volume 40; Issue 20

Main
Nucleic Acids Research
Volume 40; Issue 20

Nucleic Acids Research

Volume 40; Issue 20

1

RNAsnap : a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria

Stead, M. B., Agrawal, A., Bowden, K. E., Nasir, R., Mohanty, B. K., Meagher, R. B., Kushner, S. R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

2

Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes

Liu, H.-w., Zhang, J., Heine, G. F., Arora, M., Gulcin Ozer, H., Onti-Srinivasan, R., Huang, K., Parvin, J. D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 9.44 MB

english, 2012

3

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlen, M., Nielsen, J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 16.56 MB

english, 2012

4

Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation

Hashimoto, H., Hong, S., Bhagwat, A. S., Zhang, X., Cheng, X.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 9.66 MB

english, 2012

5

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Namiki, T., Hachiya, T., Tanaka, H., Sakakibara, Y.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 2.51 MB

english, 2012

6

Oligomerization and DNA binding of Ler, a master regulator of pathogenicity of enterohemorrhagic and enteropathogenic Escherichia coli

Garcia, J., Cordeiro, T. N., Prieto, M. J., Pons, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 8.58 MB

english, 2012

7

UVA-induced DNA double-strand breaks result from the repair of clustered oxidative DNA damages

Greinert, R., Volkmer, B., Henning, S., Breitbart, E. W., Greulich, K. O., Cardoso, M. C., Rapp, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.62 MB

english, 2012

8

Modelling and simulating generic RNA-Seq experiments with the flux simulator

Griebel, T., Zacher, B., Ribeca, P., Raineri, E., Lacroix, V., Guigo, R., Sammeth, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 8.22 MB

english, 2012

9

A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity

Liang, J. C., Chang, A. L., Kennedy, A. B., Smolke, C. D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 2.49 MB

english, 2012

10

RTL-P: a sensitive approach for detecting sites of 2'-O-methylation in RNA molecules

Dong, Z.-W., Shao, P., Diao, L.-T., Zhou, H., Yu, C.-H., Qu, L.-H.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.80 MB

english, 2012

11

Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli

Tsai, Y.-C., Du, D., Dominguez-Malfavon, L., Dimastrogiovanni, D., Cross, J., Callaghan, A. J., Garcia-Mena, J., Luisi, B. F.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.69 MB

english, 2012

12

A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop

Wanrooij, P. H., Uhler, J. P., Shi, Y., Westerlund, F., Falkenberg, M., Gustafsson, C. M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.64 MB

english, 2012

13

Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase

Ito, K., Murakami, R., Mochizuki, M., Qi, H., Shimizu, Y., Miura, K.-i., Ueda, T., Uchiumi, T.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.87 MB

english, 2012

14

Multipartite control of the DNA translocase, Mfd

Smith, A. J., Pernstich, C., Savery, N. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.97 MB

english, 2012

15

PARP activation regulates the RNA-binding protein NONO in the DNA damage response to DNA double-strand breaks

Krietsch, J., Caron, M.-C., Gagne, J.-P., Ethier, C., Vignard, J., Vincent, M., Rouleau, M., Hendzel, M. J., Poirier, G. G., Masson, J.-Y.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 2.74 MB

english, 2012

16

MutS and histone deacetylase complexes promote expansions of trinucleotide repeats in human cells

Gannon, A.-M. M., Frizzell, A., Healy, E., Lahue, R. S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 2.63 MB

english, 2012

17

Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways

Terekhova, K., Gunn, K. H., Marko, J. F., Mondragon, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 2.39 MB

english, 2012

18

The antibiotic Furvina(R) targets the P-site of 30S ribosomal subunits and inhibits translation initiation displaying start codon bias

Fabbretti, A., Brandi, L., Petrelli, D., Pon, C. L., Castanedo, N. R., Medina, R., Gualerzi, C. O.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.16 MB

english, 2012

19

Complementary strand relocation may play vital roles in RecA-based homology recognition

Peacock-Villada, A., Yang, D., Danilowicz, C., Feinstein, E., Pollock, N., McShan, S., Coljee, V., Prentiss, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.46 MB

english, 2012

20

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

Iwata, H., Gotoh, O.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 456 KB

english, 2012

21

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

Sievers, C., Schlumpf, T., Sawarkar, R., Comoglio, F., Paro, R.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 520 KB

english, 2012

22

Promoter propagation in prokaryotes

Matus-Garcia, M., Nijveen, H., van Passel, M. W. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.12 MB

english, 2012

23

Specific contacts of the -35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression

Csiszovszki, Z., Lewis, D. E. A., Le, P., Sneppen, K., Semsey, S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.74 MB

english, 2012

24

Identification of a two-layer regulatory network of proliferation-related microRNAs in hepatoma cells

Huang, Y., Chen, H.-C., Chiang, C.-W., Yeh, C.-T., Chen, S.-J., Chou, C.-K.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 12.91 MB

english, 2012

25

The architecture of eukaryotic translation

Chu, D., von der Haar, T.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 264 KB

english, 2012

26

Metal and ligand binding to the HIV-RNase H active site are remotely monitored by Ile556

Zheng, X., Mueller, G. A., DeRose, E. F., London, R. E.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.30 MB

english, 2012

27

miR-182 inhibits Schwann cell proliferation and migration by targeting FGF9 and NTM, respectively at an early stage following sciatic nerve injury

Yu, B., Qian, T., Wang, Y., Zhou, S., Ding, G., Ding, F., Gu, X.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.83 MB

english, 2012

28

Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments

Garcia-Alonso, L., Alonso, R., Vidal, E., Amadoz, A., de Maria, A., Minguez, P., Medina, I., Dopazo, J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.43 MB

english, 2012

29

Cell-cycle-regulated control of VSG expression site silencing by histones and histone chaperones ASF1A and CAF-1b in Trypanosoma brucei

Alsford, S., Horn, D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.63 MB

english, 2012

30

Mitochondrial DNA copy number is regulated in a tissue specific manner by DNA methylation of the nuclear-encoded DNA polymerase gamma A

Kelly, R. D. W., Mahmud, A., McKenzie, M., Trounce, I. A., St John, J. C.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 11.34 MB

english, 2012

31

New paradigms for conserved, multifactorial, cis-acting regulation of meiotic recombination

Wahls, W. P., Davidson, M. K.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.82 MB

english, 2012

32

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

Ocwieja, K. E., Sherrill-Mix, S., Mukherjee, R., Custers-Allen, R., David, P., Brown, M., Wang, S., Link, D. R., Olson, J., Travers, K., Schadt, E., Bushman, F. D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.72 MB

english, 2012

33

In vivo identification of essential nucleotides in tRNALeu to its functions by using a constructed yeast tRNALeu knockout strain

Huang, Q., Yao, P., Eriani, G., Wang, E.-D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.16 MB

english, 2012

34

Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA

Punekar, A. S., Shepherd, T. R., Liljeruhm, J., Forster, A. C., Selmer, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 16.08 MB

english, 2012

35

The slicing activity of miRNA-specific Argonautes is essential for the miRNA pathway in C. elegans

Bouasker, S., Simard, M. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.20 MB

english, 2012

36

Regulation of the nucleosome unwrapping rate controls DNA accessibility

North, J. A., Shimko, J. C., Javaid, S., Mooney, A. M., Shoffner, M. A., Rose, S. D., Bundschuh, R., Fishel, R., Ottesen, J. J., Poirier, M. G.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.93 MB

english, 2012

37

HapZipper: sharing HapMap populations just got easier

Chanda, P., Elhaik, E., Bader, J. S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.83 MB

english, 2012

38

Yeast CAF-1 assembles histone (H3-H4)2 tetramers prior to DNA deposition

Winkler, D. D., Zhou, H., Dar, M. A., Zhang, Z., Luger, K.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 1.90 MB

english, 2012

39

PALB2 self-interaction controls homologous recombination

Buisson, R., Masson, J.-Y.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.14 MB

english, 2012

40

Nrf2-MafG heterodimers contribute globally to antioxidant and metabolic networks

Hirotsu, Y., Katsuoka, F., Funayama, R., Nagashima, T., Nishida, Y., Nakayama, K., Douglas Engel, J., Yamamoto, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.82 MB

english, 2012

41

Nucleic Acids Research - Editorial Board

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 58 KB

english, 2012

42

Nucleic Acids Research: VOLUME 40 ISSUE 20 2012

Journal:

Nucleic Acids Research

Year:

2012

File:

PDF, 508 KB

2012

43

Subscriptions

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 51 KB

english, 2012

44

En bloc transfer of polyubiquitin chains to PCNA in vitro is mediated by two different human E2-E3 pairs

Masuda, Y., Suzuki, M., Kawai, H., Hishiki, A., Hashimoto, H., Masutani, C., Hishida, T., Suzuki, F., Kamiya, K.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.40 MB

english, 2012

45

Misacylation of tRNA with methionine in Saccharomyces cerevisiae

Wiltrout, E., Goodenbour, J. M., Frechin, M., Pan, T.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 8.23 MB

english, 2012

46

Nucleosome dynamics: HMGB1 relaxes canonical nucleosome structure to facilitate estrogen receptor binding

Joshi, S. R., Sarpong, Y. C., Peterson, R. C., Scovell, W. M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.20 MB

english, 2012

47

DNA repair endonuclease ERCC1-XPF as a novel therapeutic target to overcome chemoresistance in cancer therapy

McNeil, E. M., Melton, D. W.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.65 MB

english, 2012

48

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

Sati, S., Ghosh, S., Jain, V., Scaria, V., Sengupta, S.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.40 MB

english, 2012

49

Repeat or not repeat?--Statistical validation of tandem repeat prediction in genomic sequences

Schaper, E., Kajava, A. V., Hauser, A., Anisimova, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 2.02 MB

english, 2012

50

DOT1A-dependent H3K76 methylation is required for replication regulation in Trypanosoma brucei

Gassen, A., Brechtefeld, D., Schandry, N., Arteaga-Salas, J. M., Israel, L., Imhof, A., Janzen, C. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.26 MB

english, 2012

51

Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast

Tagwerker, C., Dupont, C. L., Karas, B. J., Ma, L., Chuang, R.-Y., Benders, G. A., Ramon, A., Novotny, M., Montague, M. G., Venepally, P., Brami, D., Schwartz, A., Andrews-Pfannkoch, C., Gibson, D. G.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.48 MB

english, 2012

52

The structural basis of differential DNA sequence recognition by restriction-modification controller proteins

Ball, N. J., McGeehan, J. E., Streeter, S. D., Thresh, S.- J., Kneale, G. G.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.55 MB

english, 2012

53

X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity

Hirata, A., Fujishima, K., Yamagami, R., Kawamura, T., Banfield, J. F., Kanai, A., Hori, H.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 16.31 MB

english, 2012

54

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

Gingold, H., Dahan, O., Pilpel, Y.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 6.26 MB

english, 2012

55

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells

Alexandrov, B. S., Fukuyo, Y., Lange, M., Horikoshi, N., Gelev, V., Rasmussen, K. O., Bishop, A. R., Usheva, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.43 MB

english, 2012

56

Promoters active in interphase are bookmarked during mitosis by ubiquitination

Arora, M., Zhang, J., Heine, G. F., Ozer, G., Liu, H.-w., Huang, K., Parvin, J. D.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 10.34 MB

english, 2012