Volume 41; Issue 1

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Nucleic Acids Research
Volume 41; Issue 1

Nucleic Acids Research

Volume 41; Issue 1

1

Mammalian cells acquire epigenetic hallmarks of human cancer during immortalization

Tommasi, S., Zheng, A., Weninger, A., Bates, S. E., Li, X. A., Wu, X., Hollstein, M., Besaratinia, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 17.02 MB

english, 2013

2

Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits

Yang, S., Sleight, S. C., Sauro, H. M.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.73 MB

english, 2013

3

Selection of a T7 promoter mutant with enhanced in vitro activity by a novel multi-copy bead display approach for in vitro evolution

Paul, S., Stang, A., Lennartz, K., Tenbusch, M., Uberla, K.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.75 MB

english, 2013

4

Comparison of mRNA features affecting translation initiation and reinitiation

Osterman, I. A., Evfratov, S. A., Sergiev, P. V., Dontsova, O. A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.25 MB

english, 2013

5

Mechanism of RNA 2',3'-cyclic phosphate end healing by T4 polynucleotide kinase-phosphatase

Das, U., Shuman, S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.41 MB

english, 2013

6

Targeting the DNA-binding activity of the human ERG transcription factor using new heterocyclic dithiophene diamidines

Nhili, R., Peixoto, P., Depauw, S., Flajollet, S., Dezitter, X., Munde, M. M., Ismail, M. A., Kumar, A., Farahat, A. A., Stephens, C. E., Duterque-Coquillaud, M., David Wilson, W., Boykin, D. W., Davi

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.32 MB

english, 2013

7

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., Glockner, F. O.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 798 KB

english, 2013

8

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

Gluncic, M., Paar, V.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.29 MB

english, 2013

9

Exome RNA sequencing reveals rare and novel alternative transcripts

Halvardson, J., Zaghlool, A., Feuk, L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.37 MB

english, 2013

10

Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution

Chen, L., Shi, K., Yin, Z., Aihara, H.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 755 KB

english, 2013

11

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Balasubramanian, D., Schneper, L., Kumari, H., Mathee, K.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 707 KB

english, 2013

12

The BET bromodomain inhibitor JQ1 activates HIV latency through antagonizing Brd4 inhibition of Tat-transactivation

Li, Z., Guo, J., Wu, Y., Zhou, Q.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.60 MB

english, 2013

13

Global analysis of mRNA stability in Mycobacterium tuberculosis

Rustad, T. R., Minch, K. J., Brabant, W., Winkler, J. K., Reiss, D. J., Baliga, N. S., Sherman, D. R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 552 KB

english, 2013

14

Dissociation and re-association of RNA polymerase with DNA during osmotic stress response in Escherichia coli

Cagliero, C., Jin, D. J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.95 MB

english, 2013

15

NGC: lossless and lossy compression of aligned high-throughput sequencing data

Popitsch, N., von Haeseler, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 961 KB

english, 2013

16

Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility

McCauley, M. J., Rueter, E. M., Rouzina, I., Maher, L. J., Williams, M. C.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.27 MB

english, 2013

17

Quantifying RNA-protein interactions in situ using modified-MTRIPs and proximity ligation

Jung, J., Lifland, A. W., Zurla, C., Alonas, E. J., Santangelo, P. J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 12.59 MB

english, 2013

18

Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR

Reginsson, G. W., Shelke, S. A., Rouillon, C., White, M. F., Sigurdsson, S. T., Schiemann, O.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.65 MB

english, 2013

19

Noncoder: a web interface for exon array-based detection of long non-coding RNAs

Gellert, P., Ponomareva, Y., Braun, T., Uchida, S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 8.00 MB

english, 2013

20

A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples

Maehara, K., Odawara, J., Harada, A., Yoshimi, T., Nagao, K., Obuse, C., Akashi, K., Tachibana, T., Sakata, T., Ohkawa, Y.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.94 MB

english, 2013

21

Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes

Rand, K. N., Young, G. P., Ho, T., Molloy, P. L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.08 MB

english, 2013

22

Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1 ,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression

Seuter, S., Heikkinen, S., Carlberg, C.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.52 MB

english, 2013

23

Metagenomic abundance estimation and diagnostic testing on species level

Lindner, M. S., Renard, B. Y.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 395 KB

english, 2013

24

Possible steps of complete disassembly of post-termination complex by yeast eEF3 deduced from inhibition by translocation inhibitors

Kurata, S., Shen, B., Liu, J. O., Takeuchi, N., Kaji, A., Kaji, H.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.47 MB

english, 2013

25

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

Liu, J., Wang, H., Yang, H., Zhang, Y., Wang, J., Zhao, F., Qi, J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 8.33 MB

english, 2013

26

Sequence verification of synthetic DNA by assembly of sequencing reads

Wilson, M. L., Cai, Y., Hanlon, R., Taylor, S., Chevreux, B., Setubal, J. C., Tyler, B. M., Peccoud, J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.37 MB

english, 2013

27

Mechanism of promoter repression by Lac repressor-DNA loops

Becker, N. A., Peters, J. P., Lionberger, T. A., Maher, L. J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.62 MB

english, 2013

28

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata

Krishna, S., Nair, A., Cheedipudi, S., Poduval, D., Dhawan, J., Palakodeti, D., Ghanekar, Y.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.10 MB

english, 2013

29

Silencing of human DNA polymerase causes replication stress and is synthetically lethal with an impaired S phase checkpoint

Zucca, E., Bertoletti, F., Wimmer, U., Ferrari, E., Mazzini, G., Khoronenkova, S., Grosse, N., van Loon, B., Dianov, G., Hubscher, U., Maga, G.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.44 MB

english, 2013

30

miRNA repression of translation in vitro takes place during 43S ribosomal scanning

Ricci, E. P., Limousin, T., Soto-Rifo, R., Rubilar, P. S., Decimo, D., Ohlmann, T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.98 MB

english, 2013

31

Genetic interactions suggest multiple distinct roles of the arch and core helicase domains of Mtr4 in Rrp6 and exosome function

Klauer, A. A., van Hoof, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.52 MB

english, 2013

32

The common ancestral core of vertebrate and fungal telomerase RNAs

Qi, X., Li, Y., Honda, S., Hoffmann, S., Marz, M., Mosig, A., Podlevsky, J. D., Stadler, P. F., Selker, E. U., Chen, J. J.- L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.52 MB

english, 2013

33

X-inactivation: quantitative predictions of protein interactions in the Xist network

Agostini, F., Cirillo, D., Bolognesi, B., Tartaglia, G. G.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.30 MB

english, 2013

34

MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.24 MB

english, 2013

35

Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends

Driessen, R. P. C., Meng, H., Suresh, G., Shahapure, R., Lanzani, G., Priyakumar, U. D., White, M. F., Schiessel, H., van Noort, J., Dame, R. T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.12 MB

english, 2013

36

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles

Highnam, G., Franck, C., Martin, A., Stephens, C., Puthige, A., Mittelman, D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.51 MB

english, 2013

37

The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1

Bazzicalupi, C., Ferraroni, M., Bilia, A. R., Scheggi, F., Gratteri, P.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.30 MB

english, 2013

38

Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation

Beaume, N., Pathak, R., Yadav, V. K., Kota, S., Misra, H. S., Gautam, H. K., Chowdhury, S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 11.03 MB

english, 2013

39

Study of E. coli Hfq's RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents

Doetsch, M., Stampfl, S., Furtig, B., Beich-Frandsen, M., Saxena, K., Lybecker, M., Schroeder, R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.50 MB

english, 2013

40

MsDetector: toward a standard computational tool for DNA microsatellites detection

Girgis, H. Z., Sheetlin, S. L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.19 MB

english, 2013

41

Heterogeneous ensemble approach with discriminative features and modified-SMOTEbagging for pre-miRNA classification

Lertampaiporn, S., Thammarongtham, C., Nukoolkit, C., Kaewkamnerdpong, B., Ruengjitchatchawalya, M.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.75 MB

english, 2013

42

Exploring functional variant discovery in non-coding regions with SInBaD

Lehmann, K.-V., Chen, T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 435 KB

english, 2013

43

Cross-talk between prion protein and quadruplex-forming nucleic acids: a dynamic complex formation

Cavaliere, P., Pagano, B., Granata, V., Prigent, S., Rezaei, H., Giancola, C., Zagari, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.83 MB

english, 2013

44

The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function

Loedige, I., Gaidatzis, D., Sack, R., Meister, G., Filipowicz, W.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.32 MB

english, 2013

45

From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software

Forster, M., Forster, P., Elsharawy, A., Hemmrich, G., Kreck, B., Wittig, M., Thomsen, I., Stade, B., Barann, M., Ellinghaus, D., Petersen, B.-S., May, S., Melum, E., Schilhabel, M. B., Keller, A., Sc

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.67 MB

english, 2013

46

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

Tanaka, K., Henry, C. S., Zinner, J. F., Jolivet, E., Cohoon, M. P., Xia, F., Bidnenko, V., Ehrlich, S. D., Stevens, R. L., Noirot, P.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.39 MB

english, 2013

47

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states

Crespo, I., Krishna, A., Le Bechec, A., del Sol, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 18.04 MB

english, 2013

48

Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques

Ortuno, F. M., Valenzuela, O., Pomares, H., Rojas, F., Florido, J. P., Urquiza, J. M., Rojas, I.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 355 KB

english, 2013

49

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

Salari, R., Kimchi-Sarfaty, C., Gottesman, M. M., Przytycka, T. M.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 465 KB

english, 2013

50

DNA expansions generated by human Pol on iterative sequences

Aza, A., Martin, M. J., Juarez, R., Blanco, L., Terrados, G.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.41 MB

english, 2013

51

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

Malboeuf, C. M., Yang, X., Charlebois, P., Qu, J., Berlin, A. M., Casali, M., Pesko, K. N., Boutwell, C. L., DeVincenzo, J. P., Ebel, G. D., Allen, T. M., Zody, M. C., Henn, M. R., Levin, J. Z.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 641 KB

english, 2013

52

Reverse engineering and analysis of large genome-scale gene networks

Aluru, M., Zola, J., Nettleton, D., Aluru, S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.66 MB

english, 2013

53

Caged circular antisense oligonucleotides for photomodulation of RNA digestion and gene expression in cells

Wu, L., Wang, Y., Wu, J., Lv, C., Wang, J., Tang, X.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.33 MB

english, 2013

54

CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data

Su, J., Yan, H., Wei, Y., Liu, H., Liu, H., Wang, F., Lv, J., Wu, Q., Zhang, Y.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.53 MB

english, 2013

55

FadE: whole genome methylation analysis for multiple sequencing platforms

Souaiaia, T., Zhang, Z., Chen, T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 280 KB

english, 2013

56

The nuclease domain of the SPP1 packaging motor coordinates DNA cleavage and encapsidation

Cornilleau, C., Atmane, N., Jacquet, E., Smits, C., Alonso, J. C., Tavares, P., Oliveira, L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.06 MB

english, 2013

57

hnRNPL and nucleolin bind LINE-1 RNA and function as host factors to modulate retrotransposition

Peddigari, S., Li, P. W.-L., Rabe, J. L., Martin, S. L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.14 MB

english, 2013

58

A minimal bacterial RNase J-based degradosome is associated with translating ribosomes

Redko, Y., Aubert, S., Stachowicz, A., Lenormand, P., Namane, A., Darfeuille, F., Thibonnier, M., De Reuse, H.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.25 MB

english, 2013

59

Subscriptions

Journal:

Nucleic Acids Research

Year:

2013

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english

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PDF, 49 KB

english, 2013

60

Contribution of intersubunit bridges to the energy barrier of ribosomal translocation

Liu, Q., Fredrick, K.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.51 MB

english, 2013

61

Nucleic Acids Research - Editorial Board

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 58 KB

english, 2013

62

Post-transcriptional regulation of CD83 expression by AUF1 proteins

Ehlers, C., Schirmer, S., Kehlenbach, R. H., Hauber, J., Chemnitz, J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.54 MB

english, 2013

63

Modulation of dendritic AMPA receptor mRNA trafficking by RNA splicing and editing

La Via, L., Bonini, D., Russo, I., Orlandi, C., Barlati, S., Barbon, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 16.34 MB

english, 2013

64

The RNA helicase DDX5/p68 is a key factor promoting c-fos expression at different levels from transcription to mRNA export

Zonta, E., Bittencourt, D., Samaan, S., Germann, S., Dutertre, M., Auboeuf, D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.68 MB

english, 2013

65

Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies

Rajan, R., Prasad, R., Taneja, B., Wilson, S. H., Mondragon, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.37 MB

english, 2013

66

Exploring Ty1 retrotransposon RNA structure within virus-like particles

Purzycka, K. J., Legiewicz, M., Matsuda, E., Eizentstat, L. D., Lusvarghi, S., Saha, A., Grice, S. F. J. L., Garfinkel, D. J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.77 MB

english, 2013

67

RNA polymerase III mutants in TFIIF -like C37 that cause terminator readthrough with no decrease in transcription output

Rijal, K., Maraia, R. J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 10.41 MB

english, 2013

68

Quadruplex formation as a molecular switch to turn on intrinsically fluorescent nucleotide analogs

Johnson, J., Okyere, R., Joseph, A., Musier-Forsyth, K., Kankia, B.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 521 KB

english, 2013

69

Nucleic Acids Research: VOLUME 41 ISSUE 1 2013

Journal:

Nucleic Acids Research

Year:

2013

File:

PDF, 521 KB

2013

70

Mitochondrial targeting of recombinant RNAs modulates the level of a heteroplasmic mutation in human mitochondrial DNA associated with Kearns Sayre Syndrome

Comte, C., Tonin, Y., Heckel-Mager, A.-M., Boucheham, A., Smirnov, A., Aure, K., Lombes, A., Martin, R. P., Entelis, N., Tarassov, I.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.73 MB

english, 2013

71

Translational fidelity maintenance preventing Ser mis-incorporation at Thr codon in protein from eukaryote

Zhou, X.-L., Ruan, Z.-R., Huang, Q., Tan, M., Wang, E.-D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.91 MB

english, 2013

72

Telomerase-dependent generation of 70-nt-long telomeric single-stranded 3' overhangs in yeast

Fridholm, H., Astromskas, E., Cohn, M.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.70 MB

english, 2013

73

The coactivator role of histone deacetylase 3 in IL-1-signaling involves deacetylation of p65 NF- B

Ziesche, E., Kettner-Buhrow, D., Weber, A., Wittwer, T., Jurida, L., Soelch, J., Muller, H., Newel, D., Kronich, P., Schneider, H., Dittrich-Breiholz, O., Bhaskara, S., Hiebert, S. W., Hottiger, M. O.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.98 MB

english, 2013

74

Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators

Jain, D., Nair, D. T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.13 MB

english, 2013

75

Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA

Smith, R. M., Jacklin, A. J., Marshall, J. J. T., Sobott, F., Halford, S. E.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.73 MB

english, 2013

76

Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA

Smith, R. M., Marshall, J. J. T., Jacklin, A. J., Retter, S. E., Halford, S. E., Sobott, F.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.17 MB

english, 2013

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