Nucleic Acids Research, ‎0305-1048

Journal

Publications

  1. 2020
  2. Published

    A non-canonical promoter element drives spurious transcription of horizontally acquired bacterial genes

    David Grainger, 21 May 2020, In: Nucleic Acids Research. 48, 9, p. 4891-4901 11 p.

    Research output: Contribution to journalArticlepeer-review

  3. E-pub ahead of print

    CircSamd4 represses myogenic transcriptional activity of PUR proteins

    Thomas Nicholson, , , , , , Simon Jones, , , & , 25 Jan 2020, (E-pub ahead of print) In: Nucleic Acids Research. 17 p.

    Research output: Contribution to journalArticlepeer-review

  4. 2019
  5. Published

    DNA barcodes for rapid, whole genome, single-molecule analyses

    Darren Andrew Smith, , Ashleigh Rushton, Steve Busby, Iain Styles & Robert Neely, 9 Jul 2019, In: Nucleic Acids Research. 47, 12, p. e68 10 p., gkz212.

    Research output: Contribution to journalArticlepeer-review

  6. Published

    Bayesian inference of origin firing time distributions, origin interference and licensing probabilities from NGS data

    Alina Bazarova, , Ildem Akerman & , 18 Mar 2019, In: Nucleic Acids Research. 47, 5, p. 2229–2243 14 p.

    Research output: Contribution to journalArticlepeer-review

  7. Published

    Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling

    Marco Catoni, , & , 20 Feb 2019, In: Nucleic Acids Research. 47, 3, p. 1311–1320 10 p.

    Research output: Contribution to journalArticlepeer-review

  8. Published
  9. 2018
  10. Published

    The APT complex is involved in non-coding RNA transcription and is distinct from CPF

    Pawel Grzechnik, , & , 30 Nov 2018, In: Nucleic Acids Research. 46, 21, p. 11528–11538

    Research output: Contribution to journalArticlepeer-review

  11. Published

    Lytic gene expression in the temperate bacteriophage GIL01 is activated by a phage-encoded LexA homologue

    Doug Browning, , , , & , 12 Oct 2018, In: Nucleic Acids Research. 46, 18, p. 9432–9443

    Research output: Contribution to journalArticlepeer-review

  12. E-pub ahead of print
  13. Published

    A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA

    Robert Neely, 20 Jun 2018, In: Nucleic Acids Research. 46, 11, e64.

    Research output: Contribution to journalArticlepeer-review

  14. 2017
  15. Published

    CsrA maximizes expression of the AcrAB multidrug resistance transporter

    Vito Ricci, , Tim Overton, David Grainger & Laura Piddock, 15 Dec 2017, In: Nucleic Acids Research. 45, 22, p. 12798–12807

    Research output: Contribution to journalArticlepeer-review

  16. Published

    The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

    Georgios Gkoutos, , , & , 23 Nov 2017, In: Nucleic Acids Research.

    Research output: Contribution to journalArticlepeer-review

  17. Published
  18. Published

    Rapid resistome mapping using nanopore sequencing

    Willem van Schaik, & , 5 May 2017, In: Nucleic Acids Research. 45, 8, e61.

    Research output: Contribution to journalArticlepeer-review

  19. Published

    Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

    Marco Catoni, & , 20 Apr 2017, In: Nucleic Acids Research. 45, 7, p. 3777-3784 8 p.

    Research output: Contribution to journalArticlepeer-review

  20. Published
  21. 2016
  22. Published
  23. Published

    Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.

    Yavor Hadzhiev, , , , , , , , Ferenc Müller & , 20 Apr 2016, In: Nucleic Acids Research. 44, 7, p. 3070-3081

    Research output: Contribution to journalArticlepeer-review

  24. Published
  25. 2015
  26. Published

    Epstein-Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression

    Jianmin Zuo, , , , , Martin Rowe, & , 20 Apr 2015, In: Nucleic Acids Research. 43, 7, p. 3563-77 15 p.

    Research output: Contribution to journalArticlepeer-review

  27. Published

    DNA recognition by Escherichia coli CbpA protein requires a conserved arginine-minor-groove interaction

    Kiran Chintakayala, Laura Sellars, , , , , & David Grainger, 27 Feb 2015, In: Nucleic Acids Research. 43, 4, p. 2282-2292

    Research output: Contribution to journalArticlepeer-review

  28. Published
  29. 2014
  30. Published

    NF-κB directly mediates epigenetic deregulation of common microRNAs in Epstein-Barr virus-mediated transformation of B-cells and in lymphomas

    Claire Shannon-Lowe, , , & , 29 Sep 2014, In: Nucleic Acids Research. 42, 17, p. 11025-11039 15 p.

    Research output: Contribution to journalArticlepeer-review

  31. Published

    Chromosome position effects on gene expression in Escherichia coli K-12

    Jack Bryant, Laura Sellars, Steve Busby & David Lee, 10 Sep 2014, In: Nucleic Acids Research. 42, 18, p. 11383-11392

    Research output: Contribution to journalArticlepeer-review

  32. Published

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

    Steve Busby & , 18 Aug 2014, In: Nucleic Acids Research. 42, 14, p. 9209-16 8 p.

    Research output: Contribution to journalArticlepeer-review

  33. Published

    SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity

    Nicholas Barnes, , , , , , , & , Jul 2014, In: Nucleic Acids Research. 42, 12, p. 7591-7610 20 p.

    Research output: Contribution to journalArticlepeer-review

  34. Published

    A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa

    Sarah Kuehne, , , , , & , Jun 2014, In: Nucleic Acids Research. 42, 11, p. 6811-6825 15 p.

    Research output: Contribution to journalArticlepeer-review

  35. Published

    Human single-stranded DNA binding protein 1 (hSSB1/NABP2) is required for the stability and repair of stalled replication forks.

    Eva Petermann, , , , , , & , Jun 2014, In: Nucleic Acids Research. 42, 10, p. 6326-6336

    Research output: Contribution to journalArticlepeer-review

  36. Published
  37. Published

    The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

    & 27 others, , , , , , , , , , , , , , , , , , , , , , , Georgios Gkoutos, , , & , 1 Jan 2014, In: Nucleic Acids Research. 42, Database issue, p. D966-974

    Research output: Contribution to journalArticlepeer-review

  38. Published

    SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

    Roland Arnold, , & , Jan 2014, In: Nucleic Acids Research. 42, D1, p. D279-D284 6 p.

    Research output: Contribution to journalArticlepeer-review

  39. Published

    Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

    Robert Neely, 2014, In: Nucleic Acids Research. 42, 7, e50.

    Research output: Contribution to journalArticlepeer-review

  40. 2013
  41. Published
  42. Published
  43. Published

    Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

    Yavor Hadzhiev, , , , , , , , , , , , , , , Ferenc Müller & , 1 Apr 2013, In: Nucleic Acids Research. 41, 6, p. 3600-18 19 p.

    Research output: Contribution to journalArticlepeer-review

  44. 2012
  45. Published

    eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

    Roland Arnold, , , , , & , Jan 2012, In: Nucleic Acids Research. 40, Database issue, p. D284-9

    Research output: Contribution to journalArticlepeer-review

  46. Published
  47. 2011
  48. Published
  49. Published

    PhenomeNET: a whole-phenome approach to disease gene discovery

    Georgios Gkoutos, 1 Oct 2011, In: Nucleic Acids Research. 39, 18, p. e119

    Research output: Contribution to journalArticlepeer-review

  50. Published

    Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

    John Colbourne, , , , & , Oct 2011, In: Nucleic Acids Research. 39, 19, p. e127

    Research output: Contribution to journalArticlepeer-review

  51. Published

    A systems biology approach sheds new light on Escherichia coli acid resistance

    Philipp Antczak, Ian Henderson, Jeff Cole, , Peter Lund & Francesco Falciani, 1 Sep 2011, In: Nucleic Acids Research. 39, 17, p. 7512-7528 17 p.

    Research output: Contribution to journalArticlepeer-review

  52. Published

    Escherichia Coli  σ70 Senses Sequence and Conformation of the Promoter Spacer Region

    Shivani Singh, , & David Grainger, 1 Jul 2011, In: Nucleic Acids Research. 39, 12, p. 5109-5118 10 p.

    Research output: Contribution to journalArticle

  53. Published
  54. Published
  55. Published

    Effective--a database of predicted secreted bacterial proteins

    Roland Arnold & , Jan 2011, In: Nucleic Acids Research. 39, Database issue, p. D591-5

    Research output: Contribution to journalArticlepeer-review

  56. 2010
  57. Published

    An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression

    Conny Bonifer, & , 1 Sep 2010, In: Nucleic Acids Research. 38, 16, p. 5336-50 15 p.

    Research output: Contribution to journalArticle

  58. Published
  59. Published
  60. Published

    Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer

    Peter Cockerill, 18 May 2010, In: Nucleic Acids Research. 38, 18, p. 6124-34 11 p.

    Research output: Contribution to journalArticlepeer-review

  61. Published

    SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters

    Roland Arnold, & , Jan 2010, In: Nucleic Acids Research. 38, Database issue, p. D223-6

    Research output: Contribution to journalArticlepeer-review

  62. 2009
  63. Published

    Characterization of RNA aptamers that disrupt the RUNX1-CBFbeta/DNA complex

    Conny Bonifer & , 1 Nov 2009, In: Nucleic Acids Research. 37, 20, p. 6818-30 13 p.

    Research output: Contribution to journalArticle

  64. Published

    Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes

    Robert Neely, , , , & , Nov 2009, In: Nucleic Acids Research. 37, 20, p. 6859-70 12 p.

    Research output: Contribution to journalArticlepeer-review

  65. Published

    CK2 phosphorylation of the PRH/Hex homeodomain functions as a reversible switch for DNA binding

    Peter Noy, , , & Padma-Sheela Jayaraman, 1 Jun 2009, In: Nucleic Acids Research. 37, 10, p. 3288-300 13 p.

    Research output: Contribution to journalArticlepeer-review

  66. Published

    Rapid Cdc13 turnover and telomere length homeostasis are controlled by Cdk1-mediated phosphorylation of Cdc13.

    Hung-Ji Tsai, , , & , 9 Apr 2009, In: Nucleic Acids Research. 37, 11, p. 3602-3611

    Research output: Contribution to journalArticlepeer-review

  67. Published
  68. Published
  69. Published

    PEDANT covers all complete RefSeq genomes

    Roland Arnold, , , , , , , , , , & , Jan 2009, In: Nucleic Acids Research. 37, Database issue, p. D408-11

    Research output: Contribution to journalArticlepeer-review

  70. Published
  71. Published
  72. 2008
  73. Published

    Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR.

    David Grainger, , & Steve Busby, 1 May 2008, In: Nucleic Acids Research. 36, 8, p. 2667-76 10 p.

    Research output: Contribution to journalArticlepeer-review

  74. Published

    Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses

    Dalan Bailey, , & , May 2008, In: Nucleic Acids Research. 36, 8, p. 2530-46 17 p.

    Research output: Contribution to journalArticlepeer-review

  75. Published
  76. Published

    DNA binding of dinuclear iron(II) metallosupramolecular cylinders. DNA unwinding and sequence preference

    Mike Hannon & , 1 Jan 2008, In: Nucleic Acids Research. 36, 11, p. 3630-3638 9 p.

    Research output: Contribution to journalArticle

  77. Published

    The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

    Steve Busby & David Grainger, 1 Jan 2008, In: Nucleic Acids Research. 36, 12, p. 3950-3955 6 p.

    Research output: Contribution to journalArticlepeer-review

  78. Published

    SIMAP--structuring the network of protein similarities

    Roland Arnold, , , , , & , Jan 2008, In: Nucleic Acids Research. 36, Database issue, p. D289-92

    Research output: Contribution to journalArticlepeer-review

  79. Published

    High throughput functional annotation and data mining with the Blast2GO suite

    Tim Williams, , , , , & , 2008, In: Nucleic Acids Research. 36, 10, p. 3420-3435 16 p.

    Research output: Contribution to journalArticlepeer-review

  80. 2007
  81. Published
  82. Published
  83. Published
  84. Published

    Transcription factor distribution in Escherichia coli: studies with FNR protein

    David Grainger, , , Doug Browning & Steve Busby, 1 Jan 2007, In: Nucleic Acids Research. 35, 1, p. 269-278 10 p.

    Research output: Contribution to journalArticle

  85. Published

    SNP discovery by mismatch-targeting of Mu transposition

    Luisa Orsini, , & , 2007, In: Nucleic Acids Research. 35, p. e44

    Research output: Contribution to journalArticlepeer-review

  86. 2006
  87. Published
  88. Published

    Cytoplasmic expression systems triggered by mRNA yield increased gene expression in post-mitotic neurons

    Rachel Spice, , , Ann Logan, & Martin Read, 28 Jun 2006, In: Nucleic Acids Research. 34(11), e80, p. 1-12 12 p.

    Research output: Contribution to journalArticle

  89. Published
  90. Published
  91. Published

    Escherichia coli K-12: a cooperatively developed annotation snapshot - 2005

    Roy Chaudhuri, , , , , , , , , , Gavin Thomas, , & , 1 Jan 2006, In: Nucleic Acids Research. 34, 1, p. 1-9 9 p.

    Research output: Contribution to journalArticle

  92. Published

    SIMAP: the similarity matrix of proteins

    Roland Arnold, , , & , 1 Jan 2006, In: Nucleic Acids Research. 34, Database issue, p. D252-6

    Research output: Contribution to journalArticlepeer-review

  93. Published

    A novel DNA damage recognition protein in Schizosaccharomyces pombe

    Ghazala Begum, , , , , & , 2006, In: Nucleic Acids Research. 34, 8, p. 2347-54 8 p.

    Research output: Contribution to journalArticlepeer-review

  94. Published
  95. 2005
  96. Published
  97. Published

    The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken

    Conny Bonifer, , & , 1 Jan 2005, In: Nucleic Acids Research. 33, 17, p. 5633-5639 7 p.

    Research output: Contribution to journalArticle

  98. Published
  99. Published
  100. Published

    Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes

    Aditi Kanhere & , 2005, In: Nucleic Acids Research. 33, 10, p. 3165-75 11 p.

    Research output: Contribution to journalArticlepeer-review

  101. Published

    Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes

    Robert Neely, , , , , & , 2005, In: Nucleic Acids Research. 33, 22, p. 6953-60 8 p.

    Research output: Contribution to journalArticlepeer-review

  102. 2004
  103. Published

    A conformational change in TFIIB is required for activator-medicated assembly of the reinitiation complex

    Tim Dafforn & , 8 Mar 2004, In: Nucleic Acids Research. 32, p. 1829-35 7 p.

    Research output: Contribution to journalArticle

  104. Published

    Identification of the CRP regulon using in vitro and in vivo transcriptional profiling

    Miller Constantinidou, Jon Hobman & Steve Minchin, 1 Jan 2004, In: Nucleic Acids Research. 32, p. 5874-5893 20 p.

    Research output: Contribution to journalArticlepeer-review

  105. Published
  106. Published
  107. 2003
  108. Published

    The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC 13129

    Lynn Dover, , Mark Pallen, & Del Besra, 15 Nov 2003, In: Nucleic Acids Research. 31, 22, p. 6516-6523 8 p.

    Research output: Contribution to journalArticle

  109. Published
  110. Published

    Identification and analysis of 'extended-10' promoters in Escherichia coli

    Jennie Mitchell, , Steve Busby & Steve Minchin, 15 Aug 2003, In: Nucleic Acids Research. 31, 16, p. 4689-4695 7 p.

    Research output: Contribution to journalArticle

  111. Published

    Impact of DNA ligase IV on the fidelity of end joining in human cells

    Boris Kysela, , , , , & , 15 Apr 2003, In: Nucleic Acids Research. 31, 8, p. 2157-67 11 p.

    Research output: Contribution to journalArticlepeer-review

  112. Published

    An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data

    Aditi Kanhere & , 2003, In: Nucleic Acids Research. 31, 10, p. 2647-58 12 p.

    Research output: Contribution to journalArticlepeer-review

  113. 2002
  114. Published

    Secondary structure and DNA binding by the C-terminal domain of the transcriptional activator NifA from Klebsiella pneumoniae.

    Kevin Smith, , & Eva Hyde, 15 Sep 2002, In: Nucleic Acids Research. 30, 18, p. 3972-80 9 p.

    Research output: Contribution to journalArticlepeer-review

  115. Published

    DNA binding of the transcription activator protein MelR from Escherichia coli and its C-terminal domain.

    Tamara Belyaeva, Steve Busby & Eva Hyde, 15 Jun 2002, In: Nucleic Acids Research. 30, 12, p. 2692-2700 9 p.

    Research output: Contribution to journalArticlepeer-review

  116. Published

    Functional dissection of the ParB homologue (KorB) from IncP-1 plasmid RK2

    Chris Thomas & , 15 Feb 2002, In: Nucleic Acids Research. 30, 4, p. 1046-1055 10 p.

    Research output: Contribution to journalArticle

  117. Published

    A critical epitope for substrate recognition by nucleosome remodelling ATPase ISWI

    Karl Nightingale & , 1 Jan 2002, In: Nucleic Acids Research. 30, p. 649-55 7 p.

    Research output: Contribution to journalArticle

  118. Published

    MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome

    Roland Arnold, & , 1 Jan 2002, In: Nucleic Acids Research. 30, 1, p. 91-3 3 p.

    Research output: Contribution to journalArticlepeer-review

  119. Published

    The chicken lysozyme chromatin domain contains a second, widely expressed gene

    Samantha Chong, & Conny Bonifer, 1 Jan 2002, In: Nucleic Acids Research. 30, 2, p. 463-467 5 p.

    Research output: Contribution to journalArticle

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