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

  120. 2001
  121. Published
  122. Published
  123. Published
  124. Published
  125. Published
  126. 2000
  127. Published
  128. 1998
  129. Published
  130. 1997
  131. Published
  132. 1996
  133. Published
  134. Published
  135. 1994
  136. Published
  137. Published

    Dissection of the Locus Control Function located on the Chicken Lysozyme Gene Domain

    Conny Bonifer, , , & , 11 Oct 1994, In: Nucleic Acids Research. 22, 20, p. 4202-4210

    Research output: Contribution to journalArticlepeer-review

  138. 1992
  139. Published
  140. Published

    A comparison of the DNA bending activities of the DNA binding proteins CRP and TFIID

    Andrew Bell, Steve Busby & , 1992, In: Nucleic Acids Research. 20, 13, p. 3391-6 6 p.

    Research output: Contribution to journalArticlepeer-review

  141. 1991
  142. Published

    The role of two surface exposed loops in transcription activation by the Escherichia coli CRP and FNR proteins

    Andrew Bell, & Steve Busby, 1991, In: Nucleic Acids Research. 19, 24, p. 6705-12 8 p.

    Research output: Contribution to journalArticlepeer-review

  143. 1990
  144. Published

    Comparison of pneumolysin genes and proteins from Streptococcus pneumoniae types 1 and 2

    Timothy Mitchell, , , & , 11 Jul 1990, In: Nucleic Acids Research. 18, 13, p. 4010

    Research output: Contribution to journalArticlepeer-review

  145. Published
  146. Published

    Nucleotide sequence of the bovine insulin-like growth factor 1 (IGF-1) and its IGF-1A precursor

    Carol Murphy & , 1990, In: Nucleic Acids Research. 18, p. 676 1 p.

    Research output: Contribution to journalArticlepeer-review

  147. 1989
  148. Published

    A new series of CAT expression vectors

    Andrew R. Clark, & , 11 Dec 1989, In: Nucleic Acids Research. 17, 23, p. 10130 1 p.

    Research output: Contribution to journalComment/debatepeer-review

  149. Published

    Up-promoter mutations in the positively-regulated mer promoter of Tn501

    Peter Lund & Nigel Brown, 25 Jul 1989, In: Nucleic Acids Research. 17, 14, p. 5517-27 11 p.

    Research output: Contribution to journalArticlepeer-review

  150. Published

    Mutational analysis of the nucleotide sequence at the FNR-dependent nirB promoter in Escherichia coli

    Padma-Sheela Jayaraman, Jeff Cole & Steve Busby, 11 Jan 1989, In: Nucleic Acids Research. 17, 1, p. 135-45 11 p.

    Research output: Contribution to journalArticlepeer-review

  151. Published