Antoine Danchin

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Articles in Scholarly Journals [Incomplete List]

  1. The extant core bacterial proteome is an archive of the origin of life
    PROTEOMICS, vol. 7, no. 6, pp. 875–889, 2007
  2. Potent and selective inhibitors of Staphylococcus epidermidis tryptophanyl-tRNA synthetase
    Journal of Antimicrobial Chemotherapy, vol. 60, no. 3, pp. 502–509, 2007
  3. Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes
    Nucleic Acids Research, vol. 35, no. 6, pp. e37–e37, 2007
  4. YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity
    Nucleic Acids Research, vol. 35, no. 13, pp. 4552–4561, 2007
  5. BMC Bioinformatics, vol. 8, no. 1, p. 47, 2007
  6. A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments
    PLoS Genetics, vol. 3, no. 4, p. e53, 2007
  7. Codon Usage Domains over Bacterial Chromosomes
    PLoS Computational Biology, vol. 2, no. 4, p. e37, 2006
  8. BMC Genomics, vol. 7, no. 1, p. 112, 2006
  9. BMC Microbiology, vol. 6, no. 1, p. 96, 2006
  10. Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells
    Nucleic Acids Research, vol. 34, no. 8, pp. 2364–2373, 2006
  11. Pleiotropic Role of Quorum-Sensing Autoinducer 2 in Photorhabdus luminescens
    Applied and Environmental Microbiology, vol. 72, no. 10, pp. 6439–6451, 2006
  12. Conversion of Methionine to Cysteine in Bacillus subtilis and Its Regulation
    Journal of Bacteriology, vol. 189, no. 1, pp. 187–197, 2006
  13. Global Control of Cysteine Metabolism by CymR in Bacillus subtilis
    Journal of Bacteriology, vol. 188, no. 6, pp. 2184–2197, 2006
  14. Persistent biases in the amino acid composition of prokaryotic proteins
    BioEssays, vol. 28, no. 7, pp. 726–738, 2006
  15. Re: Request from the international advisory committee to DDBJ/EMBL/GenBank
    Journal of Medical Virology, vol. 78, no. 7, pp. 995–995, 2006
  16. Proteome analysis of the phenotypic variation process inPhotorhabdus luminescens
    PROTEOMICS, vol. 6, no. 9, pp. 2705–2725, 2006
  17. Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125
    Extremophiles, vol. 10, no. 6, pp. 483–491, 2006
  18. Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome
    Biochimie, vol. 88, no. 6, pp. 595–606, 2006
  19. Request from the International Advisory Committee to DDBJ/EMBL/GenBank
    Journal of Virological Methods, vol. 135, no. 2, pp. 297–297, 2006
  20. 3-phenylpropionate catabolism and the oxidative stress response
    Research in Microbiology, vol. 156, no. 3, pp. 312–321, 2005
  21. Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism?
    Research in Microbiology, vol. 156, no. 5-6, pp. 611–618, 2005
  22. The PatB protein of is a C-S-lyase
    Biochimie, vol. 87, no. 2, pp. 231–238, 2005
  23. Universal biases in protein composition of model prokaryotes
    Proteins: Structure, Function, and Bioinformatics, vol. 60, no. 1, pp. 27–35, 2005
  24. How Essential Are Nonessential Genes?
    Molecular Biology and Evolution, vol. 22, no. 11, pp. 2147–2156, 2005
  25. Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays
    Nucleic Acids Research, vol. 33, no. 1, pp. 409–421, 2005
  26. Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays
    Nucleic Acids Research, vol. 33, no. 8, pp. 2764–2764, 2005
  27. Molecular diagnosis of human cancer type by gene expression profiles and independent component analysis
    European Journal of Human Genetics, vol. 13, no. 12, Article ID 5201495, 8 pages, 2005
  28. Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
    Genome Research, vol. 15, no. 10, pp. 1325–1335, 2005
  29. BMC Bioinformatics, vol. 6, no. 1, p. 206, 2005
  30. BMC Genomics, vol. 6, no. 1, p. 14, 2005
  31. Subacute Cutaneous Lupus erythematosus Associated with Tamoxifen Therapy: Two Cases
    Dermatology, vol. 210, no. 3, pp. 251–252, 2005
  32. Regulation of the Bacillus subtilis ytmI Operon, Involved in Sulfur Metabolism
    Journal of Bacteriology, vol. 187, no. 17, pp. 6019–6030, 2005
  33. BMC Microbiology, vol. 5, no. 1, p. 57, 2005
  34. Genome Diversity: A Grammar of Microbial Genomes
    Complexus, vol. 2, no. 2, pp. 61–70, 2004
  35. BMC Microbiology, vol. 4, no. 1, p. 1, 2004
  36. BMC Cancer, vol. 4, no. 1, p. 72, 2004
  37. Microbial Cell Factories, vol. 3, no. 1, p. 13, 2004
  38. AstR-AstS, a new two-component signal transduction system, mediates swarming, adaptation to stationary phase and phenotypic variation in Photorhabdus luminescens
    Microbiology, vol. 150, no. 4, pp. 897–910, 2004
  39. GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli
    Microbiology, vol. 150, no. 1, pp. 61–72, 2004
  40. Three Different Systems Participate in L-Cystine Uptake in Bacillus subtilis
    Journal of Bacteriology, vol. 186, no. 15, pp. 4875–4884, 2004
  41. The PhoP-PhoQ Two-Component Regulatory System of Photorhabdus luminescens Is Essential for Virulence in Insects
    Journal of Bacteriology, vol. 186, no. 5, pp. 1270–1279, 2004
  42. Cytosine Methylation Is Not the Major Factor Inducing CpG Dinucleotide Deficiency in Bacterial Genomes
    Journal of Molecular Evolution, vol. 58, no. 6, pp. 692–700, 2004
  43. Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus
    Archives of Virology, vol. 150, no. 1, pp. 1–20, 2004
  44. The metNPQ operon of Bacillus subtilis encodes an ABC permease transporting methionine sulfoxide, ?- and ?-methionine
    Research in Microbiology, vol. 155, no. 2, pp. 80–86, 2004
  45. Infection of society
    EMBO Reports, vol. 4, no. 4, Article ID embor809, 2 pages, 2003
  46. Gene essentiality determines chromosome organisation in bacteria
    Nucleic Acids Research, vol. 31, no. 22, pp. 6570–6577, 2003
  47. Corrigenda
    Nucleic Acids Research, vol. 31, no. 23, pp. 7056–7056, 2003
  48. An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins
    Molecular Biology and Evolution, vol. 21, no. 1, pp. 108–116, 2003
  49. A Novel H-NS-like Protein from an Antarctic Psychrophilic Bacterium Reveals a Crucial Role for the N-terminal Domain in Thermal Stability
    Journal of Biological Chemistry, vol. 278, no. 21, pp. 18754–18760, 2003
  50. Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing
    Nature, vol. 422, no. 6934, Article ID nature01597, 5 pages, 2003
  51. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
    Nature Biotechnology, vol. 21, no. 11, Article ID nbt886, 6 pages, 2003
  52. Essentiality, not expressiveness, drives gene-strand bias in bacteria
    Nature Genetics, vol. 34, no. 4, Article ID ng1209, 1 pages, 2003
  53. A strand-specific model for chromosome segregation in bacteria
    Molecular Microbiology, vol. 49, no. 4, pp. 895–903, 2003
  54. UMP kinase from the Gram-positive bacterium Bacillus subtilis is strongly dependent on GTP for optimal activity
    European Journal of Biochemistry, vol. 270, no. 15, pp. 3196–3204, 2003
  55. Essential Bacillussubtilis genes
    Proceedings of the National Academy of Sciences, vol. 100, no. 8, pp. 4678–4683, 2003
  56. Escherichia coli Response to Exogenous Pyrophosphate and Analogs
    Journal of Molecular Microbiology and Biotechnology, vol. 5, no. 1, pp. 37–45, 2003
  57. Transcription Regulation Coupling of the Divergent argG and metY Promoters in Escherichia coli K-12
    Journal of Bacteriology, vol. 185, no. 10, pp. 3139–3146, 2003
  58. MvaT proteins in Pseudomonas spp.: a novel class of H-NS-like proteins
    Microbiology, vol. 149, no. 11, pp. 3047–3050, 2003
  59. BMC Infectious Diseases, vol. 3, no. 1, p. 19, 2003
  60. BMC Bioinformatics, vol. 4, no. 1, p. 43, 2003
  61. BMC Bioinformatics, vol. 3, no. 1, p. 5, 2002
  62. BMC Microbiology, vol. 2, no. 1, p. 1, 2002
  63. BMC Microbiology, vol. 2, no. 1, p. 8, 2002
  64. The secE Gene of Helicobacter pylori
    Journal of Bacteriology, vol. 184, no. 10, pp. 2837–2840, 2002
  65. Identification of Bacillus subtilis CysL, a Regulator of the cysJI Operon, Which Encodes Sulfite Reductase
    Journal of Bacteriology, vol. 184, no. 17, pp. 4681–4689, 2002
  66. Global Expression Profile of Bacillus subtilis Grown in the Presence of Sulfate or Methionine
    Journal of Bacteriology, vol. 184, no. 18, pp. 5179–5186, 2002
  67. Identification, Characterization, and Regulation of a Cluster of Genes Involved in Carbapenem Biosynthesis in Photorhabdus luminescens
    Applied and Environmental Microbiology, vol. 68, no. 8, pp. 3780–3789, 2002
  68. Not every truth is good: The dangers of publishing knowledge about potential bioweapons
    EMBO Reports, vol. 3, no. 2, pp. 102–104, 2002
  69. SubtiList: the reference database for the Bacillus subtilis genome
    Nucleic Acids Research, vol. 30, no. 1, pp. 62–65, 2002
  70. Génomes et évolution
    Annales de l'Institut Pasteur/Actualités, vol. 11, pp. 9–18, 2002
  71. Base composition bias might result from competition for metabolic resources
    Trends in Genetics, vol. 18, no. 6, pp. 291–294, 2002
  72. Effect of mild acid pH on the functioning of bacterial membranes in Vibrio cholerae
    PROTEOMICS, vol. 2, no. 5, p. 571, 2002
  73. H-NS and H-NS-like proteins in Gram-negative bacteria andtheir multiple role in the regulation of bacterial metabolism
    Biochimie, vol. 83, no. 2, pp. 235–241, 2001
  74. Acute generalized exanthematous pustulosis induced by amoxycillin with clavulanate
    Contact Dermatitis, vol. 44, no. 2, pp. 105–106, 2001
  75. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS
    Molecular Microbiology, vol. 40, no. 1, pp. 20–36, 2001
  76. Control of Bacterial Motility by Environmental Factors in Polarly Flagellated and Peritrichous Bacteria Isolated from Lake Baikal
    Applied and Environmental Microbiology, vol. 67, no. 9, pp. 3852–3859, 2001
  77. CotA of Bacillus subtilis Is a Copper-Dependent Laccase
    Journal of Bacteriology, vol. 183, no. 18, pp. 5426–5430, 2001
  78. Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis
    Genome Research, vol. 11, no. 6, pp. 946–958, 2001
  79. BMC Microbiology, vol. 1, no. 1, p. 1, 2001
  80. BMC Microbiology, vol. 1, no. 1, p. 15, 2001
  81. Mapping the bacterial cell architecture into the chromosome
    Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 355, no. 1394, pp. 179–190, 2000
  82. Isolation and Characterization of vicH, Encoding a New Pleiotropic Regulator in Vibrio cholerae
    Journal of Bacteriology, vol. 182, no. 7, pp. 2026–2032, 2000
  83. S-adenosylmethionine decarboxylase of Bacillus subtilis is closely related to archaebacterial counterparts
    Molecular Microbiology, vol. 36, no. 5, pp. 1135–1147, 2000
  84. The DB case: pattern matching evidence is not significant. MicroCorrespondence
    Molecular Microbiology, vol. 37, no. 1, pp. 216–218, 2000
  85. A SeqA hyperstructure and its interactions direct the replication and sequestration of DNA
    Molecular Microbiology, vol. 37, no. 4, pp. 696–702, 2000
  86. A brief history of genome research and bioinformatics in France
    Bioinformatics, vol. 16, no. 1, pp. 65–75, 2000
  87. Sulphur islands in the Escherichia coli genome: markers of the cell?s architecture?
    FEBS Letters, vol. 476, no. 1-2, pp. 8–11, 2000
  88. Implication of gene distribution in the bacterial chromosome for the bacterial cell factory
    Journal of Biotechnology, vol. 78, no. 3, pp. 209–219, 2000
  89. Pyrophosphate increases the efficiency of enterobactin-dependent iron uptake in Escherichia coli
    Biochimie, vol. 81, no. 3, pp. 245–253, 1999
  90. From function to sequence, an integrated view of the genome texts
    Physica A: Statistical Mechanics and its Applications, vol. 273, no. 1-2, pp. 92–98, 1999
  91. Functional and evolutionary roles of long repeats in prokaryotes
    Research in Microbiology, vol. 150, no. 9-10, pp. 725–733, 1999
  92. Codon usage and lateral gene transfer in Bacillus subtilis
    Current Opinion in Microbiology, vol. 2, no. 5, pp. 524–528, 1999
  93. From protein sequence to function
    Current Opinion in Structural Biology, vol. 9, no. 3, pp. 363–367, 1999
  94. Bacterial DNA strand compositional asymmetry: Response
    Trends in Microbiology, vol. 7, no. 8, p. 308, 1999
  95. Imagene: an integrated computer environment for sequence annotation and analysis
    Bioinformatics, vol. 15, no. 1, pp. 2–15, 1999
  96. Identification of yrrU as the Methylthioadenosine Nucleosidase Gene in Bacillus subtilis
    DNA Research, vol. 6, no. 5, pp. 255–264, 1999
  97. Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis
    Nucleic Acids Research, vol. 27, no. 17, pp. 3567–3576, 1999
  98. Biochemistry, vol. 38, no. 8, pp. 2287–2294, 1999
  99. The structural and functional organization of H-NS-like proteins is evolutionarily conserved in Gram-negative bacteria
    Molecular Microbiology, vol. 31, no. 1, pp. 319–329, 1999
  100. Mta, a global MerR-type regulator of the Bacillus subtilis multidrug-efflux transporters
    Molecular Microbiology, vol. 31, no. 5, pp. 1549–1559, 1999
  101. Universal replication biases in bacteria
    Molecular Microbiology, vol. 32, no. 1, pp. 11–16, 1999
  102. Detecting and Analyzing DNA Sequencing Errors: Toward a Higher Quality of the Bacillus subtilis Genome Sequence
    Genome Research, vol. 9, no. 11, pp. 1116–1127, 1999
  103. Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons
    Nucleic Acids Research, vol. 26, no. 12, pp. 2971–2980, 1998
  104. On proteins of the microsporidian invasive apparatus: complete sequence of a polar tube protein of Encephalitozoon cuniculi
    Molecular Microbiology, vol. 29, no. 3, pp. 825–834, 1998
  105. Characterization of polyamine synthesis pathway in Bacillus subtilis 168
    Molecular Microbiology, vol. 29, no. 3, pp. 851–858, 1998
  106. Indigo: a World-Wide-Web review of genomes and gene functions
    FEMS Microbiology Reviews, vol. 22, no. 4, pp. 207–227, 1998
  107. Global analysis of genomic texts: The distribution of AGCT tetranucleotides in theEscherichia coli andBacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes
    Electrophoresis, vol. 19, no. 4, pp. 515–527, 1998
  108. Mapping of repetitive and non-repetitive DNA probes to chromosomes of the microsporidian Encephalitozoon cuniculi
    Gene, vol. 191, no. 1, pp. 39–45, 1997
  109. The map of the cell is in the chromosome
    Current Opinion in Genetics & Development, vol. 7, no. 6, pp. 852–854, 1997
  110. Comparison Between the Escherichia coli and Bacillus subtilis Genomes Suggests That a Major Function of Polynucleotide Phosphorylase is to Synthesize CDP
    DNA Research, vol. 4, no. 1, pp. 9–18, 1997
  111. Using Codon Usage to Predict Genes Origin: Is the Escherichia coli Outer Membrane a Patchwork of Products from Different Genomes?
    DNA Research, vol. 4, no. 4, pp. 257–265, 1997
  112. CMP Kinase from Escherichia coli Is Structurally Related to Other Nucleoside Monophosphate Kinases
    Journal of Biological Chemistry, vol. 271, no. 5, pp. 2856–2862, 1996
  113. Uneven Distribution of GATC Motifs in theEscherichia coliChromosome, its Plasmids and its Phages
    Journal of Molecular Biology, vol. 257, no. 3, pp. 574–585, 1996
  114. Effet du pyrophosphate exogène sur la croissance et la survie en phase stationnaire de Escherichia coli
    Research in Microbiology, vol. 147, no. 8, pp. 597–608, 1996
  115. Comparative analysis of the cya locus in enterobacteria and related Gram-negative facultative anaerobes
    Biochimie, vol. 78, no. 4, pp. 277–287, 1996
  116. By way of introduction: Some constraints of the cell physics that are usually forgotten, but should be taken into account for in silico genome analysis
    Biochimie, vol. 78, no. 5, pp. 299–301, 1996
  117. mRNA turnover and DNA synthesis: a lesson from bacterial genome comparisons
    Molecular Microbiology, vol. 20, no. 4, pp. 895–897, 1996
  118. La liaison protéine H-NS/ADN chez Escherichia coli est l'une des premières àêtre synthétisée après un apport nutritionnel
    Research in Microbiology, vol. 146, no. 1, pp. 5–16, 1995
  119. Cloning and sequence of the Bordetella bronchiseptica adenylate cyclase-hemolysin-encoding gene: comparison with the Bordetella pertussis gene
    Gene, vol. 162, no. 1, pp. 165–166, 1995
  120. Analysis of a Bacillus subtilis genome fragment using a co-operative computer system prototype
    Gene, vol. 165, no. 1, pp. GC37–GC51, 1995
  121. Functional analysis of subunits III and IV of Bacillus subtilis aa3-600 quinol oxidase by in vitro mutagenesis and gene replacement
    Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1232, no. 1-2, pp. 67–74, 1995
  122. The catalytic domain of Escherichia coli K-12 adenylate cyclase as revealed by deletion analysis of the cya gene
    Molecular Genetics and Genomics, vol. 243, no. 4, pp. 409–416, 1994
  123. The role of H-NS in one carbon metabolism
    Biochimie, vol. 76, no. 10-11, pp. 1063–1070, 1994
  124. Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325? to 333deg;
    Molecular Microbiology, vol. 10, no. 2, pp. 371–384, 1993
  125. Structural flexibility of the calmodulin-binding locus in Bordetella pertussis adenylate cyclase. Reconstitution of catalytically active species from fragments or inactive forms of the enzyme
    European Journal of Biochemistry, vol. 217, no. 2, pp. 581–586, 1993
  126. Structural and physico-chemical characteristics of Bordetella pertussis adenylate kinase, a tryptophan-containing enzyme
    European Journal of Biochemistry, vol. 218, no. 3, pp. 921–927, 1993
  127. From adenylate cyclase to guanylate cyclase *1Mutational analysis of a change in substrate specificity
    Journal of Molecular Biology, vol. 225, no. 4, pp. 933–938, 1992
  128. Positive regulation of the expression of the Escherichia coli pts operon Identification of the regulatory regions
    Journal of Molecular Biology, vol. 226, no. 3, pp. 623–635, 1992
  129. Mutational analysis of the enzyme IIIGlc of the phosphoenolpyruvate phosphotransferase system in Escherichia coli
    Research in Microbiology, vol. 143, no. 3, pp. 251–261, 1992
  130. Mutations inbglY, the structural gene for the DNA-binding protein H1 ofEscherichia coli, increase the expression of the kanamycin resistance gene carried by plasmid pGR71
    MGG Molecular & General Genetics, vol. 233, no. 1-2, pp. 184–192, 1992
  131. Identification of two fructose transport and phosphorylation pathways in Xanthomonas campestris pv. campestris
    MGG Molecular & General Genetics, vol. 227, no. 3, pp. 465–472, 1991
  132. From data banks to data bases
    Research in Microbiology, vol. 142, no. 7-8, pp. 913–916, 1991
  133. Evidence for horizontal gene transfer in Escherichia coli speciation
    Journal of Molecular Biology, vol. 222, no. 4, pp. 851–856, 1991
  134. Multiple IS insertion sequences near the replication terminus in Escherichia coli K-12
    Biochimie, vol. 73, no. 11, pp. 1361–1374, 1991
  135. Isolation and characterization of catalytic and calmodulin-binding domains of Bordetella pertussis adenylate cyclase
    European Journal of Biochemistry, vol. 196, no. 2, pp. 469–474, 1991
  136. Escherichia coli molecular genetic map (1500 kbp): update II
    Molecular Microbiology, vol. 5, no. 11, pp. 2629–2640, 1991
  137. A gene encoding a tyrosine tRNA synthetase is located near Sacs in Bacillus subtilis
    DNA Sequence, vol. 1, no. 4, pp. 251–261, 1991
  138. Mapping of sequenced genes (700 kbp) in the restriction map of the Escherichia coli chromosome
    Molecular Microbiology, vol. 4, no. 2, pp. 169–187, 1990
  139. Escherichia coli molecular genetic map (1000Kbp):update
    Molecular Microbiology, vol. 4, no. 9, pp. 1443–1454, 1990
  140. Cyclic AMP synthesis in Escherichia coli strains bearing known deletions in the pts phosphotransferase operon
    Gene, vol. 86, no. 1, pp. 27–33, 1990
  141. Mutations in the bglY Gene Increase the Frequency of Spontaneous Deletions in Escherichia coli K-12
    Proceedings of the National Academy of Sciences, vol. 87, no. 1, pp. 360–363, 1990
  142. Biochemistry, vol. 29, no. 35, pp. 8126–8130, 1990
  143. Biochemistry, vol. 28, no. 5, pp. 1964–1967, 1989
  144. Cloning and expression of mouse-brain calmodulin as an activator of Bordetella pertussis adenylate cyclase in Escherichia coli
    Gene, vol. 80, no. 1, pp. 145–149, 1989
  145. Genetics of the PTS components in Escherichia coli K-12
    FEMS Microbiology Reviews, vol. 63, no. 1-2, pp. 61–67, 1989
  146. A locus involved in kanamycin, chloramphenicol and L-serine resistance is located in the bglY-galU region of the Escherichia coli K12 chromosome
    MGG Molecular & General Genetics, vol. 218, no. 2, pp. 361–363, 1989
  147. Structural homology between virulence-associated bacterial adenylate cyclases
    Gene, vol. 71, no. 2, pp. 293–298, 1988
  148. Cloning and expression of the calmodulin-sensitive Bacillus anthracis adenylate cyclase in Escherichia coli
    Gene, vol. 64,