SELECTED PUBLICATIONS

COIN PRESSE RÉSUMÉ HISTOIRE DE LA BIOLOGIE SUMMARY JOURNALIST'S CORNER

Understanding scientific publications requires to have some insight on the practice of bibliometrics.
A reflection on this practice is provided at this link

Before 2005, only those publications that were cited more than 30 times at the ISI are shown
The 87 publications cited more than 50 times at the ISI are shown in green

Google Scholar provides a more complete list of citations than the ISI for recent years

1967-1975 1993 1999 2005 2011 2017
1976-1979 1994 2000 2006 2012 2018
1980-1985 1995 2001 2007 2013 2019
1986-1990 1996 2002 2008 2014 2020
1991 1997 2003 2009 2015  
1992 1998 2004 2010 2016  

M Cohn, A Danchin, M Grunberg-Manago
Proton magnetic relaxation studies of manganous complexes of transfer RNA and related compounds
J Mol Biol (1969) 39: 199-217

A Danchin, M Guéron
Proton magnetic relaxation study of the manganese transfer RNA complex
J Chem Phys (1970) 53: 3599-3609

A Danchin, M Guéron
Cooperative binding of manganese (II) to transfer RNA
Eur J Biochem (1970) 16: 532-536

A Danchin, M Grunberg-Manago
Differences in binding of oligo C to charged and uncharged tRNA
FEBS Lett (1970) 9: 327-330

A Danchin
tRNA structure and binding sites for cations
Biopolymers (1972) 11: 1317-1333


JP Changeux, P Courrège, A Danchin
A theory of the epigenesis of neuronal networks by selective stabilisation of synapses
Proc Natl Acad Sci USA (1973) 70: 2974-2978

A Danchin
Does formylation of initiator tRNA act as a regulatory signal in E coli ?
FEBS Letters (1973) 34: 327-332

MM Werber, A Oplatka, A Danchin
Affinity labelling of rabbity muscle myosin with a cobalt(III) adenosine triphosphate complex
Biochemistry (1974) 13: 2683-2688


1976-1979

M Uzan, A Danchin
A rapid test for the relA mutation in E coli
Biochem Biophys Res Comm (1976) 69: 751-758

HU Petersen, A Danchin, M Grunberg-Manago
Toward an understanding of the formylation of initiator tRNA methionine in prokaryotic protein synthesis II A two-state model for the 70S ribosome
Biochemistry (1976) 15: 1357-1362

HU Petersen, E Joseph, A Ullmann, A Danchin
Formylation of initiator tRNA methionine in prokaryotic protein synthesis: in vivo polarity in lactose operon expression
J Bacteriol (1978) 135: 453-459

M Uzan, A Danchin
Correlation between the serine sensibility and derepressibility of the ilv genes in Ecoli relA mutants
Molec Gen Genet (1978) 165: 21-30

A Ullmann, E Joseph, A Danchin
Cyclic AMP as a modulator of polarity in polycistronic transcriptional units
Proc Natl Acad Sci USA (1979) 76: 3194-3198


1980-1985

C Guidi-Rontani, A Danchin, A Ullmann
Catabolite repression in Escherichia coli mutants lacking cyclic AMP receptor protein
Proc Natl Acad Sci USA (1980) 77: 5799-5801

A Roy, A Danchin
Restriction map of the cya region of Escherichia coli K 12 chromosome
Biochimie (1981) 63: 719-722

C Guidi-Rontani, A Danchin, A Ullmann
Isolation and characterization of a mutant affected in the regulation of adenylate cyclase of Escherichia coli
J Bacteriol (1981) 148: 753-761

A Roy, A Danchin
The cya locus of Escherichia coli K 12: organization and gene products
Molec Gen Genet (1982) 188: 465-471

J Daniel, L Dondon, A Danchin
2-ketobutyrate: a putative Escherichia coli K 12 alarmone
Molec Gen Genet (1983) 190: 452-458

A Roy, C Haziza, A Danchin
Regulation of adenylate cyclase synthesis in Escherichia coli: nucleotide sequence of the control region
EMBO J (1983) 2: 791-797

A Roy, A Danchin, E Joseph, A Ullmann
Two functional domains in adenylate cyclase of Escherichia coli
J Mol Biol (1983) 165: 197-202

F Traincard, T Ternynck, A Danchin, S Avrameas
Une technique immunoenzymatique pour la mise en évidence de l'hybridation moléculaire entre acides nucléiques
Ann Immunol (Pasteur) (1983) 134D: 399-405

A Ullmann, A Danchin
Role of cyclic AMP in bacteria
Adv Cyc Nucl Res (1983) 15: 1-53

A Danchin, L Dondon, J Daniel
Metabolic alterations mediated by 2-ketobutyrate in Escherichia coli K 12
Mol Gen Genet (1984) 193: 473-478

H Aiba, K Mori, M Tanaka, T Ooi, A Roy, A Danchin
The complete nucleotide sequence of the adenylate cyclase gene of Escherichia coli
Nucl Acid Res (1984) 12: 9427-9440

C Jacq, [...], A Danchin
Antibodies against a fused "LacZ-yeast mitochondrial intron" gene product allow identification of the mRNA-maturase encoded by the fourth intron of the yeast cob-box gene
EMBO J (1984) 3: 1567-1572

H De Reuse, A Roy, A Danchin
Analysis of the ptsH- ptsI- crr region in Escherichia coli K-12 nucleotide sequence of the ptsH gene
Gene (1985) 35: 199-20

L Hedegaard, A Danchin
The cya gene region of Erwinia chrysanthemi B374: organisation and gene products
Mol Gen Genet (1985) 201: 38-42


Creation of the Regulation of Gene Expression Unit

1986-1990

O Gascuel, A Danchin
Protein export in prokaryotes and eukaryotes: indications for a difference in the mechanism of exportation
J Mol Evol (1986) 24: 130-141

I St Girons, [...] A Danchin, O Barzu
Structural and catalytic characteristics of E coli adenylate kinase
J Biol Chem (1987) 262: 622-629

P Glaser, [...] A Danchin
The calmodulin-sensitive adenylate cyclase of Bordetella pertussis: cloning and expression in Escherichia
Mol Microbiol (1988) 2: 19-30
The adenylate cyclase toxin of Bordetella pertussis bacteria is stimulated by the human regulatory protein, calmodulin. A general strategy, using the adenylate-cyclase-calmodulin interaction as a tool, allowed cloning and expression of the toxin in Escherichia coli in the absence of any B. pertussis trans-activating factor. We show that the protein is synthesized as a large precursor composed of 1706 amino acids. The calmodulin-stimulated catalytic activity lies in the amino-terminal 450 amino acids of the adenylate cyclase. Expressed in E. coli the toxin is recognized in Western blots by antibodies directed against purified B. pertussis adenylate cyclase, and its activity is inhibited by these antibodies

H De Reuse, A Danchin
The ptsH, ptsI and crr genes of the Escherichia coli PEP dependent phosphotransferase system (PTS): a complex operon with several modes of transcription
J Bacteriol (1988) 170: 3827-3837

M Mock, [...] A Danchin, A Ullmann
Cloning and expression of the calmodulin-sensitive Bacillus anthracis adenylate cyclase in Escherichia coli
Gene (1988) 64: 277-284

S Lévy, A Danchin
Phylogeny of metabolic pathways: O-acetylserine sulfhydrylase A is homologous to tryptophan synthase beta subunit
Mol Microbiol (1988) 2: 777-783

P Glaser, [...] A Danchin
Secretion of cyclolysin, the calmodulin-sensitive adenylate cyclase-haemolysin bifunctional protein of B. pertussis
EMBO J (1988) 7: 3997-4004

V Escuyer, [...] A Danchin, M Mock
Structural homology between virulence associated bacterial adenylate cyclases
Gene (1988) 71: 293-298

P Glaser, [...] A Danchin
Identification of residues essential for catalysis and binding of calmodulin in B. pertussis adenylate cyclase by site-directed mutagenesis
EMBO J (1989) 8: 967-972

P Bertin, [...] A Danchin
Mutations in bglY, the structural gene for the DNA-binding protein H1, affect expression of several Escherichia coli genes
Biochimie (1990) 72:889-891

S Lévy, GQ Zeng, A Danchin
Cyclic AMP synthesis in Escherichia coli strains bearing known deletions in the pts phosphotransferase operon
Gene (1990) 86: 27-33

A Danchin
Homeotopic transformation and the origin of translation
Progress in Biophysics and Molecular Biology (1990) 54: 81-86

P Lejeune, A Danchin
Mutations in the bglY gene increase the frequency of spontaneous deletions in E coli K-12
Proc Natl Acad Sci (1990) 87: 360-363

A Beuve, [...] A Danchin, F O'Gara
Rhizobium meliloti adenylate cyclase is related to eukaryotic adenylate and guanylate cyclases
J Bacteriol (1990) 172: 2614-2621

V De Crécy-Lagard, [...] A Danchin
A Xanthomonas campestris pv campestris protein similar to catabolite activationfactor is involved in the regulation of phytopathogenicity
J Bacteriol (1990) 172: 5877-5883


1991-1995

H de Reuse, A Danchin
Positive regulation of the pts operon of E coli genetic evidence for a signal transduction mechanism
J Bacteriol (1991) 173: 727-733

H Munier, [...] O Barzu
Isolation and characterization of catalytic and calmodulin-binding domains of Bordetella pertussis adenylate cyclase
Eur J Biochem (1991) 196: 469-474

C Médigue, [...]A Danchin
Escherichia coli molecular genetic map (1500 kbp): update II
Mol Microbiol (1991) 5: 2629-2640
The DNA sequence data for Escherichia coli deposited in the EMBL library (release 27), together with miscellaneous data obtained from several laboratories, have been localized on an updated and corrected version of the restriction map of the chromosome generated by Kohara et al. (1987) and modified by others. This second update adds a further 500 kbp, increasing the amount of the E. coli chromosome sequenced to about one third of the total: 1510 kbp of sequenced DNA is included in the present data base. The accuracy of the map is assessed, and allows us to propose a precise genetic map position for every sequenced gene. The location of rare-cutting sites such as AvrII, NotI and SfiI have also been included in the update in order to combine the data obtained from different sources into one single file. The distribution of palindromic sequences (to which most restriction sites belong) has been studied in coding sequences. There appears to be a significant counter-selection against several such sequences in E. coli coding sequences (but not in other organisms such as Saccharomyces cerevisiae), suggesting the existence of constraints on DNA structure in E. coli, perhaps indicative of a functional role for horizontal gene transfer, preserving coding sequences, in this type of bacteria

C Médigue, [...] A Danchin
Evidence for horizontal gene transfer in Escherichia coli speciation
J Mol Biol (1991) 222: 851-856
After extracting more than 780 identified Escherichia coli genes from available data libraries, we investigated the codon usage of the corresponding coding sequences and extended the study of gene classes, thus obtained, to the nature and intensity of short nucleotide sequence selection, related to constraints operating at the nucleotide level. Using Correspondence Analysis we found that three classes ought to be included in order to match all data now available. The first two classes, as known, encompass genes expressed either continuously at a high level, or at a low level and/or rarely; the third class consists of genes corresponding to surface elements of the cell, genes coming from mobile elements as well as genes resulting in a high fidelity of DNA replication. This suggests that bacterial strains cultivated in the laboratory have been fixed by specific use of antimutator genes that are horizontally exchanged

M Santana, [...] A Danchin, P Glaser
Molecular cloning, sequencing and physiological characterization of the qox operon from Bacillus subtilis encoding the aa3-600 quinol oxidase
J Biol Chem (1992) 267: 10225-10231

H De Reuse, A Kolb, A Danchin
Positive regulation of the expression of the Escherichia coli pts operon Identification of the regulatory regions
J Mol Biol (1992) 226: 623-635

A Danchin
Phylogeny of adenylyl cyclases
Adv Cyc Nuc Prot Phos Res (1993) 27: 109-162

C Médigue, [...] A Danchin
Colibri: a functional data base for the Escherichia coli genome
Microbiol Rev (1993) 57: 623-654

P Glaser, [...] A Danchin
Bacillus subtilis genome project: cloning and sequencing of the 97 Kb region from 325o to 333o
Mol Microbiol (1993) 10: 371-384

O Barzu, A Danchin
Adenylyl cyclases: a heterogeneous class of ATP-utilizing enzymes
Prog Nucleic Acid Res Mol Biol (1994) 49: 241-283

P Bertin, [...] A Danchin , E Collatz
The H-NS protein is involved in the biogenesis of flagella in Escherichia coli
J Bacteriol (1994) 176: 5537-5540

M Santana, [...] A Danchin, P Glaser
Bacillus subtilis Fo F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants
J Bacteriol (1994) 176: 6802-6811

P Glaser, A Danchin, [...]M Nakano
Identification and isolation of a gene required for nitrate assimilation and anaerobic growth of Bacillus subtilis
J Bacteriol (1995) 177: 1112-1115

I Moszer, P Glaser, A Danchin
SubtiList: a relational database for the Bacillus subtilis genome
Microbiology (1995) 141: 261-268

L Serina, [...] A Danchin, [...] O Barzu
Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP
Biochemistry (1995) 34: 5066-5074

M Borodovsky, [...] A Danchin
Detection of new genes in the bacterial genome using Markov models for three gene classes
Nucleic Acids Res (1995) 23: 3554-3562

H Cruz-Ramos, [...] A Danchin, P Glaser
Anaerobic transcription activation in Bacillus subtilis: identification of distinct FNR-dependent and independant regulatory mechanisms
EMBO J (1995) 14: 5984-5994


1996-1999

N Bucurenci, [...] A Danchin, O Barzu, AM Gilles
CMP-Kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases
J Biol Chem (1996) 271: 2856-2862

A Hénaut, [...] A Danchin
Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages
J Mol Biol (1996) 257: 574-585

MM Nakano, [...] A Danchin, FM Hulett
Two-component regulatory proteins ResD-ResE are required for transcriptional activation of fnr upon oxygen limitation in Bacillus subtilis
J Bacteriol (1996) 178: 3796-3802

C Laurent-Winter, S Ngo, A Danchin, P Bertin
Role of Escherichia coli histone-like nucleoid structuring protein in bacterial metabolism and stress response: identification of targets by two-dimensional electrophoresis
Eur J Biochem (1997) 244: 767-773

F Kunst, N Ogasawara, I Moszer, [...] H Yoshikawa, A Danchin
The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
Nature (1997) 390: 249-256

O Sismeiro, [...] A Danchin
Aeromonas hydrophila Adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic Archaebacteria
J Bacteriol (1998) 180: 3339-3344

E Rocha, A Viari, A Danchin
Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons
Nucleic Acids Res (1998) 26: 2971-2980

A Sekowska, P Bertin, A Danchin
Characterization of polyamines synthesis pathway in Bacillus subtilis 168
Mol Microbiol (1998) 29: 851-858

F Delbac, [...] A Danchin, C P Vivarès
On proteins of the microsporidian invasive apparatus: complete sequence of a polar tube protein of Encephalitozoon cuniculi
Mol Microbiol (1998) 29: 825-834

P Nitschké, [...] A Danchin
Indigo: a World-Wide-Web review of genomes and gene functions
FEMS Microbiology Reviews (1998) 22: 207-227

EP Rocha, A Danchin , A Viari
Universal replication biases in bacteria
Mol Microbiol (1999) 32: 11-16

E Presecan-Siedel, [...] A Danchin, P Glaser, I Martin-Verstraete
Catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis
J Bacteriol (1999) 181: 6889-6897

I Moszer, E P Rocha, A Danchin
Codon usage and lateral gene transfer in Bacillus subtilis
Current Opinion in Microbiology (1999) 2: 524-528

NN Baranova, A Danchin, AA Neyfakh
Mta, a global MerR-type regulator of the Bacillus subtilis multidrug-efflux transporters
Molecular Microbiology (1999) 31: 1549-1559

EP Rocha, A Danchin, A Viari
Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes
Molecular Biology, Evolution (1999) 16: 1219-1230

EPC Rocha, A Danchin, A Viari
Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis
Nucleic Acids Res (1999) 27: 3567-3576

C Médigue, F Rechenmann, A Danchin, A Viari
Imagene: an integrated computer environment for sequence annotation and analysis
Bioinformatics (1999) 15: 2-15

O Soutourina, [...] A Danchin, P Bertin
Multiple control of flagellum biosynthesis in Escherichia coli: Role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon
Journal of Bacteriology (1999) 181: 7500-7508

P Bertin, [...] A Danchin, R Brasseur
The structural and functional organization of H-NS-like proteins is evolutionarily conserved in gram-negative bacteria
Molecular Microbiology (1999) 31: 319-329


2000 (publications in collaboration with the HKU-Pasteur Centre in Hong Kong)

A Sekowska, HF Kung, A Danchin
Sulfur metabolism in Escherichia coli and related bacteria, facts and fiction
J Mol Microbiol Biotechnol (2000) 2 : 145-177

A Sekowska, A Danchin, JL Risler
Phylogeny of related functions: the case of polyamine biosynthetic enzymes
Microbiology (2000) 146: 1815-1828

Creation of the Genetics of Bacterial Genomes Unit

2001 (star: publications in collaboration with the HKU-Pasteur Research Centre in Hong Kong)


F Hommais, [...] A Danchin, P Bertin
Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS
Mol Microbiol (2001) 40: 20-36

P Bertin , [...] A Danchin
H-NS and H-NS-like proteins in Gram-negative bacteria and their multiple role in the regulation of bacterial metabolism
Biochimie (2001) 83: 235-241

*A Sekowska, [...] A Danchin
Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis
GenomeBiology (2001) 2: 191-1912


*EPC Rocha, A Danchin, A Viari
Evolutionary role of restriction/modification systems as revealed by comparative genome analysis
Genome Research (2001) 10: 946-958

*A Sekowska, [...] A Danchin
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis
BMC Microbiology (2001) 1: 15

MF Hullo, I Moszer, A Danchin, I Martin-Verstraete
CotA of Bacillus subtilis is a copper-dependent laccase
J Bacteriol (2001) 183: 5426-5430

* EPC Rocha, A Danchin
Ongoing evolution of strand composition in bacterial genomes
Mol Biol Evol (2001) 18: 1789-1799

2002 (star: publications in collaboration with the HKU-Pasteur Centre in Hong Kong)

OA Soutourina, [...]A Danchin, P Bertin
Regulation of bacterial motility in response to low pH in Escherichia coli: the role of H-NS protein
Microbiology (2002) 148: 1543-1551

*S Auger, A Danchin, I Martin-Verstraete
Global expression profile of Bacillus subtilis grown in the presence of sulfate or methionine
J Bacteriol (2002) 184: 5179-5186

I Guillouard, [...] A Danchin, I Martin-Verstraete
Identification of Bacillus subtilis CysL, a regulator of the cysJI operon, which encodes sulfite reductase
J Bacteriol (2002) 184: 4681-4689


S Derzelle, [...] A Danchin, P Bertin
Identification, characterization, and regulation of a cluster of genes involved in carbapenem biosynthesis in Photorhabdus luminescens
Appl Environ Microbiol (2002) 68: 3780-3789

*EPC Rocha, A Danchin
Base composition bias might result from competition for metabolic resources
Trends in Genetics (2002) 18: 291-294

*A Sekowska , A Danchin
The methionine salvage pathway in Bacillus subtilis
BMC Microbiol (2002) 2: 8
*S Bocs, A Danchin, C Médigue
Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes
BMC Bioinformatics (2002) 3: 5

*S Auger, [...] I Martin-Verstraete
The metIC methionine biosynthesis operon is controlled by transcription antitermination in Bacillus subtilis
Microbiology (2002) 148: 507-518

*I Moszer, [...] A Danchin
SubtiList: the reference database for the Bacillus subtilis genome
Nucleic Acids Research (2002) 30: 62-65

2003 (star: publications in collaboration with the HKU-Pasteur Centre in Hong Kong)

*SX Ren, [...], A Danchin, [...] GP Zhao
Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing
Nature (2003) 422: 888-893 Associated to the LeptoList database


*K Kobayashi, [...], A Danchin, [...], H Yoshikawa, U Zuber, N Ogasawara
Essential Bacillus subtilis genes
Proceedings of the National Academy of Sciences, USA, (2003) 100: 4678-4683

* EPC Rocha, A Danchin
Essentiality, not expressiveness, drives gene-strand bias in bacteria
Nature Genet (2003) 34: 377-378

*YQ Zhang, [...] A Danchin, YM Wen
Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228)
Mol Microbiol (2003) 49: 1577-1593 Associated to the SepiList database


E Duchaud, [...], A Danchin, F Kunst
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
Nature Biotechnol (2003) 21: 1307-1313


* EPC Rocha, A Danchin
Gene essentiality determines chromosome organisation in bacteria
Nucleic Acids Res (2003) 31: 6570-6577

2004 (star: publications in collaboration with the HKU-Pasteur Centre in Hong Kong)


* EPC Rocha, A Danchin
An analysis of determinants of amino-acids substitution rates in bacterial proteins
Mol Biol Evol (2004) 21: 108-116

F Hommais, [...] A Danchin, P Bertin
GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli
Microbiology (2004) 150: 61-72

S Derzelle, [...] A Danchin
The PhoP-PhoQ two-component regulatory system of Photorhabdus luminescens is essential for virulence in insects
J Bacteriol (2004) 186: 1270-1279

MF Hullo, [...]A Danchin, I Martin-Verstraete
The metNPQ operon of Bacillus subtilis encodes an ABC permease transporting methionine sulfoxide, D- and L-methionine
Res Microbiol (2004) 155: 80-86

* A Sekowska, [...] A Danchin
Bacterial variations on the methionine salvage pathway
BMC Microbiol (2004) 4: 9

P Burguière, [...] A Danchin, I Martin-Verstraete
Three different systems participate in L-cystine uptake in Bacillus subtilis
J Bacteriol (2004) 186: 4875-4884


2005 (star: publications in collaboration with the HKU-Pasteur Research Centre


H Ashida, A Danchin, A Yokota
Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism?
Res Microbiol (2005) 156: 611-618

HD Song, [...] A Danchin, [...] GP Zhao
Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human
Proc Natl Acad Sci USA (2005) 102: 2430-2435

* G Fang, [...] A Danchin
Specialized microbial databases for inductive exploration of microbial genome sequences
BMC Genomics (2005) 6: 14

S Auger, MP Gomez, A Danchin, I Martin-Verstraete
The PatB protein of Bacillus subtilis is a C-S-lyase
Biochimie (2005) 87: 231-238

E Turlin, [...] A Danchin, F Biville
3-phenylpropionate catabolism and the Escherichia coli oxidative stress response
Res Microbiol (2005) 156: 312-321

* G Pascal, C Médigue, A Danchin
Universal biases in protein composition of model prokaryotes
Proteins (2005) 60: 27-35

* YL Yap, [...] A Danchin, MP Wong
Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays
Nucleic Acids Res (2005) 14: 409-421


G Fang, EPC Rocha, A Danchin
How essential are non-essential genes?
Mol Biol Evol (2005) 22: 2147-2156

C Médigue, [...], G von Heijne, A Danchin
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
Genome Res (2005) 15: 1325-1335

2006


M Bailly-Bechet, A Danchin,[...] M Vergassola
Codon usage domains over bacterial chromosomes
PLoS Computational Biology (2006) 2: e37

C Carapito, [...] A Danchin, [...] MC Lett
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 (2006) 8: 595-606

A Danchin
Beneficial biological warfare
EMBO Rep (2006) 7:767

S Even, [...] A Danchin, I Martin-Verstraete
Global control of cysteine metabolism by CymR in Bacillus subtilis
J Bacteriol (2006) 188: 2184-2197

U Mechold, [...] A Danchin
Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells
Nucleic Acids Res (2006) 34: 2364-2373

G Pascal, C Médigue, A Danchin
Persistent biases in the amino-acid composition of prokaryotic proteins
Bioessays (2006) 28: 726-738

Z Qin, [...] A Danchin, H Jiang, D Qu
Structure-based discovery of inhibitors of the YycG histidine kinase: New chemical leads to combat Staphylococcus epidermidis infections
BMC Microbiology (2006) 6: 96

E Turlin, [...] A Danchin, S Derzelle
Proteome analysis of the phenotypic variation process in Photorhabdus luminescens
Proteomics (2006) 6: 2705-2725

W Wei, [...] A Danchin, YX Li
Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228
BMC Genomics (2006) 7: 112

2007

S Chalabaev, [...] A Danchin, Biville F
The HcaR regulatory protein of Photorhabdus luminescens affects the production of proteins involved in oxidative stress and toxemia
Proteomics (2007) 7: 4499-4510

A Danchin
Archives or palimpsests? Bacterial genomes unveil a scenario for the origin of life
Biological Theory (2007) 2: 52-61


A Danchin, G Fang, S Noria
The extant core bacterial proteome is an archive of the origin of life
Proteomics (2007) 7: 875-889

MF Hullo, [...] A Danchin, I Martin-Verstraete
The conversion of methionine to cysteine in Bacillus subtilis and its regulation
J Bacteriol (2007) 189: 187-197

Y Makita, MJL de Hoon, A Danchin
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
BMC Bioinformatics (2007) 8: 47

U Mechold, [...] A Danchin
YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity
Nucleic Acids Res (2007) 35: 4552-4561


D Muller, [...] A Danchin, PN Bertin
A tale of two oxidation states: bacterial colonization of arsenic-rich environments
PLoS Genetics (2007) 3: e53

TW Ng, [...] A Danchin
A parasite vector-host epidemic model for TSE propagation
Medical Science Monitor (2007) 13: 59-66


RM Watt, [...] A Danchin, JD Huang
Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes
Nucleic Acids Res (2007) 35: e37

Y Wu, [...] A Danchin, [...] H Jiang
Potent and selective inhibitors of Staphylococcus epidermidis tryptophanyl-tRNA synthetase
J Antimicrobial Chemotherapy (2007) 60: 502-509


2008

G André, [...] A Danchin, I Martin-Verstraete, O Soutourina
S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum
Nucleic Acids Res (2008) 36: 5955-5969 

H Ashida, [...] A Danchin, A Yokota
RuBisCO-like proteins as the enolase enzyme in the methionine salvage pathway: functional and evolutionary relationships between RuBisCO-like proteins and photosynthetic RuBisCO
J Exp Bot (2008) 59: 1543-1554.

S Chalabaev, [...] A Danchin, F Biville
Cinnamic acid, an autoinducer of its own biosynthesis, is processed via Hca enzymes in Photorhabdus luminescens
Appl Environ Microbiol (2008) 74:1717-1725


V de Lorenzo, A Danchin
Synthetic biology: discovering new worlds and new words
EMBO Rep (2008) 9: 822-827 pubmed

G Fang, EP Rocha, A Danchin
Persistence drives gene clustering in bacterial genomes
BMC Genomics (2008) 9: 4

E Krin, [...] A Danchin
Regulatory role of UvrY in adaptation of Photorhabdus luminescens growth inside the insect
Environmental Microbiology (2008) 10: 1118–1134


M Riley, JT Staley, A Danchin,[...] LS Thompson
Genomics of an extreme psychrophile, Psychromonas ingrahamii
BMC Genomics 9: 210

2009

V Barbe, [...] A Danchin
From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later
Microbiology (2009) 155: 1758-1775

uk-flagThis article describes the re-sequencing of the Bacillus subtilis genome. It is dedicated to the memory of Frank Kunst, who was instrumental in the whole B. subtilis genome project, victim of an unjust law which forces active scientists to retire, without any consideration for their contribution to creation and diffusion of knowledge.

  fr-flagCet article rapporte le reséquençage du génome de Bacillus subtilis. Il est dédié à la mémoire de Frank Kunst, sans qui le projet n'aurait jamais pu être mené à son terme en 1997. Frank Kunst a été victime d'une loi inique qui force les chercheurs encore actifs à cesser leur activité sans aucune considération de l'apport qu'ils peuvent avoir à la création et la diffusion du savoir.
In memoriam Frank Kunst, let us remember that, when the article reporting the first complete sequencing of the genome appeared in 1997, Chet Raymo, for the Boston Globe wrote (january 5th, 1998):
Beauty bare on the spiral staircase
[…]
« Euclid alone has looked on Beauty bare, » wrote the poet Edna St. Vincent Millay. Here, in this exquisite geometrical molecule [DNA], we look on Beauty bare.
I felt the same response recently when I looked at a schematic map of the complete genome (genetic material) of the bacterium Bacillus subtilis in the journal Nature.
[…]
I was looking at the gene map for Bacillus subtilis in the college library, with the 8-page foldout spread across a table. Several students stopped to look over my shoulder, curious as to what the colorful chart might be.
« This is the blueprint for making a living organism, » I said. I started to provide a more complete explanation, but fell silent. The map spoke for itself. Elegant. Simple. Unfathomably profound.
Beauty bare.
A Danchin
Natural selection and immortality
Biogerontology (2009) 10: 503-516

A Danchin
Bacteria as computers making computers
FEMS Microbiol Rev (2009) 33: 3-26

A Danchin
A phylogenetic view of bacterial ribonucleases
Prog Nucleic Acid Res Mol Biol (2009) 85: 1-41

A Danchin
Nature, artifice and emerging diseases
EMBO Reports (2009) 10: 418-419

A Danchin
Cells need safety valves
Bioessays (2009) 31: 769-773

In Escherichia coli, the role of lacA, the third gene of the lactose operon, has remained an enigma. I suggest that its role is the consequence of the need for cells to have safety valves that protect them from the osmotic effect created by their permeases. Safety valves allow them to cope with the buildup of osmotic pressure under accidental transient conditions. Multidrug resistance (MDR) efflux, thus named because of our anthropocentrism, is ubiquitous. Yet, the formation of simple leaks would result in futile influx/efflux cycles. Versatile modification enzymes with low sensitivity solve the problem if the modified metabolite is the one exported by MDR permeases. This may account for the pervasive presence of acetyltransferases, such as LacA, associated to acetyl-metabolite exporters. This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells

A Danchin
Sélection naturelle et immortalité
in: Les mondes darwiniens (T Heams, P Huneman, G Lecointre, M Silberstein, eds), Syllepse (2009) pp 445-470

Tous les organismes – bactéries incluses – vieillissent et meurent. En raison de l’incroyable diversité de ce processus (les plantes vieillissent lentement, par exemple), c’est un lieu commun des études sur le vieillissement que de considérer qu’il s’agit d’un paradoxe, qui requiert par conséquent une explication en profondeur. Cette observation a suscité une profusion d’études fascinantes (et de discussions enflammées) destinées à mettre au jour la variété des causes et des mécanismes impliqués dans le vieillissement. Dans ce contexte, l’« immortalité » est considérée comme la norme. Pourquoi et comment vieillissons-nous ? Ce n’est pas cette question que je traiterai ici, je vais prendre le chemin exactement opposé. Considérant que le vieillissement est une conséquence directe de la physique – et c’est en effet l’une des conclusions majeures à laquelle parviennent ceux qui analysent le vieillissement en profondeur quand il repensent les théories de l’« avalanche d’erreurs» d’Orgel ou le « cliquet de Muller –, j’observe au contraire que c’est l’immortalité (que nous observons dans le cancer) qui soulève un paradoxe...

唐善﹒安東
向合成细胞迈进:细胞与计算机的复制过程中的遗传问题
微生物与感染 Journal of Microbes and Infection (2009) 4: 12

A. Danchin
Information of the chassis and information of the program in synthetic cells
Syst Synth Biol (2009) 3: 125-134

A Danchin, A Sekowska
Physico-chemical prerequisites for the construction of a synthetic cell
in: Synthetic Chemistry, May 26th - 30th, 2008, Bozen, Italy
Beilstein Institut for the Advancement of Chemical Sciences (2009) 1-13

M Fang, [...] A Danchin, U Mechold
Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis
Nucleic Acids Res (2009) 37: 5114-5125

Y Jin, RM Watt, A Danchin, JD Huang
Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli
BMC Genomics (2009) 10: 165

Y Saito, [...] A Danchin, A Sekowska, A Yokota
Structural and functional similarities between a RuBisCO-like protein from Bacillus subtilis and photosynthetic RuBisCO
J Biol Chem (2009) 284:13256-13264

E Parrilli, [...] A Danchin, G Marino, ML Tutino
PhPssA is required for alpha-amylase secretion in Antarctic Pseudoalteromonas haloplanktis
Microbiology (2009) 156: 211-219

A Sekowska, [...] A Danchin, M Vergassola
Repulsion and metabolic switches in the collective behavior of bacterial colonies
Biophys J (2009) 97: 688-698

O Soutourina,[...] A Danchin, T Msadek, I Martin-Verstraete
CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulfur source utilization and plays a role in biofilm formation
Mol Microbiol (2009) 73: 194-211

J Thornton and the BioSapiens Network
Annotations for all by all - the BioSapiens network
Genome Biology (2009) 10: 2


M Touchon, [...], A Danchin, [...], C Médigue, EPC Rocha, E Denamur
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
PLoS Genetics (2009) 5: e1000344

2010

A Danchin
Perfect time or perfect crime?
EMBO Reports (2010) 11: 74

A Danchin
Motivated research
EMBO Reports (2010) 11: 488


Opening: Three years ago, a senior politician attended his country’s Annual Congress for the Advancement of Science to give the introductory lecture. He asked the attending scientists to make science and research more attractive to young students and the general public, and asked his countrymen to support scientists to address the urgent challenges of global climate change, energy needs and dwindling water resources. It was neither a European nor a US politician, but the Indian Prime Minister Manmohan Singh who made this speech about the relationship between research and its practical applications. This is such an important topic that one might think it deserves appropriate attention in Europe, yet we fail to address it properly. Instead, we just discuss how science should serve society or contribute to the ‘knowledge-based economy’, or how ‘basic’ or ‘fundamental’ research is opposed to ‘applied’ or ‘industrial’ research and how funding for ‘big science’ comes at the expense of ‘little academic’ research.

A Danchin
A path from predation to mutualism
Molecular Microbiology (2010) 77: 1346-1350

A Danchin
Science and arsenic fool's gold: a toxic broth
Journal of Cosmology (2010) 13 : 3617-3620

A Danchin, G Fang
Babies are born very young. The synthesis of change
Journal of Cosmology (2010) 7: May 2010 Artificial Life

A Danchin, A Sekowska
The role of information in evolutionary genomics of bacteria
In: Evolutionary genomics and systems biology (G Caetano-Anollés, Editor), Wiley, sons, Hoboken, NJ (2010) pp 81-94

E Krin, A Danchin, O Soutourina
RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli
Res Microbiol (2010) 161: 363-371

E Krin, A Danchin, O Soutourina
Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli
BMC Microbiology (2010) 10: 273

E Parrilli, [...] A Danchin, G Marino, ML Tutino
PhPssA is required for alpha-amylase secretion in Antarctic Pseudoalteromonas haloplanktis
Microbiology (2010) 156: 211-219


F Piette, [...] A Danchin, P Leprince, G Feller
Proteomics of life at low temperatures: trigger factor is the primary chaperone in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125
Molecular Microbiology (2010) 76: 120-132

M Vayssier-Taussat, D Le Rhun, HK Deng, F Biville, S Cescau, A Danchin, G Marignac, E Lenaour, HJ Boulouis, M Mavris, L Arnaud, H Yang, J Wang, M Quebatte, P Engel, H Saenz, C Dehio
The Trw type IV secretion system of Bartonella mediates host-specific adhesion to erythrocytes
PLoS Pathogens (2010) 6: e1000946


PM Binder, A Danchin
Life's demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life?
EMBO Reports (2011) 12: 495-499


In his seventeenth-century classic, Novum Organum, Francis Bacon wrote, “we cannot command nature except by obeying her” (Bacon, 2010). Although our knowledge of living systems is much improved since Bacon’s time, we are still far from understanding—or commanding—all the complex mechanisms of life. To take full advantage of living organisms for the benefit of mankind, we will need to understand those mechanisms to the furthest possible extent. To do so will require that the concept of information and the theories of information science take a more-prominent role in the understanding of living systems...

A Danchin
Les gènes du démon de Maxwell : est-il possible de construire une usine cellulaire ? Maxwell’s demon’s genes: Can we build a cell factory?
Comptes Rendus de l'Académie des Sciences, Chimie (2011) 14: 413-419


A Danchin, PM Binder, S Noria
Antifragility and tinkering in biology (and in business): Flexibility provides an efficient epigenetic way to manage risk
Genes (2011), 2: 998-1016; doi:10.3390/genes2040998

F Piette, [...] A Danchin, P Leprince, G Feller
Life in the cold: a proteomic study of cold-repressed proteins in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125
Applied and Environmental Microbiology (2011) 77: 3881-3883

M Porcar, A Danchin, [...] A Moya
The ten grand challenges of synthetic life
Systems and Synthetic Biology (2011) 5: 1-9

H Rohde, [...], A Danchin, [...] J Xu, the E. coli O104:H4 Genome Analysis Crowd-sourcing consortium, MJ Pallen, J Wang, M Aepfelbacher, R Yang
Open-source genomics of an isolate from a german family outbreak of Shiga-toxin-producing Escherichia coli O104:H4
New England Journal of Medicine (2011) 365: 718-724

Y Wang, [...] A Danchin, P-Y Qian
Bacterial niche-specific genome expansion Is coupled with highly frequent gene disruptions in deep-sea sediments
PLoS ONE (2011) 6: e29149

Y Wang, [...], A Danchin, PY Qian
Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea
ISME J (2011) 5: 1652-1659

B Wilmes, [...] A Danchin, [...] M Schweder
Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125
Applied and Environmental Microbiology (2011) 77: 1276-1283   


RM Couture, A Sekowska, G Fang, A Danchin
Linking selenium biogeochemistry to the sulfur-dependent biological detoxification of arsenic
Environ Microbiol (2012) 14: 1612-1623. doi: 10.1111/j.1462-2920.2012.02758.x.

A Danchin
Scaling up synthetic biology: Do not forget the chassis
FEBS Letters (2012) 586: 2129-2137

A Danchin
Synthetic biology's flywheel
EMBO Reports (2012) 13: 92

A Danchin
I geni del diavoletto di Maxwell
Prometeo 117: 120-125


S Engelen, D Vallenet, C Médigue, A Danchin
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
BMC Genomics (2012) 13: 69

Karsch-Mizrachi I, Nakamura Y, Cochrane G
International Nucleotide Sequence Database Collaboration Advisors:
Miyano S, Nakamura H, Sugano S, Danchin A, Savakis B, Weissenbach J, Weng Z, Salzberg S

The International Nucleotide Sequence Database Collaboration
Nucleic Acids Research (2012) 40: D33-D37

MF Liu, [...] A Danchin, HJ Boulouis, F Biville
Identification of a new nanoRNase in Bartonella
Microbiology (2012)158: 886-895


G Postic, A Danchin, U Mechold
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae
RNA (2012) 18: 155-165

E Toledano, V Ogryzko, A Danchin, D Ladant, U Mechold
3’‐5’phosphoadenosine phosphate is an inhibitor of Poly(ADP-ribose) Polymerase 1 and a potential mediator of the lithium-dependent inhibition of PARP‐1 in vivo
Biochemical Journal (2012) 443: 485-490


CG Acevedo-Rocha, G Fang, M Schmidt, DW Ussery, A Danchin
From essential to persistent genes: a functional approach to constructing synthetic life
Trends Genet (2013) 29: 273-279

E Belda E, A Sekowska, F Le Fèvre, A Morgat, D Mornico, C Ouzounis, D Vallenet, C Médigue, A Danchin
An updated metabolic view of the Bacillus subtilis 168 genome
Microbiology (2013) 159: 757-770

A Danchin, A Sekowska
Constraints in the design of the synthetic bacterial chassis
Methods in Microbiology (2013) 40: 39-68


CM Chan, A Danchin, P Marlière, A Sekowska
Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis
Environ Microbiol (2014) 16: 101-117

A Danchin, A Sekowska
The logic of metabolism and its fuzzy consequences
Environ Microbiol (2014) 16: 19-28

Kyrpides, [...] Danchin, A, [...] Klenk, H-P
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strain
PLoS Biology (2014) 12: e1001920


M Porcar, A Danchin, V de Lorenzo
Confidence, tolerance, and allowance in biological engineering: The nuts and bolts of living things
BioEssays (2015) 37: 95-102
Abstract The emphasis of systems and synthetic biology on quantitative understanding of biological objects and their eventual re-design has raised the question of whether description and construction standards that are commonplace in electric and mechanical engineering are applicable to live systems. The tuning of genetic devices to deliver a given activity is generally context-dependent, thereby undermining the re-usability of parts, and predictability of function, necessary for manufacturing new biological objects. Tolerance (acceptable limits within the unavoidable divergence of a nominal value) and allowance (deviation introduced on purpose for the sake of flexibility and hence modularity, i.e. fitting together with a variety of other components) are key aspects of standardization that need to be brought to biological design. These should endow functional building blocks with a pre-specified level of confidence for bespoke biosystems engineering. However, in the absence of more fundamental knowledge, fine-tuning necessarily relies on evolutionary/combinatorial gravitation toward a fixed objective

V de Lorenzo, A Sekowska, A Danchin,
Chemical reactivity drives spatiotemporal organisation of bacterial metabolism
FEMS Microbiology Reviews (2015) 39: 96-119
Abstract We examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects

 


M Blaxter, A Danchin, B Savakis, K Fukami-Kobayashi, K Kurokawa, S Sugano, RJ Roberts, SL Salzberg, CI Wu
Reminder to deposit DNA sequences
Science (2016) 352: 780

E Belda, RG van Heck, MJ Lopez-Sanchez, S Cruveiller, V Barbe, C Fraser, HP Klenk, J Petersen, A Morgat, PI Nikel, D Vallenet, Z Rouy, A Sekowska, VA Martins Dos Santos, V de Lorenzo, A Danchin, C Médigue
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Environ Microbiol (2016) doi: 10.1111/1462-2920.13230

A Danchin
From function to structure take the archaeal TRAM
Environ Microbiol (2016) 18: 2776-2778

A Danchin
Nature or manufacture: What should we fear most?
C R Biol (2016) doi: 10.1016/j.crvi.2016.05.001

A Danchin, G Fang
Unknown unknowns: essential genes in quest for function
Microb Biotechnol. (2016) doi: 10.1111/1751-7915.12384

PI Nikel, M Chavarría, A Danchin, V de Lorenzo
From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions
Curr Opin Chem Biol (2016) 34: 20-29

Y Wang, JM Huang, SL Wang, ZM Gao, AQ Zhang, A Danchin, LS He
Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp.
Environ Microbiol (2016) doi: 10.1111/1462-2920.13411
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