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Note that we had to cancel many links. The WWW is unfortunately very unstable and does not faithfully keep memories...
Programme |
Databases |
Home |
All publications |
Note that we had to cancel many links. The WWW is unfortunately very unstable and does not faithfully keep memories...
Philosophy, Epistemology, Ethics
A Note on bibliometrics : What is the impact factor? Assessing the citation quality of journals, authors and institutions (number of citations, citations after 20 years...)
A New International Publication Policy: Search PubMed, PubMed Central, BioMed Central
•
Peer-review assumes unbiased reviewing. Unfortunately, people do not always 'speak their minds', and people do not always 'know their minds'. Understanding such divergences is important to scientific psychology, in particular during the review process. The Implicit Association Test website presents a new method that demonstrates public-private and conscious-unconscious divergences much more convincingly than has been possible with previous methods. It also displays the method in the form of a do-it-yourself demonstration.
This new method is called the Implicit Association Test, or IAT for short.
In addition to several do-it-yourself demonstrations of the IAT, the Implicit Association Test web site contains various related information. The value of the demonstrations may be greatest if you try at least one by clicking above before browsing the rest of the site. Also note that the IAT itself is not be immune to its own biases.
2003
E.
P. C. Rocha & A. Danchin
Essentiality, not expressiveness, drives gene-strand bias
in bacteria.
Nature Genetics (2003) E-publication ahead of print, july
6th.
S.X.
Ren, G. Fu, X.G. Jiang, R. Zeng, Y.G. Miao, H. Xu, Y.X. Zhang, H.
Xiong, G. Lu, L.F. Lu, H.Q. Jiang, J. Jia, Y.F. Tu, J.X. Jiang, W.Y.
Gu, Y.Q. Zhang, Z. Cai, H.H. Sheng, H.F. Yin, Y. Zhang, G.F. Zhu, M.
Wan, H.L. Huang, Z. Qian, S.Y. Wang, W. Ma, Z.J. Yao, Y. Shen, B.Q.
Qiang, Q.C. Xia, X.K. Guo, A. Danchin, I. Saint Girons, R.L.
Somerville, Y.M. Wen, M.H. Shi, Z. Chen, J.G. Xu & G.P. Zhao
Unique physiological and pathogenic features of Leptospira
interrogans revealed by whole-genome sequencing.
Nature (2003) 422:888-893. [PDF]
Associated to the LeptoList database. See Comments at BioMed
Central, with links.
K.Y.
Yuen, G. Pascal, S.S. Wong, P. Glaser, P.C. Woo, F. Kunst, J.J. Cai,
E.Y. Cheung, C. Médigue & A. Danchin
Exploring the Penicillium marneffei genome.
Arch Microbiol. (2003) 179:339-353.
C.
Tendeng, E. Krin, O.A. Soutourina, A. Marin, A. Danchin & P.N.
Bertin
A
novel H-NS-like protein from an antarctic psychrophilic bacterium
reveals a crucial role for the N-terminal domain in thermal
stability.
J Biol Chem. (2003) 278:18754-18760.
| K.
Kobayashi, S.D. Ehrlich, A. Albertini, G. Amati, K.K.
Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, P.
Bessières, F. Boland, S.C. Brignell, S. Bron, K. Bunai, J.
Chapuis, L.C. Christiansen, A. Danchin, M. Débarbouillé, E.
Dervyn, E. Deuerling, K. Devine, S.K. Devine, O. Dreesen, J.
Errington, S. Fillinger, S.J. Foster, Y. Fujita, A. Galizzi,
R. Gardan, C. Eschevins, T. Fukushima, K. Haga, C.R.
Harwood, M. Hecker, D. Hosoya, M.F. Hullo, H. Kakeshita, D.
Karamata, Y. Kasahara, F. Kawamura, K. Koga, P. Koski, R.
Kuwana, D. Imamura, M. Ishimaru, S. Ishikawa, I. Ishio, D.
Le Coq, A. Mason, C. Mauël, R. Meima, R.P. Mellado, A. Moir,
S. Moriya, E. Nagakawa, H. Nanamiya, S. Nakai, P. Nygaard,
M. Ogura, T. Ohanan, M. O’Reilly, M. O’Rourke, Z. Pragai,
H.M. Pooley, G. Rapoport, J.P. Rawlins, L.A. Rivas, C.
Rivolta, A. Sadaie, Y. Sadaie, M. Sarvas, T. Sato, H.H.
Saxild, E. Scanlan, W. Schumann, J.F.M.L.Seegers, J.
Sekiguchi, A. Sekowska, S. Séror, M. Simon, P.Stragier, R.
Studer, H. Takamatsu, T. Tanaka, M. Takeuchi, H.B.Thomaides,
, V. Vagner, J.M. van Dijl, K. Watabe, A. Wipat, H.Yamamoto,
M. Yamamoto, Y. Yamamoto, K. Yamane, K. Yata, K.Yoshida, H.
Yoshikawa, U. Zuber & N. Ogasawara Essential Bacillus subtilis genes Proceedings of the National Academy of Sciences, USA, (2003) 100: 4678-4683. [PDF] |
A.
Danchin
Genomes and evolution
Curr Issues Mol Biol. (2003) 5:37-42.
V.
Tosato, K. Gjuracic, K. Vlahovicek, S. Pongor, A. Danchin & C.V.
Bruschi
The DNA secondary structure of the Bacillus
subtilis genome
FEMS Microbiol Lett. (2003) 218: 23-30.
2002
X. Xia, T.
Wei, Z. Xie & A. Danchin
Genomic changes in
nucleotide and dinucleotide frequencies in Pasteurella multocida
cultured under high temperature
Genetics (2002) 161:
1385-1394.
L.P. Wong,
P.C. Woo, A.Y. Wu & K.Y. Yuen
DNA immunization
using a secreted cell wall antigen Mp1p is protective against Penicillium
marneffei infection
Vaccine (2002) 20:2878-86.
X. Xia
& Z. Xie
Protein structure,
neighbor effect, and a new index of amino-acid dissimilarities
Mol. Biol. Evol. (2002)
19:58-67.
S. Auger,
A. Danchin & I. Martin-Verstraete
Global expression
profile of Bacillus subtilis grown in the presence of
sulfate or methionine
Journal of Bacteriology
(2002) 184: 5179-5186.
| S.
Derzelle, E. Duchaud, F. Kunst, A. Danchin & P. Bertin Identification, haracterization, and regulation of a cluster of genes involved in carbapenem biosynthesis in Photorhabdus luminescens Appl Environ Microbiol (2002) 68: 3780-3789. |
E.P.C.
Rocha & A. Danchin
Base composition
bias might result from competition for metabolic resources.
Trends in Genetics (2002)
18: 291-294. [PDF]
A.
Sekowska & A. Danchin
The
methionine salvage pathway in Bacillus subtilis
BMC Microbiol 2002 2: 8
C.
Médigue, B. C.-Y. Wong, M. C.-M. Lin, S. Bocs & A. Danchin
The secE
gene of Helicobacter pylori
Journal of Bacteriology
(2002) 184: 2837-2840.
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 (E-Publication).
S. Auger,
W.H. Yuen, A. Danchin & I. Martin-Verstraete
The metIC
methionine biosynthesis operon is controlled by transcription
antitermination in Bacillus subtilis
Microbiology (2002) 148:
507-518.
I. Moszer,
L.M. Jones, S. Moreira, C. Fabry & A. Danchin
SubtiList: the
reference database for the Bacillus subtilis genome
Nucleic Acids Research
(2002) 30: 62-65.
2001
[work
entirely performed at the Microbiology Department, HKU
P.C.Y. Woo, S.S.Y Wong, P.N.L Lum, W.T. Hui & K.Y. Yuen
Cell-wall-deficient
bacteria and culture-negative febrile episodes in
bone-marrow-transplant recipients
Lancet (2001) 357:
675-679.]
J.-Y.
Coppée, S. Auger, E. Turlin, A. Sekowska, J.-P. Le Caer, V. Labas,
V. Vagner, A. Danchin & I. Martin-Verstraete
Sulfur-limitation-regulated
proteins in Bacillus subtilis: a two-dimensional gel
electrophoresis study
Microbiology (2001) 147:
1631-1640.
A.
Sekowska, S. Robin, J.-J. Daudin, A. Hénaut & A. Danchin
Extracting
biological information from DNA arrays: an unexpected link between
arginine and methionine metabolism in Bacillus subtilis
GenomeBiology (2001) 2:
19.1-19.12. (E-publication)
E.P.C.
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, L. Mulard, S. Krogh, J. Tse & A. Danchin MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis BMC Microbiology (2001) 1: 15. (E-publication) See a Comment about the future of E-Publication in Nature. |
|
E.P.C.
Rocha & A. Danchin
Ongoing evolution of strand
composition in bacterial genomes
Mol. Biol. Evol. (2001) 18: 1789-1799.
2000
A.
Sekowska, H.-F. Kung & A. Danchin
Sulfur metabolism in Escherichia coli and related bacteria,
facts and fiction
J. Mol. Microbiol. Biotechnol. (2000) 2: 145-177. [PDF]
E.P.C.
Rocha, A. Sekowska & A. Danchin
Sulphur islands in the Escherichia coli genome: markers
of the cell's architecture?
FEBS Lett. (2000) 476: 8-11.
A.
Sekowska, J.Y. Coppée, J.-P. Le Caer, I. Martin-Verstraete & A.
Danchin
S-adenosylmethionine decarboxylase of Bacillus subtilis is
closely related to archaebacterial counterparts
Mol. Microbiol. (2000) 36: 1135-1147.
A.
Sekowska, A. Danchin, & J.-L. Risler
Phylogeny of related functions: the case of polyamine
biosynthetic enzymes
Microbiology (2000) 146: 1815-1828.
A.
Danchin & A. Sekowska
Expression
profiling in reference bacteria: dreams and reality
GenomeBiology (2000) 1: 1024.1-1024.5
E.P.C.
Rocha, A. Danchin & A. Viari
The DB
case: pattern matching evidence is not significant
Mol.
Microbiol. (2000) 37: 216-218.
Book Reviews
2002
A.
Danchin
Préhistoire
de Pasteur
La Recherche (2002) 352: .
A.
Danchin
Les
Instituts Pasteur d'Outre-Mer
La Recherche (2002) 352: .
2001
A. Danchin
On our tiniest foes
EMBO Reports (2001) 2: 468-469.
2000
A.
Danchin
The
natural war
EMBO Reports (2000) 1: 216.
Book Chapters, Books
2003
2002
A.
Danchin
The Delphic Boat, Harvard University Press, Cambridge, USA
S.
Noria & A. Danchin
Just so genome stories: what does my neighbor tell me?, 3-13.
Genome science: towards a new paradigm? (Hiroshi
Yoshikawa, Naotake Ogasawara, Noriyuki Satoh, Editors) Elsevier.
Genomics of GC-rich Gram-positive Bacteria, A.
Danchin, editor, (2002)
Functional Genomics Series (Milton H. Saier, Series Editor),
Caister, Academic Press.
A.
Danchin
Genomes and Evolution, Chapter 1, 1-14.
2001
| A.
Danchin & K.Y. Yuen Bacterial Genomics in the Study of Virulence in Molecular Medical Microbiology (M. Sussman, editor), Harcourt (2001) Chapter 18 pp. 000-000. |
 |
A. Danchin
Bacillus subtilis
Biotechnology Volume
5b: Genomics and
Bioinformatics (M. Puehler, C. Sensen, editors), Wiley-VCH (2001)
000-000.
A. Danchin
Bacillus subtilis
Encyclopedia of Genetics,
(S. Brenner, J. H. Miller, editors) Academic Press (2001) 135-144.
Note that most of these layman-oriented texts are published in French; a translation of La Recherche exists in Spanish (Mundo Scientifico, Barcelona, Spain).
2003
A.
Danchin
Chercheurs d'or,
microbes et évolution
La Recherche (2003) 360: 00.
2002
A. Danchin
Au début; était
l'ordre des gènes
La Recherche Hors série
(2002) 9:14-18.
A. Danchin
Lifeline
Lancet (2002) 360:1030.
A. Danchin
Un Jurassic Park
moléculaire
La Recherche (2002) 358:
00.
A. Danchin
Faibles doses
La Recherche (2002) 357:
00.
A. Danchin
Mémoires et
apprentissages
La Recherche (2002) 356:
00.
A. Danchin
La soif du colibri
La Recherche (2002) 354:
00.
A. Danchin
Les Princes de
Serendip
La Recherche (2002) 353:
00.
A. Danchin
Mystère ou problème?
La Recherche (2002) 352:
00.
A. Danchin
Roméo, Juliette et
la bactérie
La Recherche (2002) 351:
91.
A. Danchin
& D. Mange
L'autonomie... des
êtres vivants
La Recherche (2002) 350:
30-32.
A. Danchin
Quand les poules
auront des dents
La Recherche (2002) 349:
22.
2001
A. Danchin
Qu'est-ce que la
génération spontanée?
in Tout ce que vous
avez toujours voulu savoir sur les sciences, Bayard Compact,
Paris, (2001) 464-466.
A.
Danchin
Les parasites de Tom
et Jerry
La Recherche (2001) 338:
22.
A.
Danchin
L'âme du monde
La Recherche (2001) 340:
24.
A.
Danchin
Où l’habit ne fait pas le
moine
La Recherche (2001) 341:
22.
A.
Danchin
Bricolage moléculaire
La Recherche (2001) 342:
90.
A.
Danchin
Mélancolie
La Recherche (2001) 343: 00
A.
Danchin
Politiques de dissuasion
La Recherche
(2001) 345: 00
A.
Danchin
Le Vivant et la
Machine de Turing
La Recherche
(2001) 345: 88-93.
A. Danchin
Entre Pas Encore et
Déjà Plus
Au-Delà 2001. Odyssée de
l'Esprit, (Emile Noël, dir.), Editions de la Radio Suisse Romande
Espace2, Genève; chapitre 5, pp 53-64.
A.
Danchin
Génomes et évolution
Annales de l'Institut
Pasteur/Actualités (2001) 11: 9-18.
A.
Danchin
Vie sociale au futur
La Recherche (2001) 347: 91
A.
Danchin
Le nombre est-il si
important?
La Recherche (2001) 348: 91
2000
A.
Danchin
Le style
fait l'espèce
La Recherche (2000) 332 : 24.
A. Danchin
Une histoire
intense, presque violente: l'histoire du programme génome humain
(English translation : A
rattling good history: the story of the Human Genome Project)
La Recherche (2000) 332: 26-34.
A. Danchin
Il nostro genoma
quotidiano 
Il Sole-24
Ore 2 Luglio 2000, 32.
A. Danchin
Science-fiction,
roman gothique ou canular ?
Le Monde 3
juillet 2000
A. Danchin
L'ADN volant
La Recherche (2000) 334: 26.
A. Danchin
Du bon usage de
l'analogie
La Recherche
(2000) 335: 24.
A. Danchin
Pas de pétrole
mais des microbes
La
Recherche (2000) 336: 20.
A. Danchin
Les
grenadiers prussiens
La Recherche
(2000) 337: 24.
A.
Danchin
La Biologia
nell'Era del Genoma (in Italian)
Spoletoscienza (2000) 20: 10.
A.
Danchin
Dalla
funzione alla struttura (in Italian)
Prometeo (2000) 71: 24-29.
Philosophy, History, Epistemology, Ethics
A.
Danchin
Infection
of society [PDF]
EMBO
Reports (2003) 4: 333-335.
S.
Brunak, A. Danchin, M. Hattori, H. Nakamura, K. Shinozaki, T.
Matise, D. Preuss
Nucleotide
sequence database policies [pdf]
Science
(2002) 298: 1333.
A.
Danchin
Not
every truth is good
EMBO
Reports (2002) 2: 102-104
A.
Danchin
II modi di
produzione del sapere: esiste une specificità occidentale? (in
Italian); the meeting
at Spoleto
Tecnocrazia
Keiron (2001) 9: 52-62
A.
Danchin
Nature et
Artifice
Dialogue Transculturel n°2
Alliage (2001) 45-46: 125-133
A.
Danchin
Sequencing
the genome of Bacillus subtilis: a Western inside story
For the Love of Genome
A Tribute to Hiroshi Yoshikawa (2001) pp. 4-9.
The Durban Declaration (5,228 signatures on october 9th, 2000)
see also the surprising (and dangerous) reaction to this declaration
at The Scientist (Editor in Chief, Eugene Garfield, the inventor of
Impact Factors...)
A. Danchin
Zi ran yu ren wei
(in Chinese) (in English 
:
Nature and Artifice)
Ke xue
yu ren wen, Transcultural Dialogue (2000), Pr Yue Daiyun, 樂 黛雲 (乐
黛云) ed., Beijing University Press 5: 1-9.
A.
Danchin
Sheng wu ji shu jie
he dian; meng huw xian shi? in Yin te wang chuang xin ji tou zi -
lai zi hua er jie he gui gu de bao gao, published by the Chinese
Association for Science and Business (in Chinese) (in English
:
The biotech connection: dream or
reality?) (2000) 166-179
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