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Peer-reviewed publications

Popularisation of Science

Philosophy, Epistemology, Ethics

Economy

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 reviewing process. The Implicit Association Test web site 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 a do-it-yourself demonstration form.

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.

Peer-reviewed publications

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 [abstract on PubMed] [FREE full text]

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.


Popularisation of Science

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.


Economy

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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