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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
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Peer-review assumes unbiased reviewing. Unfortunately, people don't always 'speak their minds', and people don't 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.
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 (BMC publications are supported by Pr P. Kourilsky, Director of the Institut Pasteur). |
|
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.
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) 12: 000-000.
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 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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