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Courses / Cours
Research
and university teaching cannot
be separated. A scientist's
career is therefore inevitably
intertwining lectures and
courses, over the years. A few
excerpts of courses and lectures
that were given in a thirty
years period are presented here.
The first formal account of the
creation of the course in
Biology, at the Ecole
Polytechnique in the mid-1970's,
with Maurice Guéron, was
summarized in a first book in
French: Ordre et Dynamique du
Vivant
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La
recherche et l'enseignement
supérieur ne peuvent être
séparés. La carrière d'un
chercheur est donc toujours
jalonnée de périodes
d'enseignement, brèves ou plus
longues. Quelques extraits de
cours et de conférences
dispensées au cours du temps
sont présentées ici. Le premier
compte-rendu détaillé de la
création du cours de Biologie à
l'Ecole Polytechnique avec
Maurice Guéron, au milieu des
années 1970, a donné lieu à un
premier livre (en français)
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A Danchin
Ordre et Dynamique du Vivant. Chemins
de la Biologie Moléculaire
Le Seuil (1978) 350 pages

1980
- 1995
1993 - 1998 Cours de
Biotechnologie à l'Ecole des Mines de
Paris
"De l'origine de la
vie à la biotechnologie"
Plan
du cours
The
biotech connection: dream or
reality?
1994 - 1995 Cours de
Microbiologie Générale de l'Institut
Pasteur
"Régulation de
l'expression génétique chez Escherichia
coli: activation et répression
du gène de l'adénylate cyclase"
2006
- 2008
- Cours de Mastère
I, Evolution, Ecole Normale Supérieure
2007
Ecole Normale
Supérieure
7 janvier 2008
« Ce que nous apprend
la structure des génomes bactériens de
l'origine de la vie à la biologie
synthétique »
Cours (2,6 Mo) ; compléments
sur l'origine de la vie

- Cours de Mastère
I, Evolution, Ecole Normale Supérieure
2007
Ecole Normale
Supérieure
9 janvier 2007
« Archives ou
palimpsestes ? Les génomes bactériens
nous parlent de l'origine de la vie »
Cours (2,9 Mo) ; compléments
sur l'origine de la vie

- Cours d'Analyse
des Génomes 2006-2007
Institut Pasteur
15 décembre 2006
« De la biologie
symplectique à la biologie synthétique
: quels gènes pour faire une cellule ?
»
Cours (2,6 Mo) ;

Lectures /
Conférences
2006-2007
- ESF Programme on frontiers of
functional genomics
European Conference on Synthetic
Biology ECSB07
Design, programming and optimisation
of biological systems
Sant Feliu de Guixols, Spain
24-29 november 2007
«Will we be able to construct a
synthetic bacterium?»
Presentation (1.3 kb)

- What are the theoretical tools most
useful for understanding biological
systems?
Quels sont les outils théoriques les
plus utiles pour comprendre les
systèmes biologiques ?
Institut des Hautes Études
Scientifiques (IHES),
Bures-sur-Yvette, France
12-15 november 2007
« The constructor and the
replicator: prerequisites for the
construction of a synthetic cell »
Presentation (1.8 kb)

- Synthetic Biology 3.0 Conference
Swiss Federal Institute of
Technology (ETH), Zürich, Switzerland
24-26 june 2007
« Can we design de novo a bacterial
genome »
Presentation (864 kb)

- 6th Annual International Symposium, Systems
Biology and the Environment
The Institute for Systems Biology,
Seattle, USA
22-23 april 2007
« Archives or palimpsests? Bacterial
genomes unveil a scenario for the
origin of life »
Presentation (1.3 Mb)

- Transcultura International Meeting
Order
and Disorder
Chinese Academy of Social Sciences,
Beijing, China
5-7 march 2007
« Survivre dans un avenir
imprévisible : quelques conséquences
malheureuses de la génération de la
diversité, et la Civilisation comme
remède »
Presentation in English (772 kb)


- Les Rencontres du Palais Thott
Ambassade de France, Kongens Nytorv,
November 23, 2006
« Nature and Artifice: a reflection
on domestication and GMOs »
Conference
(628 kb)
BioCampus Conference « Public
Perception of GMO »
November 24, 2006, The Old University
building, Copenhagen
« An avatar of domestication: GMOs »
Summary (428 kb)
Questions and Answers on the Danish TV
(DR2)

- L'Homme Artificiel, au service de la
Société
Collège de France, Paris
12-13 octobre 2006
« De la biologie symplectique à la
biologie synthétique : saurons-nous
construire un organisme vivant ? »
Conférence (1,4 Mo)

- 40 years Spetsai Summer School
Anniversary Workshop on Molecular and
Cell Biology at Spetsai: Past, Present
and Future — A Forty Years's Anniversary
Spetses Hotel, Island of Spetses,
Greece
1-5 september 2006
« From symplectic biology to
synthetic biology: Universals in
microbial genomes »
Lecture (1.4 Mb)

« Symplectic
biology: lessons from microbes »
Video
« Coping
with cold and aging: lessons from the
genome of Pseudoalteromonas
haloplanktis »
Video

« Symplectic biology: Universals in
microbial genomes »
Presentation
(1.4 Mb)
- Taipei, Taiwan
22 february 2006
« Symplectic biology: Lessons from
microbial genomes »
- Newcastle-upon-Tyne
25 january 2006
« Coping with cold and aging: Lessons
from the genome of the versatile
Antarctica bacteria Pseudoalteromonas
haloplanktis TAC125 »
1995
- 2005


- Le Logique et
le Biologique
Université Paris I Sorbonne
22 avril 2005
Paris, France
« La métaphore de l’ordinateur
est-elle appropriée pour décrire les
organismes vivants? Stabilisation
fonctionnelle sélective »
Présentation (0,88 Mo)

- How complex is functional genomics?
Sixth Bologna Winter School
13-19 February 2005
Bologna, Italy
Related
publications:
C Médigue, T Rouxel, P Vigier, A Hénaut,
A Danchin
Evidence for horizontal
gene transfer in Escherichia coli
speciation
J Mol Biol (1991) 222:
851-856
M Borodovsky, JD McIninch, EV Koonin, KE
Rudd, C Médigue, A Danchin
Detection of new genes
in a bacterial genome using Markov
models for three gene classes
Nucleic Acids Res (1995) 23:
3554-3562
A
Danchin
mRNA turnover and DNA
synthesis: a lesson from bacterial
genome comparisons Mol Microbiol
(1996) 20: 895-897
A Danchin
Comparison between the
Escherichia coli and Bacillus
subtilis genomes suggests that a
major function of polynucleotide
phosphorylase is to synthesize CDP
DNA Res (1997) 4: 9-18

P Nitschké, P Guerdoux-Jamet, H
Chiapello, G Faroux, C Hénaut, A Hénaut,
A Danchin
Indigo: a
World-Wide-Web review of genomes and
gene functions
FEMS Microbiol Rev (1998) 22:
207-227
EPC 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, V Dénervaud, H Ashida, K
Michoud, D Haas, A Yokota, A Danchin
Bacterial variations on
the methionine salvage pathway
BMC Microbiol (2004) 4: 9


- First EuroScience Open Forum
(ESOF2004)
25-28 August 2004
Stockholm City Conference Centre in
Stockholm, Sweden


- 8th Altenberg
Workshop in Theoretical Biology
11-14 July 2002
Biological Information Beyond Metaphor
Organized by Werner Callebaut and
Sahotra Sarkar
Konrad Lorenz Institute for Evolution
and Cognition Research, Altenberg,
Austria
"Living Turing Machines"
Summary 1
Summary 2

- 25-28 September 1996
Final EU Conference of the "Yeast Genome
Sequencing Network"
Trieste, Italy.
"In silico comparison of bacterial
genomes"
P Glaser, F Kunst, M
Arnaud, M-P Coudart, W Gonzales, M-F
Hullo, M Ionescu, B Lubochinsky, L
Marcelino, I Moszer, E Presecan, M
Santana, E Schneider, J Schweizer, A
Vertes, G Rapoport, A Danchin
Bacillus subtilis
genome project: cloning and sequencing of
the 97 Kb region from 325o to
333o
Mol Microbiol (1993) 10:
371-384
- 10 -14 September 1992 "Colibri: a
functional database for the Escherichia
coli genome"
First Escherichia coli genome
meeting - Madison, USA
C
Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional
data base for the Escherichia coli
genome
Microbiol Rev (1993) 57:
623-654

A Danchin
A brief history of
genome research and bioinformatics in
France
Bioinformatics (2000) 16:
65-75
- 2-6 October 1994 "On genomes and
cosmologies: the Bacillus subtilis
example"
Twentieth EMBO Annual Symposium 1994
"Genomes and Chromosomes", Heidelberg,
Germany
- 4 -12 November 1994 "Large scale
analysis of the E. coli genome"
Third International Escherichia coli
Genome Meeting - Woods Hole MA, USA
C Médigue, T Rouxel,
P Vigier, A Hénaut, A Danchin
Evidence for horizontal
gene transfer in Escherichia coli
speciation
J Mol Biol (1991) 222:
851-856
The concept of
neighborhood, later to be the basis for a
new area of bioinformatics
has been proposed as a basis for inductive
reasoning in genome studies and illustrated
in all the following lectures:
Slide
(1995) of an unlimited list of
relevant neighborhoods to be combined
to construct an inductive approach to
biological functions

- 25-28 June 1995
Eighth Bacillus subtilis
international conference, Standord, Ca,
USA
"New insights from the study of B.
subtilis in silico"
P Nitschké, P
Guerdoux-Jamet, H Chiapello, G Faroux, C
Hénaut, A Hénaut, A Danchin
Indigo: a World-Wide-Web
review of genomes and gene functions
FEMS Microbiol Rev (1998) 22:
207-227

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- 5-8 October 1996
Eighth International Genome Sequencing
and Analysis Conference
Hilton Head Island, Savannah, USA
"Small genomes: sequencing,
functional characterization and
comparative genomics"
- 23-27 October 1996
Genome Symposium, Seoul, South Korea
"Lessons from in silico comparison
of bacterial genomes"
- 27-30 October 1996
"Recent Advance in Genome Biology of
Micro-organisms". International
symposium, Kasuza DNA Research
Institute, Japan
"Bacterial genomes in silico"
- 25-28 January 1997
Small genomes: sequencing, functional
characterization and comparative
genomics (TIGR Science Education
Foundation, inc;), Hilton Head,
Savannah, USA.
"Lessons from bacterial genomes
comparison in silico"
- 6-9 April 1997 Integrating Genetic,
Biochemical and other Data in the
Post-Genomics Era
The Banbury Center, Cold Spring Harbor
Laboratory, USA
- 24-27 June 1997
The Fifth International Conference on
Intelligent Systems for Molecular
Biology (ISMB-97) Hakidiki, Greece.
"The concept of neighborhood in
genome exploration"

Related publications:
A Danchin
The Delphic boat or what the genomic texts
tell us
Bioinformatics (1998) 14:
383
A
Danchin
From protein sequence to
function
Curr Opin Struct Biol (1999) 9:
363-367


- Université de tous les savoirs
Qu'est-ce que la vie?
Conservatoire des Arts et Métiers,
quatrième confèrence, 4 Janvier 2000
Paris
Extraits vidéo de la conférence
Publication associée:
A Danchin
L'identité génétique
Volume 1: Qu'est-ce que la vie? coordonné
par Yves Michaud, Odile Jacob (2000) p
59-68

- 7th Western
Pacific Congress on Chemotherapy and
Infectious Diseases
WPCCID, 11-14 December 2000
Hong Kong, China
S Brunak, A Danchin,
M Hattori, H Nakamura, K Shinozaki, T
Matise, D Preuss
Nucleotide sequence
database policies
Science (2002) 298: 1333

- Mining bacterial genomes
National Research Council, April 16-17,
1999
Roma, Italy
"The map of the cell is in the
chromosome"
Related
publication:
A
Danchin, A Hénaut
The
map of the cell is in the chromosome
Curr Opin Genet Dev (1997) 7:
852-854

- Eighth Workshop on Genome
Informatics (GIW '97)
University of Tokyo
12- 13 December 1997
Tokyo, Japan
"The map of the cell is in the
chromosome"

- 8th European Congress on
Biotechnology
70th Event of the European Federation of
the Biotechnology
17- 21 August 1997
Budapest, Hungary
"Biotechnology and genomes"
Summary of
the presentation

1995 l'année Pasteur
Related
publications:
A Danchin
Homeotopic transformation and the origin of translation
Progress in Biophysics and Molecular Biology (1989) 54: 81-86 
S Lévy, A Danchin
Phylogeny of metabolic pathways: O-acetylserine sulphydrylase
A is homologous to the tryptophan synthase beta subunit
Mol Microbiol (1988) 2: 777-783
A
Danchin
Une Aurore de Pierres. Aux
origines de la vie
Le Seuil (1990), 276 pp
A
Danchin
"Uma aurora de pedras. Nas origens da vida",
Portuguese translation; Almedina, Coimbra 1992
A
Danchin
Dai minerali alla vita
Prometeo (1996) 14: 16-21
A
Danchin
Des minéraux à
la vie: une alternative à la soupe prébiotique
In: Dictionnaire de l'ignorance, Aux frontières de la
Science (PUF) (1998) pp 196-212
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