Antoine Danchin
Encyclopedia
Antoine Danchin PhD DSc is a French geneticist
known for his research in several fields of biology, from the structure and function of adenylate cyclase
, to modelisation of learning in the nervous system and the early development of genomics
and bioinformatics
. He is the Chairman of the startup AMAbiotics http://www.amabiotics.com/, specialised in metabolic bioremediation and synthetic biology http://synbio.ku.dk/augustworkshop2010/. He was the director of the Department Genomes and Genetics at the Institut Pasteur in Paris
where he headed the Genetics of Bacterial Genomes Unit.
Trained as a mathematician at the Institut Henri Poincaré
and a physicist at the Ecole Polytechnique
, Danchin has an Erdős number
of 3 (via Eugene Koonin
). Working first with Mildred Cohn
, Marianne Grunberg-Manago
and Ionel Solomon in Nuclear Magnetic Resonance
, Danchin became an experimental microbiologist
in the early seventies.
He created with Philippe Courrège and Jean-Pierre Changeux
at the Institut de Biologie Physico-Chimique in Paris, France, a working seminar where they worked together on the construction of mathematical models of learning and memory.
Interested in University training he created, with Maurice Guéron, the first semester of Biology at the Ecole Polytechnique
, and developed his teaching during four years. Among his first students one can find Daniel Kahn, Patrick Charnay, and many others. The main goal of his research has been to try to understand how genes can function collectively in the cell. This led him to work on regulation systems which control global gene expression in bacteria. Part of his work was devoted to the study of the enzymes that synthesize cyclic AMP. He established the reference classification of adenylate cyclases after his laboratory successfully cloned and sequenced the genes of adenylyl cyclase toxins from the whooping cough agent as well as from the agent of anthrax
. This work led him to trigger ethical reflections on the practices of molecular genetics and genomics at a time when this was not considered important.
Danchin started in 1985 a collaboration with computer scientists for evaluation of artificial intelligence
techniques to the study of integrated problems in molecular genetics
. This convinced him that it was time to investigate genomes as wholes, provided that an important effort in computer sciences was initiated in parallel (in silico
biology). Early in 1987 he proposed that a sequencing program should be undertaken for Bacillus subtilis
. This proposal was actualized by a European joint effort on this genome, starting in 1988. The complete sequence was published in 1997. The first significant and unexpected discovery of this work was, in 1991, that many genes (at the time, half of the genes) were of completely unknown function. This led him to try to organize bioinformatics
in France with the help of several colleagues at universities, CNRS and INRIA, through the creation of a nation-wide group, GDR 1029 (1991–1995) and subsequently through the coordination of the bioinformatics programme of the Groupement de Recherche et d'Etudes des Genomes (1992–1996), then at the Comité de Coordination des Sciences du Vivant (1998–2000). Re-sequencing and re-annotation of the B. subtilis genome was completed in 2009 to update the sequence and annotation of this reference genome
.
In year 2000, Danchin created the HKU-Pasteur Research Centre in Hong Kong, meant to develop microbial genomics in the region, with the help of the Innovation and Technology Commission of the Hong Kong SAR government to develop bioinformatics (programme Biosupport).
Danchin is now developing theoretical reflections and experiments in the domain of synthetic biology
, trying to make explicit the idea that cells behave as computers (Turing machines) making computers. Together with Victor de Lorenzo he created the free and open access journal Symplectic Biology, devoted to publishing innovative ideas in systems and synthetic biology http://knol.google.com/k/symplectic-biology#
Geneticist
A geneticist is a biologist who studies genetics, the science of genes, heredity, and variation of organisms. A geneticist can be employed as a researcher or lecturer. Some geneticists perform experiments and analyze data to interpret the inheritance of skills. A geneticist is also a Consultant or...
known for his research in several fields of biology, from the structure and function of adenylate cyclase
Adenylate cyclase
Adenylate cyclase is part of the G protein signalling cascade, which transmits chemical signals from outside the cell across the membrane to the inside of the cell ....
, to modelisation of learning in the nervous system and the early development of genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
and bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
. He is the Chairman of the startup AMAbiotics http://www.amabiotics.com/, specialised in metabolic bioremediation and synthetic biology http://synbio.ku.dk/augustworkshop2010/. He was the director of the Department Genomes and Genetics at the Institut Pasteur in Paris
Paris
Paris is the capital and largest city in France, situated on the river Seine, in northern France, at the heart of the Île-de-France region...
where he headed the Genetics of Bacterial Genomes Unit.
Trained as a mathematician at the Institut Henri Poincaré
Institut Henri Poincaré
The Institut Henri Poincaré is a mathematical institute in Paris which has established itself over its eighty year history as an important meeting place for French and international mathematicians and theoretical physicists...
and a physicist at the Ecole Polytechnique
École Polytechnique
The École Polytechnique is a state-run institution of higher education and research in Palaiseau, Essonne, France, near Paris. Polytechnique is renowned for its four year undergraduate/graduate Master's program...
, Danchin has an Erdős number
Erdos number
The Erdős number describes the "collaborative distance" between a person and mathematician Paul Erdős, as measured by authorship of mathematical papers.The same principle has been proposed for other eminent persons in other fields.- Overview :...
of 3 (via Eugene Koonin
Eugene Koonin
Eugene V. Koonin is a Senior Investigator at the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA...
). Working first with Mildred Cohn
Mildred Cohn
Mildred Cohn was an American biochemist. She graduated from high school at 14 and went on to receive her Bachelor's from Hunter College in 1931, her master's in 1932 from Columbia University, and her PhD in physical chemistry in 1938 from Columbia...
, Marianne Grunberg-Manago
Marianne Grunberg-Manago
Dr. Marianne Grunberg-Manago, PhD, is an French biochemist.Grunberg-Manago was born into a family of artists who adhered to the teachings of the Swiss educational reformer Johann Pestalozzi. When she was 9 months old, her parents emigrated from the Soviet Union to France...
and Ionel Solomon in Nuclear Magnetic Resonance
Nuclear magnetic resonance
Nuclear magnetic resonance is a physical phenomenon in which magnetic nuclei in a magnetic field absorb and re-emit electromagnetic radiation...
, Danchin became an experimental microbiologist
Microbiologist
A microbiologist is a scientist who works in the field of microbiology. Microbiologists study organisms called microbes. Microbes can take the form of bacteria, viruses, fungi, and protists...
in the early seventies.
He created with Philippe Courrège and Jean-Pierre Changeux
Jean-Pierre Changeux
Jean-Pierre Changeux is a French neuroscientist known for his research in several fields of biology, from the structure and function of proteins , to the early development of the nervous system up to cognitive functions...
at the Institut de Biologie Physico-Chimique in Paris, France, a working seminar where they worked together on the construction of mathematical models of learning and memory.
Interested in University training he created, with Maurice Guéron, the first semester of Biology at the Ecole Polytechnique
École Polytechnique
The École Polytechnique is a state-run institution of higher education and research in Palaiseau, Essonne, France, near Paris. Polytechnique is renowned for its four year undergraduate/graduate Master's program...
, and developed his teaching during four years. Among his first students one can find Daniel Kahn, Patrick Charnay, and many others. The main goal of his research has been to try to understand how genes can function collectively in the cell. This led him to work on regulation systems which control global gene expression in bacteria. Part of his work was devoted to the study of the enzymes that synthesize cyclic AMP. He established the reference classification of adenylate cyclases after his laboratory successfully cloned and sequenced the genes of adenylyl cyclase toxins from the whooping cough agent as well as from the agent of anthrax
Anthrax
Anthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and other animals...
. This work led him to trigger ethical reflections on the practices of molecular genetics and genomics at a time when this was not considered important.
Danchin started in 1985 a collaboration with computer scientists for evaluation of artificial intelligence
Artificial intelligence
Artificial intelligence is the intelligence of machines and the branch of computer science that aims to create it. AI textbooks define the field as "the study and design of intelligent agents" where an intelligent agent is a system that perceives its environment and takes actions that maximize its...
techniques to the study of integrated problems in molecular genetics
Molecular genetics
Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. The field studies how the genes are transferred from generation to generation. Molecular genetics employs the methods of genetics and molecular biology...
. This convinced him that it was time to investigate genomes as wholes, provided that an important effort in computer sciences was initiated in parallel (in silico
In silico
In silico is an expression used to mean "performed on computer or via computer simulation." The phrase was coined in 1989 as an analogy to the Latin phrases in vivo and in vitro which are commonly used in biology and refer to experiments done in living organisms and outside of living organisms,...
biology). Early in 1987 he proposed that a sequencing program should be undertaken for Bacillus subtilis
Bacillus subtilis
Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...
. This proposal was actualized by a European joint effort on this genome, starting in 1988. The complete sequence was published in 1997. The first significant and unexpected discovery of this work was, in 1991, that many genes (at the time, half of the genes) were of completely unknown function. This led him to try to organize bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
in France with the help of several colleagues at universities, CNRS and INRIA, through the creation of a nation-wide group, GDR 1029 (1991–1995) and subsequently through the coordination of the bioinformatics programme of the Groupement de Recherche et d'Etudes des Genomes (1992–1996), then at the Comité de Coordination des Sciences du Vivant (1998–2000). Re-sequencing and re-annotation of the B. subtilis genome was completed in 2009 to update the sequence and annotation of this reference genome
Reference genome
A reference genome is a digital nucleic acid sequence database, assembled by scientists as a representative example of a species' genetic code. As they are often assembled from the sequencing of DNA from a number of donors, reference genomes do not accurately represent the genetic code of any...
.
In year 2000, Danchin created the HKU-Pasteur Research Centre in Hong Kong, meant to develop microbial genomics in the region, with the help of the Innovation and Technology Commission of the Hong Kong SAR government to develop bioinformatics (programme Biosupport).
Danchin is now developing theoretical reflections and experiments in the domain of synthetic biology
Synthetic biology
Synthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions...
, trying to make explicit the idea that cells behave as computers (Turing machines) making computers. Together with Victor de Lorenzo he created the free and open access journal Symplectic Biology, devoted to publishing innovative ideas in systems and synthetic biology http://knol.google.com/k/symplectic-biology#
Selected works
- The Delphic Boat: What Genomes Tell Us, Translated by Alison Quayle, Harvard University PressHarvard University PressHarvard University Press is a publishing house established on January 13, 1913, as a division of Harvard University, and focused on academic publishing. In 2005, it published 220 new titles. It is a member of the Association of American University Presses. Its current director is William P...
, 2003.