Etienne G.J. Danchin

evolutionary and comparative genomics

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Publications - Publications 2003-2007

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Publications
Publications 2003-2007
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2007

16) Benoit I, Danchin E.G.J, Bleichrodt R.J., de Vries R.P. Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity. Biotechnology Letters 2007;30(3):387-96. (View Online)

15) Da Lage J-L, Danchin E.G.J, Casane D. Where do animal alpha-amylases come from? An interkingdom trip. FEBS Letters 2007; 581(21):3927-35. (View Online)

14) Levasseur A, Orlando L, Bailly X, Milinkovitch M.C, Danchin E.G.J, Pontarotti P. Conceptual bases for quantifying the role of environmental changes on gene evolution: the participation of positive selection and neutral evolution. Biological Reviews 2007;82(4):551-72. (View Online).

13) Pel H.J., de Winde J.H.,..., Coutinho P.M, Danchin E.G.J.,..., Henrissat B,..., Visser J., Stam H. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol, 2007; 25(2):221-231. (View Online).

2006

12) Stam M.R., Danchin E.G.J., Rancurel C., Coutinho P.M., Henrissat B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. PEDS, 2006; 19: 555-62  (Open access).

11) Asther M, Record E, Gimbert I, Sigoillot J-C, Levasseur A, Danchin E.G.J, Coutinho P.M., Monot F. Des champignons qui carburent: de létude du génome à la production industrielle. Biofutur, 28 (269), 2006 (View Online).

10) Danchin E.G.J, Levasseur A, Lopez-Rascol V, Gouret P, Pontarotti P. The use of evolutionary biology concepts for genome annotation. J. Exp. Zoology Part B: Mol. and Dev. Evol, 2006; 308B:26-36. (View online).

9) Danchin E.G.J, Gouret P, Pontarotti P. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals. BMC Evolutionary Biology, 2006;6: 5. (Open Access)

2005

8) Balandraud N, Gouret P, Danchin E.G.J, Blanc M, Zinn D, Roudier J, Pontarotti P. A rigorous method for multigenic families’ functional annotation: the peptidyl arginine deiminase (PAD) proteins family example. BMC Genomics, 2005; 6:153. (Open Access)

7) Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin E.G.J. FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinformatics, 2005; 6: 198. (Open Access)

2004

6) Danchin EGJ, Pontarotti P. Towards reconstructing the bilaterian ancestral pre-MHC region. Trends Genet. Dec 2004; 20 (12 ): 587-591. (View Online)

5) Danchin EG, Pontarotti P. Statistical evidence for a more than 800 Million years old evolutionary conserved genomic region in our genome. Journal of  Molecular Evolution. 2004 Nov;59(5):587-597. (View Online).

4) Meglécz E,  Petenian F, Danchin E, Coeur D’Acier A, Rasplus JY,  Faure E. High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera : Parnassius apollo and Euphydryas aurinia. Molecular Ecology. 2004 Jun;13(6):1693-700. (View Online)

3) Danchin E, Vitiello V, Vienne A, Richard O, Gouret P, McDermott MF, Pontarotti P. The Major Histocompatibiliy Complex Origin. Immunological reviews. 2004 April;198(1):216-232.( View Online) (Online Supplement).

2003

2) Vienne A, Shiina T, Abi Rached L, Danchin E, Vitiello V, Cartault F, Inoko H, P Pontarotti. Evolution of the proto-MHC ancestral region: more evidence for the plesiomorphic organisation of human chromosome 9q34 region. Immunogenetics. 2003 Oct;55(7):429-36. (View Online)

1) Danchin EG, Abi-Rached L, Gilles A, Pontarotti P. Conservation of the MHC-like region throughout evolution. Immunogenetics. 2003 Jun;55(3):141-8. (View Online)

2010 Top
25) Ma L., van der Does C., Borkovich K.A., Coleman J.J., ... , Danchin E.G.J., ... , Galagan J., Cuomo C.A., Kistler H.C., Rep M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum. Nature 2010; Mar 18;464(7287):367-73.
Online
Must Read
F1000 Factor 6.5
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2009 Top
24) Levasseur A, Lopez-Rascol V, Chabrol O, Gruseas S, Gouret P, Danchin EGJ, Pontarotti P. C.A.S.S.I.O.P.E.: A Multi-agent system for conserved regions searches. BMC Bioinformatics. 2009 Sep 10;10(1):284.

23) Coleman J.J, Rounsley S.D, Rodriguez-Carres M, Kuo A, ... , Danchin EGJ, Henrissat B, Coutinho P.M, ... , Covert S.F, Temporini E,  VanEtten H.D. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. Plos Genetics. 2009, Aug;5(8):e1000618..
Online
22) Bird D.M, Williamson V.M, Abad P, McCarter J,  Danchin EGJ, Castagnone-Sereno P, Opperman C.H.. The genomes of root-knot nematodes. Annu. Rev. Phytopatol. 2009, online on May 4, 2009.
Online
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2008 Top
21) Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EGJ,..., Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol. Advance online 2008 July 28.


Online
F1000 Factor 3.2
INRA, CNRS, Press release
20) Darbo E, Danchin EGJ, Mc Dermott MF, Pontarotti P. Evolution of major histocompatibility complex by "en bloc" duplication before mammalian radiation. Immunogenetics. 2008 June 17.
Online
19) Espagne E, Lespinet O, Malagnac F, ... , de Vries RP, Battaglia E, Coutinho PM, Danchin EGJ, Henrissat B, ... , Debuchy R, Wincker P, Weissenbach J, Silar P. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol. 2008 May 6;9(5):R77.
Online
18) Martinez D, Berka RM, Henrissat B, Saloheimo M, ... , Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV, ... , Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol. 2008, May;26(5):553-60.
Must Read
F1000 Factor 6.0

Online

Editor's choice
17) Martin F, Aerts A, Ahrén D, Brun A, Danchin E.G.J,...,Coutinho P.M,..., Henrissat B,...,Tuskan G & Grigoriev I. V. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008, Mar 6;452(7183):88-92.
Online
INRA Press release
F1000 Factor 3.0
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2007 Top
16) Benoit I, Danchin E.G.J, Bleichrodt R.J., de Vries R.P. Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity. Biotechnology Letters 2007;30(3):387-96.
Online
15) Da Lage J-L, Danchin E.G.J, Casane D. Where do animal alpha-amylases come from? An interkingdom trip. FEBS Letters 2007; 581(21):3927-35.
Online
14) Levasseur A, Orlando L, Bailly X, Milinkovitch M.C, Danchin E.G.J, Pontarotti P. Conceptual bases for quantifying the role of environmental changes on gene evolution: the participation of positive selection and neutral evolution. Biological Reviews 2007;82(4):551-72.
Online
13) Pel H.J., de Winde J.H.,..., Coutinho P.M, Danchin E.G.J.,..., Henrissat B,..., Visser J., Stam H. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol, 2007; 25(2):221-231. (View Online).
Online
NBT cover
_
2006 Top
12) Stam M.R., Danchin E.G.J., Rancurel C., Coutinho P.M., Henrissat B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. PEDS, 2006; 19: 555-62  (View online).
Online
11) Asther M, Record E, Gimbert I, Sigoillot J-C, Levasseur A, Danchin E.G.J, Coutinho P.M., Monot F. Des champignons qui carburent: de létude du génome à la production industrielle. Biofutur, 28 (269), 2006 (Link). Link
10) Danchin E.G.J, Levasseur A, Lopez-Rascol V, Gouret P, Pontarotti P. The use of evolutionary biology concepts for genome annotation. J. Exp. Zoology Part B: Mol. and Dev. Evol, 2006; 308B:26-36. (View online).

Online

9) Danchin E.G.J, Gouret P, Pontarotti P. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals. BMC Evolutionary Biology, 2006;6: 5. (Open Access)


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2005 Top
8) Balandraud N, Gouret P, Danchin E.G.J, Blanc M, Zinn D, Roudier J, Pontarotti P. A rigorous method for multigenic families’ functional annotation: the peptidyl arginine deiminase (PAD) proteins family example. BMC Genomics, 2005; 6:153. (Open Access)

7) Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin E.G.J. FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinformatics, 2005; 6: 198. (Open Access)


_
2004 Top
6) Danchin EGJ, Pontarotti P. Towards reconstructing the bilaterian ancestral pre-MHC region. Trends Genet. Dec 2004; 20 (12 ): 587-591 (Link)
5) Danchin EG, Pontarotti P. Statistical evidence for a more than 800 Million years old evolutionary conserved genomic region in our genome. Journal of  Molecular Evolution. 2004 Nov;59(5):587-597.Online Supplement. Link
4) Meglécz E,  Petenian F, Danchin E, Coeur D’Acier A, Rasplus JY,  Faure E. High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera : Parnassius apollo and Euphydryas aurinia. Molecular Ecology. 2004 Jun;13(6):1693-700. Online Supplement
3) Danchin E, Vitiello V, Vienne A, Richard O, Gouret P, McDermott MF, Pontarotti P. The Major Histocompatibiliy Complex Orgin. Immunological reviews. 2004 April;198(1):216-232.Online Supplement. Link
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2003 Top
2) Vienne A, Shiina T, Abi Rached L, Danchin E, Vitiello V, Cartault F, Inoko H, P Pontarotti. Evolution of the proto-MHC ancestral region: more evidence for the plesiomorphic organisation of human chromosome 9q34 region. Immunogenetics. 2003 Oct;55(7):429-36.
1) Danchin EG, Abi-Rached L, Gilles A, Pontarotti P. Conservation of the MHC-like region throughout evolution. Immunogenetics. 2003 Jun;55(3):141-8. Online Supplement
Must Read
F1000 Factor 6.0


 

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