Publications

Publications in peer-reviewed journals

2022

85) Koutsovoulos G, Granjeon Noriot S, Bailly-Bechet M, Danchin EGJ and Rancurel C. AvP: a software package for automatic phylogenetic detection of candidate horizontal gene transfers. PLoS Computational Biology. 2022 (View Online).

84) Siddique S, Radakovic Z, Hiltl C, Pellegrin C, Baum T, Beasley H, Bent A, Chitambo O, Chopra D, Danchin E.G.J., Grenier E, Habash S, Shamim Hasan M, Helder J, Hewezi T, Holbein J, Holterman M, Janakowski S, Koutsovoulos G.D., Kranse O, Lozano-Torres J, Maier T, Masonbrink R, Mendy B, Reimer E, Sobczak M, USonawala U, Sterken M, Thorpe P, van Steenbrugge J, Zahid N, Grundler F, and Eves-van den Akker S. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nature Communications. 2022 (View Online).

83) Belliardo C, Koutsovoulos G, Rancurel C, Clement M, Lipuma J, Bailly-Bechet M, Danchin EGJ.  Improvement of Eukaryotic Proteins Prediction from Soil Metagenomes. Scientific Data. 2022 (View Online).

2021

82) Hassanaly-Goulamhoussen R., De Carvalho Augusto R., Marteu-Garello N., Péré A., Favery B., Da Rocha M., Danchin E.G.J., Abad P., Grunau C., Perfus-Barbeoch L. Chromatin Landscape Dynamics in Development of the Plant Parasitic Nematode Meloidogyne incognita. Frontiers in Cell and Developmental Biology. 2021 (View Online).

81) Vieira P, Myers RY, Pellegrin C, Wram C, Hesse C, Maier TR, Shao J, Koutsovoulos GD, Zasada I,
Matsumoto T, Danchin EGJ, Baum TJ, Eves-van den Akker S, Nemchinovet LG. Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis. PLoS Pathogens. 17(11): e1010036. 2021 (View online)

80) Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Rodriguez Gaudray F, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Lliros M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot J-F, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Science Advances. 2021 (View online).

79) Da Rocha M., Bournaud C., Dazenière J., Thorpe P., Pellegrin C., Bailly-Bechet M., Péré A., Grynberg P., Perfus-Barbeoch L., Eves-van den Akker S., Danchin E.G.J. Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes. GENES. 2021 (View online).

78) Kozlowski DKL , Hassanaly-Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly-Bechet M, Danchin  EGJ. Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. Evolutionary Applications. 2021 (View online), recommended in PCI Evolutionary Biology. 2020 (Recommendation).

2020

77) Arraes F.B.M., Martins-de-Sa D., Noriega Vasquez D.D., Paes Melo B., Faheem M., Lima Pepino de Macedo L., Morgante C.V., Barbosa J.A.R.G., Coiti Togawa R., Moreira V.J.V, Danchin E.G.J., Grossi-de-Sa M.F. Dissecting Protein Domain Variability In The Core RNA Interference Machinery Of Five Insect Orders. RNA Biology. 2020. (View Online).

76) Grynberg P., Coiti Togawa R., Dias de Freitas L., Antonino J.D., Rancurel C., Mota do Carmo Costa M., Grossi-de-Sa M.F., Miller R.N.G., Brasileiro A.C.M., Messenberg Guimaraes P., Danchin E.G.J. Comparative genomics reveals novel target genes towards specific control of plant-parasitic nematodes. Genes. 2020. (View Online).

75) Montarry J., Mimee B., Danchin EGJ., Koutsovoulos G.D., Ste-Croix DT and Grenier E. Recent advances in population genomics of plant-parasitic nematodes. Phytopathology. 2020 (View Online).

74) Koutsovoulos G.D., Poullet M., El Ashry A., Kozlowski D.K., Sallet E., Da Rocha M., Martin-Jimenez C., Perfus-Barbeoch L., Frey J-E, Ahrens C., Kiewnick S., Danchin E.G.J. Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. Scientific Data. 2020 (View Online).

73) Vinson CC, Zotta Mota AP, Porto BN, Oliveira TN, Sampaio I, Lacerda AL, Danchin EGJ, Guimaraes PM, Williams TCR, Brasileiro ACM. Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses. Scientific Reports. 2020 (View online).

72) Phan NT, Orjuela J, Danchin EGJ, Klopp C, Perfus-Barbeoch L, Kozlowski DK, Koutsovoulos GD, Lopez-Roques C, Bouchez O, Zahm M , Besnard G, Bellafiore S. Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola). Ecology & Evolution. 2020 (View online).

71) Zotta Mota AP.; Fernandez D.; Arraes FBM; Petitot A-S; Paes de Melo B; Lisei de Sa ME; Grynberg P; Passos Saraiva MA; Messenberg Guimaraes P; Brasileiro ACM; Albuquerque EVS; Danchin EGJ*; Grossi–de–Sa MF*. Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics. Molecular Genetics And Genomics 2020 (View Online). *:co-last

70) Susič N, Koutsovoulos GD, Riccio C, Danchin EGJ, Blaxter ML, Lunt DH, Strajnar P, Širca S, Urek G, Gerič Stare B. Genome Sequence of the Root-Knot Nematode Meloidogyne luci. Journal of Nematology 2020 (View Online)

2019

69) Schiffer PH, Danchin EGJ, Burnell AM, Creevey C, Wong S, Dix I,  O’Mahony G, Culleton BA, Rancurel C, Stier G, Martinez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M. Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes. iScience 2019 (View Online)

68) Bresso E., Fernandez D., Amora D.X., Noel P., Petitot A-S., Lisei de Sa M-E., Albuquerque E.V.S, Danchin E.G.J., Maigret B., Martins N.F. A chemosensory GPCR as a potential target to control the root-knot nematode Meloidogyne incognita parasitism in plants. Molecules 2019 (View Online)

67) Koutsovoulos G.D., Marques E., Arguel M-J, Duret L., Machado A.C.Z., Carneiro R.M.D.G., Kozlowski D.K., Bailly-Bechet M., Castagnone-Sereno, Albuquerque E.V.S, Danchin E.G.J. Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest. Evolutionary Applications 2019 (View Online) *Peer-reviewed and recommended in PCI Evolutionary Biology 2019 (View Online)

66) Michelet C., Danchin E.G.J, Jaouannet M., Bernhagen J., Panstruga R., Kogel K-H., Keller H., Coustau C. Cross-Kingdom Analysis of Diversity, Evolutionary History, and Site Selection within the Eukaryotic Macrophage Migration Inhibitory Factor Superfamily. Genes 2019 (View Online)

65) Busch A., Danchin E.G.J., Pauchet Y. Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in Phytophaga beetles. BMC Evolutionary Biology 2019 (View Online)

64) Zotta Mota A.P., Nicolini Oliveira T., Cleo Vinson C., Rhys Williams T.C., Mota do Carmo Costa M., Guerra Araujo A.C., Danchin E.G.J., Grossi-De-Sa M.F., Messenberg Guimaraes P., Miranda Brasileiro A.C. Contrasting effects of wild Arachis dehydrin under abiotic and biotic stresses. Frontiers In Plant Science 2019 (View Online)

63) Castagnone-Sereno P., Mulet K., Danchin E.G.J, Koutsovoulos G.D., Karaulic M., Da Rocha M., Bailly-Bechet M., Pratx L., Perfus-Barbeoch L., Abad P. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita. Molecular Ecology 2019 (View Online)

2018

62) Vitale S, Luongo L, Danchin EGJ, Mughini G, Gras M, Galli M, Belisario A. Coniothyrium/Teratosphaeria stem canker disease on Eucalypt in Italy. European Journal of Plant Pathology, 2018 (View Online)

61) Zotta Mota A.P., Vidigal B., Danchin E.G.J., Coiti Togawa R., Leal-Bertioli S.C.M., Bertioli D.J., Guerra Araujo A.C., Brasileiro A.C.M., Messenberg Guimaraes P. Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance. BMC Plant Biology, 2018 (View Online)

60) Pratx L., Rancurel C., Da Rocha M.; Danchin E.G.J., Castagnone-Sereno P., Abad P., Perfus-Barbeoch L. Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes Meloidogyne spp., with a focus on the asexual species. BMC Genomics, 2018 (View Online)

2017

59) Danchin E.G.J., Perfus-Barbeoch L., Rancurel C., Thorpe P., Da Rocha M., Bajew S., Neilsen R., Sokolova (Guzeeva) E., Da Silva C., Guy J., Labadie K., Esmenjaud D., Helder J., Jones J.T., Eves-van den Akker S. The transcriptomes of Xiphinema index and Longidorus elongatus reveal independent acquisition of parasitism genes by horizontal gene transfer in early-branching plant-parasitic nematodes. Genes 2017 (View Online).

58) Rancurel, C., Legrand, L., Danchin, E.G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes 2017 (View Online).

57) Blanc-Mathieu R., Perfus-Babeoch L., Aury JM., Da Rocha M., Gouzy J., Sallet E., Martin-Jimenez C., Bailly-Bechet M., Castagnone-Sereno P., Flot JF., Kozlowski DK., Cazareth J., Couloux A., Da Silva C., Guy J., Kim-Jo YJ, Rancurel C., Schiex T., Abad P., Wincker P., Danchin E.G.J. Hybridization and Polyploidy Enable Genomic Plasticity Without Sex in the Most Devastating Plant-Parasitic Nematodes. PLoS Genetics 2017 (View Online).

56) Arrais Guimaraes L., Zotta Mota A.P., Guerra Araujo A.C., de Alencar Figueiredo L.F., Medeiros Pereira B., de Passos Saraiva M.A., Bispo Silva R., Danchin E.G.J., Messenberg Guimaraes P., Brasileiro A.C.M. Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene. Plant Mol. Biol. 2017 (View Online).

2016

55) Danchin E.G.J. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? BMC Biology. 2016 (commentary, View Online)

54) Fatouros N., Cusumano A., Danchin E.G.J., Colazza S. Prospects of herbivore egg-killing plant defences for sustainable crop protection. Ecology and Evolution. 2016 (View Online).

53) Eves-van den Akker S., Laetsch D.R., Thorpe P., Lilley C.J., Danchin E.G.J, Da Rocha M., Rancurel C, Holroyd N.E., Cotton J.A., Szitenberg A, Grenier E., Montarry J., Mimee B., Duceppe M-O, Boyes I, Marvin JMC, Jones LM, …, Koutsovoulos G., Blok V, Mantelin S, Cock PJA, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT. The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence. Genome Biology. 2016 (View Online).

52) Shelomi M., Danchin E.G.J., Heckel D., Wipfler B., Bradler S., Zhou X., Pauchet Y. Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects. Scientific Reports. 2016 (View Online).

51) Damiani I., Drain A., Guichard M., Balzergue S., Boscari A., Boyer J-C, Brunaud V., Cottaz S., Rancurel C., Da Rocha M., Fizames C., Fort S., Gaillard I., Danchin E.G.J., Maillol V., Rouached H., Samain E., Su Y-H, Thouin J., Touraine B., Puppo A., Frachisse J-M, Pauly N., Sentenac H. Nod factor effects on root hair-specific transcriptome of Medicago truncatula: focus on plasma membrane transport systems and reactive oxygen species networks. Frontiers in Plant Science. 2016 (View Online).

50) Danchin E.G.J., Guzeeva E., Mantelin S., Berepiki A., Jones J.T. Horizontal gene transfer from bacteria has enabled nematodes to feed on plant-derived sucrose. Molecular Biology & Evolution. 2016; 33 (6): 1571-1579. (View Online).

2015

49) Bird D.M., Jones J.T., Opperman C.H., Kikuchi T., Danchin E.G.J. Signatures of adaptation to plant parasitism in nematode genomes. Parasitology. 2015 (View Online).

2014

48) Veneault-Fourrey C., Commun C., Kohler A., Morin E., Balestrini R., Plett J., Danchin E.G.J., Coutinho P., Wiebenga A., de Vries R., Henrissat B., Martin F. Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment. Fungal Genetics & Biology. 2014 (View Online).

47) Eves-van den Akker S., Lilley C.,  Danchin E.G.J., Rancurel C., Cock P., Urwin P., Jones J.T. The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes. Genome Biol. Evol. 2014 (View Online).

46) Castagnone-Sereno P., Danchin E.G.J. Parasitic success without sex – the nematode experience. Journal of Evol. Biol. 2014 (View Online).

2013

45) Danchin EGJ, Arguel M-J, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso M-N, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining. PLoS Pathogens 2013 (View Online, Pubmed).

44) Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EGJ, Hejnol A, Henrissat B,…, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 2013 (View Online, PubMed).

43) Jones J. T., Haegeman A., Danchin E.G.J., Gaur H.S., Helder J., Jones M., Kikuchi T., Manzanilla-Lopez R., Palomares-Rius J., Wesemael W., Perry R.N. Top 10 plant parasitic nematodes in molecular plant pathology. Mol Plant Path 2013 (View Online, PubMed). Highly Cited Paper

42) Castagnone-Sereno P., Danchin E.G.J., Perfus-Barbeoch L. and Abad P. Diversity and evolution of root-knot nematodes, genus Meloidogyne: new insights from the genomic era. Annual Review of Phytopathology 2013 (View Online, PubMed).

2012

41) Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, Abad P, Danchin EGJ. Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes. PLoS One 2012 (View Online, PubMed).

40) Arias MC, Danchin EGJ, Coutinho PM, Henrissat B, Ball S. Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants. Mobile Genetic Elements 2012 (View Online, Pubmed).

39) Jaouannet M, Perfus-Barbeoch L, Deleury E, Magliano M, Engler G, Vieira P, Danchin EGJ, Da Rocha M, Coquillard P, Abad P, Rosso MN. A root-knot nematode secreted protein is injected into giant-cells and targeted to the nuclei. New Phytol. 2012 (View Online, PubMed).

38) Danchin E.G.J, Rosso MN. Lateral gene transfers have polished animal genomes: lessons from Nematodes. Front. Cell. Inf. Microbio. 2012 (View Online, Pubmed).

37) Coutard B, Danchin E.G.J, Oubelaid R, Canard B, Bignon C. Single pH buffer refolding screen for protein from inclusion bodies. Protein Expression and Purification 2012 (View Online, Pubmed).

2011

36) Danchin E.G.J. What Nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals ? Mobile Genetic Elements 2011 Nov/Dec 1(4):1-5 (View Online, PubMed).

35) Amselem J., Cuomo C.A., van Kan J.A.L., Viaud M., Benito E.P., Couloux A., Coutinho P.M, de Vries R.P.,…,Danchin E.G., Da Silva C.,…,Rollins J.A., Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics 2011Aug;7(8):e1002230 (View Online). Highly-Cited

34) Hok S., Danchin E.G.J., Allasia V., Panabières F., Attard A., Keller H. An Arabidopsis (malectin-like) leucine-rich repeat receptor-like kinase contributes to downy mildew disease. Plant, Cell & Environment 2011 Jun 28. doi: 10.1111/j.1365-3040.2011.02390.x. (View Online).

33) Haegeman A., Jones J., Danchin E.G.J. Horizontal gene transfer in nematodes: a catalyst for plant parasitism? MPMI 2011 Aug;24(8):879-87. (View Online).

32) Vens C., Rosso MN., Danchin E.G.J. Identifying discriminative classification-based motifs in biological sequences. Bioinformatics 2011; 27 (9): 1231-1238.(View Online) (Download the Software).

31) Marino D., Andrio E., Danchin E.G.J., Oger E., Gucciardo S., Lambert A., Puppo A., Pauly N. A Medicago truncatula NADPH oxidase is involved in symbiotic nodule functioning. New Phytol. 2011; Jan;189(2):580-92. 13(Open access).

30) Arguel M-J, Campan-Fournier A, Perfus-Barbeoch L, Danchin EGJ, Rosso M-N, Da Silva C, Labadie K, Marteu N, Artiguenave F, Abad P. Identification of plant-parasitism genes in nematodes in silico screening and in vivo validation in Meloidogyne incognita. Commun Agric Appl Biol Sci. 2011;76(3):409-12. (PubMed).

2010

29) Vieira P., Danchin E.G.J., Neveu C., Crozat C., Jaubert S., Hussey R.S., Engler G., Abad P., de Almeida-Engler J., Castagnone-Sereno P., Rosso M.N. The plant apoplasm is an important recipient compartment for nematode secreted proteins . J Exp Bot. 2011 Jan;62(3):1241-53. (Open access).

28) Castagnone-Sereno P., Deleury E., Perfus-Barbeoch L., Danchin E.G.J., Abad P. Data-mining of the Meloidogyne incognita degradome and comparative analysis of proteases in nematode. Genomics 2011; Jan;97(1):29-36. (View Online)

27) Castagnone-Sereno P, Danchin E.G.J., Deleury E, Guillemaud T, Malausa T, Abad P. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics. 2010 Oct 25; 11:598. (Open access)

26) Danchin E.G.J., Rosso M-N., Vieira P., de Almeida-Engler J., Coutinho P, Henrissat B., Abad P. Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. PNAS 2010; Oct 12;107(41):17651-6. (Open access) Highly-Cited

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. Nature 2010; Mar 18;464(7287):367-73. (View Online) Highly-Cited

2009

24) Lopez-Rascol V, Levasseur A, Chabrol O, Gruseas S, Gouret P, Danchin EGJ, Pontarotti P. CASSIOPE: an expert system for conserved regions searches. BMC Bioinformatics. 2009 Sep 10;10(1):284. (Open Access)

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. (Open access)

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. (View Online).

2008

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. (View Online). Highly-Cited

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. (View 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. (Open Access).

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. (View Online). Highly-Cited

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. (View Online). Highly-Cited

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)

 

Higly cited paper explanation

As of November/December 2018, this highly cited paper received enough citations to place it in the top 1% of its academic field based on a highly cited threshold for the field and publication year. (Data from Essential Science Indicators)