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Items: 18

1.

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.

Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP.

Database (Oxford). 2019 Jan 1;2019. pii: baz077. doi: 10.1093/database/baz077.

2.

Community-Driven Data Analysis Training for Biology.

Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B.

Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012.

3.

De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae).

Gschloessl B, Dorkeld F, Audiot P, Bretaudeau A, Kerdelhué C, Streiff R.

Data Brief. 2018 Feb 1;17:781-787. doi: 10.1016/j.dib.2018.01.073. eCollection 2018 Apr.

4.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae).

Gschloessl B, Dorkeld F, Berges H, Beydon G, Bouchez O, Branco M, Bretaudeau A, Burban C, Dubois E, Gauthier P, Lhuillier E, Nichols J, Nidelet S, Rocha S, Sauné L, Streiff R, Gautier M, Kerdelhué C.

Mol Ecol Resour. 2018 May;18(3):602-619. doi: 10.1111/1755-0998.12756. Epub 2018 Feb 12.

PMID:
29352511
5.

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.

Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagné N, Darboux I, Kuwar S, Chertemps T, Siaussat D, Bretschneider A, Moné Y, Ahn SJ, Hänniger S, Grenet AG, Neunemann D, Maumus F, Luyten I, Labadie K, Xu W, Koutroumpa F, Escoubas JM, Llopis A, Maïbèche-Coisne M, Salasc F, Tomar A, Anderson AR, Khan SA, Dumas P, Orsucci M, Guy J, Belser C, Alberti A, Noel B, Couloux A, Mercier J, Nidelet S, Dubois E, Liu NY, Boulogne I, Mirabeau O, Le Goff G, Gordon K, Oakeshott J, Consoli FL, Volkoff AN, Fescemyer HW, Marden JH, Luthe DS, Herrero S, Heckel DG, Wincker P, Kergoat GJ, Amselem J, Quesneville H, Groot AT, Jacquin-Joly E, Nègre N, Lemaitre C, Legeai F, d'Alençon E, Fournier P.

Sci Rep. 2017 Sep 25;7(1):11816. doi: 10.1038/s41598-017-10461-4.

6.

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J.

Mol Ecol. 2017 Sep;26(18):4700-4711. doi: 10.1111/mec.14240. Epub 2017 Aug 14.

7.

Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid.

Richard G, Legeai F, Prunier-Leterme N, Bretaudeau A, Tagu D, Jaquiéry J, Le Trionnaire G.

Epigenetics Chromatin. 2017 Jun 15;10:30. doi: 10.1186/s13072-017-0137-1. eCollection 2017.

8.

Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Apr 4;18(1):63. doi: 10.1186/s13059-017-1202-6. No abstract available.

9.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Feb 13;18(1):27. doi: 10.1186/s13059-016-1145-3. Erratum in: Genome Biol. 2017 Apr 4;18(1):63.

10.

De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms.

Rispe C, Legeai F, Papura D, Bretaudeau A, Hudaverdian S, Le Trionnaire G, Tagu D, Jaquiéry J, Delmotte F.

BMC Genomics. 2016 Mar 11;17:219. doi: 10.1186/s12864-016-2530-8.

11.

Tools and data services registry: a community effort to document bioinformatics resources.

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.

Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

12.

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ.

Bretaudeau A, Monjeaud C, Le Bras Y, Legeai F, Collin O.

Gigascience. 2015 May 9;4:22. doi: 10.1186/s13742-015-0063-8. eCollection 2015.

13.

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

Legeai F, Gimenez S, Duvic B, Escoubas JM, Gosselin Grenet AS, Blanc F, Cousserans F, Séninet I, Bretaudeau A, Mutuel D, Girard PA, Monsempes C, Magdelenat G, Hilliou F, Feyereisen R, Ogliastro M, Volkoff AN, Jacquin-Joly E, d'Alençon E, Nègre N, Fournier P.

BMC Genomics. 2014 Aug 23;15:704. doi: 10.1186/1471-2164-15-704.

14.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

Ouedraogo M, Bettembourg C, Bretaudeau A, Sallou O, Diot C, Demeure O, Lecerf F.

PLoS One. 2012;7(11):e50653. doi: 10.1371/journal.pone.0050653. Epub 2012 Nov 28.

15.

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions.

Bretaudeau A, Coste F, Humily F, Garczarek L, Le Corguillé G, Six C, Ratin M, Collin O, Schluchter WM, Partensky F.

Nucleic Acids Res. 2013 Jan;41(Database issue):D396-401. doi: 10.1093/nar/gks1091. Epub 2012 Nov 21.

16.

PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.

Mahé S, Duhamel M, Le Calvez T, Guillot L, Sarbu L, Bretaudeau A, Collin O, Dufresne A, Kiers ET, Vandenkoornhuyse P.

PLoS One. 2012;7(9):e43117. doi: 10.1371/journal.pone.0043117. Epub 2012 Sep 13.

17.

Seqcrawler: biological data indexing and browsing platform.

Sallou O, Bretaudeau A, Roult A.

BMC Bioinformatics. 2012 Jul 24;13:175. doi: 10.1186/1471-2105-13-175.

18.

AnnotQTL: a new tool to gather functional and comparative information on a genomic region.

Lecerf F, Bretaudeau A, Sallou O, Desert C, Blum Y, Lagarrigue S, Demeure O.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W328-33. doi: 10.1093/nar/gkr361. Epub 2011 May 19.

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