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Items: 31

1.

Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design.

Daval S, Belcour A, Gazengel K, Legrand L, Gouzy J, Cottret L, Lebreton L, Aigu Y, Mougel C, Manzanares-Dauleux MJ.

Genomics. 2018 Nov 15. pii: S0888-7543(18)30141-1. doi: 10.1016/j.ygeno.2018.11.013. [Epub ahead of print]

PMID:
30447277
2.

Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii.

Pecrix Y, Buendia L, Penouilh-Suzette C, Maréchaux M, Legrand L, Bouchez O, Rengel D, Gouzy J, Cottret L, Vear F, Godiard L.

Plant J. 2018 Nov 13. doi: 10.1111/tpj.14157. [Epub ahead of print]

PMID:
30422341
3.

LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization.

Buendia L, Girardin A, Wang T, Cottret L, Lefebvre B.

Front Plant Sci. 2018 Oct 24;9:1531. doi: 10.3389/fpls.2018.01531. eCollection 2018. Review.

4.

Evolutionary History of Plant LysM Receptor Proteins Related to Root Endosymbiosis.

Gough C, Cottret L, Lefebvre B, Bono JJ.

Front Plant Sci. 2018 Jul 4;9:923. doi: 10.3389/fpls.2018.00923. eCollection 2018.

5.

MetExplore: collaborative edition and exploration of metabolic networks.

Cottret L, Frainay C, Chazalviel M, Cabanettes F, Gloaguen Y, Camenen E, Merlet B, Heux S, Portais JC, Poupin N, Vinson F, Jourdan F.

Nucleic Acids Res. 2018 Jul 2;46(W1):W495-W502. doi: 10.1093/nar/gky301.

6.

The Rosa genome provides new insights into the domestication of modern roses.

Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrère S, Caissard JC, Couloux A, Cottret L, Aury JM, Szécsi J, Latrasse D, Madoui MA, François L, Fu X, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P, Bendahmane M.

Nat Genet. 2018 Jun;50(6):772-777. doi: 10.1038/s41588-018-0110-3. Epub 2018 Apr 30.

7.

Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen.

Peyraud R, Cottret L, Marmiesse L, Genin S.

Nat Commun. 2018 Jan 29;9(1):418. doi: 10.1038/s41467-017-02660-4.

8.

Genomic Prediction of Sunflower Hybrids Oil Content.

Mangin B, Bonnafous F, Blanchet N, Boniface MC, Bret-Mestries E, Carrère S, Cottret L, Legrand L, Marage G, Pegot-Espagnet P, Munos S, Pouilly N, Vear F, Vincourt P, Langlade NB.

Front Plant Sci. 2017 Sep 21;8:1633. doi: 10.3389/fpls.2017.01633. eCollection 2017.

9.

MetExploreViz: web component for interactive metabolic network visualization.

Chazalviel M, Frainay C, Poupin N, Vinson F, Merlet B, Gloaguen Y, Cottret L, Jourdan F.

Bioinformatics. 2017 Sep 15. doi: 10.1093/bioinformatics/btx588. [Epub ahead of print]

10.

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.

Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Brière C, Owens GL, Carrère S, Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Bérard A, Bergès H, Blanchet N, Boniface MC, Brunel D, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, Le Paslier MC, Lippi Y, Lorenzon L, Mandel JR, Marage G, Marchand G, Marquand E, Bret-Mestries E, Morien E, Nambeesan S, Nguyen T, Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E, Schiex T, Thomas J, Vandecasteele C, Varès D, Vear F, Vautrin S, Crespi M, Mangin B, Burke JM, Salse J, Muños S, Vincourt P, Rieseberg LH, Langlade NB.

Nature. 2017 Jun 1;546(7656):148-152. doi: 10.1038/nature22380. Epub 2017 May 22.

PMID:
28538728
11.

Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula.

Satgé C, Moreau S, Sallet E, Lefort G, Auriac MC, Remblière C, Cottret L, Gallardo K, Noirot C, Jardinaud MF, Gamas P.

Nat Plants. 2016 Oct 31;2(11):16166. doi: 10.1038/nplants.2016.166.

PMID:
27797357
12.

A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum.

Peyraud R, Cottret L, Marmiesse L, Gouzy J, Genin S.

PLoS Pathog. 2016 Oct 12;12(10):e1005939. doi: 10.1371/journal.ppat.1005939. eCollection 2016 Oct.

13.

A Laser Dissection-RNAseq Analysis Highlights the Activation of Cytokinin Pathways by Nod Factors in the Medicago truncatula Root Epidermis.

Jardinaud MF, Boivin S, Rodde N, Catrice O, Kisiala A, Lepage A, Moreau S, Roux B, Cottret L, Sallet E, Brault M, Emery RJ, Gouzy J, Frugier F, Gamas P.

Plant Physiol. 2016 Jul;171(3):2256-76. doi: 10.1104/pp.16.00711. Epub 2016 May 23.

14.

FlexFlux: combining metabolic flux and regulatory network analyses.

Marmiesse L, Peyraud R, Cottret L.

BMC Syst Biol. 2015 Dec 15;9:93. doi: 10.1186/s12918-015-0238-z.

15.

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.

Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F.

Nucleic Acids Res. 2015 Jan;43(Database issue):D637-44. doi: 10.1093/nar/gku944. Epub 2014 Oct 9.

16.

Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes.

Khafif M, Cottret L, Balagué C, Raffaele S.

BMC Bioinformatics. 2014 Jun 26;15:222. doi: 10.1186/1471-2105-15-222.

17.

An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing.

Roux B, Rodde N, Jardinaud MF, Timmers T, Sauviac L, Cottret L, Carrère S, Sallet E, Courcelle E, Moreau S, Debellé F, Capela D, de Carvalho-Niebel F, Gouzy J, Bruand C, Gamas P.

Plant J. 2014 Mar;77(6):817-37. doi: 10.1111/tpj.12442. Epub 2014 Feb 24.

18.

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.

Milreu PV, Klein CC, Cottret L, Acuña V, Birmelé E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF.

Bioinformatics. 2014 Jan 1;30(1):61-70. doi: 10.1093/bioinformatics/btt597. Epub 2013 Oct 27.

19.

Transcriptome database resource and gene expression atlas for the rose.

Dubois A, Carrere S, Raymond O, Pouvreau B, Cottret L, Roccia A, Onesto JP, Sakr S, Atanassova R, Baudino S, Foucher F, Le Bris M, Gouzy J, Bendahmane M.

BMC Genomics. 2012 Nov 20;13:638. doi: 10.1186/1471-2164-13-638.

20.

Exploration of the core metabolism of symbiotic bacteria.

Klein CC, Cottret L, Kielbassa J, Charles H, Gautier C, Ribeiro de Vasconcelos AT, Lacroix V, Sagot MF.

BMC Genomics. 2012 Aug 31;13:438. doi: 10.1186/1471-2164-13-438.

21.

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

Acuña V, Milreu PV, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot MF.

Bioinformatics. 2012 Oct 1;28(19):2474-83. Epub 2012 Jul 10.

PMID:
22782547
22.

A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: reduced transporter sets and variable membrane organisations.

Charles H, Balmand S, Lamelas A, Cottret L, Pérez-Brocal V, Burdin B, Latorre A, Febvay G, Colella S, Calevro F, Rahbé Y.

PLoS One. 2011;6(12):e29096. doi: 10.1371/journal.pone.0029096. Epub 2011 Dec 27.

23.

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S.

Database (Oxford). 2011 Apr 7;2011:bar008. doi: 10.1093/database/bar008. Print 2011.

24.

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Cottret L, Milreu PV, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF.

PLoS Comput Biol. 2010 Sep 2;6(9). pii: e1000904. doi: 10.1371/journal.pcbi.1000904.

25.

Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining.

Jourdan F, Cottret L, Huc L, Wildridge D, Scheltema R, Hillenweck A, Barrett MP, Zalko D, Watson DG, Debrauwer L.

Metabolomics. 2010 Jun;6(2):312-321. Epub 2010 Jan 6.

26.

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. doi: 10.1093/nar/gkq312. Epub 2010 May 5.

27.

Graph methods for the investigation of metabolic networks in parasitology.

Cottret L, Jourdan F.

Parasitology. 2010 Aug;137(9):1393-407. doi: 10.1017/S0031182010000363. Epub 2010 May 6. Review.

PMID:
20444302
28.

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

Brinza L, Viñuelas J, Cottret L, Calevro F, Rahbé Y, Febvay G, Duport G, Colella S, Rabatel A, Gautier C, Fayard JM, Sagot MF, Charles H.

C R Biol. 2009 Nov;332(11):1034-49. doi: 10.1016/j.crvi.2009.09.007. Epub 2009 Oct 14. Review.

PMID:
19909925
29.

Deciphering the connectivity structure of biological networks using MixNet.

Picard F, Miele V, Daudin JJ, Cottret L, Robin S.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S17. doi: 10.1186/1471-2105-10-S6-S17.

30.

An introduction to metabolic networks and their structural analysis.

Lacroix V, Cottret L, Thébault P, Sagot MF.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec;5(4):594-617. doi: 10.1109/TCBB.2008.79. Review.

PMID:
18989046
31.

Metabolic network visualization eliminating node redundance and preserving metabolic pathways.

Bourqui R, Cottret L, Lacroix V, Auber D, Mary P, Sagot MF, Jourdan F.

BMC Syst Biol. 2007 Jul 3;1:29.

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