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Items: 1 to 50 of 68

1.

Erythroid differentiation displays a peak of energy consumption concomitant with glycolytic metabolism rearrangements.

Richard A, Vallin E, Romestaing C, Roussel D, Gandrillon O, Gonin-Giraud S.

PLoS One. 2019 Sep 4;14(9):e0221472. doi: 10.1371/journal.pone.0221472. eCollection 2019.

2.

WASABI: a dynamic iterative framework for gene regulatory network inference.

Bonnaffoux A, Herbach U, Richard A, Guillemin A, Gonin-Giraud S, Gros PA, Gandrillon O.

BMC Bioinformatics. 2019 May 2;20(1):220. doi: 10.1186/s12859-019-2798-1.

3.

Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts.

Duchesne R, Guillemin A, Crauste F, Gandrillon O.

In Silico Biol. 2019;13(1-2):55-69. doi: 10.3233/ISB-190471.

4.

Model-Based Assessment of the Role of Uneven Partitioning of Molecular Content on Heterogeneity and Regulation of Differentiation in CD8 T-Cell Immune Responses.

Girel S, Arpin C, Marvel J, Gandrillon O, Crauste F.

Front Immunol. 2019 Feb 19;10:230. doi: 10.3389/fimmu.2019.00230. eCollection 2019.

5.

Automated cell cycle and cell size measurements for single-cell gene expression studies.

Guillemin A, Richard A, Gonin-Giraud S, Gandrillon O.

BMC Res Notes. 2018 Feb 1;11(1):92. doi: 10.1186/s13104-018-3195-y.

6.

Inferring gene regulatory networks from single-cell data: a mechanistic approach.

Herbach U, Bonnaffoux A, Espinasse T, Gandrillon O.

BMC Syst Biol. 2017 Nov 21;11(1):105. doi: 10.1186/s12918-017-0487-0.

7.

Investigating the role of the experimental protocol in phenylhydrazine-induced anemia on mice recovery.

Angulo O, Gandrillon O, Crauste F.

J Theor Biol. 2018 Jan 21;437:286-298. doi: 10.1016/j.jtbi.2017.10.031. Epub 2017 Nov 2.

PMID:
29102644
8.

SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles.

Papili Gao N, Ud-Dean SMM, Gandrillon O, Gunawan R.

Bioinformatics. 2017 Sep 14. doi: 10.1093/bioinformatics/btx575. [Epub ahead of print]

9.

Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment.

Moussy A, Cosette J, Parmentier R, da Silva C, Corre G, Richard A, Gandrillon O, Stockholm D, Páldi A.

PLoS Biol. 2017 Jul 27;15(7):e2001867. doi: 10.1371/journal.pbio.2001867. eCollection 2017 Jul.

10.

Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny.

Crauste F, Mafille J, Boucinha L, Djebali S, Gandrillon O, Marvel J, Arpin C.

Cell Syst. 2017 Mar 22;4(3):306-317.e4. doi: 10.1016/j.cels.2017.01.014. Epub 2017 Feb 22.

11.

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process.

Richard A, Boullu L, Herbach U, Bonnafoux A, Morin V, Vallin E, Guillemin A, Papili Gao N, Gunawan R, Cosette J, Arnaud O, Kupiec JJ, Espinasse T, Gonin-Giraud S, Gandrillon O.

PLoS Biol. 2016 Dec 27;14(12):e1002585. doi: 10.1371/journal.pbio.1002585. eCollection 2016 Dec.

12.

IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8(+) T cell-APC: a multiscale modeling study.

Gao X, Arpin C, Marvel J, Prokopiou SA, Gandrillon O, Crauste F.

BMC Syst Biol. 2016 Aug 17;10(1):77. doi: 10.1186/s12918-016-0323-y.

13.

Erratum to: Temperature-induced variation in gene expression burst size in metazoan cells.

Arnaud O, Meyer S, Vallin E, Beslon G, Gandrillon O.

BMC Mol Biol. 2016 Feb 3;17:2. doi: 10.1186/s12867-015-0054-4. No abstract available.

14.

Temperature-induced variation in gene expression burst size in metazoan cells.

Arnaud O, Meyer S, Vallin E, Beslon G, Gandrillon O.

BMC Mol Biol. 2015 Nov 25;16:20. doi: 10.1186/s12867-015-0048-2. Erratum in: BMC Mol Biol. 2016;17:2.

15.

Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts.

Cellier P, Charnois T, Plantevit M, Rigotti C, Crémilleux B, Gandrillon O, Kléma J, Manguin JL.

J Biomed Semantics. 2015 May 18;6:27. doi: 10.1186/s13326-015-0023-3. eCollection 2015.

16.

Predicting pathogen-specific CD8 T cell immune responses from a modeling approach.

Crauste F, Terry E, Mercier IL, Mafille J, Djebali S, Andrieu T, Mercier B, Kaneko G, Arpin C, Marvel J, Gandrillon O.

J Theor Biol. 2015 Jun 7;374:66-82. doi: 10.1016/j.jtbi.2015.03.033. Epub 2015 Apr 3.

17.

Stochastic fluctuations and distributed control of gene expression impact cellular memory.

Corre G, Stockholm D, Arnaud O, Kaneko G, Viñuelas J, Yamagata Y, Neildez-Nguyen TM, Kupiec JJ, Beslon G, Gandrillon O, Paldi A.

PLoS One. 2014 Dec 22;9(12):e115574. doi: 10.1371/journal.pone.0115574. eCollection 2014.

18.

The role of spatial organization of cells in erythropoiesis.

Eymard N, Bessonov N, Gandrillon O, Koury MJ, Volpert V.

J Math Biol. 2015 Jan;70(1-2):71-97. doi: 10.1007/s00285-014-0758-y. Epub 2014 Feb 5.

PMID:
24496930
19.

V-erbA generates ribosomes devoid of RPL11 and regulates translational activity in avian erythroid progenitors.

Nguyen-Lefebvre AT, Leprun G, Morin V, Viñuelas J, Couté Y, Madjar JJ, Gandrillon O, Gonin-Giraud S.

Oncogene. 2014 Mar 20;33(12):1581-9. doi: 10.1038/onc.2013.93. Epub 2013 Apr 8.

PMID:
23563180
20.

Differential miRNA expression profiles in proliferating or differentiated keratinocytes in response to gamma irradiation.

Joly-Tonetti N, Viñuelas J, Gandrillon O, Lamartine J.

BMC Genomics. 2013 Mar 16;14:184. doi: 10.1186/1471-2164-14-184.

21.

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.

Viñuelas J, Kaneko G, Coulon A, Vallin E, Morin V, Mejia-Pous C, Kupiec JJ, Beslon G, Gandrillon O.

BMC Biol. 2013 Feb 25;11:15. doi: 10.1186/1741-7007-11-15.

22.

Chance at the heart of the cell.

Gandrillon O, Kolesnik-Antoine D, Kupiec JJ, Beslon G.

Prog Biophys Mol Biol. 2012 Sep;110(1):1-4. doi: 10.1016/j.pbiomolbio.2012.05.006. Epub 2012 May 30. No abstract available.

PMID:
22682931
23.

Towards experimental manipulation of stochasticity in gene expression.

Viñuelas J, Kaneko G, Coulon A, Beslon G, Gandrillon O.

Prog Biophys Mol Biol. 2012 Sep;110(1):44-53. doi: 10.1016/j.pbiomolbio.2012.04.010. Epub 2012 May 16.

PMID:
22609563
24.

Modeling erythroblastic islands: using a hybrid model to assess the function of central macrophage.

Fischer S, Kurbatova P, Bessonov N, Gandrillon O, Volpert V, Crauste F.

J Theor Biol. 2012 Apr 7;298:92-106. doi: 10.1016/j.jtbi.2012.01.002. Epub 2012 Jan 11.

PMID:
22245622
25.

Cholesterol synthesis-related enzyme oxidosqualene cyclase is required to maintain self-renewal in primary erythroid progenitors.

Mejia-Pous C, Damiola F, Gandrillon O.

Cell Prolif. 2011 Oct;44(5):441-52. doi: 10.1111/j.1365-2184.2011.00771.x.

PMID:
21951287
26.

Mathematical model of the primary CD8 T cell immune response: stability analysis of a nonlinear age-structured system.

Terry E, Marvel J, Arpin C, Gandrillon O, Crauste F.

J Math Biol. 2012 Aug;65(2):263-91. doi: 10.1007/s00285-011-0459-8. Epub 2011 Aug 13.

PMID:
21842166
27.

Novel genes differentially expressed between posterior and median silk gland identified by SAGE-aided transcriptome analysis.

Royer C, Briolay J, Garel A, Brouilly P, Sasanuma S, Sasanuma M, Shimomura M, Keime C, Gandrillon O, Huang Y, Chavancy G, Mita K, Couble P.

Insect Biochem Mol Biol. 2011 Feb;41(2):118-24. doi: 10.1016/j.ibmb.2010.11.003. Epub 2010 Nov 13.

PMID:
21078388
28.

Identification of human, rat and chicken ribosomal proteins by a combination of two-dimensional polyacrylamide gel electrophoresis and mass spectrometry.

Nguyen-Lefebvre AT, Gonin-Giraud S, Scherl A, Arboit P, Granger L, Sanchez JC, Diaz JJ, Gandrillon O, Madjar JJ.

J Proteomics. 2011 Feb 1;74(2):167-85. doi: 10.1016/j.jprot.2010.10.007. Epub 2010 Nov 3.

PMID:
21055487
29.

On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter.

Coulon A, Gandrillon O, Beslon G.

BMC Syst Biol. 2010 Jan 8;4:2. doi: 10.1186/1752-0509-4-2.

30.

Mathematical study of feedback control roles and relevance in stress erythropoiesis.

Crauste F, Demin I, Gandrillon O, Volpert V.

J Theor Biol. 2010 Apr 7;263(3):303-16. doi: 10.1016/j.jtbi.2009.12.026. Epub 2010 Jan 4.

PMID:
20043921
31.

A multi-scale model of erythropoiesis.

Demin I, Crauste F, Gandrillon O, Volpert V.

J Biol Dyn. 2010 Jan;4(1):59-70. doi: 10.1080/17513750902777642.

PMID:
22881070
32.

A combination of transposable elements and magnetic cell sorting provides a very efficient transgenesis system for chicken primary erythroid progenitors.

Mejia-Pous C, Viñuelas J, Faure C, Koszela J, Kawakami K, Takahashi Y, Gandrillon O.

BMC Biotechnol. 2009 Sep 18;9:81. doi: 10.1186/1472-6750-9-81.

33.

Extracting signature motifs from promoter sets of differentially expressed genes.

Mitasiŭnaite I, Rigotti C, Schicklin S, Meyniel L, Boulicaut JF, Gandrillon O.

In Silico Biol. 2009;9(1-2):S17-39.

PMID:
19537163
34.

Constraint-based knowledge discovery from SAGE data.

Klémal J, Blachon S, Soulet A, Crémilleux B, Gandrillon O.

In Silico Biol. 2008;8(2):157-75.

PMID:
18928203
35.

Stem cell antigen 2: a new gene involved in the self-renewal of erythroid progenitors.

Bresson-Mazet C, Gandrillon O, Gonin-Giraud S.

Cell Prolif. 2008 Oct;41(5):726-38. doi: 10.1111/j.1365-2184.2008.00554.x.

PMID:
18823497
36.

SQUAT: A web tool to mine human, murine and avian SAGE data.

Leyritz J, Schicklin S, Blachon S, Keime C, Robardet C, Boulicaut JF, Besson J, Pensa RG, Gandrillon O.

BMC Bioinformatics. 2008 Sep 18;9:378. doi: 10.1186/1471-2105-9-378.

37.

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome.

Hanriot L, Keime C, Gay N, Faure C, Dossat C, Wincker P, Scoté-Blachon C, Peyron C, Gandrillon O.

BMC Genomics. 2008 Sep 16;9:418. doi: 10.1186/1471-2164-9-418.

38.

Large multiprotein structures modeling and simulation: the need for mesoscopic models.

Coulon A, Beslon G, Gandrillon O.

Methods Mol Biol. 2008;484:537-58. doi: 10.1007/978-1-59745-398-1_32.

PMID:
18592200
39.

Involvement of the TGF-beta and mTOR/p70S6Kinase pathways in the transformation process induced by v-ErbA.

Gonin-Giraud S, Bresson-Mazet C, Gandrillon O.

Leuk Res. 2008 Dec;32(12):1878-88. doi: 10.1016/j.leukres.2008.05.010. Epub 2008 Jun 24.

PMID:
18573525
40.

Clustering formal concepts to discover biologically relevant knowledge from gene expression data.

Blachon S, Pensa RG, Besson J, Robardet C, Boulicaut JF, Gandrillon O.

In Silico Biol. 2007;7(4-5):467-83.

PMID:
18391238
41.

Adding self-renewal in committed erythroid progenitors improves the biological relevance of a mathematical model of erythropoiesis.

Crauste F, Pujo-Menjouet L, Génieys S, Molina C, Gandrillon O.

J Theor Biol. 2008 Jan 21;250(2):322-38. Epub 2007 Oct 6.

PMID:
17997418
42.

Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action.

Bresson C, Keime C, Faure C, Letrillard Y, Barbado M, Sanfilippo S, Benhra N, Gandrillon O, Gonin-Giraud S.

BMC Genomics. 2007 Oct 26;8:390.

43.

Unexpected observations after mapping LongSAGE tags to the human genome.

Keime C, Sémon M, Mouchiroud D, Duret L, Gandrillon O.

BMC Bioinformatics. 2007 May 15;8:154.

44.

SAGE analysis of mosquito salivary gland transcriptomes during Plasmodium invasion.

Rosinski-Chupin I, Briolay J, Brouilly P, Perrot S, Gomez SM, Chertemps T, Roth CW, Keime C, Gandrillon O, Couble P, Brey PT.

Cell Microbiol. 2007 Mar;9(3):708-24. Epub 2006 Oct 18.

PMID:
17054438
45.

Broadening of DNA replication origin usage during metazoan cell differentiation.

Dazy S, Gandrillon O, Hyrien O, Prioleau MN.

EMBO Rep. 2006 Aug;7(8):806-11. Epub 2006 Jun 16.

46.
47.

Serial analysis of gene expression in the silkworm, Bombyx mori.

Huang J, Miao X, Jin W, Couble P, Mita K, Zhang Y, Liu W, Zhuang L, Shen Y, Keime C, Gandrillon O, Brouilly P, Briolay J, Zhao G, Huang Y.

Genomics. 2005 Aug;86(2):233-41.

PMID:
15963683
48.

Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.

Keime C, Damiola F, Mouchiroud D, Duret L, Gandrillon O.

BMC Bioinformatics. 2004 Oct 6;5:143.

49.

Global transcription analysis of immature avian erythrocytic progenitors: from self-renewal to differentiation.

Damiola F, Keime C, Gonin-Giraud S, Dazy S, Gandrillon O.

Oncogene. 2004 Oct 7;23(46):7628-43.

PMID:
15378009
50.

The MEK-1/ERKs signalling pathway is differentially involved in the self-renewal of early and late avian erythroid progenitor cells.

Dazy S, Damiola F, Parisey N, Beug H, Gandrillon O.

Oncogene. 2003 Dec 18;22(58):9205-16.

PMID:
14681680

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