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Items: 19

1.

Applying ecological resistance and resilience to dissect bacterial antibiotic responses.

Meredith HR, Andreani V, Ma HR, Lopatkin AJ, Lee AJ, Anderson DJ, Batt G, You L.

Sci Adv. 2018 Dec 5;4(12):eaau1873. doi: 10.1126/sciadv.aau1873. eCollection 2018 Dec.

2.

Identification of individual cells from z-stacks of bright-field microscopy images.

Lugagne JB, Jain S, Ivanovitch P, Ben Meriem Z, Vulin C, Fracassi C, Batt G, Hersen P.

Sci Rep. 2018 Jul 30;8(1):11455. doi: 10.1038/s41598-018-29647-5.

3.

Balancing a genetic toggle switch by real-time feedback control and periodic forcing.

Lugagne JB, Sosa Carrillo S, Kirch M, Köhler A, Batt G, Hersen P.

Nat Commun. 2017 Nov 17;8(1):1671. doi: 10.1038/s41467-017-01498-0.

4.

Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway.

Palaniappan SK, Bertaux F, Pichené M, Fabre E, Batt G, Genest B.

Bioinformatics. 2017 Jul 1;33(13):1980-1986. doi: 10.1093/bioinformatics/btx095.

PMID:
28200026
5.

Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform.

Versari C, Stoma S, Batmanov K, Llamosi A, Mroz F, Kaczmarek A, Deyell M, Lhoussaine C, Hersen P, Batt G.

J R Soc Interface. 2017 Feb;14(127). pii: 20160705. doi: 10.1098/rsif.2016.0705.

6.

What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.

Llamosi A, Gonzalez-Vargas AM, Versari C, Cinquemani E, Ferrari-Trecate G, Hersen P, Batt G.

PLoS Comput Biol. 2016 Feb 9;12(2):e1004706. doi: 10.1371/journal.pcbi.1004706. eCollection 2016 Feb.

7.

In silico control of biomolecular processes.

Uhlendorf J, Miermont A, Delaveau T, Charvin G, Fages F, Bottani S, Hersen P, Batt G.

Methods Mol Biol. 2015;1244:277-85. doi: 10.1007/978-1-4939-1878-2_13.

PMID:
25487102
8.

A platform for rapid prototyping of synthetic gene networks in mammalian cells.

Duportet X, Wroblewska L, Guye P, Li Y, Eyquem J, Rieders J, Rimchala T, Batt G, Weiss R.

Nucleic Acids Res. 2014 Dec 1;42(21):13440-51. doi: 10.1093/nar/gku1082. Epub 2014 Nov 5.

9.

Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance.

Bertaux F, Stoma S, Drasdo D, Batt G.

PLoS Comput Biol. 2014 Oct 23;10(10):e1003893. doi: 10.1371/journal.pcbi.1003893. eCollection 2014 Oct.

10.

STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification.

Stoma S, Donzé A, Bertaux F, Maler O, Batt G.

PLoS Comput Biol. 2013;9(5):e1003056. doi: 10.1371/journal.pcbi.1003056. Epub 2013 May 9.

11.

Composition and abstraction of logical regulatory modules: application to multicellular systems.

Mendes ND, Lang F, Le Cornec YS, Mateescu R, Batt G, Chaouiya C.

Bioinformatics. 2013 Mar 15;29(6):749-57. doi: 10.1093/bioinformatics/btt033. Epub 2013 Jan 22.

PMID:
23341501
12.

Long-term model predictive control of gene expression at the population and single-cell levels.

Uhlendorf J, Miermont A, Delaveau T, Charvin G, Fages F, Bottani S, Batt G, Hersen P.

Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):14271-6. doi: 10.1073/pnas.1206810109. Epub 2012 Aug 14.

13.

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.

Batt G, Besson B, Ciron PE, de Jong H, Dumas E, Geiselmann J, Monte R, Monteiro PT, Page M, Rechenmann F, Ropers D.

Methods Mol Biol. 2012;804:439-62. doi: 10.1007/978-1-61779-361-5_22.

PMID:
22144166
14.

Towards real-time control of gene expression: controlling the HOG signaling cascade.

Uhlendorf J, Bottani S, Fages F, Hersen P, Batt G.

Pac Symp Biocomput. 2011:338-49.

15.

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.

Batt G, Page M, Cantone I, Goessler G, Monteiro P, de Jong H.

Bioinformatics. 2010 Sep 15;26(18):i603-10. doi: 10.1093/bioinformatics/btq387.

16.

A general computational method for robustness analysis with applications to synthetic gene networks.

Rizk A, Batt G, Fages F, Soliman S.

Bioinformatics. 2009 Jun 15;25(12):i169-78. doi: 10.1093/bioinformatics/btp200.

17.

Robustness analysis and tuning of synthetic gene networks.

Batt G, Yordanov B, Weiss R, Belta C.

Bioinformatics. 2007 Sep 15;23(18):2415-22. Epub 2007 Jul 27.

PMID:
17660209
18.

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.

Batt G, Ropers D, de Jong H, Geiselmann J, Mateescu R, Page M, Schneider D.

Bioinformatics. 2005 Jun;21 Suppl 1:i19-28.

PMID:
15961457
19.

Qualitative simulation of the initiation of sporulation in Bacillus subtilis.

De Jong H, Geiselmann J, Batt G, Hernandez C, Page M.

Bull Math Biol. 2004 Mar;66(2):261-99.

PMID:
14871567

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