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Items: 1 to 50 of 83

1.

CiliaCarta: An integrated and validated compendium of ciliary genes.

van Dam TJP, Kennedy J, van der Lee R, de Vrieze E, Wunderlich KA, Rix S, Dougherty GW, Lambacher NJ, Li C, Jensen VL, Leroux MR, Hjeij R, Horn N, Texier Y, Wissinger Y, van Reeuwijk J, Wheway G, Knapp B, Scheel JF, Franco B, Mans DA, van Wijk E, Képès F, Slaats GG, Toedt G, Kremer H, Omran H, Szymanska K, Koutroumpas K, Ueffing M, Nguyen TT, Letteboer SJF, Oud MM, van Beersum SEC, Schmidts M, Beales PL, Lu Q, Giles RH, Szklarczyk R, Russell RB, Gibson TJ, Johnson CA, Blacque OE, Wolfrum U, Boldt K, Roepman R, Hernandez-Hernandez V, Huynen MA.

PLoS One. 2019 May 16;14(5):e0216705. doi: 10.1371/journal.pone.0216705. eCollection 2019.

2.

A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data.

Le Treut G, Képès F, Orland H.

Biophys J. 2018 Dec 18;115(12):2286-2294. doi: 10.1016/j.bpj.2018.10.032. Epub 2018 Nov 10.

PMID:
30527448
3.

Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis.

Nouri H, Monnier AF, Fossum-Raunehaug S, Maciag-Dorszynska M, Cabin-Flaman A, Képès F, Wegrzyn G, Szalewska-Palasz A, Norris V, Skarstad K, Janniere L.

DNA Res. 2018 Dec 1;25(6):641-653. doi: 10.1093/dnares/dsy031.

4.

Correction to 'Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity'.

Paschalis V, Le Chatelier E, Green M, Képès F, Soultanas P, Janniere L.

Open Biol. 2017 Nov;7(11). pii: 170234. doi: 10.1098/rsob.170234. No abstract available.

5.

Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity.

Paschalis V, Le Chatelier E, Green M, Nouri H, Képès F, Soultanas P, Janniere L.

Open Biol. 2017 Sep;7(9). pii: 170146. doi: 10.1098/rsob.170146. Erratum in: Open Biol. 2017 Nov;7(11):.

6.

From multiple pathogenicity islands to a unique organized pathogenicity archipelago.

Bouyioukos C, Reverchon S, Képès F.

Sci Rep. 2016 Jun 15;6:27978. doi: 10.1038/srep27978.

7.

Analysis tools for the interplay between genome layout and regulation.

Bouyioukos C, Elati M, Képès F.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:191. doi: 10.1186/s12859-016-1047-0.

8.

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJ, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJ, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, Roepman R; UK10K Rare Diseases Group.

Nat Commun. 2016 May 13;7:11491. doi: 10.1038/ncomms11491.

9.

GREAT: a web portal for Genome Regulatory Architecture Tools.

Bouyioukos C, Bucchini F, Elati M, Képès F.

Nucleic Acids Res. 2016 Jul 8;44(W1):W77-82. doi: 10.1093/nar/gkw384. Epub 2016 May 5.

10.

Phase Behavior of DNA in the Presence of DNA-Binding Proteins.

Le Treut G, Képès F, Orland H.

Biophys J. 2016 Jan 5;110(1):51-62. doi: 10.1016/j.bpj.2015.10.027.

11.

Thermodynamics of long supercoiled molecules: insights from highly efficient Monte Carlo simulations.

Lepage T, Képès F, Junier I.

Biophys J. 2015 Jul 7;109(1):135-43. doi: 10.1016/j.bpj.2015.06.005.

12.

[Scientific and technological conditions of the emergence of synthetic biology].

Képès F.

Med Sci (Paris). 2013 May;29 Spec No 2:13-5. doi: 10.1051/medsci/201329s204. Epub 2013 Jun 7. French. No abstract available.

13.

PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

Elati M, Nicolle R, Junier I, Fernández D, Fekih R, Font J, Képès F.

Nucleic Acids Res. 2013 Feb 1;41(3):1406-15. doi: 10.1093/nar/gks1286. Epub 2012 Dec 14.

14.

CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus.

Junier I, Dale RK, Hou C, Képès F, Dean A.

Nucleic Acids Res. 2012 Sep;40(16):7718-27. doi: 10.1093/nar/gks536. Epub 2012 Jun 16.

15.

The layout of a bacterial genome.

Képès F, Jester BC, Lepage T, Rafiei N, Rosu B, Junier I.

FEBS Lett. 2012 Jul 16;586(15):2043-8. doi: 10.1016/j.febslet.2012.03.051. Epub 2012 Mar 31. Review.

16.

Genomic organization of evolutionarily correlated genes in bacteria: limits and strategies.

Junier I, Hérisson J, Képès F.

J Mol Biol. 2012 Jun 22;419(5):369-86. doi: 10.1016/j.jmb.2012.03.009. Epub 2012 Mar 21.

PMID:
22446685
17.

Introduction to special issue ECCS'09 in Theory in Biosciences.

Kirkilionis M, Kepes F.

Theory Biosci. 2011 Sep;130(3):153. doi: 10.1007/s12064-011-0123-2. No abstract available.

PMID:
21451965
18.

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing.

Norris V, Zemirline A, Amar P, Audinot JN, Ballet P, Ben-Jacob E, Bernot G, Beslon G, Cabin A, Fanchon E, Giavitto JL, Glade N, Greussay P, Grondin Y, Foster JA, Hutzler G, Jost J, Kepes F, Michel O, Molina F, Signorini J, Stano P, Thierry AR.

Theory Biosci. 2011 Sep;130(3):211-28. doi: 10.1007/s12064-010-0118-4. Epub 2011 Mar 8. Review.

19.

Periodic pattern detection in sparse boolean sequences.

Junier I, Hérisson J, Képès F.

Algorithms Mol Biol. 2010 Sep 10;5:31. doi: 10.1186/1748-7188-5-31.

20.

Challenges in experimental data integration within genome-scale metabolic models.

Bourguignon PY, Samal A, Képès F, Jost J, Martin OC.

Algorithms Mol Biol. 2010 Apr 22;5:20. doi: 10.1186/1748-7188-5-20.

21.

Spatial and topological organization of DNA chains induced by gene co-localization.

Junier I, Martin O, Képès F.

PLoS Comput Biol. 2010 Feb 12;6(2):e1000678. doi: 10.1371/journal.pcbi.1000678.

22.

[Synthetic and integrative biology].

Képès F.

Med Sci (Paris). 2009 May;25 Spec No 2:39-42. doi: 10.1051/medsci/2009252s39. Review. French.

23.

Gene-based bin analysis of genome-wide association studies.

Omont N, Forner K, Lamarine M, Martin G, Képès F, Wojcik J.

BMC Proc. 2008 Dec 17;2 Suppl 4:S6.

24.

[First French team success during iGEM synthetic biology competition].

Bikard D, Képès F; L'Equipe iGEM Paris.

Med Sci (Paris). 2008 May;24(5):541-4. doi: 10.1051/medsci/2008245541. French. No abstract available.

25.

Topology-based abstraction of complex biological systems: application to the Golgi apparatus.

Poudret M, Arnould A, Comet JP, Le Gall P, Meseure P, Képès F.

Theory Biosci. 2008 Jun;127(2):79-88. doi: 10.1007/s12064-008-0030-3. Epub 2008 May 6. Review.

PMID:
18458977
26.

A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle.

Sriram K, Bernot G, Képès F.

IET Syst Biol. 2007 Nov;1(6):326-41.

PMID:
18203579
27.

Incremental and unifying modelling formalism for biological interaction networks.

Yartseva A, Klaudel H, Devillers R, Képès F.

BMC Bioinformatics. 2007 Nov 8;8:433.

28.

Question 7: the first units of life were not simple cells.

Norris V, Hunding A, Kepes F, Lancet D, Minsky A, Raine D, Root-Bernstein R, Sriram K.

Orig Life Evol Biosph. 2007 Oct;37(4-5):429-32. Epub 2007 Jul 10.

PMID:
17624805
29.

Model of interactions in biology and application to heterogeneous network in yeast.

Smidtas S, Yartseva A, Schächter V, Képès F.

C R Biol. 2006 Dec;329(12):945-52. Epub 2006 Aug 7.

PMID:
17126798
30.

Guidelines: From artificial evolution to computational evolution: a research agenda.

Banzhaf W, Beslon G, Christensen S, Foster JA, Képès F, Lefort V, Miller JF, Radman M, Ramsden JJ.

Nat Rev Genet. 2006 Sep;7(9):729-35. doi: 10.1038/nrg1921. Epub 2006 Aug 8. Review.

PMID:
16894364
31.

The adaptive filter of the yeast galactose pathway.

Smidtas S, Schächter V, Képès F.

J Theor Biol. 2006 Sep 21;242(2):372-81. Epub 2006 Apr 27.

PMID:
16643954
32.

Compositional complementarity and prebiotic ecology in the origin of life.

Hunding A, Kepes F, Lancet D, Minsky A, Norris V, Raine D, Sriram K, Root-Bernstein R.

Bioessays. 2006 Apr;28(4):399-412.

PMID:
16547956
33.

A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae.

Mercier G, Berthault N, Touleimat N, Képès F, Fourel G, Gilson E, Dutreix M.

Nucleic Acids Res. 2005 Nov 30;33(20):6635-43. Print 2005.

34.

[Epigenetics as an aspect of post-genomics].

Képès F.

Med Sci (Paris). 2005 Apr;21(4):371-6. Review. French.

35.

Morphodynamics of the secretory pathway.

Képès F, Rambourg A, Satiat-Jeunemaître B.

Int Rev Cytol. 2005;242:55-120. Review.

PMID:
15598467
36.

Codon bias signatures, organization of microorganisms in codon space, and lifestyle.

Carbone A, Képès F, Zinovyev A.

Mol Biol Evol. 2005 Mar;22(3):547-61. Epub 2004 Nov 10. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1158.

PMID:
15537809
37.

Periodic transcriptional organization of the E.coli genome.

Képès F.

J Mol Biol. 2004 Jul 23;340(5):957-64.

PMID:
15236959
38.

Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication.

Omont N, Képès F.

Bioinformatics. 2004 Nov 1;20(16):2719-25. Epub 2004 May 14.

PMID:
15145803
39.

Soi3p/Rav1p functions at the early endosome to regulate endocytic trafficking to the vacuole and localization of trans-Golgi network transmembrane proteins.

Sipos G, Brickner JH, Brace EJ, Chen L, Rambourg A, Kepes F, Fuller RS.

Mol Biol Cell. 2004 Jul;15(7):3196-209. Epub 2004 Apr 16.

40.

Codon adaptation index as a measure of dominating codon bias.

Carbone A, Zinovyev A, Képès F.

Bioinformatics. 2003 Nov 1;19(16):2005-15.

PMID:
14594704
41.
42.

Hyperstructures, genome analysis and I-cells.

Amar P, Ballet P, Barlovatz-Meimon G, Benecke A, Bernot G, Bouligand Y, Bourguine P, Delaplace F, Delosme JM, Demarty M, Fishov I, Fourmentin-Guilbert J, Fralick J, Giavitto JL, Gleyse B, Godin C, Incitti R, Képès F, Lange C, Le Sceller L, Loutellier C, Michel O, Molina F, Monnier C, Natowicz R, Norris V, Orange N, Pollard H, Raine D, Ripoll C, Rouviere-Yaniv J, Saier M Jr, Soler P, Tambourin P, Thellier M, Tracqui P, Ussery D, Vincent JC, Vannier JP, Wiggins P, Zemirline A.

Acta Biotheor. 2002;50(4):357-73. Review.

PMID:
12675536
43.

Secretory compartments as instances of dynamic self-evolving structures.

Képès F.

Acta Biotheor. 2002;50(4):209-21.

PMID:
12675528
44.

Membrane traffic in virtual reality.

Képès F.

Traffic. 2003 Jan;4(1):13-7. No abstract available.

45.

Characterization of a putative type IV aminophospholipid transporter P-type ATPase.

Flamant S, Pescher P, Lemercier B, Clément-Ziza M, Képès F, Fellous M, Milon G, Marchal G, Besmond C.

Mamm Genome. 2003 Jan;14(1):21-30.

PMID:
12532265
46.

Modelling macromolecular networks: two meetings in Paris, July, 2002.

Képès F, Carbone A.

Bioessays. 2002 Dec;24(12):1188-90. No abstract available.

PMID:
12447983
47.

Effects of brefeldin A and nordihydroguaiaretic acid on endomembrane dynamics and lipid synthesis in plant cells.

Mérigout P, Képès F, Perret AM, Satiat-Jeunemaitre B, Moreau P.

FEBS Lett. 2002 May 8;518(1-3):88-92.

48.

Topological and causal structure of the yeast transcriptional regulatory network.

Guelzim N, Bottani S, Bourgine P, Képès F.

Nat Genet. 2002 May;31(1):60-3. Epub 2002 Apr 22.

PMID:
11967534
49.

Sec7p directs the transitions required for yeast Golgi biogenesis.

Deitz SB, Rambourg A, Képès F, Franzusoff A.

Traffic. 2000 Feb;1(2):172-83.

50.

Morphogenesis and dynamics of the yeast Golgi apparatus.

Morin-Ganet MN, Rambourg A, Deitz SB, Franzusoff A, Képès F.

Traffic. 2000 Jan;1(1):56-68.

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