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Items: 1 to 50 of 89

1.

Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells.

Tidin O, Friman ET, Naef F, Suter DM.

Sci Rep. 2019 Mar 29;9(1):5372. doi: 10.1038/s41598-019-41870-2.

2.

Memory and relatedness of transcriptional activity in mammalian cell lineages.

Phillips NE, Mandic A, Omidi S, Naef F, Suter DM.

Nat Commun. 2019 Mar 14;10(1):1208. doi: 10.1038/s41467-019-09189-8.

3.

Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock.

Gachon F, Yeung J, Naef F.

Genes Dev. 2018 Nov 1;32(21-22):1359-1360. doi: 10.1101/gad.320911.118. Review.

4.

The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism.

Weger BD, Gobet C, Yeung J, Martin E, Jimenez S, Betrisey B, Foata F, Berger B, Balvay A, Foussier A, Charpagne A, Boizet-Bonhoure B, Chou CJ, Naef F, Gachon F.

Cell Metab. 2019 Feb 5;29(2):362-382.e8. doi: 10.1016/j.cmet.2018.09.023. Epub 2018 Oct 18.

5.

Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior.

Yeung J, Naef F.

Trends Genet. 2018 Dec;34(12):915-926. doi: 10.1016/j.tig.2018.09.005. Epub 2018 Oct 8. Review.

PMID:
30309754
6.

Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates.

Alber AB, Paquet ER, Biserni M, Naef F, Suter DM.

Mol Cell. 2018 Sep 20;71(6):1079-1091.e9. doi: 10.1016/j.molcel.2018.07.023. Epub 2018 Aug 23.

PMID:
30146318
7.

Modulation of transcriptional burst frequency by histone acetylation.

Nicolas D, Zoller B, Suter DM, Naef F.

Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):7153-7158. doi: 10.1073/pnas.1722330115. Epub 2018 Jun 18.

8.

Clock-dependent chromatin topology modulates circadian transcription and behavior.

Mermet J, Yeung J, Hurni C, Mauvoisin D, Gustafson K, Jouffe C, Nicolas D, Emmenegger Y, Gobet C, Franken P, Gachon F, Naef F.

Genes Dev. 2018 Mar 1;32(5-6):347-358. doi: 10.1101/gad.312397.118. Epub 2018 Mar 23.

9.

Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver.

Wang J, Symul L, Yeung J, Gobet C, Sobel J, Lück S, Westermark PO, Molina N, Naef F.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1916-E1925. doi: 10.1073/pnas.1715225115. Epub 2018 Feb 5.

10.

Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs.

Yeung J, Mermet J, Jouffe C, Marquis J, Charpagne A, Gachon F, Naef F.

Genome Res. 2018 Feb;28(2):182-191. doi: 10.1101/gr.222430.117. Epub 2017 Dec 18.

11.

Guidelines for Genome-Scale Analysis of Biological Rhythms.

Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB.

J Biol Rhythms. 2017 Oct;32(5):380-393. doi: 10.1177/0748730417728663. Epub 2017 Nov 3.

12.

Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome.

Mauvoisin D, Atger F, Dayon L, Núñez Galindo A, Wang J, Martin E, Da Silva L, Montoliu I, Collino S, Martin FP, Ratajczak J, Cantó C, Kussmann M, Naef F, Gachon F.

Cell Rep. 2017 Aug 15;20(7):1729-1743. doi: 10.1016/j.celrep.2017.07.065.

13.

What shapes eukaryotic transcriptional bursting?

Nicolas D, Phillips NE, Naef F.

Mol Biosyst. 2017 Jun 27;13(7):1280-1290. doi: 10.1039/c7mb00154a. Review.

PMID:
28573295
14.

Transcriptional regulatory logic of the diurnal cycle in the mouse liver.

Sobel JA, Krier I, Andersin T, Raghav S, Canella D, Gilardi F, Kalantzi AS, Rey G, Weger B, Gachon F, Dal Peraro M, Hernandez N, Schibler U, Deplancke B, Naef F; CycliX consortium.

PLoS Biol. 2017 Apr 17;15(4):e2001069. doi: 10.1371/journal.pbio.2001069. eCollection 2017 Apr.

15.

A new promoter element associated with daily time keeping in Drosophila.

Sharp B, Paquet E, Naef F, Bafna A, Wijnen H.

Nucleic Acids Res. 2017 Jun 20;45(11):6459-6470. doi: 10.1093/nar/gkx268.

16.

Ribosome profiling and dynamic regulation of translation in mammals.

Gobet C, Naef F.

Curr Opin Genet Dev. 2017 Apr;43:120-127. doi: 10.1016/j.gde.2017.03.005. Epub 2017 Mar 28. Review.

17.

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World.

Mermet J, Yeung J, Naef F.

Cold Spring Harb Perspect Biol. 2017 Mar 1;9(3). pii: a028720. doi: 10.1101/cshperspect.a028720. Review.

18.

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver.

Wang J, Mauvoisin D, Martin E, Atger F, Galindo AN, Dayon L, Sizzano F, Palini A, Kussmann M, Waridel P, Quadroni M, Dulić V, Naef F, Gachon F.

Cell Metab. 2017 Jan 10;25(1):102-117. doi: 10.1016/j.cmet.2016.10.003. Epub 2016 Nov 3.

19.

Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp.

Gotic I, Omidi S, Fleury-Olela F, Molina N, Naef F, Schibler U.

Genes Dev. 2016 Sep 1;30(17):2005-17. doi: 10.1101/gad.287094.116. Epub 2016 Sep 15.

20.

Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling.

Bischofberger M, Iacovache I, Boss D, Naef F, van der Goot FG, Molina N.

Biophys J. 2016 Apr 12;110(7):1574-1581. doi: 10.1016/j.bpj.2016.02.035.

21.

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver.

Atger F, Gobet C, Marquis J, Martin E, Wang J, Weger B, Lefebvre G, Descombes P, Naef F, Gachon F.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6579-88. doi: 10.1073/pnas.1515308112. Epub 2015 Nov 9.

22.

Structure of silent transcription intervals and noise characteristics of mammalian genes.

Zoller B, Nicolas D, Molina N, Naef F.

Mol Syst Biol. 2015 Jul 27;11(7):823. doi: 10.15252/msb.20156257.

23.

The effect of chronic shoulder pain on maximal force of shoulder abduction.

Naef F, Grace S, Crowley-McHattan Z, Hardy D, McLeod A.

J Bodyw Mov Ther. 2015 Jul;19(3):410-6. doi: 10.1016/j.jbmt.2014.08.005. Epub 2014 Aug 17.

PMID:
26118510
24.

CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings.

Blanchoud S, Nicolas D, Zoller B, Tidin O, Naef F.

Methods. 2015 Sep 1;85:3-11. doi: 10.1016/j.ymeth.2015.04.023. Epub 2015 Apr 28.

PMID:
25934263
25.

Quantitative analysis and modeling probe polarity establishment in C. elegans embryos.

Blanchoud S, Busso C, Naef F, Gönczy P.

Biophys J. 2015 Feb 17;108(4):799-809. doi: 10.1016/j.bpj.2014.12.022.

26.

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription.

Knight B, Kubik S, Ghosh B, Bruzzone MJ, Geertz M, Martin V, Dénervaud N, Jacquet P, Ozkan B, Rougemont J, Maerkl SJ, Naef F, Shore D.

Genes Dev. 2014 Aug 1;28(15):1695-709. doi: 10.1101/gad.244434.114. Erratum in: Genes Dev. 2014 Oct 1;28(19):2188.

27.

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells.

Bieler J, Cannavo R, Gustafson K, Gobet C, Gatfield D, Naef F.

Mol Syst Biol. 2014 Jul 15;10:739. doi: 10.15252/msb.20145218.

28.

Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells.

Hoffmann J, Symul L, Shostak A, Fischer T, Naef F, Brunner M.

PLoS One. 2014 Jul 9;9(7):e102238. doi: 10.1371/journal.pone.0102238. eCollection 2014.

29.

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters.

Quinodoz M, Gobet C, Naef F, Gustafson KB.

Genome Biol. 2014 Jun 12;15(6):R85. doi: 10.1186/gb-2014-15-6-r85.

30.

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.

Mauvoisin D, Wang J, Jouffe C, Martin E, Atger F, Waridel P, Quadroni M, Gachon F, Naef F.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):167-72. doi: 10.1073/pnas.1314066111. Epub 2013 Dec 16.

31.

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene.

Molina N, Suter DM, Cannavo R, Zoller B, Gotic I, Naef F.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20563-8. doi: 10.1073/pnas.1312310110. Epub 2013 Dec 2.

32.

Analysis of precision in chemical oscillators: implications for circadian clocks.

d'Eysmond T, De Simone A, Naef F.

Phys Biol. 2013 Oct;10(5):056005. doi: 10.1088/1478-3975/10/5/056005. Epub 2013 Sep 16.

PMID:
24043227
33.

A chemostat array enables the spatio-temporal analysis of the yeast proteome.

Dénervaud N, Becker J, Delgado-Gonzalo R, Damay P, Rajkumar AS, Unser M, Shore D, Naef F, Maerkl SJ.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15842-7. doi: 10.1073/pnas.1308265110. Epub 2013 Sep 9.

34.

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics.

Simicevic J, Schmid AW, Gilardoni PA, Zoller B, Raghav SK, Krier I, Gubelmann C, Lisacek F, Naef F, Moniatte M, Deplancke B.

Nat Methods. 2013 Jun;10(6):570-6. doi: 10.1038/nmeth.2441. Epub 2013 Apr 14.

35.

The circadian clock coordinates ribosome biogenesis.

Jouffe C, Cretenet G, Symul L, Martin E, Atger F, Naef F, Gachon F.

PLoS Biol. 2013;11(1):e1001455. doi: 10.1371/journal.pbio.1001455. Epub 2013 Jan 3.

36.

Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles.

Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U, Rougemont J, Guex N, Hernandez N, Naef F; CycliX Consortium.

PLoS Biol. 2012;10(11):e1001442. doi: 10.1371/journal.pbio.1001442. Epub 2012 Nov 27.

37.

Circadian Dbp transcription relies on highly dynamic BMAL1-CLOCK interaction with E boxes and requires the proteasome.

Stratmann M, Suter DM, Molina N, Naef F, Schibler U.

Mol Cell. 2012 Oct 26;48(2):277-87. doi: 10.1016/j.molcel.2012.08.012. Epub 2012 Sep 13.

38.

Cold-inducible RNA-binding protein modulates circadian gene expression posttranscriptionally.

Morf J, Rey G, Schneider K, Stratmann M, Fujita J, Naef F, Schibler U.

Science. 2012 Oct 19;338(6105):379-83. doi: 10.1126/science.1217726. Epub 2012 Aug 23.

39.

Origins and consequences of transcriptional discontinuity.

Suter DM, Molina N, Naef F, Schibler U.

Curr Opin Cell Biol. 2011 Dec;23(6):657-62. doi: 10.1016/j.ceb.2011.09.004. Epub 2011 Sep 29. Review.

PMID:
21963300
40.

Computational analysis of protein-DNA interactions from ChIP-seq data.

Rougemont J, Naef F.

Methods Mol Biol. 2012;786:263-73. doi: 10.1007/978-1-61779-292-2_16.

PMID:
21938632
41.

Analysis of the dynamics of limb transcriptomes during mouse development.

Gyurján I, Sonderegger B, Naef F, Duboule D.

BMC Dev Biol. 2011 Jul 29;11:47. doi: 10.1186/1471-213X-11-47.

42.

Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains.

Bieler J, Pozzorini C, Naef F.

Biophys J. 2011 Jul 20;101(2):287-96. doi: 10.1016/j.bpj.2011.05.060.

43.

Mammalian genes are transcribed with widely different bursting kinetics.

Suter DM, Molina N, Gatfield D, Schneider K, Schibler U, Naef F.

Science. 2011 Apr 22;332(6028):472-4. doi: 10.1126/science.1198817. Epub 2011 Mar 17.

44.

Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver.

Rey G, Cesbron F, Rougemont J, Reinke H, Brunner M, Naef F.

PLoS Biol. 2011 Feb;9(2):e1000595. doi: 10.1371/journal.pbio.1000595. Epub 2011 Feb 22.

45.

ASSET: a robust algorithm for the automated segmentation and standardization of early Caenorhabditis elegans embryos.

Blanchoud S, Budirahardja Y, Naef F, Gönczy P.

Dev Dyn. 2010 Dec;239(12):3285-96. doi: 10.1002/dvdy.22486.

46.

Information processing in cells and tissues (IPCAT'2009): from small scale dynamics to understanding systems behavior.

Egri-Nagy A, Galliot B, Naef F, Nehaniv CL.

Biosystems. 2010 Oct;102(1):1-2. doi: 10.1016/j.biosystems.2010.07.015. Epub 2010 Aug 17. No abstract available.

PMID:
20723577
47.

Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico.

Stoll G, Bischofberger M, Rougemont J, Naef F.

Biosystems. 2010 Oct;102(1):3-10. doi: 10.1016/j.biosystems.2010.07.014. Epub 2010 Jul 22.

PMID:
20655356
48.

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae.

Preti M, Ribeyre C, Pascali C, Bosio MC, Cortelazzi B, Rougemont J, Guarnera E, Naef F, Shore D, Dieci G.

Mol Cell. 2010 May 28;38(4):614-20. doi: 10.1016/j.molcel.2010.04.016.

49.

Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors.

Parisi F, Sonderegger B, Wirapati P, Delorenzi M, Naef F.

BMC Genomics. 2009 Aug 18;10:381. doi: 10.1186/1471-2164-10-381.

50.

Network inference by combining biologically motivated regulatory constraints with penalized regression.

Parisi F, Koeppl H, Naef F.

Ann N Y Acad Sci. 2009 Mar;1158:114-24. doi: 10.1111/j.1749-6632.2008.03751.x.

PMID:
19348637

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