| Year |
Citation |
Score |
| 2022 |
Hurni C, Weger BD, Gobet C, Naef F. Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver. Plos Genetics. 18: e1009903. PMID 35921362 DOI: 10.1371/journal.pgen.1009903 |
0.345 |
|
| 2021 |
Gobet C, Naef F. Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data. Methods (San Diego, Calif.). PMID 34673173 DOI: 10.1016/j.ymeth.2021.10.004 |
0.324 |
|
| 2021 |
Phillips NE, Hugues A, Yeung J, Durandau E, Nicolas D, Naef F. The circadian oscillator analysed at the single-transcript level. Molecular Systems Biology. 17: e10135. PMID 33719202 DOI: 10.15252/msb.202010135 |
0.378 |
|
| 2021 |
Mermet J, Yeung J, Naef F. Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle. Plos Genetics. 17: e1009350. PMID 33524027 DOI: 10.1371/journal.pgen.1009350 |
0.357 |
|
| 2021 |
Weger BD, Gobet C, David FPA, Atger F, Martin E, Phillips NE, Charpagne A, Weger M, Naef F, Gachon F. Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33452134 DOI: 10.1073/pnas.2015803118 |
0.329 |
|
| 2020 |
Talamanca L, Naef F. How to tell time: advances in decoding circadian phase from omics snapshots. F1000research. 9. PMID 33014340 DOI: 10.12688/F1000Research.26759.1 |
0.336 |
|
| 2020 |
Gobet C, Weger BD, Marquis J, Martin E, Neelagandan N, Gachon F, Naef F. Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver. Proceedings of the National Academy of Sciences of the United States of America. PMID 32295881 DOI: 10.1073/Pnas.1918145117 |
0.358 |
|
| 2019 |
Droin C, Paquet ER, Naef F. Low-dimensional Dynamics of Two Coupled Biological Oscillators. Nature Physics. 15: 1086-1094. PMID 32528550 DOI: 10.1038/S41567-019-0598-1 |
0.337 |
|
| 2019 |
Hor CN, Yeung J, Jan M, Emmenegger Y, Hubbard J, Xenarios I, Naef F, Franken P. Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex. Proceedings of the National Academy of Sciences of the United States of America. PMID 31776259 DOI: 10.1073/Pnas.1910590116 |
0.367 |
|
| 2019 |
Tidin O, Friman ET, Naef F, Suter DM. Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells. Scientific Reports. 9: 5372. PMID 30926874 DOI: 10.1038/S41598-019-41870-2 |
0.454 |
|
| 2019 |
Phillips NE, Mandic A, Omidi S, Naef F, Suter DM. Memory and relatedness of transcriptional activity in mammalian cell lineages. Nature Communications. 10: 1208. PMID 30872573 DOI: 10.1038/S41467-019-09189-8 |
0.451 |
|
| 2018 |
Gachon F, Yeung J, Naef F. Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock. Genes & Development. 32: 1359-1360. PMID 30385518 DOI: 10.1101/Gad.320911.118 |
0.377 |
|
| 2018 |
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. The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism. Cell Metabolism. PMID 30344015 DOI: 10.1016/J.Cmet.2018.09.023 |
0.352 |
|
| 2018 |
Yeung J, Naef F. Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior. Trends in Genetics : Tig. PMID 30309754 DOI: 10.1016/J.Tig.2018.09.005 |
0.426 |
|
| 2018 |
Alber AB, Paquet ER, Biserni M, Naef F, Suter DM. Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates. Molecular Cell. PMID 30146318 DOI: 10.1016/J.Molcel.2018.07.023 |
0.35 |
|
| 2018 |
Nicolas D, Zoller B, Suter DM, Naef F. Modulation of transcriptional burst frequency by histone acetylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29915087 DOI: 10.1073/Pnas.1722330115 |
0.402 |
|
| 2018 |
Mermet J, Yeung J, Hurni C, Mauvoisin D, Gustafson K, Jouffe C, Nicolas D, Emmenegger Y, Gobet C, Franken P, Gachon F, Naef F. Clock-dependent chromatin topology modulates circadian transcription and behavior. Genes & Development. PMID 29572261 DOI: 10.1101/Gad.312397.118 |
0.448 |
|
| 2018 |
Wang J, Symul L, Yeung J, Gobet C, Sobel J, Lück S, Westermark PO, Molina N, Naef F. Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver. Proceedings of the National Academy of Sciences of the United States of America. PMID 29432155 DOI: 10.1073/Pnas.1715225115 |
0.726 |
|
| 2017 |
Yeung J, Mermet J, Jouffe C, Marquis J, Charpagne A, Gachon F, Naef F. Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs. Genome Research. PMID 29254942 DOI: 10.1101/Gr.222430.117 |
0.427 |
|
| 2017 |
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, ... ... Naef F, et al. Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms. 748730417728663. PMID 29098954 DOI: 10.1177/0748730417728663 |
0.319 |
|
| 2017 |
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. Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome. Cell Reports. 20: 1729-1743. PMID 28813682 DOI: 10.1016/J.Celrep.2017.07.065 |
0.391 |
|
| 2017 |
Nicolas D, Phillips NE, Naef F. What shapes eukaryotic transcriptional bursting? Molecular Biosystems. PMID 28573295 DOI: 10.1039/C7Mb00154A |
0.463 |
|
| 2017 |
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, et al. Transcriptional regulatory logic of the diurnal cycle in the mouse liver. Plos Biology. 15: e2001069. PMID 28414715 DOI: 10.1371/Journal.Pbio.2001069 |
0.458 |
|
| 2017 |
Sharp B, Paquet E, Naef F, Bafna A, Wijnen H. A new promoter element associated with daily time keeping in Drosophila. Nucleic Acids Research. PMID 28407113 DOI: 10.1093/Nar/Gkx268 |
0.442 |
|
| 2017 |
Gobet C, Naef F. Ribosome profiling and dynamic regulation of translation in mammals. Current Opinion in Genetics & Development. 43: 120-127. PMID 28363112 DOI: 10.1016/J.Gde.2017.03.005 |
0.406 |
|
| 2016 |
Mermet J, Yeung J, Naef F. Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World. Cold Spring Harbor Perspectives in Biology. PMID 27920039 DOI: 10.1101/Cshperspect.A028720 |
0.42 |
|
| 2016 |
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. Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver. Cell Metabolism. PMID 27818260 DOI: 10.1016/J.Cmet.2016.10.003 |
0.424 |
|
| 2016 |
Gotic I, Omidi S, Fleury-Olela F, Molina N, Naef F, Schibler U. Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp. Genes & Development. PMID 27633015 DOI: 10.1101/Gad.287094.116 |
0.728 |
|
| 2016 |
Bischofberger M, Iacovache I, Boss D, Naef F, van der Goot FG, Molina N. Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling. Biophysical Journal. 110: 1574-81. PMID 27074682 DOI: 10.1016/J.Bpj.2016.02.035 |
0.678 |
|
| 2015 |
Atger F, Gobet C, Marquis J, Martin E, Wang J, Weger B, Lefebvre G, Descombes P, Naef F, Gachon F. Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver. Proceedings of the National Academy of Sciences of the United States of America. PMID 26554015 DOI: 10.1073/Pnas.1515308112 |
0.481 |
|
| 2015 |
Zoller B, Nicolas D, Molina N, Naef F. Structure of silent transcription intervals and noise characteristics of mammalian genes. Molecular Systems Biology. 11: 823. PMID 26215071 DOI: 10.15252/Msb.20156257 |
0.752 |
|
| 2015 |
Blanchoud S, Nicolas D, Zoller B, Tidin O, Naef F. CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings. Methods (San Diego, Calif.). 85: 3-11. PMID 25934263 DOI: 10.1016/J.Ymeth.2015.04.023 |
0.427 |
|
| 2014 |
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. Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription. Genes & Development. 28: 1695-709. PMID 25085421 DOI: 10.1101/Gad.244434.114 |
0.403 |
|
| 2014 |
Bieler J, Cannavo R, Gustafson K, Gobet C, Gatfield D, Naef F. Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells. Molecular Systems Biology. 10: 739. PMID 25028488 DOI: 10.15252/Msb.20145218 |
0.361 |
|
| 2014 |
Hoffmann J, Symul L, Shostak A, Fischer T, Naef F, Brunner M. Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells. Plos One. 9: e102238. PMID 25007071 DOI: 10.1371/Journal.Pone.0102238 |
0.495 |
|
| 2014 |
Quinodoz M, Gobet C, Naef F, Gustafson KB. Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biology. 15: R85. PMID 24972996 DOI: 10.1186/Gb-2014-15-6-R85 |
0.462 |
|
| 2014 |
Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM, Herr W, Hernandez N, Delorenzi M, Deplancke B, Desvergne B, Guex N, Naef F, Rougemont J, et al. Quantifying ChIP-seq data: A spiking method providing an internal reference for sample-to-sample normalization Genome Research. 24: 1157-1168. PMID 24709819 DOI: 10.1101/Gr.168260.113 |
0.705 |
|
| 2014 |
Gilardi F, Migliavacca E, Naldi A, Baruchet M, Canella D, Le Martelot G, Guex N, Desvergne B, Delorenzi M, Deplancke B, Herr W, Naef F, Rougemont J, Schibler U, Andersin T, et al. Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals Plos Genetics. 10. PMID 24603613 DOI: 10.1371/journal.pgen.1004155 |
0.734 |
|
| 2014 |
Mauvoisin D, Wang J, Jouffe C, Martin E, Atger F, Waridel P, Quadroni M, Gachon F, Naef F. Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proceedings of the National Academy of Sciences of the United States of America. 111: 167-72. PMID 24344304 DOI: 10.1073/Pnas.1314066111 |
0.409 |
|
| 2013 |
Molina N, Suter DM, Cannavo R, Zoller B, Gotic I, Naef F. Stimulus-induced modulation of transcriptional bursting in a single mammalian gene. Proceedings of the National Academy of Sciences of the United States of America. 110: 20563-8. PMID 24297917 DOI: 10.1073/Pnas.1312310110 |
0.738 |
|
| 2013 |
d'Eysmond T, De Simone A, Naef F. Analysis of precision in chemical oscillators: implications for circadian clocks. Physical Biology. 10: 056005. PMID 24043227 DOI: 10.1088/1478-3975/10/5/056005 |
0.34 |
|
| 2013 |
Dénervaud N, Becker J, Delgado-Gonzalo R, Damay P, Rajkumar AS, Unser M, Shore D, Naef F, Maerkl SJ. A chemostat array enables the spatio-temporal analysis of the yeast proteome. Proceedings of the National Academy of Sciences of the United States of America. 110: 15842-7. PMID 24019481 DOI: 10.1073/Pnas.1308265110 |
0.32 |
|
| 2013 |
Simicevic J, Schmid AW, Gilardoni PA, Zoller B, Raghav SK, Krier I, Gubelmann C, Lisacek F, Naef F, Moniatte M, Deplancke B. Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods. 10: 570-6. PMID 23584187 DOI: 10.1038/Nmeth.2441 |
0.425 |
|
| 2013 |
Jouffe C, Cretenet G, Symul L, Martin E, Atger F, Naef F, Gachon F. The circadian clock coordinates ribosome biogenesis. Plos Biology. 11: e1001455. PMID 23300384 DOI: 10.1371/Journal.Pbio.1001455 |
0.463 |
|
| 2012 |
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, ... ... Naef F, et al. Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. Plos Biology. 10: e1001442. PMID 23209382 DOI: 10.1371/Journal.Pbio.1001442 |
0.449 |
|
| 2012 |
Stratmann M, Suter DM, Molina N, Naef F, Schibler U. Circadian Dbp transcription relies on highly dynamic BMAL1-CLOCK interaction with E boxes and requires the proteasome. Molecular Cell. 48: 277-87. PMID 22981862 DOI: 10.1016/J.Molcel.2012.08.012 |
0.755 |
|
| 2012 |
Morf J, Rey G, Schneider K, Stratmann M, Fujita J, Naef F, Schibler U. Cold-inducible RNA-binding protein modulates circadian gene expression posttranscriptionally. Science (New York, N.Y.). 338: 379-83. PMID 22923437 DOI: 10.1126/Science.1217726 |
0.466 |
|
| 2012 |
Rougemont J, Naef F. Computational analysis of protein-DNA interactions from ChIP-seq data. Methods in Molecular Biology (Clifton, N.J.). 786: 263-73. PMID 21938632 DOI: 10.1007/978-1-61779-292-2_16 |
0.385 |
|
| 2011 |
Suter DM, Molina N, Naef F, Schibler U. Origins and consequences of transcriptional discontinuity. Current Opinion in Cell Biology. 23: 657-62. PMID 21963300 DOI: 10.1016/J.Ceb.2011.09.004 |
0.746 |
|
| 2011 |
Gyurján I, Sonderegger B, Naef F, Duboule D. Analysis of the dynamics of limb transcriptomes during mouse development. Bmc Developmental Biology. 11: 47. PMID 21801425 DOI: 10.1186/1471-213X-11-47 |
0.399 |
|
| 2011 |
Bieler J, Pozzorini C, Naef F. Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains. Biophysical Journal. 101: 287-96. PMID 21767480 DOI: 10.1016/J.Bpj.2011.05.060 |
0.385 |
|
| 2011 |
Suter DM, Molina N, Gatfield D, Schneider K, Schibler U, Naef F. Mammalian genes are transcribed with widely different bursting kinetics. Science (New York, N.Y.). 332: 472-4. PMID 21415320 DOI: 10.1126/Science.1198817 |
0.756 |
|
| 2011 |
Rey G, Cesbron F, Rougemont J, Reinke H, Brunner M, Naef F. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. Plos Biology. 9: e1000595. PMID 21364973 DOI: 10.1371/Journal.Pbio.1000595 |
0.46 |
|
| 2010 |
Stoll G, Bischofberger M, Rougemont J, Naef F. Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico. Bio Systems. 102: 3-10. PMID 20655356 DOI: 10.1016/J.Biosystems.2010.07.014 |
0.311 |
|
| 2010 |
Preti M, Ribeyre C, Pascali C, Bosio MC, Cortelazzi B, Rougemont J, Guarnera E, Naef F, Shore D, Dieci G. The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae. Molecular Cell. 38: 614-20. PMID 20513435 DOI: 10.1016/J.Molcel.2010.04.016 |
0.443 |
|
| 2009 |
Parisi F, Sonderegger B, Wirapati P, Delorenzi M, Naef F. Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors. Bmc Genomics. 10: 381. PMID 19689805 DOI: 10.1186/1471-2164-10-381 |
0.371 |
|
| 2009 |
Parisi F, Koeppl H, Naef F. Network inference by combining biologically motivated regulatory constraints with penalized regression. Annals of the New York Academy of Sciences. 1158: 114-24. PMID 19348637 DOI: 10.1111/J.1749-6632.2008.03751.X |
0.315 |
|
| 2009 |
Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biology. 10: R17. PMID 19210792 DOI: 10.1186/Gb-2009-10-2-R17 |
0.443 |
|
| 2009 |
Dibner C, Sage D, Unser M, Bauer C, d'Eysmond T, Naef F, Schibler U. Circadian gene expression is resilient to large fluctuations in overall transcription rates. The Embo Journal. 28: 123-34. PMID 19078963 DOI: 10.1038/Emboj.2008.262 |
0.49 |
|
| 2008 |
Rougemont J, Naef F. Stochastic phase oscillator models for circadian clocks. Advances in Experimental Medicine and Biology. 641: 141-9. PMID 18783177 DOI: 10.1007/978-0-387-09794-7_10 |
0.35 |
|
| 2008 |
Sauvain MO, Dorr AP, Stevenson B, Quazzola A, Naef F, Wiznerowicz M, Schütz F, Jongeneel V, Duboule D, Spitz F, Trono D. Genotypic features of lentivirus transgenic mice. Journal of Virology. 82: 7111-9. PMID 18463153 DOI: 10.1128/Jvi.00623-08 |
0.341 |
|
| 2008 |
Paquet ER, Rey G, Naef F. Modeling an evolutionary conserved circadian cis-element. Plos Computational Biology. 4: e38. PMID 18282089 DOI: 10.1371/Journal.Pcbi.0040038 |
0.415 |
|
| 2007 |
Rougemont J, Naef F. Stochastic phase oscillators and circadian bioluminescence recordings. Cold Spring Harbor Symposia On Quantitative Biology. 72: 405-11. PMID 18419298 DOI: 10.1101/Sqb.2007.72.044 |
0.347 |
|
| 2007 |
Boothroyd CE, Wijnen H, Naef F, Saez L, Young MW. Integration of light and temperature in the regulation of circadian gene expression in Drosophila. Plos Genetics. 3: e54. PMID 17411344 DOI: 10.1371/Journal.Pgen.0030054 |
0.403 |
|
| 2007 |
Rougemont J, Naef F. Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks. Molecular Systems Biology. 3: 93. PMID 17353935 DOI: 10.1038/Msb4100130 |
0.352 |
|
| 2007 |
Parisi F, Wirapati P, Naef F. Identifying synergistic regulation involving c-Myc and sp1 in human tissues. Nucleic Acids Research. 35: 1098-107. PMID 17264126 DOI: 10.1093/Nar/Gkl1157 |
0.374 |
|
| 2006 |
Retelska D, Iseli C, Bucher P, Jongeneel CV, Naef F. Similarities and differences of polyadenylation signals in human and fly. Bmc Genomics. 7: 176. PMID 16836751 DOI: 10.1186/1471-2164-7-176 |
0.328 |
|
| 2006 |
Wijnen H, Naef F, Boothroyd C, Claridge-Chang A, Young MW. Control of daily transcript oscillations in Drosophila by light and the circadian clock. Plos Genetics. 2: e39. PMID 16565745 DOI: 10.1371/Journal.Pgen.0020039 |
0.399 |
|
| 2006 |
Lim DA, Suárez-Fariñas M, Naef F, Hacker CR, Menn B, Takebayashi H, Magnasco M, Patil N, Alvarez-Buylla A. In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis. Molecular and Cellular Neurosciences. 31: 131-48. PMID 16330219 DOI: 10.1016/J.Mcn.2005.10.005 |
0.727 |
|
| 2006 |
Naef F, Wijnen H, Magnasco M. Reply to "comment on 'Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays'" Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 73. DOI: 10.1103/Physreve.73.063902 |
0.575 |
|
| 2005 |
Naef F. Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria. Molecular Systems Biology. 1: 2005.0019. PMID 16729054 DOI: 10.1038/Msb4100027 |
0.413 |
|
| 2005 |
Naef F, Huelsken J. Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks. Nucleic Acids Research. 33: e111. PMID 16030348 DOI: 10.1093/Nar/Gni104 |
0.38 |
|
| 2005 |
Gardner TJ, Naef F, Nottebohm F. Freedom and rules: the acquisition and reprogramming of a bird's learned song. Science (New York, N.Y.). 308: 1046-9. PMID 15890887 DOI: 10.1126/Science.1108214 |
0.44 |
|
| 2005 |
Wijnen H, Naef F, Young MW. Molecular and statistical tools for circadian transcript profiling. Methods in Enzymology. 393: 341-65. PMID 15817298 DOI: 10.1016/S0076-6879(05)93015-2 |
0.357 |
|
| 2005 |
Schibler U, Naef F. Cellular oscillators: rhythmic gene expression and metabolism. Current Opinion in Cell Biology. 17: 223-9. PMID 15780601 DOI: 10.1016/J.Ceb.2005.01.007 |
0.414 |
|
| 2004 |
Nagoshi E, Saini C, Bauer C, Laroche T, Naef F, Schibler U. Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell. 119: 693-705. PMID 15550250 DOI: 10.1016/J.Cell.2004.11.015 |
0.402 |
|
| 2003 |
Asmal M, Colgan J, Naef F, Yu B, Lee Y, Magnasco M, Luban J. Production of ribosome components in effector CD4+ T cells is accelerated by TCR stimulation and coordinated by ERK-MAPK. Immunity. 19: 535-48. PMID 14563318 DOI: 10.1016/S1074-7613(03)00268-1 |
0.619 |
|
| 2003 |
Naef F, Magnasco MO. Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 68: 011906. PMID 12935175 DOI: 10.1103/Physreve.68.011906 |
0.596 |
|
| 2003 |
Sato N, Sanjuan IM, Heke M, Uchida M, Naef F, Brivanlou AH. Molecular signature of human embryonic stem cells and its comparison with the mouse. Developmental Biology. 260: 404-13. PMID 12921741 DOI: 10.1016/S0012-1606(03)00256-2 |
0.312 |
|
| 2003 |
Hekstra D, Taussig AR, Magnasco M, Naef F. Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Research. 31: 1962-8. PMID 12655013 DOI: 10.1093/Nar/Gkg283 |
0.61 |
|
| 2003 |
Naef F, Socci ND, Magnasco M. A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations. Bioinformatics (Oxford, England). 19: 178-84. PMID 12538237 DOI: 10.1093/Bioinformatics/19.2.178 |
0.621 |
|
| 2002 |
Naef F, Lim DA, Patil N, Magnasco M. DNA hybridization to mismatched templates: a chip study. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 040902. PMID 12005798 DOI: 10.1103/Physreve.65.040902 |
0.619 |
|
| 2002 |
Naef F, Hacker CR, Patil N, Magnasco M. Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biology. 3: RESEARCH0018. PMID 11983059 DOI: 10.1186/Gb-2002-3-4-Research0018 |
0.601 |
|
| 2002 |
Naef F, Hacker CR, Patil N, Magnasco M. Characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biology. 3: PREPRINT0001. PMID 11806820 |
0.566 |
|
| 2002 |
Naef F, Lim DA, Patil N, Magnasco M. DNA hybridization to mismatched templates: A chip study Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 65: 040902/1-040902/4. DOI: 10.1103/PhysRevE.65.040902 |
0.52 |
|
| 2001 |
Claridge-Chang A, Wijnen H, Naef F, Boothroyd C, Rajewsky N, Young MW. Circadian regulation of gene expression systems in the Drosophila head. Neuron. 32: 657-71. PMID 11719206 DOI: 10.1016/S0896-6273(01)00515-3 |
0.448 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2006 |
Stoll G, Rougemont J, Naef F. Few crucial links assure checkpoint efficiency in the yeast cell-cycle network. Bioinformatics (Oxford, England). 22: 2539-46. PMID 16895923 DOI: 10.1093/Bioinformatics/Btl432 |
0.298 |
|
| 2006 |
Ben-Haim N, Lu C, Guzman-Ayala M, Pescatore L, Mesnard D, Bischofberger M, Naef F, Robertson EJ, Constam DB. The nodal precursor acting via activin receptors induces mesoderm by maintaining a source of its convertases and BMP4. Developmental Cell. 11: 313-23. PMID 16950123 DOI: 10.1016/J.Devcel.2006.07.005 |
0.297 |
|
| 2015 |
Blanchoud S, Busso C, Naef F, Gönczy P. Quantitative analysis and modeling probe polarity establishment in C. elegans embryos. Biophysical Journal. 108: 799-809. PMID 25692585 DOI: 10.1016/J.Bpj.2014.12.022 |
0.289 |
|
| 2009 |
Bénazet JD, Bischofberger M, Tiecke E, Gonçalves A, Martin JF, Zuniga A, Naef F, Zeller R. A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning. Science (New York, N.Y.). 323: 1050-3. PMID 19229034 DOI: 10.1126/Science.1168755 |
0.285 |
|
| 2007 |
Stoll G, Rougemont J, Naef F. Representing perturbed dynamics in biological network models. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 011917. PMID 17677504 DOI: 10.1103/Physreve.76.011917 |
0.284 |
|
| 2010 |
Blanchoud S, Budirahardja Y, Naef F, Gönczy P. ASSET: a robust algorithm for the automated segmentation and standardization of early Caenorhabditis elegans embryos. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 239: 3285-96. PMID 21089077 DOI: 10.1002/Dvdy.22486 |
0.276 |
|
| 2019 |
Manfrin A, Tabata Y, Paquet ER, Vuaridel AR, Rivest FR, Naef F, Lutolf MP. Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells. Nature Methods. 16: 640-648. PMID 31249412 DOI: 10.1038/S41592-019-0455-2 |
0.275 |
|
| 2020 |
Neelagandan N, Lamberti I, Carvalho HJF, Gobet C, Naef F. What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis. Open Biology. 10: 200292. PMID 33292102 DOI: 10.1098/rsob.200292 |
0.275 |
|
| 2023 |
Talamanca L, Gobet C, Naef F. Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans. Science (New York, N.Y.). 379: 478-483. PMID 36730411 DOI: 10.1126/science.add0846 |
0.264 |
|
| 2006 |
Rougemont J, Naef F. Collective synchronization in populations of globally coupled phase oscillators with drifting frequencies. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 73: 011104. PMID 16486119 DOI: 10.1103/Physreve.73.011104 |
0.262 |
|
| 2008 |
Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F. Probabilistic base calling of Solexa sequencing data. Bmc Bioinformatics. 9: 431. PMID 18851737 DOI: 10.1186/1471-2105-9-431 |
0.261 |
|
| 2021 |
Droin C, Kholtei JE, Bahar Halpern K, Hurni C, Rozenberg M, Muvkadi S, Itzkovitz S, Naef F. Space-time logic of liver gene expression at sub-lobular scale. Nature Metabolism. PMID 33432202 DOI: 10.1038/s42255-020-00323-1 |
0.26 |
|
| 2021 |
Abruzzi KC, Gobet C, Naef F, Rosbash M. Comment on "Circadian rhythms in the absence of the clock gene ". Science (New York, N.Y.). 372. PMID 33859000 DOI: 10.1126/science.abf0922 |
0.247 |
|
| 2018 |
Floriancic MG, Meerveld Iv, Smoorenburg M, Margreth M, Naef F, Kirchner JW, Molnar P. Spatio‐temporal variability in contributions to low flows in the high Alpine Poschiavino catchment Hydrological Processes. 32: 3938-3953. DOI: 10.1002/Hyp.13302 |
0.245 |
|
| 2010 |
Egri-Nagy A, Galliot B, Naef F, Nehaniv CL. Information processing in cells and tissues (IPCAT'2009): from small scale dynamics to understanding systems behavior. Bio Systems. 102: 1-2. PMID 20723577 DOI: 10.1016/J.Biosystems.2010.07.015 |
0.244 |
|
| 2005 |
Fishilevich E, Domingos AI, Asahina K, Naef F, Vosshall LB, Louis M. Chemotaxis behavior mediated by single larval olfactory neurons in Drosophila. Current Biology : Cb. 15: 2086-96. PMID 16332533 DOI: 10.1016/J.Cub.2005.11.016 |
0.231 |
|
| 2002 |
Naef F, Scherrer S, Weiler M. A process based assessment of the potential to reduce flood runoff by land use change Journal of Hydrology. 267: 74-79. DOI: 10.1016/S0022-1694(02)00141-5 |
0.218 |
|
| 1997 |
Zotos X, Naef F, Prelovšek P. Transport and conservation laws Physical Review B - Condensed Matter and Materials Physics. 55: 11029-11032. DOI: 10.1103/Physrevb.55.11029 |
0.214 |
|
| 2000 |
Naef F, Wang X. Nuclear spin relaxation rates in two-Leg spin ladders Physical Review Letters. 84: 1320-3. PMID 11017508 DOI: 10.1103/Physrevlett.84.1320 |
0.213 |
|
| 2003 |
Scherrer S, Naef F. A decision scheme to indicate dominant hydrological flow processes on temperate grassland Hydrological Processes. 17: 391-401. DOI: 10.1002/Hyp.1131 |
0.206 |
|
| 2000 |
Zotos X, Naef F, Long M, Prelovsek P. Reactive hall response Physical Review Letters. 85: 377-80. PMID 10991287 DOI: 10.1103/Physrevlett.85.377 |
0.205 |
|
| 2002 |
Bourdon V, Naef F, Rao PH, Reuter V, Mok SC, Bosl GJ, Koul S, Murty VV, Kucherlapati RS, Chaganti RS. Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes. Cancer Research. 62: 6218-23. PMID 12414650 |
0.192 |
|
| 2010 |
D'Eysmond T, Naef F. Systems biology and modeling of circadian rhythms Protein Reviews. 12: 283-293. DOI: 10.1007/978-1-4419-1262-6-11 |
0.138 |
|
| 2023 |
Martini T, Naef F, Tchorz JS. Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology. Annual Review of Pathology. 18: 439-466. PMID 36693201 DOI: 10.1146/annurev-pathmechdis-031521-024831 |
0.129 |
|
| 2024 |
Lederer AR, Leonardi M, Talamanca L, Herrera A, Droin C, Khven I, Carvalho HJF, Valente A, Mantes AD, Arabí PM, Pinello L, Naef F, Manno G. Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. Biorxiv : the Preprint Server For Biology. PMID 38328127 DOI: 10.1101/2024.01.18.576093 |
0.12 |
|
| 2023 |
Phillips NE, Collet TH, Naef F. Uncovering personalized glucose responses and circadian rhythms from multiple wearable biosensors with Bayesian dynamical modeling. Cell Reports Methods. 3: 100545. PMID 37671030 DOI: 10.1016/j.crmeth.2023.100545 |
0.119 |
|
| 1991 |
Naef F, Bezzola GR. Hydrology and morphological consequences of the 1987 flood event in the upper Reuss valley . |
0.115 |
|
| 2002 |
Naef F. How often do extreme events occur? Iahs-Aish Publication. 65-70. |
0.113 |
|
| 2008 |
Kienzier PM, Naef F. Temporal variability of subsurface stormflow formation Hydrology and Earth System Sciences. 12: 257-265. |
0.113 |
|
| 1997 |
Faeh AO, Scherrer S, Naef F. A combined field and numerical approach to investigate flow processes in natural macroporous soils under extreme precipitation Hydrology and Earth System Sciences. 1: 787-800. |
0.11 |
|
| 2010 |
Schmocker-Fackel P, Naef F. More frequent flooding? Changes in flood frequency in Switzerland since 1850 Journal of Hydrology. 381: 1-8. DOI: 10.1016/j.jhydrol.2009.09.022 |
0.101 |
|
| 2000 |
Naef F, Kull D, Thoma C. How do floodplains influence the discharge of extreme floods? Pik Report. 628-636. |
0.101 |
|
| 2010 |
Schmocker-Fackel P, Naef F. Changes in flood frequencies in Switzerland since 1500 Hydrology and Earth System Sciences. 14: 1581-1594. DOI: 10.5194/hess-14-1581-2010 |
0.1 |
|
| 1989 |
Naef F. Hydrology of the Bodensee and its tributaries | Hydrologie des Bodensees und seiner Zuflusse Mensuration, Photogrammetrie, Genie Rural. 1: 15-17. |
0.097 |
|
| 1998 |
Weiler M, Naef F, Leibungut C. Study of runoff generation on hillslopes using tracer experiments and a physically-based numerical hillslope model Iahs-Aish Publication. 248: 353-360. |
0.096 |
|
| 1990 |
Naef F. Assessing changes of hydrological regime on the basis of present-day hydrological data The Hydrological Basis For Water Resources Management. Proc. Symposium, Beijing, 1990. 387-394. |
0.094 |
|
| 1981 |
Naef F. Can we model the rainfall-runoff process today? Hydrological Sciences Bulletin. 26: 281-289. DOI: 10.1080/02626668109490887 |
0.093 |
|
| 1966 |
Spreafico M, Naef F. Observation and analysis of flood discharges - experiences from Switzerland . |
0.087 |
|
| 2021 |
Phillips NE, Mareschal J, Schwab N, Manoogian ENC, Borloz S, Ostinelli G, Gauthier-Jaques A, Umwali S, Rodriguez EG, Aeberli D, Hans D, Panda S, Rodondi N, Naef F, Collet TH. The Effects of Time-Restricted Eating versus Standard Dietary Advice on Weight, Metabolic Health and the Consumption of Processed Food: A Pragmatic Randomised Controlled Trial in Community-Based Adults. Nutrients. 13. PMID 33807102 DOI: 10.3390/nu13031042 |
0.087 |
|
| 1999 |
Naef F, Wang X, Zotos X, Von Der Linden W. Autocorrelations from the transfer-matrix density-matrix renormalization-group method Physical Review B - Condensed Matter and Materials Physics. 60: 359-368. |
0.087 |
|
| 1999 |
Weiler M, Scherrer S, Naef F, Burlando P. Hydrograph separation of runoff components based on measuring hydraulic state variables, tracer experiments, and weighting methods Iahs-Aish Publication. 249-255. |
0.085 |
|
| 2000 |
Weiler M, Scherer S, Thoma C, Fackel P, Naef F. The potential to influence runoff processes by changes in land use Pik Report. 286-294. |
0.083 |
|
| 2007 |
Schmocker-Fackel P, Naef F, Scherrer S. Identifying runoff processes on the plot and catchment scale Hydrology and Earth System Sciences. 11: 891-906. |
0.078 |
|
| 2022 |
Li TY, Gao AW, Li X, Li H, Liu YJ, Lalou A, Neelagandan N, Naef F, Schoonjans K, Auwerx J. V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans. The Journal of Cell Biology. 222. PMID 36314986 DOI: 10.1083/jcb.202205045 |
0.075 |
|
| 2007 |
Scherrer S, Naef F, Fach AO, Cordery I. Formation of runoff at the hillslope scale during intense precipitation Hydrology and Earth System Sciences. 11: 907-922. |
0.075 |
|
| 1984 |
Naef FE. ARTIFICIAL INTELLIGENCE EXPERT PROGRAM FOR A RESTRICTED MEMORY MICROCOMPUTER Proceedings - Ieee Computer Society International Conference. 4-10. |
0.062 |
|
| 2004 |
Naef FH, Sener B, Bürgi-Tiedemann C, Schmidlin PR. [Calculus removal efficiency and injury potential of vertically oscillating metallic and carbon ultrasonic tips]. Schweizer Monatsschrift FüR Zahnmedizin = Revue Mensuelle Suisse D'Odonto-Stomatologie = Rivista Mensile Svizzera Di Odontologia E Stomatologia / Sso. 114: 1116-23. PMID 15587598 |
0.061 |
|
| 1990 |
Faeh R, Koella E, Naef F. The flood in the Reuss valley in August 1987: a computer aided reconstruction of a flood in a mountainous region International Conference On River Flood Hydraulics. Wallingford, 1990. 65-74. |
0.06 |
|
| 2004 |
Giersch W, Naef F. γ,δ- and δ,ε-unsaturated aldehydes from γ- and δ-lactones in one step: Preliminary communication Helvetica Chimica Acta. 87: 1697-1703. DOI: 10.1002/hlca.200490153 |
0.059 |
|
| 2008 |
Kienzler PM, Naef F. Subsurface storm flow formation at different hillslopes and implications for the 'old water paradox' Hydrological Processes. 22: 104-116. DOI: 10.1002/hyp.6687 |
0.053 |
|
| 1988 |
Naef F, Haeberli W, Jaggi M, Rickenmann D. Morphological changes in the Swiss Alps as a result of the summer 1987 storms Oesterr. Wasserwirtsch.. 40: 134-138. |
0.049 |
|
| 1975 |
TRIMBLE LC, NAEF FE. OCEAN THERMAL ENERGY CONVERSION Proc. 7th Annual Offshore Technol. Conf. (Houston, Texas). 2: MAY 5-8, 1975. |
0.048 |
|
| 2003 |
Weiler M, Naef F. Simulating surface and subsurface initiation of macropore flow Journal of Hydrology. 273: 139-154. DOI: 10.1016/S0022-1694(02)00361-X |
0.045 |
|
| 1980 |
Naef FE, Burwell DN. Mini-OTEC results . |
0.042 |
|
| 1990 |
Naef F, Horat P, Milnes AG, Hoehn E. Anomalous hydrological behaviour of an Alpine stream (Varuna, Poschiavo, southern Switzerland) and its interpretation in terms of the geology of the catchment Hydrology in Mountainous Regions Ii. 347-354. |
0.042 |
|
| 2003 |
Weiler M, Naef F. An experimental tracer study of the role of macropores in infiltration in grassland soils Hydrological Processes. 17: 477-493. DOI: 10.1002/hyp.1136 |
0.041 |
|
| 2004 |
Giersch W, Naef F. Unsymmetrical unsaturated ketones from lactones and carboxylic acids in one step Helvetica Chimica Acta. 87: 1704-1710. DOI: 10.1002/hlca.200490154 |
0.04 |
|
| 2012 |
Lones MA, Smith SL, Teichmann S, Naef F, Walker JA, Trefzer MA. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7223: V-VI. |
0.032 |
|
| 1998 |
Naef F, Zotos X. Spin and energy correlations in the one dimensional spin-1/2 Heisenberg model Journal of Physics Condensed Matter. 10: L183-L190. DOI: 10.1088/0953-8984/10/12/001 |
0.027 |
|
| 1986 |
Naef F, Decorzant R. Grignard and hydride addition to a ketene intermediate: a novel access to α-damascone and α-cyclocitral Tetrahedron. 42: 3245-3250. DOI: 10.1016/S0040-4020(01)87388-9 |
0.027 |
|
| 1974 |
Naef F, Ohloff G. A short stereoselective total synthesis of racemic patchouli alcohol: preliminary communication Helvetica Chimica Acta. 57: 1868-1870. |
0.025 |
|
| 2009 |
Van Der Loo B, Naef F, Spring S, Rousson V, Amann-Vesti B, Koppensteiner R. Lack of major gender-related differences in patients undergoing elective endovascular or surgical repair of abdominal aortic aneurysm. International Angiology : a Journal of the International Union of Angiology. 28: 50-5. PMID 19190556 |
0.024 |
|
| 2008 |
Tetzlaff D, McDonnell JJ, Uhlenbrook S, McGuire KJ, Bogaart PW, Naef F, Baird AJ, Dunn SM, Soulsby C. Conceptualizing catchment processes: Simply too complex? Hydrological Processes. 22: 1727-1730. DOI: 10.1002/Hyp.7069 |
0.019 |
|
| 2015 |
Naef F, Grace S, Crowley-McHattan Z, Hardy D, McLeod A. The effect of chronic shoulder pain on maximal force of shoulder abduction. Journal of Bodywork and Movement Therapies. 19: 410-6. PMID 26118510 DOI: 10.1016/j.jbmt.2014.08.005 |
0.012 |
|
| 2012 |
Schmocker-Fackel P, Naef F. Floods in Switzerland Iahs-Aish Publication. 335-343. |
0.01 |
|
| 1993 |
Naef F. Hans M. Keller Hydrological Sciences Journal. 38: 567-568. DOI: 10.1080/02626669309492708 |
0.01 |
|
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