Felix Naef - Publications

Affiliations: 
2001-2003 EPF Lausanne, Lausanne, Vaud, Switzerland 

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2002 Naef F. How often do extreme events occur? Iahs-Aish Publication. 65-70.  1
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  1
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  1
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  1
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.  1
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  1
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