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Boothroyd, C. E., Wijnen, H., Naef, F., Saez, L., and Young, M. W. (2007). Integration of Light and Temperature in the Regulation of Circadian Gene Expression in Drosophila. PLoS Genet 3, e54. Abstract
Parisi, F., Wirapati, P., and Naef, F. (2007). Identifying synergistic regulation involving c-Myc and sp1 in human tissues. Nucleic Acids Res 35, 1098-1107. Abstract
Rougemont, J., and Naef, F. (2007). Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks. Mol Syst Biol 3, Article 93. Abstract
Stoll, G., Rougemont, J., and Naef, F. (2007). Representing perturbed dynamics in biological network models. Phys Rev E Stat Nonlin Soft Matter Phys 76, 011917. Abstract
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Ben-Haim, N., Lu, C., Guzman-Ayala, M., Pescatore, L., Mesnard, D., Bischofberger, M., Naef, F., Robertson, E. J., and Constam, D. B. (2006). The nodal precursor acting via activin receptors induces mesoderm by maintaining a source of its convertases and BMP4. Dev Cell 11, 313-323. Abstract
Lim, D. A., Suarez-Farinas, M., Naef, F., Hacker, C. R., Menn, B., Takebayashi, H., Magnasco, M., Patil, N., and Alvarez-Buylla, A. (2006). In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis. Mol Cell Neurosci 31, 131-148. Abstract
Naef, F., Wijnen, H., and Magnasco, M. (2006). Reply to "Comment on 'Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays'". Phys Rev E Stat Nonlin Soft Matter Phys 73, 063902. Abstract
Retelska, D., Iseli, C., Bucher, P., Jongeneel, C. V., and Naef, F. (2006). Similarities and differences of polyadenylation signals in human and fly. BMC Genomics 7, 176. Abstract
Rougemont, J., and Naef, F. (2006). Collective synchronization in populations of globally coupled phase oscillators with drifting frequencies. Phys Rev E Stat Nonlin Soft Matter Phys 73, 011104. Abstract
Stoll, G., Rougemont, J., and Naef, F. (2006). Few crucial links assure checkpoint efficiency in the yeast cell-cycle network. Bioinformatics 22, 2539-2546. Abstract
Wijnen, H., Naef, F., Boothroyd, C., Claridge-Chang, A., and Young, M. W. (2006). Control of daily transcript oscillations in Drosophila by light and the circadian clock. PLoS Genet 2, e39. Abstract
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Fishilevich, E., Domingos, A. I., Asahina, K., Naef, F., Vosshall, L. B. , and Louis, M. (2005). Chemotaxis behavior mediated by single larval olfactory neurons in Drosophila. Curr Biol 15, 2086-2096. Abstract
Gardner, T. J., Naef, F. , and Nottebohm, F. (2005). Freedom and rules: the acquisition and reprogramming of a bird's learned song. Science 308, 1046-1049. Abstract
Naef, F. , and Huelsken, J. (2005). Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks. Nucleic Acids Res 33, e111. Abstract
Schibler, U. , and Naef, F. (2005). Cellular oscillators: rhythmic gene expression and metabolism. Curr Opin Cell Biol 17, 223-229. Abstract
Wijnen, H., Naef, F. , and Young, M. W. (2005). Molecular and statistical tools for circadian transcript profiling. Methods Enzymol 393, 341-365. Abstract
Naef, F. (2005). Circadian clocks go in vitro : purely post-translational oscillators in cyanobacteria. Molecular Systems Biology, msb4100027, E1-E5. Full Text
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Nagoshi, E., Saini, C., Bauer, C., Laroche, T., Naef, F., and Schibler, U. (2004). Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell 119, 693-705. Abstract
Naef, F., Stoll, G. (2004) Effects of perturbations on dynamical properties of biological networks. In : CompBioNets 2004, Recife, December 15-18 2004, Vol 3 : Algorithms and computational methods for biochemical and evolutionary networks, 115-126.
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Naef, F., Socci, N., and Magnasco, M. (2003). A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations. Bioinformatics 19, 178-184. Abstract
Hekstra, D., Taussig, A.R., Magnasco, M., Naef, F. (2003). Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res. 31, 1962-1968. Abstract
Naef, F., and Magnasco, M. (2003). Solving the riddle of the bright mismatches: the physics of hybridization. Phys. Rev. E68, 011906. Abstract
Sato, N., Munoz Sanjuan, I., Heke, M., Uchida, M., Naef, F., and Brivanlou, A.H. (2003). Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev. Biol. 260, 404-413. Abstract
Asmal, M., Colgan, J., Naef, F., Yu, B., Lee, Y., Magnasco, M., Luban, J. (2003). Production of ribosome components in effector CD4+ T cells is accelerated by TCR stimulation and coordinated by ERK MAPK. Immunity 19, 535-548. Abstract
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Naef, F., Hacker, C., Patil, N., and Magnasco, M. (2002). Characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol. 3, RESEARCH0018. Abstract
Naef, F., Lim, D.A., Patil, N., and Magnasco, M. (2002). DNA hybridization to mismatched templates: a chip study. Phys. Rev. E 65, 040902. Abstract
Bourdon, V., Naef, F., Rao, P.H., Reuter, V., Mok, S., Bosl, G.J., Koul, S., Murty, V.V.V.S., Kucherlapati, R., and Chaganti, R.S.K. (2002). Genomic and expression analysis of the 12p11 p12 amplicon using EST arrays identifies two novelamplified and over-expressed genes. Cancer Res. 62, 6218-6223. Abstract
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