Felix Naef

Summary

Affiliation: The Rockefeller University
Country: USA

Publications

  1. ncbi request reprint Characterization of the expression ratio noise structure in high-density oligonucleotide arrays
    Felix Naef
    Mathematical Physics Laboratory, Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Ave, NY 10021, USA
    Genome Biol 3:PREPRINT0001. 2002
  2. pmc Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays
    Felix Naef
    Mathematical Physics Laboratory, Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Ave, NY 10021, USA
    Genome Biol 3:RESEARCH0018. 2002
  3. ncbi request reprint A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations
    Felix Naef
    Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, NY 10021, USA
    Bioinformatics 19:178-84. 2003
  4. pmc Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays
    Doeke Hekstra
    Center for Studies in Physics and Biology, Laboratory of Mathematical Physics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 31:1962-8. 2003
  5. ncbi request reprint DNA hybridization to mismatched templates: a chip study
    Felix Naef
    Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 65:040902. 2002
  6. ncbi request reprint Molecular and statistical tools for circadian transcript profiling
    Herman Wijnen
    Laboratory of Genetics, The Rockefeller University, New York, New York 10021, USA
    Methods Enzymol 393:341-65. 2005
  7. ncbi request reprint Chemotaxis behavior mediated by single larval olfactory neurons in Drosophila
    Elane Fishilevich
    Laboratory of Neurogenetics and Behavior, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Curr Biol 15:2086-96. 2005
  8. ncbi request reprint Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays
    Felix Naef
    Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 68:011906. 2003
  9. ncbi request reprint Molecular signature of human embryonic stem cells and its comparison with the mouse
    Noboru Sato
    Laboratory of Vertebrate Molecular Embryology, The Rockefeller University, 1230, York Avenue, New York, NY 10021, USA
    Dev Biol 260:404-13. 2003
  10. pmc Modeling an evolutionary conserved circadian cis-element
    Eric R Paquet
    Swiss Institute of Bioinformatics SIB, Lausanne, Switzerland
    PLoS Comput Biol 4:e38. 2008

Collaborators

Detail Information

Publications15

  1. ncbi request reprint Characterization of the expression ratio noise structure in high-density oligonucleotide arrays
    Felix Naef
    Mathematical Physics Laboratory, Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Ave, NY 10021, USA
    Genome Biol 3:PREPRINT0001. 2002
    ..Both the PM (Perfect Match) probes and PM-MM differentials (MM is the single MisMatch) are considered as raw intensities. We then characterize the log-ratio noise structure using robust estimates of their intensity dependent variance...
  2. pmc Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays
    Felix Naef
    Mathematical Physics Laboratory, Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Ave, NY 10021, USA
    Genome Biol 3:RESEARCH0018. 2002
    ..We undertake an empirical characterization of the experimental repeatability of results by carrying out statistical analysis of a large number of duplicate HDONA experiments...
  3. ncbi request reprint A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations
    Felix Naef
    Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, NY 10021, USA
    Bioinformatics 19:178-84. 2003
    ..Given a certain transcript concentration, it is of particular interest to know whether current analysis methods are capable of detecting differential expression ratios of 2 or higher...
  4. pmc Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays
    Doeke Hekstra
    Center for Studies in Physics and Biology, Laboratory of Mathematical Physics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 31:1962-8. 2003
    ..Additionally, by accounting for chemical saturation, we substantially reduce the compressive bias of differential expression estimates that normally occurs toward high concentrations...
  5. ncbi request reprint DNA hybridization to mismatched templates: a chip study
    Felix Naef
    Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 65:040902. 2002
    ..Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and suggest estimators for the target RNA concentration...
  6. ncbi request reprint Molecular and statistical tools for circadian transcript profiling
    Herman Wijnen
    Laboratory of Genetics, The Rockefeller University, New York, New York 10021, USA
    Methods Enzymol 393:341-65. 2005
    ..Both comparative and temporal study designs are discussed, and their use in circadian research is illustrated with examples. Data analysis methods to assess periodic components in time series data are outlined in detail...
  7. ncbi request reprint Chemotaxis behavior mediated by single larval olfactory neurons in Drosophila
    Elane Fishilevich
    Laboratory of Neurogenetics and Behavior, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Curr Biol 15:2086-96. 2005
    ..The extent to which a single OR contributes to chemotaxis behavior is not known. We investigated this question in Drosophila larvae, which represent a powerful genetic system to analyze the contribution of individual OSNs to odor coding...
  8. ncbi request reprint Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays
    Felix Naef
    Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 68:011906. 2003
    ..A simple model for the binding of labeled oligonucleotides sheds light on the interplay between binding energies and labeling probability...
  9. ncbi request reprint Molecular signature of human embryonic stem cells and its comparison with the mouse
    Noboru Sato
    Laboratory of Vertebrate Molecular Embryology, The Rockefeller University, 1230, York Avenue, New York, NY 10021, USA
    Dev Biol 260:404-13. 2003
    ....
  10. pmc Modeling an evolutionary conserved circadian cis-element
    Eric R Paquet
    Swiss Institute of Bioinformatics SIB, Lausanne, Switzerland
    PLoS Comput Biol 4:e38. 2008
    ..Finally, a deeper phylogenetic analysis reveals that the link between the CLOCK/BMAL1 complex and the circadian cis-element dates back to before insects and vertebrates diverged...
  11. pmc Integration of light and temperature in the regulation of circadian gene expression in Drosophila
    Catharine E Boothroyd
    Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
    PLoS Genet 3:e54. 2007
    ..Taken together, these findings suggest that information from both light and temperature is integrated by the transcriptional clock mechanism in the adult fly head...
  12. pmc Identifying synergistic regulation involving c-Myc and sp1 in human tissues
    Fabio Parisi
    Swiss Institute for Experimental Cancer Research ISREC and NCCR Molecular Oncology, Lausanne, Switzerland
    Nucleic Acids Res 35:1098-107. 2007
    ..Our approach shows how integrated functional analyses can uncover tissue-specific and combinatorial regulatory dependencies in mammals...
  13. pmc Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
    Felix Naef
    Swiss Institute for Experimental Cancer Research ISREC, NCCR Molecular Oncology Chemin des Boveresses 155, 1066 Epalinges, Switzerland
    Nucleic Acids Res 33:e111. 2005
    ..This approach can be applied to xenograft models studying tumor-host interactions, morphogenesis or immune responses...
  14. ncbi request reprint Cellular oscillators: rhythmic gene expression and metabolism
    Ueli Schibler
    Department of Molecular Biology and NCCR Frontiers in Genetics, Sciences III, University of Geneva, 30, Quai Ernest Ansermet, CH 1211 Geneva 4, Switzerland
    Curr Opin Cell Biol 17:223-9. 2005
    ..Circadian oscillators and the ultradian yeast respiratory clock share at least four properties: they follow limit-cycle kinetics, interweave with cellular metabolism, are temperature-compensated and influence the cell division clock...
  15. ncbi request reprint Stochastic phase oscillator models for circadian clocks
    Jacques Rougemont
    Swiss Institute of Bioinformatics, Lausanne, Switzerland
    Adv Exp Med Biol 641:141-9. 2008