534 citations · 1k across the 11 of their papers we have counts for
11 papers
Representing perturbed dynamics in biological network models
Gautier Stoll, Jacques Rougemont, Felix Naef
We study the dynamics of gene activities in relatively small size biological networks (up to a few tens of nodes), e.g. the activities of cell-cycle proteins during the mitotic cel…
Collective synchronization in populations of globally coupled phase oscillators with drifting frequencies
Jacques Rougemont, Felix Naef
We generalize the Kuramoto model for coupled phase oscillators by allowing the frequencies to drift in time according to Ornstein-Uhlenbeck dynamics. Such drifting frequencies were…
Solving the riddle of the bright mismatches: hybridization in oligonucleotide arrays
Felix Naef, Marcelo O. Magnasco
HDONA technology is predicated on two ideas. First, the differential between high-affinity (perfect match, PM) and lower-affinity (mismatch, MM) probes is used to minimize cross-hy…
A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations
Felix Naef, Nicholas D. Socci, Marcelo Magnasco
Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now be…
DNA hybridization to mismatched templates: a chip study
Felix Naef, Daniel A. Lim, Nila Patil +1
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration…
From features to expression: High-density oligonucleotide array analysis revisited
Felix Naef, Daniel A. Lim, Nila Patil +1
One of the most popular tools for large scale gene expression studies are high-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20 small probe cells (``feature…