475 citations · 1.1k across the 6 of their papers we have counts for
6 papers
Comprehensive evaluation of differential expression analysis methods for RNA-seq data
Franck Rapaport, Raya Khanin, Yupu Liang +5
High-throughput sequencing of RNA transcripts (RNA-seq) has become the method of choice for detection of differential expression (DE). Concurrent with the growing popularity of thi…
Non-equilibrium raft-like membrane domains under continuous recycling
Matthew S. Turner, Pierre Sens, Nicholas D. Socci
We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that the domai…
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…
Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels
N. D. Socci, J. N. Onuchic, P. G. Wolynes
The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and f…
Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique
Nicholas D. Socci, José Nelson Onuchic
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of var…
Folding Kinetics of Protein Like Heteropolymers
Nicholas D. Socci, Jose' Nelson Onuchic
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers lo…