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BMCBI
2011
14 years 11 months ago
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
Background: Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diver...
Ozkan U. Nalbantoglu, Samuel F. Way, Steven H. Hin...
BMCBI
2011
14 years 11 months ago
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring
Background: Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. I...
Mi-Youn K. Brusniak, Sung-Tat Kwok, Mark Christian...
BMCBI
2011
14 years 11 months ago
Appearance frequency modulated gene set enrichment testing
Background: Gene set enrichment testing has helped bridge the gap from an individual gene to a systems biology interpretation of microarray data. Although gene sets are defined a ...
Jun Ma, Maureen A. Sartor, H. V. Jagadish
CORR
2011
Springer
158views Education» more  CORR 2011»
14 years 11 months ago
SqFreeEVAL: An (almost) optimal real-root isolation algorithm
Let f be a univariate polynomial with real coefficients, f ∈ R[X]. Subdivision algorithms based on algebraic techniques (e.g., Sturm or Descartes methods) are widely used for is...
Michael Burr, Felix Krahmer
CORR
2011
Springer
167views Education» more  CORR 2011»
14 years 11 months ago
Fast global convergence of gradient methods for high-dimensional statistical recovery
Many statistical M-estimators are based on convex optimization problems formed by the weighted sum of a loss function with a norm-based regularizer. We analyze the convergence rat...
Alekh Agarwal, Sahand Negahban, Martin J. Wainwrig...
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