Systematic tests for position-dependent additive shear bias

Quantifying Position-Dependent Codon Usage Bias

Although the mapping of codon to amino acid is conserved across nearly all species, the frequency at which synonymous codons are used varies both between organisms and between genes from the same organism. This variation affects diverse cellular processes including protein expression, regulation, and folding. Here, we mathematically model an additional layer of complexity and show that individu...

Systematic Bias in Cosmic Shear: Beyond the Fisher Matrix

We describe a method for computing the biases that systematic signals introduce in parameter estimation using a simple extension of the Fisher matrix formalism. This allows us to calculate the offset of the best fit parameters relative to the fiducial model, in addition to the usual statistical error ellipse. As an application, we study the impact that residual systematics in tomographic weak l...

Generalized Likelihood Ratio Tests for Additive Models

Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion

BACKGROUND The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surf...

Position Automata for Kleene Algebra with Tests

Kleene algebra with tests (KAT) is an equational system that combines Kleene and Boolean algebras. One can model basic programming constructs and assertions in KAT, which allows for its application in compiler optimization, program transformation and dataflow analysis. To provide semantics for KAT expressions, Kozen first introduced automata on guarded strings, showing that the regular sets of ...