Determination of sample size in genome-scale RNAi screens - Motivation: For genome-scale RNAi research, it is critical to investigate sample size required for the achievement of reasonably low false negative rate (FNR) and false positive rate.

The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding - Motivation: In current databases, there are many genes with inconsistent mapping positions between their cytogenetic annotations and sequence map positions.

Accurate identification of orthologous segments among multiple genomes - Motivation: The accurate detection of orthologous segments (also referred to as syntenic segments) plays a key role in comparative genomics, as it is useful for inferring genome rearrangement scenarios and computing whole-genome

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods - Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates.

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction - Motivation: Identifying regulatory elements in genomic sequences is a key component in understanding the control of gene expression.

SIMPRO: simple protein homology detection method by using indirect signals - Motivation: Detecting homologous proteins is one of the fundamental problems in computational biology.

A flexible rank-based framework for detecting copy number aberrations from array data - Motivation: DNA copy number aberration—both inherited and sporadic—is a significant contributor to a variety of human diseases. Copy number characterization is therefore an area of intense research.

Genome-wide association analysis by lasso penalized logistic regression - Motivation: In ordinary regression, imposition of a lasso penalty makes continuous model selection straightforward.

MSMAD: a computationally efficient method for the analysis of noisy array CGH data - Motivation: Genome analysis has become one of the most important tools for understanding the complex process of cancerogenesis.

Papers on normalization, variable selection, classification or clustering of microarray data