GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data

MOTIVATION Microarray designs containing millions to hundreds of millions of probes that tile entire genomes are currently being released. Within the next 2 months, our group will release a microarray data set containing over 12,000,000 microarray measurements taken from 37 mouse tissues. A problem that will become increasingly significant in the upcoming era of genome-wide exon-tiling microarr...

Iterated Conditional Modes for Cross-Hybridization Compensation in DNA Microarray Data

Predicting CpG Islands and DNA Methlation in the Cow Genome Using DNA Microarray Meta-Analysis and Genome Wide Scanning

DNA methylation is a type of epigenetic changes that directly affects DNA. In mammals, DNA methylation is essential for fetal development and stem cell differentiation and this phenomenon essentially occurs within the CpG islands. In this study, two methods were used to study the DNA methylation profile of cow genome. In the first method, the DNA methylation profile of the differentially expres...

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model

Genome-wide microarray designs containing millions to tens of millions of probes will soon become available for a variety of mammals, including mouse and human. These “tiling arrays” can potentially lead to significant advances in science and medicine, e.g., by indicating new genes and alternative primary and secondary transcripts. While bottomup pattern matching techniques (e.g., hierarchical ...

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data

Genome-wide microarray designs containing millions to hundreds of millions of probes are available for a variety of mammals, including mouse and human. These genome tiling arrays can potentially lead to significant advances in science and medicine, e.g., by indicating new genes and alternative primary and secondary transcripts. While bottom-up pattern matching techniques (e.g., hierarchical clu...