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Search: authors:"Andrey A. Shabalin"

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Convergence of evidence from a methylome-wide CpG-SNP association study and GWAS of major depressive disorder

AffiliationsCenter for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USAKarolina A. Aberg, Andrey A. Shabalin, Robin F. Chan, Min Zhao, Gaurav Kumar, Shaunna L. Clark, Lin ...  & Brenda W. J. H. Penninx AuthorsSearch for Karolina A. Aberg in:Nature Research journals • PubMed • Google Scholar Search for Andrey A. Shabalin in:Nature Research journals • PubMed • Google Scholar

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

Andrey A. Shabalin 0 Associate Editor: Trey Ideker 0 Department of Biostatistics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599 , USA Motivation: Expression quantitative trait

seeQTL: a searchable database for human eQTLs

Summary: seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots. Availability and implementation: seeQTL is freely available for non-commercial use at...

Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival

Breast cancer is a heterogeneous disease with known expression-defined tumor subtypes. DNA copy number studies have suggested that tumors within gene expression subtypes share similar DNA Copy number aberrations (CNA) and that CNA can be used to further sub-divide expression classes. To gain further insights into the etiologies of the intrinsic subtypes, we classified tumors...

Merging two gene-expression studies via cross-platform normalization

Motivation: Gene-expression microarrays are currently being applied in a variety of biomedical applications. This article considers the problem of how to merge datasets arising from different gene-expression studies of a common organism and phenotype. Of particular interest is how to merge data from different technological platforms. Results: The article makes two contributions...

The Set2/Rpd3S Pathway Suppresses Cryptic Transcription without Regard to Gene Length or Transcription Frequency

In cells lacking the histone methyltransferase Set2, initiation of RNA polymerase II transcription occurs inappropriately within the protein-coding regions of genes, rather than being restricted to the proximal promoter. It was previously reported that this “cryptic” transcription occurs preferentially in long genes, and in genes that are infrequently transcribed. Here, we mapped...

FastMap: Fast eQTL mapping in homozygous populations

Motivation: Gene expression Quantitative Trait Locus (eQTL) mapping measures the association between transcript expression and genotype in order to find genomic locations likely to regulate transcript expression. The availability of both gene expression and high-density genotype data has improved our ability to perform eQTL mapping in inbred mouse and other homozygous populations...

Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies

Polymorphisms in the target mRNA sequence can greatly affect the binding affinity of microarray probe sequences, leading to false-positive and false-negative expression quantitative trait locus (QTL) signals with any other polymorphisms in linkage disequilibrium. We provide the most complete solution to this problem, by using the latest genome and exome sequence reference data to...