Impact of Natural Genetic Variation on Gene Expression Dynamics

Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing

(2012) Thomas Sakoparnig et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Teamwork: Improved eQTL Mapping Using Combinations of Machine Learning Methods

(2012) Marit Ackermann et al.   PLoS One

Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression

(2012) Jingyuan Fu et al.   PLoS Genetics

SNPInterForest: A new method for detecting epistatic interactions

(2011) Makiko Yoshida et al.   BMC BIOINFORMATICS

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease

(2011) Rudi Alberts et al.   BMC GENOMICS

Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

(2011) J. E. Powell et al.   GENOME RESEARCH

The role of sirtuin 2 activation by nicotinamide phosphoribosyltransferase in the aberrant proliferation and survival of myeloid leukemia cells

(2011) L. Dan et al.   HAEMATOLOGICA

A genome-wide screen of gene–gene interactions for rheumatoid arthritis susceptibility

(2011) Chunyu Liu et al.   HUMAN GENETICS

Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest

(2011) Usman Roshan et al.   NUCLEIC ACIDS RESEARCH

Protein Networks as Logic Functions in Development and Cancer

(2011) Janusz Dutkowski et al.   PLoS Computational Biology

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

(2011) Alkes L. Price et al.   PLoS Genetics

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Variation Within DNA Repair Pathway Genes and Risk of Multiple Sclerosis

(2010) Farren B. S. Briggs et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Gene Expression in Skin and Lymphoblastoid Cells: Refined Statistical Method Reveals Extensive Overlap in cis-eQTL Signals

(2010) Jun Ding et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An application of Random Forests to a genome-wide association dataset: Methodological considerations & new findings

(2010) Benjamin A Goldstein et al.   BMC GENETICS

Data-driven assessment of eQTL mapping methods

(2010) Jacob J Michaelson et al.   BMC GENOMICS

Use of Wrapper Algorithms Coupled with a Random Forests Classifier for Variable Selection in Large-Scale Genomic Association Studies

(2010) Andrei S. Rodin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Integrative Analysis of Low- and High-Resolution eQTL

(2010) Salvatore Loguercio et al.   PLoS One

Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

(2010) Hua Zhong et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Loss-of-function Additional sex combs like 1 mutations disrupt hematopoiesis but do not cause severe myelodysplasia or leukemia

(2009) C. L. Fisher et al.   BLOOD

The effects of disruption of genes for peroxiredoxin-2, glutathione peroxidase-1, and catalase on erythrocyte oxidative metabolism

(2009) Robert M. Johnson et al.   FREE RADICAL BIOLOGY AND MEDICINE

Expression quantitative trait loci detected in cell lines are often present in primary tissues

(2009) Kevin Bullaughey et al.   HUMAN MOLECULAR GENETICS

MAPK signaling pathways in the regulation of hematopoiesis

(2009) Christian R. Geest et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State

(2009) Alice Gerrits et al.   PLoS Genetics

Oxidative Stress in the Regulation of Normal and Neoplastic Hematopoiesis

(2008) Saghi Ghaffari   ANTIOXIDANTS & REDOX SIGNALING

Enriched random forests

(2008) D. Amaratunga et al.   BIOINFORMATICS

EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis

(2008) Sophia S. F. Lee et al.   BIOINFORMATICS

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL

A comparison of analytical methods for genetic association studies

(2008) Alison A. Motsinger-Reif et al.   GENETIC EPIDEMIOLOGY

Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny

(2008) Alice Gerrits et al.   IMMUNOGENETICS

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

From gene expression to disease risk

(2008) Emmanouil T Dermitzakis   NATURE GENETICS

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits

(2008) Erin L Heinzen et al.   PLOS BIOLOGY

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY