Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

(2015) Emma Pierson et al.   PLoS Computational Biology

Expression of Human CD46 Modulates Inflammation Associated With GalTKO Lung Xenograft Injury

(2014) L. Burdorf et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The H3K27me3 demethylase UTX is a gender-specific tumor suppressor in T-cell acute lymphoblastic leukemia

(2014) Joni Van der Meulen et al.   BLOOD

Associations between CD36 gene polymorphisms and susceptibility to coronary artery heart disease

(2014) Y. Zhang et al.   BRAZILIAN JOURNAL OF MEDICAL AND BIOLOGICAL RESEARCH

Aberrant Chloride Intracellular Channel 4 Expression Contributes to Endothelial Dysfunction in Pulmonary Arterial Hypertension

(2014) Beata Wojciak-Stothard et al.   CIRCULATION

CXCR3 deficiency enhances tumor progression by promoting macrophage M2 polarization in a murine breast cancer model

(2014) Steve Oghumu et al.   IMMUNOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Siglec-E is a negative regulator of acute pulmonary neutrophil inflammation and suppresses CD11b  2-integrin-dependent signaling

(2013) S. J. McMillan et al.   BLOOD

A Core Human Primary Tumor Angiogenesis Signature Identifies the Endothelial Orphan Receptor ELTD1 as a Key Regulator of Angiogenesis

(2013) Massimo Masiero et al.   CANCER CELL

Angiogenesis and Vascular Functions in Modulation of Obesity, Adipose Metabolism, and Insulin Sensitivity

(2013) Yihai Cao   Cell Metabolism

MiR-26b is down-regulated in carcinoma-associated fibroblasts from ER-positive breast cancers leading to enhanced cell migration and invasion

(2013) Eldo T Verghese et al.   JOURNAL OF PATHOLOGY

Age-Related and Depot-Specific Changes in White Adipose Tissue of Growth Hormone Receptor-Null Mice

(2013) Lucila Sackmann-Sala et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Evidence for a role ofLPGAT1in influencing BMI and percent body fat in Native Americans

(2013) Michael T. Traurig et al.   Obesity

Passing Messages between Biological Networks to Refine Predicted Interactions

(2013) Kimberly Glass et al.   PLoS One

Nontelomeric Role for Rap1 in Regulating Metabolism and Protecting against Obesity

(2013) Frank Yeung et al.   Cell Reports

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

(2013) Christopher D. Brown et al.   PLoS Genetics

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

Dynamic Regulation of the Cerebral Cavernous Malformation Pathway Controls Vascular Stability and Growth

(2012) Xiangjian Zheng et al.   DEVELOPMENTAL CELL

The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

(2012) Abed AlFatah Mansour et al.   NATURE

Arhgef15 Promotes Retinal Angiogenesis by Mediating VEGF-Induced Cdc42 Activation and Potentiating RhoJ Inactivation in Endothelial Cells

(2012) Sentaro Kusuhara et al.   PLoS One

Integrated cross-species transcriptional network analysis of metastatic susceptibility

(2012) Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sparse Bayesian infinite factor models

(2011) A. Bhattacharya et al.   BIOMETRIKA

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

(2011) L. T. MacNeil et al.   GENOME RESEARCH

Diet-induced obesity affects expression of adiponutrin/PNPLA3 and adipose triglyceride lipase, two members of the same family

(2011) P Oliver et al.   INTERNATIONAL JOURNAL OF OBESITY

The wnt/β-catenin signaling pathway: A potential therapeutic target in the treatment of triple negative breast cancer

(2011) Taj D. King et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

CD46 Protects against Chronic Obstructive Pulmonary Disease

(2011) Sandra Grumelli et al.   PLoS One

Thymidine Kinase 2 Deficiency-Induced Mitochondrial DNA Depletion Causes Abnormal Development of Adipose Tissues and Adipokine Levels in Mice

(2011) Joan Villarroya et al.   PLoS One

FABIA: factor analysis for bicluster acquisition

(2010) Sepp Hochreiter et al.   BIOINFORMATICS

The horseshoe estimator for sparse signals

(2010) C. M. Carvalho et al.   BIOMETRIKA

Searching for functional gene modules with interaction component models

(2010) Juuso A Parkkinen et al.   BMC Systems Biology

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

Down-regulation of CD3zeta is a breast cancer biomarker associated with immune suppression

(2010) Bin Yu et al.   CELL BIOLOGY INTERNATIONAL

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Correction for hidden confounders in the genetic analysis of gene expression

(2010) J. Listgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis

(2010) Barbara E. Engelhardt et al.   PLoS Genetics

Identification of functional modules that correlate with phenotypic difference: the influence of network topology

(2010) Jui-Hung Hung et al.   GENOME BIOLOGY

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

(2009) Sara C Madeira et al.   Algorithms for Molecular Biology

Differential Expression of the Antioxidant Repair Enzyme Methionine Sulfoxide Reductase (MSRA and MSRB) in Human Skin

(2009) Wirach M Taungjaruwinai et al.   AMERICAN JOURNAL OF DERMATOPATHOLOGY

Detailing regulatory networks through large scale data integration

(2009) C. Huttenhower et al.   BIOINFORMATICS

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

The candidate gene approach in asthma: what happens with the neighbours?

(2009) Naomi E Reijmerink et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics

(2009) Carlos M. Carvalho et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

(2009) Guojun Li et al.   NUCLEIC ACIDS RESEARCH

Clustering high-dimensional data

(2009) Hans-Peter Kriegel et al.   ACM Transactions on Knowledge Discovery from Data

Clustering cancer gene expression data: a comparative study

(2008) Marcilio C. P. de Souto et al.   BMC BIOINFORMATICS

Bayesian biclustering of gene expression data

(2008) Jiajun Gu et al.   BMC GENOMICS

Loss of 13q is associated with genes involved in cell cycle and proliferation in dedifferentiated hepatocellular carcinoma

(2008) Britta Skawran et al.   MODERN PATHOLOGY

Dok1 mediates high-fat diet–induced adipocyte hypertrophy and obesity through modulation of PPAR-γ phosphorylation

(2008) Tetsuya Hosooka et al.   NATURE MEDICINE

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High-fat Diet Alters PP2A, TC10, and CIP4 Expression in Visceral Adipose Tissue of Rats

(2008) Hye-Seung Jun et al.   Obesity

Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast

(2008) Maria I. Davidich et al.   PLoS One

Biclustering in data mining

(2007) Stanislav Busygin et al.   COMPUTERS & OPERATIONS RESEARCH