Chromatin variation associated with liver metabolism is mediated by transposable elements

How retrotransposons shape genome regulation

(2016) Paolo Mita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Persistent Chromatin Modifications Induced by High Fat Diet

(2016) Amy Leung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice

(2015) Luz D. Orozco et al.   Cell Metabolism

Genetic and epigenetic variation among inbred mouse littermates: identification of inter-individual differentially methylated regions

(2015) Harald Oey et al.   Epigenetics & Chromatin

quantro: a data-driven approach to guide the choice of an appropriate normalization method

(2015) Stephanie Hicks et al.   GENOME BIOLOGY

Liver ENPP1 protein increases with remission of type 2 diabetes after gastric bypass surgery

(2014) Vinko Besic et al.   BMC GASTROENTEROLOGY

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Open Chromatin Profiling in Mice Livers Reveals Unique Chromatin Variations Induced by High Fat Diet

(2014) Amy Leung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evolution of Alu Elements toward Enhancers

(2014) Ming Su et al.   Cell Reports

Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules

(2013) Keunsoo Kang et al.   BMC GENOMICS

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Genetic Control of Obesity and Gut Microbiota Composition in Response to High-Fat, High-Sucrose Diet in Mice

(2013) Brian W. Parks et al.   Cell Metabolism

Mouse strain-dependent variation in obesity and glucose homeostasis in response to high-fat feeding

(2013) M. K. Montgomery et al.   DIABETOLOGIA

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

High Fat Diet Induces Liver Steatosis and Early Dysregulation of Iron Metabolism in Rats

(2013) Rosaria Meli et al.   PLoS One

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Causes and Consequences of Chromatin Variation between Inbred Mice

(2013) Mona Hosseini et al.   PLoS Genetics

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

STAT proteins – Key regulators of anti-viral responses, inflammation, and tumorigenesis in the liver

(2012) Bin Gao et al.   JOURNAL OF HEPATOLOGY

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

STAT1:DNA sequence-dependent binding modulation by phosphorylation, protein:protein interactions and small-molecule inhibition

(2012) Andrew J. Bonham et al.   NUCLEIC ACIDS RESEARCH

Metabolic reprogramming by class I and II histone deacetylases

(2012) Maria M. Mihaylova et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Growth hormone-STAT5 regulation of growth, hepatocellular carcinoma, and liver metabolism

(2011) Myunggi Baik et al.   Annals of the New York Academy of Sciences

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Human Fatty Liver Disease: Old Questions and New Insights

(2011) J. C. Cohen et al.   SCIENCE

Genome-wide transcription factor binding: beyond direct target regulation

(2011) Kyle L. MacQuarrie et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes

(2010) A. D. Ewing et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Effects of Retroviruses on Host Genome Function

(2008) Patric Jern et al.   Annual Review of Genetics

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Limited variation in the major urinary proteins of laboratory mice

(2008) Sarah A. Cheetham et al.   PHYSIOLOGY & BEHAVIOR