3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression

(2020) Maria Fasolino et al.   IMMUNITY

Update on NAFLD genetics: from new variants to the clinic

(2020) Eric Trépo et al.   JOURNAL OF HEPATOLOGY

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

Targeted nanopore sequencing with Cas9-guided adapter ligation

(2020) Timothy Gilpatrick et al.   NATURE BIOTECHNOLOGY

Agonist of RORA Attenuates Non-Alcoholic Fatty Liver Progression in Mice via Upregulation of microRNA 122

(2020) Chofit Chai et al.   GASTROENTEROLOGY

Genetic and epigenetic factors determining NAFLD risk

(2020) Wenke Jonas et al.   Molecular Metabolism

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

(2019) Irene Miguel-Escalada et al.   NATURE GENETICS

Control of DNA replication timing in the 3D genome

(2019) Claire Marchal et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Knockout of the non-essential gene SUGCT creates diet-linked, age-related microbiome disbalance with a diabetes-like metabolic syndrome phenotype

(2019) Joanna Niska-Blakie et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Herbal drug discovery for the treatment of nonalcoholic fatty liver disease

(2019) Tingting Yan et al.   Acta Pharmaceutica Sinica B

The rs626283 Variant in the MBOAT7 Gene is Associated with Insulin Resistance and Fatty Liver in Caucasian Obese Youth

(2018) Giuseppina R Umano et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

(2018) David A. Quigley et al.   CELL

Genetics and epigenetics of NAFLD and NASH: Clinical impact

(2018) Mohammed Eslam et al.   JOURNAL OF HEPATOLOGY

Genetic Variants Associated With Obesity and Insulin Resistance in Hispanic Boys With Nonalcoholic Fatty Liver Disease

(2018) John C. Rausch et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding the 3D genome: Emerging impacts on human disease

(2018) Anton Krumm et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

(2018) James H. Sun et al.   CELL

Non-alcoholic fatty liver disease – A global public health perspective

(2018) Zobair M. Younossi   JOURNAL OF HEPATOLOGY

Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice

(2017) Chun-Qing Song et al.   GASTROENTEROLOGY

Identification of the genomic region under epigenetic regulation during non-alcoholic fatty liver disease progression

(2017) Kikuko Hotta et al.   HEPATOLOGY RESEARCH

Chromatin Conformation Links Distal Target Genes to CKD Loci

(2017) Maarten M. Brandt et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

(2017) Xiao-Tao Wang et al.   NUCLEIC ACIDS RESEARCH

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

(2017) Pengze Wu et al.   Nature Communications

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

Ezetimibe, an NPC1L1 inhibitor, is a potent Nrf2 activator that protects mice from diet-induced nonalcoholic steatohepatitis

(2016) Da Hyun Lee et al.   FREE RADICAL BIOLOGY AND MEDICINE

Genetic Factors That Affect Risk of Alcoholic and Nonalcoholic Fatty Liver Disease

(2016) Quentin M. Anstee et al.   GASTROENTEROLOGY

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

(2016) Phillippa C. Taberlay et al.   GENOME RESEARCH

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

HiCdat: a fast and easy-to-use Hi-C data analysis tool

(2015) Marc W. Schmid et al.   BMC BIOINFORMATICS

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Telomerase activation by genomic rearrangements in high-risk neuroblastoma

(2015) Martin Peifer et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

(2013) Z. Kan et al.   GENOME RESEARCH

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE