Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection

When 3D genome technology meets viral infection, including SARS‐CoV‐2

(2022) Weizheng Liang et al.   JOURNAL OF MEDICAL VIROLOGY

Hepatocellular carcinoma

(2021) Josep M. Llovet et al.   Nature Reviews Disease Primers

Hepatitis B virus integrations promote local and distant oncogenic driver alterations in hepatocellular carcinoma

(2021) Camille Péneau et al.   GUT

Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE

(2021) Jiangping He et al.   Nature Communications

Transcriptionally inactive hepatitis B virus episome DNA preferentially resides in the vicinity of chromosome 19 in 3D host genome upon infection

(2021) Dingbin Tang et al.   Cell Reports

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis

(2021) Ian J. Groves et al.   PLoS Pathogens

RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription

(2021) Ke Xiao et al.   Science Advances

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

(2020) Pierre Bost et al.   CELL

Epstein-Barr Virus episome physically interacts with active regions of the host genome in lymphoblastoid cells

(2020) Luopin Wang et al.   JOURNAL OF VIROLOGY

Yin-Yang 1 and HBx protein activate HBV transcription by mediating the spatial interaction of cccDNA minichromosome with cellular chromosome 19p13.11

(2020) Congle Shen et al.   Emerging Microbes & Infections

Whole exome HBV DNA integration is independent of the intrahepatic HBV reservoir in HBeAg-negative chronic hepatitis B

(2020) Valentina Svicher et al.   GUT

Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression

(2020) Guohe Song et al.   Cell Discovery

3D landscape of Hepatitis B virus interactions with human chromatins

(2020) Bo Yang et al.   Cell Discovery

Profiling of LINE-1-Related Genes in Hepatocellular Carcinoma

(2019) Tomoyuki Honda et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Circular ecDNA promotes accessible chromatin and high oncogene expression

(2019) Sihan Wu et al.   NATURE

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

(2019) Yu Kong et al.   Nature Communications

Genome organization at different scales: nature, formation and function

(2018) Jacques Serizay et al.   CURRENT OPINION IN CELL BIOLOGY

Hepatocellular carcinoma

(2018) Alejandro Forner et al.   LANCET

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis

(2018) Anat Melamed et al.   eLife

Parvovirus Minute Virus of Mice Interacts with Sites of Cellular DNA Damage to Establish and Amplify its Lytic Infection

(2018) Kinjal Majumder et al.   eLife

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Integrative detection and analysis of structural variation in cancer genomes

(2018) Jesse R. Dixon et al.   NATURE GENETICS

The changing epidemiology of liver diseases in the Asia–Pacific region

(2018) Martin C. S. Wong et al.   Nature Reviews Gastroenterology & Hepatology

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

(2018) Pierrick Moreau et al.   Nature Communications

EnhancerDB: a resource of transcriptional regulation in the context of enhancers

(2018) Ran Kang et al.   Database-The Journal of Biological Databases and Curation

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma

(2016) Ling-Hao Zhao et al.   Nature Communications

Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression

(2016) Yixuan Gong et al.   Oncotarget

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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