Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription

Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses

(2022) Kevin B. Einkauf et al.   CELL

Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

(2021) John M. Coffin et al.   PLoS Pathogens

Radial Organization in the Mammalian Nucleus

(2020) Nicola Crosetto et al.   Frontiers in Genetics

HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains

(2020) Ashwanth C. Francis et al.   Nature Communications

Distinct viral reservoirs in individuals with spontaneous control of HIV-1

(2020) Chenyang Jiang et al.   NATURE

The relative contributions of infectious and mitotic spread to HTLV-1 persistence

(2020) Daniel J. Laydon et al.   PLoS Computational Biology

Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries

(2020) Aizhan Bizhanova et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin

(2019) Anastassiia Vertii et al.   GENOME RESEARCH

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Control of DNA replication timing in the 3D genome

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

Human T Cell Leukemia Virus Type 1: Persistence and Pathogenesis

(2018) Charles R.M. Bangham   Annual Review of Immunology

Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells

(2018) Mohamed Mahgoub et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Anat Melamed et al.   eLife

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

(2017) Michael I. Robson et al.   GENOME RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions

(2017) Charles C. Berry et al.   Molecular Therapy-Methods & Clinical Development

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome

(2016) Yorifumi Satou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid dissemination of human T-lymphotropic virus type 1 during primary infection in transplant recipients

(2016) Lucy B. M. Cook et al.   Retrovirology

HTLV-1 drives vigorous clonal expansion of infected CD8+ T cells in natural infection

(2015) Anat Melamed et al.   Retrovirology

The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia/lymphoma

(2014) L. B. Cook et al.   BLOOD

Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection

(2014) T. A. Wagner et al.   SCIENCE

Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

(2014) F. Maldarelli et al.   SCIENCE

Quantification of HTLV-1 Clonality and TCR Diversity

(2014) Daniel J. Laydon et al.   PLoS Computational Biology

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Genome-wide Determinants of Proviral Targeting, Clonal Abundance and Expression in Natural HTLV-1 Infection

(2013) Anat Melamed et al.   PLoS Pathogens

Estimating abundances of retroviral insertion sites from DNA fragment length data

(2012) Charles C. Berry et al.   BIOINFORMATICS

HTLV-1-infected T cells contain a single integrated provirus in natural infection

(2012) L. B. Cook et al.   BLOOD

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones

(2011) N. A. Gillet et al.   BLOOD

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

(2010) Silvana van Koningsbruggen et al.   MOLECULAR BIOLOGY OF THE CELL

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation

(2009) Nicolas Chomont et al.   NATURE MEDICINE

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics

HTLV-1 Integration into Transcriptionally Active Genomic Regions Is Associated with Proviral Expression and with HAM/TSP

(2008) Kiran N. Meekings et al.   PLoS Pathogens