Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

(2019) Marlies E. Oomen et al.   GENOME RESEARCH

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Physical principles of retroviral integration in the human genome

(2019) D. Michieletto et al.   Nature Communications

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration

(2019) Bojana Lucic et al.   Nature Communications

Mapping Active Gene-Regulatory Regions in Human Repopulating Long-Term HSCs

(2018) Peer Wünsche et al.   Cell Stem Cell

Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells

(2018) John L. Johnson et al.   IMMUNITY

Interactions between Retroviruses and the Host Cell Genome

(2018) Valentina Poletti et al.   Molecular Therapy-Methods & Clinical Development

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers

(2018) Radwa Sharaf et al.   JOURNAL OF CLINICAL INVESTIGATION

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells

(2018) Joseph A. Fraietta et al.   NATURE

A Cosine Similarity-Based Method to Infer Variability of Chromatin Accessibility at the Single-Cell Level

(2018) Stanley Cai et al.   Frontiers in Genetics

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration

(2017) Julien Matysiak et al.   Retrovirology

INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes

(2017) Eric Sherman et al.   Molecular Therapy-Methods & Clinical Development

Histones Are Rapidly Loaded onto Unintegrated Retroviral DNAs Soon after Nuclear Entry

(2016) Gary Z. Wang et al.   Cell Host & Microbe

What Integration Sites Tell Us about HIV Persistence

(2016) Stephen H. Hughes et al.   Cell Host & Microbe

HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay

(2016) Sara Sunshine et al.   JOURNAL OF VIROLOGY

Nuclear landscape of HIV-1 infection and integration

(2016) Marina Lusic et al.   NATURE REVIEWS MICROBIOLOGY

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes

(2016) Wei Shao et al.   Retrovirology

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

(2016) Jakub Mieczkowski et al.   Nature Communications

HIV-1 Integration Landscape during Latent and Active Infection

(2015) Lillian B. Cohn et al.   CELL

LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes

(2015) Parmit Kumar Singh et al.   GENES & DEVELOPMENT

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Structural basis for retroviral integration into nucleosomes

(2015) Daniel P. Maskell et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Nuclear architecture dictates HIV-1 integration site selection

(2015) Bruna Marini et al.   NATURE

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells

(2014) Makoto Kurachi et al.   NATURE IMMUNOLOGY

MLV integration site selection is driven by strong enhancers and active promoters

(2014) Matthew C. LaFave et al.   NUCLEIC ACIDS RESEARCH

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

Integration Site and Clonal Expansion in Human Chronic Retroviral Infection and Gene Therapy

(2014) Heather Niederer et al.   Viruses-Basel

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

HIV latency and integration site placement in five cell-based models

(2013) Scott Sherrill-Mix et al.   Retrovirology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS