Genome organization and DNA accessibility control antigenic variation in trypanosomes

African trypanosomes evade immune clearance by O-glycosylation of the VSG surface coat

(2018) Jason Pinger et al.   Nature Microbiology

Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq

(2017) Carolin Wedel et al.   EXPERIMENTAL PARASITOLOGY

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

(2017) Houda Belaghzal et al.   METHODS

Companion: a web server for annotation and analysis of parasite genomes

(2016) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Defining chromosomal translocation risks in cancer

(2016) Marc A. Hogenbirk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VEX1 controls the allelic exclusion required for antigenic variation in trypanosomes

(2016) Lucy Glover et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

The in vivo dynamics of antigenic variation in Trypanosoma brucei

(2015) M. R. Mugnier et al.   SCIENCE

Discovery of Unconventional Kinetochores in Kinetoplastids

(2014) Bungo Akiyoshi et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

Antigenic variation in African trypanosomes

(2014) David Horn   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427

(2014) George A.M. Cross et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Spatial Dynamics of Chromosome Translocations in Living Cells

(2013) V. Roukos et al.   SCIENCE

Nuclear Organization and Genome Function

(2012) Kevin Van Bortle et al.   Annual Review of Cell and Developmental Biology

Cell-cycle-regulated control of VSG expression site silencing by histones and histone chaperones ASF1A and CAF-1b in Trypanosoma brucei

(2012) Sam Alsford et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

The chromatin insulator CTCF and the emergence of metazoan diversity

(2012) P. Heger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF, cohesin, and histone variants: connecting the genome

(2011) Jean-François Millau et al.   Biochemistry and Cell Biology

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Insulators and promoters: closer than we think

(2010) Jesse R. Raab et al.   NATURE REVIEWS GENETICS

Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites

(2010) Tim Nicolai Siegel et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide Analysis of Heterochromatin Associates Clonally Variant Gene Regulation with Perinuclear Repressive Centers in Malaria Parasites

(2009) Jose-Juan Lopez-Rubio et al.   Cell Host & Microbe

Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

(2009) T. N. Siegel et al.   GENES & DEVELOPMENT

Cohesin regulatesVSGmonoallelic expression in trypanosomes

(2009) David Landeira et al.   JOURNAL OF CELL BIOLOGY

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens

(2009) Kirk W. Deitsch et al.   NATURE REVIEWS MICROBIOLOGY

The emerging role of nuclear architecture in DNA repair and genome maintenance

(2009) Tom Misteli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional characterization of cohesin subunit SCC1 inTrypanosoma bruceiand dissection of mutant phenotypes in two life cycle stages

(2008) Eva Gluenz et al.   MOLECULAR MICROBIOLOGY

A Histone Methyltransferase Modulates Antigenic Variation in African Trypanosomes

(2008) Luisa M Figueiredo et al.   PLOS BIOLOGY

CRE recombinase-based positive–negative selection systems for genetic manipulation in Trypanosoma brucei

(2007) Michael D. Scahill et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY