Contribution of CTCF binding to transcriptional activity at the HOXA locus in NPM1-mutant AML cells

A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation

(2019) Guangsong Su et al.   NUCLEIC ACIDS RESEARCH

NPM1c impedes CTCF functions through cytoplasmic mislocalization in acute myeloid leukemia

(2019) Atom J. Wang et al.   LEUKEMIA

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia

(2018) Huacheng Luo et al.   BLOOD

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

(2018) John C. Stansfield et al.   BMC BIOINFORMATICS

Mutant NPM1 Maintains the Leukemic State through HOX Expression

(2018) Lorenzo Brunetti et al.   CANCER CELL

SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression

(2017) Kaixiang Cao et al.   GENES & DEVELOPMENT

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells

(2015) D H Spencer et al.   LEUKEMIA

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

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

(2014) Suhas S.P. Rao et al.   CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

(2014) Christopher A. Miller et al.   PLoS Computational Biology

Classifying leukemia types with chromatin conformation data

(2014) Mathieu Rousseau et al.   GENOME BIOLOGY

Potent inhibition of DOT1L as treatment of MLL-fusion leukemia

(2013) S. R. Daigle et al.   BLOOD

Leukemic transformation by the MLL-AF6 fusion oncogene requires the H3K79 methyltransferase Dot1l

(2013) A. J. Deshpande et al.   BLOOD

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The PAF Complex Synergizes with MLL Fusion Proteins at HOX Loci to Promote Leukemogenesis

(2010) Andrew G. Muntean et al.   CANCER CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY