Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes

Specific expression of novel long non-coding RNAs in high-hyperdiploid childhood acute lymphoblastic leukemia

(2017) Mathieu Lajoie et al.   PLoS One

Canvas: versatile and scalable detection of copy number variants

(2016) Eric Roller et al.   BIOINFORMATICS

Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia

(2016) Henrik Lilljebjörn et al.   Nature Communications

LncRNA Expression Discriminates Karyotype and Predicts Survival in B-Lymphoblastic Leukemia

(2015) T. R. Fernando et al.   MOLECULAR CANCER RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages

(2015) David Casero et al.   NATURE IMMUNOLOGY

Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures

(2015) Seung-Tae Lee et al.   NUCLEIC ACIDS RESEARCH

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus

(2015) Sandra Lazorthes et al.   Nature Communications

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs

(2014) V. Adoue et al.   Molecular Systems Biology

Integration of High-Resolution Methylome and Transcriptome Analyses to Dissect Epigenomic Changes in Childhood Acute Lymphoblastic Leukemia

(2013) S. Busche et al.   CANCER RESEARCH

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer

(2013) Georges St Laurent et al.   GENOME BIOLOGY

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular genetics of B-precursor acute lymphoblastic leukemia

(2012) Charles G. Mullighan   JOURNAL OF CLINICAL INVESTIGATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network

(2012) Seung-Tae Lee et al.   NUCLEIC ACIDS RESEARCH

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan 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

Late Effects in Long-Term Survivors After Treatment for Childhood Acute Leukemia

(2009) Theresa B. Haddy et al.   CLINICAL PEDIATRICS

Long-term results of Dana-Farber Cancer Institute ALL Consortium protocols for children with newly diagnosed acute lymphoblastic leukemia (1985–2000)

(2009) L B Silverman et al.   LEUKEMIA

Twenty-five-year follow-up among survivors of childhood acute lymphoblastic leukemia: a report from the Childhood Cancer Survivor Study

(2008) R. Mody et al.   BLOOD

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY