Epigenomic profiling of neuroblastoma cell lines

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

The Expanding World of N-MYC–Driven Tumors

(2018) David S. Rickman et al.   Cancer Discovery

Neuroblastoma is composed of two super-enhancer-associated differentiation states

(2017) Tim van Groningen et al.   NATURE GENETICS

Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries

(2017) Valentina Boeva et al.   NATURE GENETICS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines

(2017) Jo Lynne Harenza et al.   Scientific Data

A Myc Activity Signature Predicts Poor Clinical Outcomes in Myc-Associated Cancers

(2016) MoonSun Jung et al.   CANCER RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Neuroblastoma

(2016) Katherine K. Matthay et al.   Nature Reviews Disease Primers

hiHMM: Bayesian non-parametric joint inference of chromatin state maps

(2015) Kyung-Ah Sohn et al.   BIOINFORMATICS

Advances in Risk Classification and Treatment Strategies for Neuroblastoma

(2015) Navin R. Pinto et al.   JOURNAL OF CLINICAL ONCOLOGY

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data

(2013) Parameswaran Ramachandran et al.   BIOINFORMATICS

Roles for MYC in the Establishment and Maintenance of Pluripotency

(2013) J. Chappell et al.   Cold Spring Harbor Perspectives in Medicine

MYCN and the epigenome

(2013) Stanley He et al.   Frontiers in Oncology

MYCN-mediated transcriptional repression in neuroblastoma: the other side of the coin

(2013) Samuele Gherardi et al.   Frontiers in Oncology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Functional MYCN signature predicts outcome of neuroblastoma irrespective of MYCN amplification

(2012) L. J. Valentijn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MYCN: from oncoprotein to tumor-associated antigen

(2012) Vito Pistoia et al.   Frontiers in Oncology

Cell-Type Independent MYC Target Genes Reveal a Primordial Signature Involved in Biomass Accumulation

(2011) Hongkai Ji et al.   PLoS One

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

Recent Advances in Neuroblastoma

(2010) John M. Maris   NEW ENGLAND JOURNAL OF MEDICINE

Treatment and outcomes of patients with relapsed, high-risk neuroblastoma: Results of German trials

(2010) Thorsten Simon et al.   PEDIATRIC BLOOD & CANCER

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

International consensus for neuroblastoma molecular diagnostics: report from the International Neuroblastoma Risk Group (INRG) Biology Committee

(2009) P F Ambros et al.   BRITISH JOURNAL OF CANCER

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY