Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations

Tumour‐derived substrate‐adherent cells promote neuroblastoma survival through secreted trophic factors

(2021) Jing Li et al.   Molecular Oncology

Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing

(2020) Povilas Gibas et al.   PLOS BIOLOGY

Hypoxia inducible factor‐2α importance for migration, proliferation, and self‐renewal of trunk neural crest cells

(2020) Camilla U. Niklasson et al.   DEVELOPMENTAL DYNAMICS

Characterization of universal features of partially methylated domains across tissues and species

(2020) Benjamin E. Decato et al.   Epigenetics & Chromatin

Neuroblastoma—A Neural Crest Derived Embryonal Malignancy

(2019) John Inge Johnsen et al.   Frontiers in Molecular Neuroscience

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

(2019) Arie B. Brinkman et al.   Nature Communications

Wnt Signaling in Neural Crest Ontogenesis and Oncogenesis

(2019) Yu Ji et al.   Cells

DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

A pan-cancer atlas of cancer hallmark-associated candidate driver lncRNAs

(2018) Yulan Deng et al.   Molecular Oncology

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

The mechanism of epithelial-mesenchymal transition induced by TGF-β1 in neuroblastoma cells

(2017) Jing-Bo Shao et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Mesenchymal stem cells: key players in cancer progression

(2017) Sarah M. Ridge et al.   Molecular Cancer

Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling

(2017) Zdislav Staševskij et al.   MOLECULAR CELL

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

Concise Review: Cancer Cells, Cancer Stem Cells, and Mesenchymal Stem Cells: Influence in Cancer Development

(2017) Federica Papaccio et al.   Stem Cells Translational Medicine

Base resolution maps reveal the importance of 5-hydroxymethylcytosine in a human glioblastoma

(2017) Eun-Ang Raiber et al.   npj Genomic Medicine

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types

(2016) Tianshun Gao et al.   BIOINFORMATICS

Hypoxia promotes production of neural crest cells in the embryonic head

(2016) Deirdre Scully et al.   DEVELOPMENT

Tumour hypoxia causes DNA hypermethylation by reducing TET activity

(2016) Bernard Thienpont et al.   NATURE

5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients

(2016) Kevin C. Johnson et al.   Nature Communications

Age-Dependent Levels of 5-Methyl-, 5-Hydroxymethyl-, and 5-Formylcytosine in Human and Mouse Brain Tissues

(2015) Mirko Wagner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Non-CG Methylation in the Human Genome

(2015) Yupeng He et al.   Annual Review of Genomics and Human Genetics

The development of cisplatin resistance in neuroblastoma is accompanied by epithelial to mesenchymal transition in vitro

(2015) Olga Piskareva et al.   CANCER LETTERS

Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer

(2015) Ke Chen et al.   CELL RESEARCH

Mutational dynamics between primary and relapse neuroblastomas

(2015) Alexander Schramm et al.   NATURE GENETICS

High expression of small GTPase Rab3D promotes cancer progression and metastasis

(2015) Jian Yang et al.   Oncotarget

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers

(2015) Michael Christoph Haffner et al.   Oncotarget

The Role of Snail in EMT and Tumorigenesis

(2014) Yifan Wang et al.   CURRENT CANCER DRUG TARGETS

Genomic distribution and possible functions of DNA hydroxymethylation in the brain

(2014) Lu Wen et al.   GENOMICS

TET1-Mediated Hydroxymethylation Facilitates Hypoxic Gene Induction in Neuroblastoma

(2014) Christopher J. Mariani et al.   Cell Reports

The genetic landscape of high-risk neuroblastoma

(2013) Trevor J Pugh et al.   NATURE GENETICS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

(2012) G. I. Dellino et al.   GENOME RESEARCH

Low values of 5-hydroxymethylcytosine (5hmC), the “sixth base,” are associated with anaplasia in human brain tumors

(2012) Theo F.J. Kraus et al.   INTERNATIONAL JOURNAL OF CANCER

Intermittent Hypoxia Regulates Stem-like Characteristics and Differentiation of Neuroblastoma Cells

(2012) Vasantha Kumar Bhaskara et al.   PLoS One

DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes

(2012) Yong H Woo et al.   Nature Communications

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Inhibition of p600 Expression Suppresses Both Invasiveness and Anoikis Resistance of Gastric Cancer

(2011) Hiroshi Sakai et al.   ANNALS OF SURGICAL ONCOLOGY

High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq

(2011) J. Schodel et al.   BLOOD

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

5-Hydroxymethylcytosine Is Strongly Depleted in Human Cancers but Its Levels Do Not Correlate with IDH1 Mutations

(2011) S.-G. Jin et al.   CANCER RESEARCH

Notch pathway regulation of neural crest cell development in vivo

(2011) Timothy J. Mead et al.   DEVELOPMENTAL DYNAMICS

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

TNF-α/NF-κB/Snail pathway in cancer cell migration and invasion

(2010) Y Wu et al.   BRITISH JOURNAL OF CANCER

Interplay between DNA replication and gene expression: a harmonious coexistence

(2010) Chrystelle Maric et al.   CURRENT OPINION IN CELL BIOLOGY

Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

(2010) Daniel Globisch et al.   PLoS One

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Enhanced Activation of Epidermal Growth Factor Receptor Caused by Tumor-Derived E-Cadherin Mutations

(2008) A. Bremm et al.   CANCER RESEARCH