RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

JC Marioni, CE Mason, SM Mane, M Stephens… - Genome …, 2008 - genome.cshlp.org
Abstract Ultra-high-throughput sequencing is emerging as an attractive alternative to
microarrays for genotyping, analysis of methylation patterns, and identification of
transcription factor binding sites. Here, we describe an application of the Illumina

[HTML][HTML] Multiple recurrent de novo CNVs, including duplications of the 7q11. 23 Williams syndrome region, are strongly associated with autism

…, MP Moreau, AR Gupta, SA Thomson, CE Mason… - Neuron, 2011 - Elsevier
Summary We have undertaken a genome-wide analysis of rare copy-number variation
(CNV) in 1124 autism spectrum disorder (ASD) families, each comprised of a single
proband, unaffected parents, and, in most kindreds, an unaffected sibling. We find significant

[HTML][HTML] Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons

…, Y Saletore, P Zumbo, O Elemento, CE Mason… - Cell, 2012 - Elsevier
Methylation of the N6 position of adenosine (m6A) is a posttranscriptional modification of
RNA with poorly understood prevalence and physiological relevance. The recent discovery
that FTO, an obesity risk gene, encodes an m6A demethylase implicates m6A as an

[HTML][HTML] Functional and evolutionary insights into human brain development through global transcriptome analysis

MB Johnson, YI Kawasawa, CE Mason, Ž Krsnik… - Neuron, 2009 - Elsevier
Our understanding of the evolution, formation, and pathological disruption of human brain
circuits is impeded by a lack of comprehensive data on the developing brain transcriptome.
A whole-genome, exon-level expression analysis of 13 regions from left and right sides of

[HTML][HTML] An integrated map of structural variation in 2,504 human genomes

…, S McCarthy, P Flicek, RA Gibbs, G Marth, CE Mason… - Nature, 2015 - ncbi.nlm.nih.gov
Summary Structural variants (SVs) are implicated in numerous diseases and make up the
majority of varying nucleotides among human genomes. Here we describe an integrated set
of eight SV classes comprising both balanced and unbalanced variants, which we

[HTML][HTML] Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

…, A Krek, P Zumbo, CE Mason… - Genome …, 2013 - genomebiology.biomedcentral.com
Abstract A large number of computational methods have been developed for analyzing
differential gene expression in RNA-seq data. We describe a comprehensive evaluation of
common methods using the SEQC benchmark dataset and ENCODE data. We consider a

Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis

…, M Hassimi, N Socci, PK Bhatt, M Gonen, CE Mason… - Nature …, 2012 - nature.com
Aging is characterized by clonal expansion of myeloid-biased hematopoietic stem cells and
by increased risk of myeloid malignancies. Exome sequencing of three elderly females with
clonal hematopoiesis, demonstrated by X-inactivation analysis, identified somatic TET2

[HTML][HTML] methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

…, A Melnick, CE Mason - Genome …, 2012 - genomebiology.biomedcentral.com
Abstract DNA methylation is a chemical modification of cytosine bases that is pivotal for
gene regulation, cellular specification and cancer development. Here, we describe an R
package, methylKit, thatrapidly analyzes genome-wide cytosine epigenetic profiles from

[HTML][HTML] L-histidine decarboxylase and Tourette's syndrome

…, K Bilguvar, BJ O'roak, CE Mason… - … England Journal of …, 2010 - Mass Medical Soc
Tourette's syndrome is a common developmental neuropsychiatric disorder characterized by
chronic motor and vocal tics. Despite a strong genetic contribution, inheritance is complex,
and risk alleles have proven difficult to identify. Here, we describe an analysis of linkage in a

The structure of aqueous guanidinium chloride solutions

PE Mason, GW Neilson, JE Enderby… - Journal of the …, 2004 - ACS Publications
The combination of neutron diffraction with isotopic substitution (NDIS) experiments and
molecular dynamics (MD) simulations to characterize the structuring in an aqueous solution
of the denaturant guanidinium chloride is described. The simulations and experiments were