ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

H Parkinson, M Kapushesky, N Kolesnikov… - Nucleic acids …, 2008 -
Abstract ArrayExpress http://www. ebi. ac. uk/arrayexpress consists of three components: the
ArrayExpress Repository—a public archive of functional genomics experiments and
supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and

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

…, M Wang, F Yu, C Zhang, J Zhang, X Zheng-Bradley… - Nature, 2015 -
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

Demographic history and rare allele sharing among human populations

S Gravel, BM Henn, RN Gutenkunst… - Proceedings of the …, 2011 - National Acad Sciences
Abstract High-throughput sequencing technology enables population-level surveys of
human genomic variation. Here, we examine the joint allele frequency distributions across
continental human populations and present an approach for combining complementary

[HTML][HTML] The functional spectrum of low-frequency coding variation

…, T Blackwell, X Zheng-Bradley… - Genome …, 2011 -
Background Rare coding variants constitute an important class of human genetic variation,
but are underrepresented in current databases that are based on small population samples.
Recent studies show that variants altering amino acid sequence and protein function are

[HTML][HTML] The 1000 Genomes Project: data management and community access

L Clarke, X Zheng-Bradley, R Smith, E Kulesha… - Nature …, 2012 -
The 1000 Genomes Project was launched as one of the largest distributed data collection
and analysis projects ever undertaken in biology. In addition to the primary scientific goals of
creating both a deep catalog of human genetic variation and extensive methods to

[HTML][HTML] Large scale comparison of global gene expression patterns in human and mouse

X Zheng-Bradley, J Rung… - Genome …, 2010 -
Background It is widely accepted that orthologous genes between species are conserved at
the sequence level and perform similar functions in different organisms. However, the level
of conservation of gene expression patterns of the orthologous genes in different species

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

…, M Romanovitch, C Zhang, X Zheng-Bradley… - Nature …, 2016 -
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26
worldwide populations by the 1000 Genomes Project. We discovered more than 65,000
variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB

TF Rayner, FI Rezwan, M Lukk, XZ Bradley… - …, 2008 -
Abstract Summary: The MAGE-TAB format for microarray data representation and exchange
has been proposed by the microarray community to replace the more complex MAGE-ML
format. We present a suite of tools to support MAGE-TAB generation and validation,

[PDF][PDF] Developing an application focused experimental factor ontology: embracing the OBO Community

J Malone, TF Rayner, XZ Bradley… - Proceedings of the …, 2008 -
A BSTRACT Motivation: The recent crop of bio-medical standards has promoted the use of
ontologies for describing data and for use in database applications. The standards
compliant ArrayExpress database contains data from> 200 species and> 110,000 samples

Applications of the 1000 Genomes Project resources

X Zheng-Bradley, P Flicek - Briefings in functional genomics, 2016 -
Abstract The 1000 Genomes Project created a valuable, worldwide reference for human
genetic variation. Common uses of the 1000 Genomes dataset include genotype imputation
supporting Genome-wide Association Studies, mapping expression Quantitative Trait Loci,