Publications

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

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Abstract Genome3D, available at http://www. genome3d. eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE,

Recommended citation: http://nar.oxfordjournals.org/content/41/D1/D499.short

The SUPERFAMILY 1.75 database in 2014: a doubling of data

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Abstract We present updates to the SUPERFAMILY 1.75 (http://supfam. org) online resource and protein sequence collection. The hidden Markov model library that provides sequence homology to SCOP structural domains remains unchanged at version 1.75. In the last 4

Recommended citation: http://nar.oxfordjournals.org/content/43/D1/D227.short

An atlas of active enhancers across human cell types and tissues

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Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5

Recommended citation: http://www.nature.com/nature/journal/v507/n7493/abs/nature12787.html

WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools

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Abstract Motivation: As the number of studies looking at differences between DNA methylation increases, there is a growing demand to develop and benchmark statistical methods to analyse these data. To date no objective approach for the comparison of these

Recommended citation: http://bioinformatics.oxfordjournals.org/content/early/2015/03/25/bioinformatics.btv114.short

SUPERFAMILY 1.75 including a domain-centric gene ontology method

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Abstract The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 metagenomes and other gene collections such as UniProt. All models

Recommended citation: http://nar.oxfordjournals.org/content/early/2010/11/08/nar.gkq1130.short

The evolution and structure prediction of coiled coils across all genomes

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Coiled coils are α-helical interactions found in many natural proteins. Various sequence-based coiled-coil predictors are available, but key issues remain: oligomeric state and protein–protein interface prediction and extension to all genomes. We present SpiriCoil

Recommended citation: http://www.sciencedirect.com/science/article/pii/S0022283610009101

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

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Abstract To help evaluate how protein function impacts on genome evolution, we introduce a new concept of 'architecture plasticity potential'–the capacity to form distinct domain architectures–both for an individual domain, or more generally for a set of domains grouped

Recommended citation: http://www.sciencedirect.com/science/article/pii/S0300908415001376

Genome3D: exploiting structure to help users understand their sequences

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Abstract Genome3D (http://www. genome3d. eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the

Recommended citation: http://scholar.google.com/https://academic.oup.com/nar/article-lookup/43/D1/D382

The evolution of human cells in terms of protein innovation

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Abstract Humans are composed of hundreds of cell types. As the genomic DNA of each somatic cell is identical, cell type is determined by what is expressed and when. Until recently, little has been reported about the determinants of human cell identity, particularly

Recommended citation: http://mbe.oxfordjournals.org/content/early/2014/04/03/molbev.mst139.short

Exploring uncertainties in the relationship between temperature, ice volume, and sea level over the past 50 million years

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Abstract [1] Over the past decade, efforts to estimate temperature and sea level for the past 50 Ma have increased. In parallel, efforts to model ice sheet changes during this period have been ongoing. We review published paleodata and modeling work to provide insights into

Recommended citation: http://onlinelibrary.wiley.com/doi/10.1029/2011RG000358/full

A daily-updated tree of (sequenced) life as a reference for genome research

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Abstract We report a daily-updated sequenced/species Tree Of Life (sTOL) as a reference for the increasing number of cellular organisms with their genomes sequenced. The sTOL builds on a likelihood-based weight calibration algorithm to consolidate NCBI taxonomy

Recommended citation: http://www.nature.com/articles/srep02015?message-global=remove&message-global%3Dremove%26WT.ec_id%3DSREP-631-20130701

A proteome quality index

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Summary We present the Proteome Quality Index (PQI; http://pqi-list. org), a much-needed resource for users of bacterial and eukaryotic proteomes. Completely sequenced genomes for which there is an available set of protein sequences (the proteome) are given a one-to

Recommended citation: http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12622/full

A predictive computational framework for direct reprogramming between human cell types

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Transdifferentiation, the process of converting from one cell type to another without going through a pluripotent state, has great promise for regenerative medicine. The identification of key transcription factors for reprogramming is currently limited by the cost of exhaustive

Recommended citation: http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3487.html

A Ca2+-based computational model for NMDA receptor-dependent synaptic plasticity at individual post-synaptic spines in the hippocampus

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Associative synaptic plasticity is synapse specific and requires coincident activity in pre-synaptic and post-synaptic neurons to activate NMDA receptors (NMDARs). The resultant Ca2+ influx is the critical trigger for the induction of synaptic plasticity. Given its centrality for

Recommended citation: http://books.google.com/books?hl=en&lr=&id=hWV6VTSeBzsC&oi=fnd&pg=PA345&dq=Owen+Rackham&ots=2BPHGPLntx&sig=0LDI46PY1uUy7md6699Sc1iRluQ