21 Result(s)

Article

Aberrant paracrine signalling for bone remodelling underlies the mutant histone-driven giant cell tumour of bone

Oncohistones represent compelling evidence for a causative role of epigenetic perturbations in cancer. Giant cell tumours of bone (GCTs) are characterised by a mutated histone H3.3 as the sole genetic driver p...

Lucia Cottone, Lorena Ligammari, Hang-Mao Lee… in Cell Death & Differentiation (2022)

Article

Author Correction: G-tract RNA removes Polycomb repressive complex 2 from genes

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Manuel Beltran, Manuel Tavares, Neil Justin… in Nature Structural & Molecular Biology (2019)

Article

Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection

Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patt...

James E. Barrett, Andrew Feber, Javier Herrero, Miljana Tanic… in BMC Bioinformatics (2017)

Article

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening

The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large v...

Anna Köferle, Karolina Worf, Christopher Breunig, Valentin Baumann… in BMC Genomics (2016)

Article

deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the...

Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S. Taylor… in Genome Biology (2016)

Article

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidat...

Olgert Denas, Richard Sandstrom, Yong Cheng, Kathryn Beal, Javier Herrero… in BMC Genomics (2015)

Article

Extending reference assembly models

The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles. However, the models and analysis assumptions that underlie the current ass...

Deanna M Church, Valerie A Schneider, Karyn Meltz Steinberg… in Genome Biology (2015)

Article

Stem cells isolated from adipose tissue of obese patients show changes in their transcriptomic profile that indicate loss in stemcellness and increased commitment to an adipocyte-like phenotype

The adipose tissue is an endocrine regulator and a risk factor for atherosclerosis and cardiovascular disease when by excessive accumulation induces obesity. Although the adipose tissue is also a reservoir for...

Blanca Oñate, Gemma Vilahur, Sandra Camino-López, Alberto Díez-Caballero… in BMC Genomics (2013)

Article

Analysis of variation at transcription factor binding sites in Drosophila and humans

Advances in sequencing technology have boosted population genomics and made it possible to map the positions of transcription factor binding sites (TFBSs) with high precision. Here we investigate TFBS variabil...

Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal… in Genome Biology (2012)

Article

Erratum to: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay… in Genome Biology (2011)

Article

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hop** mammals that symbolize Australia to be sequenced...

Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay… in Genome Biology (2011)

Article

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol2010, 11:R16.

Albert J Vilella, Ewan Birney, Paul Flicek, Javier Herrero in Genome Biology (2011)

Article

eHive: An Artificial Intelligence workflow system for genomic analysis

The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomi...

Jessica Severin, Kathryn Beal, Albert J Vilella, Stephen Fitzgerald… in BMC Bioinformatics (2010)