11 Result(s)
within
Javier Herrero
Bioinformatics
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Article
Open AccessQuantification 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...
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Article
Saturation analysis for whole-genome bisulfite sequencing data
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Article
Open AccessdeconstructSigs: 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...
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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...
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Article
Open AccessAnalysis 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...
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Article
Erratum to: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
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Article
Open AccessGenome 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...
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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.
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Article
Open AccesseHive: 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...
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Article
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
An inability to estimate absolute DNA methylation levels has slowed progress in understanding the role of this epigenetic modification in health and disease. Down et al. describe an algorithm for analyzing methyl...
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Chapter and Conference Paper
Using Perceptrons for Supervised Classification of DNA Microarray Samples: Obtaining the Optimal Level of Information and Finding Differentially Expressed Genes
The success of the application of neural networks to DNA microarray data comes from their efficiency in dealing with noisy data. Here we describe a combined approach that provides, at the same time, an accurat...
