12 Result(s)
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Javier Herrero
Human Genetics
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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
Correction: Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
Nat. Genet. 45, 701–706 (2013); published online 28 April 2013; corrected after print 28 May 2014 In the version of this article initially published, the claim that the ghrelin gene was lost specifically in th...
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Article
Open AccessThe duck genome and transcriptome provide insight into an avian influenza virus reservoir species
Ning Li and colleagues report the whole-genome sequence of the duck, Anas platyrhynchos, a natural host of avian influenza viruses. They examine host response to infection by comparing the lung transcriptomes of ...
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Article
Open AccessThe draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
Naoki Irie and colleagues report the draft genomes of the soft-shell and green sea turtles. Their genome-wide phylogenetic analysis supports the hypothesis that turtles are a sister group of crocodilians and b...
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Article
Open AccessSequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution
Jeramiah Smith, Weiming Li and colleagues report the whole-genome sequence of the sea lamprey, Petromyzon marinus, representing a vertebrate lineage diverged from humans ~500 million years ago. Their analyses def...
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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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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
TranscriptSNPView: a genome-wide catalog of mouse coding variation
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Chapter
Supervised Neural Networks for Clustering Conditions in DNA Array Data After Reducing Noise by Clustering Gene Expression Profiles
In this paper we compare various applications of supervised and unsupervised neural networks to the analysis of the gene expression profiles produced using DNA microarrays. In particular we are interested in t...
