14 Result(s)

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

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...

Zhuo Wang, Juan Pascual-Anaya, Amonida Zadissa, Wenqi Li… in Nature Genetics (2014)

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

The 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 ...

Yinhua Huang, Yingrui Li, David W Burt, Hualan Chen, Yong Zhang… in Nature Genetics (2013)

Article

The 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...

Zhuo Wang, Juan Pascual-Anaya, Amonida Zadissa, Wenqi Li… in Nature Genetics (2013)

Article

Sequencing 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...

Jeramiah J Smith, Shigehiro Kuraku, Carson Holt, Tatjana Sauka-Spengler… in Nature Genetics (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

TranscriptSNPView: a genome-wide catalog of mouse coding variation

Fiona Cunningham, Daniel Rios, Mark Griffiths, James Smith, Zemin Ning… in Nature Genetics (2006)