01.05.2013 | Stephen B. Montgomery; David L. Goode; Erika Kvikstad; Cornelis A. Albers; Zhengdong D. Zhang; Xinmeng Jasmine Mu; G ..., Genome Research, 2013

Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 ...

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01.05.2013 | Wang, Y., Lu, J., Yu, J., Gibbs, R. A., Yu, F., Genome Research, 2013

Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage ...

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01.05.2013 | Nathan C. Sheffield; Robert E. Thurman; Lingyun Song; Alexias Safi; John A. Stamatoyannopoulos; Boris Lenhard; Grego ..., Genome Research, 2013

Regulatory elements recruit transcription factors that modulate gene expression distinctly across cell types, but the relationships among these remains elusive. To address this, we analyzed matched DNase-seq and gene expression data for 112 human samples representing 72 cell types. We first ...

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01.05.2013 | Malhotra, A., Lindberg, M., Faust, G. G., Leibowitz, M. L., Clark, R. A., Layer, R. M., Quinlan, A. R., Hall, I. M., Genome Research, 2013

Tumor genomes are generally thought to evolve through a gradual accumulation of mutations, but the observation that extraordinarily complex rearrangements can arise through single mutational events suggests that evolution may be accelerated by punctuated changes in genome architecture. To ...

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01.05.2013 | Jeffrey S. McLean; Mary-Jane Lombardo; Michael G. Ziegler; Mark Novotny; Joyclyn Yee-Greenbaum; Jonathan H. Badger; ..., Genome Research, 2013

Although biofilms have been shown to be reservoirs of pathogens, our knowledge of the microbial diversity in biofilms within critical areas, such as health care facilities, is limited. Available methods for pathogen identification and strain typing have some inherent restrictions. In ...

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01.05.2013 | Pouya Kheradpour; Jason Ernst; Alexandre Melnikov; Peter Rogov; Li Wang; Xiaolan Zhang; Jessica Alston; Tarjei S. Mi ..., Genome Research, 2013

Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained unfeasible at the genome scale. Here, we use a massively parallel ...

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01.05.2013 | Fitzsimons, M. S., Novotny, M., Lo, C.-C., Dichosa, A. E. K., Yee-Greenbaum, J. L., Snook, J. P., Gu, W., Chertkov, ..., Genome Research, 2013

The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is ...

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01.05.2013 | Gelfman, S., Cohen, N., Yearim, A., Ast, G., Genome Research, 2013

DNA methylation is known to regulate transcription and was recently found to be involved in exon recognition via cotranscriptional splicing. We recently observed that exon–intron architectures can be grouped into two classes: one with higher GC content in exons compared to the flanking ...

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01.05.2013 | Aaron M. Wenger; Shoa L. Clarke; Harendra Guturu; Jenny Chen; Bruce T. Schaar; Cory Y. McLean; Gill Bejerano, Genome Research, 2013

The human genome encodes 1500–2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant ...

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01.05.2013 | Kirkness, E. F., Grindberg, R. V., Yee-Greenbaum, J., Marshall, C. R., Scherer, S. W., Lasken, R. S., Venter, J. C., Genome Research, 2013

There is increasing evidence that the phenotypic effects of genomic sequence variants are best understood in terms of variant haplotypes rather than as isolated polymorphisms. Haplotype analysis is also critically important for uncovering population histories and for the study of ...

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