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2,633
Resource Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
"... Transcription factors (TFs) and their specific interactions with targets are crucial for specifying geneexpression programs. To gain insights into the transcriptional regulatory networks in embryonic stem (ES) cells, we use chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequenc ..."
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Transcription factors (TFs) and their specific interactions with targets are crucial for specifying geneexpression programs. To gain insights into the transcriptional regulatory networks in embryonic stem (ES) cells, we use chromatin immunoprecipitation coupled with ultra-high-throughput DNA
Versatile Low Power Media Access for Wireless Sensor Networks
, 2004
"... We propose B-MAC, a carrier sense media access protocol for wireless sensor networks that provides a flexible interface to obtain ultra low power operation, effective collision avoidance, and high channel utilization. To achieve low power operation, B-MAC employs an adaptive preamble sampling scheme ..."
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Cited by 1099 (19 self)
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We propose B-MAC, a carrier sense media access protocol for wireless sensor networks that provides a flexible interface to obtain ultra low power operation, effective collision avoidance, and high channel utilization. To achieve low power operation, B-MAC employs an adaptive preamble sampling
A comparison of bayesian methods for haplotype reconstruction from population genotype data.
- Am J Hum Genet
, 2003
"... In this report, we compare and contrast three previously published Bayesian methods for inferring haplotypes from genotype data in a population sample. We review the methods, emphasizing the differences between them in terms of both the models ("priors") they use and the computational str ..."
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Cited by 557 (7 self)
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PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/ software.html). Current high-throughput genotyping technologies, when applied to DNA from a diploid individual, are able to determine which two alleles are present at each locus but not the haplotype information (that is
An analysis of the feasibility of short read sequencing
, 2005
"... Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that rese ..."
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Cited by 23 (1 self)
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Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown
Human DNA methylomes at base resolution show widespread epigenomic differences.
- Nature,
, 2009
"... DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryo ..."
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Cited by 401 (6 self)
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Arabidopsis thaliana were previously achieved using MethylC-Seq 15 or BS-Seq 16 . In this method, genomic DNA is treated with sodium bisulphite (BS) to convert cytosine, but not methylcytosine, to uracil, and subsequent high-throughput sequencing. We performed MethylC-Seq for two human cell lines, H1 human
doi:10.1093/nar/gni170 An analysis of the feasibility of short read sequencing
, 2005
"... Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that rese ..."
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Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
- Nucleic Acids Res
, 2008
"... Novel sequencing technologies permit the rapid production of large sequence data sets. These tech-nologies are likely to revolutionize genetics and bio-medical research, but a thorough characterization of the ultra-short read output is necessary. We gen-erated and analyzed two Illumina 1G ultra-shor ..."
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Cited by 121 (0 self)
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Novel sequencing technologies permit the rapid production of large sequence data sets. These tech-nologies are likely to revolutionize genetics and bio-medical research, but a thorough characterization of the ultra-short read output is necessary. We gen-erated and analyzed two Illumina 1G ultra
Review Article Novel RNA Markers in Prostate Cancer: Functional Considerations and Clinical Translation
"... The availability of ultra-high throughput DNA and RNA sequencing technologies in recent years has led to the identification of numerous novel transcripts, whose functions are unknown as yet. Evidence is accumulating that many of these molecules are deregulated in diseases, including prostate cancer ..."
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The availability of ultra-high throughput DNA and RNA sequencing technologies in recent years has led to the identification of numerous novel transcripts, whose functions are unknown as yet. Evidence is accumulating that many of these molecules are deregulated in diseases, including prostate
Bayesian Analysis of High-Throughput Quantitative Measurement of Protein-DNA Interactions
, 2011
"... Transcriptional regulation depends upon the binding of transcription factor (TF) proteins to DNA in a sequence-dependent manner. Although many experimental methods address the interaction between DNA and proteins, they generally do not comprehensively and accurately assess the full binding repertoir ..."
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repertoire (the complete set of sequences that might be bound with at least moderate strength). Here, we develop and evaluate through simulation an experimental approach that allows simultaneous high-throughput quantitative analysis of TF binding affinity to thousands of potential DNA ligands. Tens
OnlineOpen: This article is available free online at www.blackwell-synergy.com
, 2008
"... synthetic biology; gene network; engineering bacteria. Engineering of synthetic gene circuits is a rapidly growing discipline, currently dominated by prokaryotic transcription networks, which can be easily rearranged or rewired to give different output behaviours. In this review, we examine both a r ..."
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organisms, showing that prokaryotic systems have the potential to tackle questions traditionally associated with developmental biology. Overall, the current advances in synthetic gene synthesis, ultra-high-throughput DNA sequencing and computation are synergizing to drive synthetic gene network design
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