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236
Genome-wide colonization of gene regulatory elements by G4 DNA motifs
- Nucleic Acids Res
, 2009
"... G-quadruplex (or G4 DNA), a stable four-stranded structure found in guanine-rich regions, is impli-cated in the transcriptional regulation of genes involved in growth and development. Previous studies on the role of G4 DNA in gene regulation mostly focused on genomic regions proximal to transcriptio ..."
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G-quadruplex (or G4 DNA), a stable four-stranded structure found in guanine-rich regions, is impli-cated in the transcriptional regulation of genes involved in growth and development. Previous studies on the role of G4 DNA in gene regulation mostly focused on genomic regions proximal to transcription start sites (TSSs). To gain a more comprehensive understanding of the regulatory role of G4 DNA, we examined the landscape of potential G4 DNA (PG4Ms) motifs in the human genome and found that G4 motifs, not restricted to those found in the TSS-proximal regions, are bias toward gene-associated regions. Significantly, ana-lyses of G4 motifs in seven types of well-known gene regulatory elements revealed a constitutive enrichment pattern and the clusters of G4 motifs tend to be colocalized with regulatory elements. Considering our analysis from a genome evolu-tionary perspective, we found evidence that the occurrence and accumulation of certain progenitors and canonical G4 DNA motifs within regulatory regions were progressively favored by natural selection. Our results suggest that G4 DNA motifs are ‘colonized ’ in regulatory regions, supporting a likely genome-wide role of G4 DNA in gene regulation. We hypothesize that G4 DNA is a regulatory apparatus situated in regulatory elements, acting as a molecular switch that can modulate the role of the host functional regions, by transition in DNA structure.
The UCSC Cancer Genomics Browser: update 2013
- Nucleic Acids Res
, 2013
"... The UCSC Cancer Genomics Browser ..."
Trap: A tree approach for fingerprinting subclonal tumor composition
- Nucleic Acids Research
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Identification of ancient remains through genomic sequencing. Genome Res
, 2008
"... Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protoco ..."
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Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla.
Method Integration of ChIP-seq and machine learning reveals
"... enhancers and a predictive regulatory sequence vocabulary in melanocytes ..."
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enhancers and a predictive regulatory sequence vocabulary in melanocytes
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
- Genome Biol
, 2009
"... Bioinformatics, epigenome, statistics, machine learning, computational epigenetics The EpiGRAPH web service ..."
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Bioinformatics, epigenome, statistics, machine learning, computational epigenetics The EpiGRAPH web service
Assisting Scientists with Complex Data Analysis Tasks through Semantic Workflows
, 2010
"... To assist scientists in data analysis tasks, we have developed semantic workflow representations that support automatic constraint propagation and reasoning algorithms to manage constraints among the individual workflow steps. Semantic constraints can be used to represent requirements of input datas ..."
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To assist scientists in data analysis tasks, we have developed semantic workflow representations that support automatic constraint propagation and reasoning algorithms to manage constraints among the individual workflow steps. Semantic constraints can be used to represent requirements of input datasets as well as best practices for the method represented in a workflow. We demonstrate how the Wings workflow system uses semantic workflows to assist users in creating workflows while validating that the workflows comply with the requirements of the software components and datasets. Wings reasons over semantic workflow representations that consist of both a traditional dataflow graph as well as a network of constraints on the data and components of the workflow.
Bauersachs S. Deep sequencing of the porcine endometrial transcriptome on day 14 of pregnancy. Biol Reprod 2013; 88:84
"... In pigs, conceptus attachment to the uterine surface epithelium starts around Day 14 of pregnancy preceded by a pronounced vascularization at the implantation zones, initiating the epitheliochorial placentation. To characterize the complex transcriptome changes in the endometrium in the course of in ..."
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In pigs, conceptus attachment to the uterine surface epithelium starts around Day 14 of pregnancy preceded by a pronounced vascularization at the implantation zones, initiating the epitheliochorial placentation. To characterize the complex transcriptome changes in the endometrium in the course of initial conceptus attachment deep sequencing of endometrial RNA samples of pregnant animals (n = 4) and corresponding cyclic controls (n = 4) was performed using Illumina RNA-Seq. The obtained sequence reads were mapped to the porcine genome and relative expression values were calculated for the analysis of differential gene expression. Statistical analysis revealed 1,933 differentially expressed genes (FDR 1%), 1,229 with higher and 704 with lower mRNA concentration in the samples from pregnant animals. Expression of selected genes was validated by the use of quantitative real-time RT-PCR. The RNA-Seq data were compared to results of a microarray study of bovine endometrium on Day 18 of pregnancy and additional related data sets. Bioinformatics analysis revealed for the genes with higher mRNA concentration in pregnant samples strong overrepresentation particularly for immune-related functional terms but also for apoptosis and cell adhesion. Overrepresented terms for the
Foundations and Tools for End-User Architecting
"... Abstract. Within an increasing number of domains an important emerging need is the ability for technically naïve users to compose computational elements into novel configurations. Examples include astronomers who create new analysis pipelines to process telescopic data, intelligence analysts who mus ..."
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Abstract. Within an increasing number of domains an important emerging need is the ability for technically naïve users to compose computational elements into novel configurations. Examples include astronomers who create new analysis pipelines to process telescopic data, intelligence analysts who must process diverse sources of unstructured text to discover socio-technical trends, and medical researchers who have to process brain image data in new ways to understand disease pathways. Creating such compositions today typically requires low-level technical expertise, limiting the use of computational methods and increasing the cost of using them. In this paper we describe an approach — which we term end-user architecting — that exploits the similarity between such compositional activities and those of software architects. Drawing on the rich heritage of software architecture languages, methods, and tools, we show how those techniques can be adapted to support end users in composing rich computational systems through domain-specific compositional paradigms and component repositories, without requiring that they have knowledge of the low-level implementation details of the components or the compositional infrastructure. Further, we outline a set of open research challenges that the area of end-user architecting raises.
Education Automated Querying of Genome Databases
"... The number of molecular biology databases continues to explode. Presently, few problems in genomic molecular biology can be addressed without analyzing data stored in them. However, these databases reside in many different ..."
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The number of molecular biology databases continues to explode. Presently, few problems in genomic molecular biology can be addressed without analyzing data stored in them. However, these databases reside in many different
