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Genome-wide map of regulatory interactions in the human genome

Genome-wide map of regulatory interactions in the human genome

Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. Researchers at Stanford University School of Medicine generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, ...

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iRegulon: From a Gene List to a Gene Regulatory Network

iRegulon: From a Gene List to a Gene Regulatory Network

Identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. Researchers at the KU Leuven Center for Human Genetics developed a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying ...

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Querying the Cancer Transcriptome

from Genetic Engineering News by Richard A. Stein, M.D., Ph.D. The complex and dynamic transcriptional patterns unveiled by the ENCyclopedia of DNA Elements (ENCODE) project, together with the finding that less than 2% of the transcriptional output of the human ...

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STAR: ultrafast universal RNA-seq aligner

To align their large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, a team of researchers at Cold Spring Harbor Laboratory developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses ...

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RNA-Seq making significant contributions to GENCODE project

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been ...

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How Many Reads are Enough?

There is no question that RNA-Seq has several major advantages over current hybridization-based approach such as microarrays. However, with the cost per sample of RNA-Seq still much higher than microarray, it would be beneficial if multiple samples could be multiplexed ...

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Another weapon in the war against bias

Another weapon in the war against bias

There have been several studies demonstrating the biases inherent to the RNA-Seq method as well as variation in results across protocols and platforms. Researchers have set about innovating methods to correct for these biases and variances, but until now, most ...

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