Tag Archives: Bioinformatics

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

Abstract Background: Tiling arrays have been the tool of choice for probing an organism’s transcriptome without prior assumptions about the transcribed regions, but RNA-Seq is becoming a viable alternative as the costs of sequencing continue to decrease. Understanding the relative … Continue reading

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Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

Abstract Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors … Continue reading

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An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping

Abstract Background: There are two main technologies for transcriptome profiling, namely, tiling microarrays and high-throughput sequencing. Recently there has been a tremendous amount of excitement about the latter because of the advent of next-generation sequencing technologies and its promises. Consequently, … Continue reading

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ENCODE/modENCODE Consortium Meeting 2009

Ashish Agarwal, LaDeana W. Hillier, Joel Rozowsky, David Koppstein, Andrea Sboner, Lukas Habegger, Jeanyoung Jo, Michael Snyder, Philip Green, Valerie Reinke, Robert H. Waterston, Mark Gerstein, “Transcriptome comparison between tiling arrays and next generation sequencing on matched worm samples, towards … Continue reading

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tYNA: An Online Tool for Analysis of Biological Networks

A summary of Kevin Yip’s tYNA software is available here.

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