Armatus – Topological Domain Finder

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Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains…

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Sailfish RNA-seq Quantification

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RNA-seq expression estimates need not take longer than a cup of coffee The quantification of gene or isoform abundance is a fundamental step in many transcriptome analysis tasks, such as determining differential expression between biological samples. Yet, estimating isoform abundance from a large set of RNA-seq reads remains a computationally…

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Sequence Bloom Trees

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Querying a short read database for a transcript of interest is a fundamental problem in biology. Yet such queries are computationally intensive and scale linearly with the size of the data being searched. This leads to a computational bottleneck in which large databases of sequencing reads are compiled but never…

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Archived News

Sep. 2016: Dan DeBlasio, Ph.D. was elected to the ISCB Student Council Leadership (as Student Council Representative to ISCB Board of Directors). Sep. 2016: Hao Wang, Ph.D. successfully defended her Ph.D. August 2016: Hao Wang, Ph.D. student in the group, receives the CPCB Research award for her research contributions during…

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