Split Sequence Bloom Trees

The Experiment Discovery Problem Public databases such at the NIH Sequencing Read Archive (SRA) now contain hundreds of thousands of short-read sequencing experiments. A major challenge now is making that raw data accessible and useful for biological analysis — researchers must be able to find the relevant and related experiments…

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Split Sequence Bloom Trees Preprint

Our pre-print on “Split Sequence Bloom Trees” has appeared on bioRxiv: Brad Solomon and Carl Kingsford. Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. See also the simultaneous posting of a related pre-print: Chen Sun, Robert S. Harris, Rayan Chikhi, and Paul Medvedev. AllSome Sequence Bloom…

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Armatus – Topological Domain Finder


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


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


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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