Things to do in Pittsburgh

A Ph.D. might span ~240 weekends. If we assume that 1 weekend / month is spent relaxing, watching movies and TV and running errands, 1 weekend / month is spent working ūüėĀ, and 4 weekends per year are spent traveling, that leaves about 100 weekends to explore Pittsburgh, if you‚Ķ

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Sailfish / Salmon User Feedback Survey

We are trying to prioritize our feature development for future versions of Sailfish / Salmon and related tools. If you’ve used our Sailfish or Salmon software, we‚Äôre interested in your thoughts and experiences. We‚Äôd really appreciate any feedback you could provide by filling out this short questionnaire: Thanks! Carl‚Ķ

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Kingsford Group, School of Computer Science, Carnegie Mellon University March 1, 2017 The Kingsford Group in the Computational Biology Department in the School of Computer Science at Carnegie Mellon University invites applications to fill several available postdoc positions.   The Kingsford Group develops a variety of algorithms and analyses related to large-scale genomics and seeks candidates whose research interests lie in that area.…

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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‚Ķ

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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‚Ķ

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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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