Kingsford Group's Current Research Interests
We are interested in designing graph and optimization algorithms to extract insight from biological data. In particular, we focus on the following classes of problems:
- Genomics & genome assembly: RNA-seq expression quantification; genome assembly; large-scale sequence search, etc. This work is currently supported by a Data-Driven Invesgator grant from the Gordon and Betty Moore Foundation. It was previously supported by NIH grant 1R21HG006913, and NSF grant CCF-1319998.
- Chromatin structure and function: Algorithms for determining the spatial organization of eukaryotic genomes from Chromosome Conformation Capture data. Supported by NIH grant R01HG007104.
- Protein interactions and networks: Evolution of interactions; protein function prediction; clustering within networks; protein structure prediction. This work was supported by NSF grant EF-0849899 and by NSF grant CCF-1053918/CCF-1256087 (CAREER award).
Previous research interests include:
- Viral evolution: Reassortment in the influenza genome. This work was supported by NIH grant 1R21AI085376.
Recent Research Highlights
Sequence Bloom Trees
Sailfish RNA-seq Quantification
Armatus – Topological Domain Finder
I’ve started a blog at monogrammedchalk.com. Check it out — CS+other stuff. Rarely, if ever, about my research (which will continue to be posted here at my group’s website).
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 😁, and 4 weekends per year are spent traveling, that leaves about 100 weekends to explore Pittsburgh, if you…
Lane Fellow Mingfu Shao was interviewed on the inaugural episode of the “The Bioinformatics Chat” podcast! He talks about his new transcriptome assembler, Scallop. Listen to hear all about Mingfu’s work! You can read a pre-print about Scallop, too.
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’re interested in your thoughts and experiences. We’d really appreciate any feedback you could provide by filling out this short questionnaire: https://goo.gl/forms/3oxntoO5RFahOQOe2 Thanks! Carl…
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.…
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…
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…
Congratulations to Brad Solomon who passed his Ph.D. proposal on Dec. 1, 2016!
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…