Colorado Computational Pharmacology (CCP)
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Our Mission


Creating novel algorithms and knowledge-based tools for the analysis and interpretation of high-throughput molecular biology data.

Our ultimate goal is augmenting the process of biological discovery through the use of advanced computational techniques. , particularly machine learning and knowledge-based approaches applied to high throughput molecular biology data. We create novel algorithms for the analysis and interpretation of gene expression arrays, proteomics, metabonomics, and combinatorial chemistry. We also create tools for building, maintaining and applying knowledge-bases of molecular biology, and for knowledge-driven inference from multiple biological data types. Finally, we are developing and applying natural language processing techniques for information extraction from and management of the biomedical literature.


Current Projects



"Something I've been doing lately that I'm pretty excited about is assignment of broad semantic classes to biomedical text."

Kevin Bretonnel Cohen

"I'm working on applying the lab's natural language processing to larger corpora (of documents) using, among others, the large Janus cluster in Boulder. . We hope to add to the knowledge base Kevin Livingston is building, KaBOB."

Chris Roeder

NLP Group

  • Improving protein function prediction through integration of evidence from text mining with protein structure analysis.
  • CRAFT NLP: A fully treebanked corpus of full-length biomedical articles, plus evaluation of the performance of text mining tools over this data.
  • Pattern learning for protein-residue relation extraction using distant learning.
  • BioLemmatizer: a lemmatization tool for morphological processing of biomedical text.
  • Exploring an approximate subgraph matching approach in biological event extraction.



Open Source Resources


The common goal of all our projects is to provide the biomedical community with freely available resources to aid scientific discovery. Here you will find a links to our resources that have been distibuted.

Many of our resources are available under the umbrella SourceForge project BioNLP. Individual resources provided there are listed in these links:







Computational Bioscience Program hompage
Computation Bioscience Program lab talks are held weekly and are open to the public.
International Society for Computational Biology (ISCB)



Contact Info


Kathy Thomas
Administrative Coordinator
Computational Bioscience Program
University of Colorado Denver, School of Medicine
12801 E. 17th Ave., Room 6103
Mailstop 8303, PO Box 6511
Aurora, CO 80045
Phone: +1-303-724-3399