Although Computational Bioscience is a young program at UCDHSC, the faculty have published in such prestigious publications as Nature, Science, and The Proceedings of the National Academy of Sciences. They have also been awarded millions of dollars in grants from the National Institutes of Health, the National Science Foundation and other highly competitive organizations.

Details of each faculty member’s research interests and relevant publications can be found on their individual home pages.

Active Grants:
Dr. Lawrence Hunter
http://compbio.uchsc.edu/ccp
Technology Development For a Molecular Biology Knowledge Base
NIH 2R01 LM008111-04A1 (Principal Investigator)
The goal of this project is to demonstrate that database integration and natural language information extraction technology are adequate to produce in automated fashion a broad, deep knowledge base for molecular biology.

Beyond Abstracts: Issues in Mining Full Texts
NIH 5R01 LM 009254-01 (Principal Investigator)
This research tests the following hypothesis: Creation of large, high-quality, biomedical corpora from full text genres will lead to significant improvement in the performance of biomedical text mining systems and the creation of new approaches to text mining tasks. Specific aims include constructing several large corpora covering a range of genres and incorporating a rich knowledge representation; identifying factors that affect differential performance on full text versus abstracts; and developing new methods for language processing, especially of full text.

Bioscience Training Program
NIH T15 LM009451-01 (Principal Investigator)
This grant supports the Colorado Bioscience Program's outstanding training program with scholarships, travel funds, and other resources.

Ontologies and Biomedical Language Processing

NIH 1R01GM083649-01A1 (Principal Investigator)

The goal of this project is to explore bot6h the potential for, and obstacles to, the mutual application of biomedical ontologies and biomedical language processing.

Construction of a Full Text Corpus for Biomedical Text Mining

NIH 1G08LM009639-01 (Principal Investigator)

The goal of this project is to build a team that includes the builder of the largest semantically annotated corpus to date, one of the pioneers of the model organism databases, and an already-assembled cadre of experienced linguistic  and domain-expert annotators.

Dr. Debra Goldberg
http://www.cs.colorado.edu/~debra

Dr. Katherina J. Kechris
http://pmb.uchsc.edu/faculty/Kechris

Recently awarded:

Genomic Regulatory Sequence Analysis For Alcohol-Related Phenotypes.  5 year NIH/NIAAA K01 Career Development Award for the project

Using Comparative Genomics to Find Functional Signatures of Human Non-Coding Sequences and Identifying Horizontal Gene Transfer in Bacterial Genomes
NIH R01 GM075312. (Co-Investigator)
The project has two primary research goals:
• Development of methodology for finding functionally predictive signatures
   of non-coding sequences highly conserved across multiple species
• Development of novel approaches for detecting horizontal gene transfer

Gene Array Technology Center for Alcohol Research
NIH R01 AA13162. (Co-Investigator)
The goal of this center is to provide a national resource for alcohol researchers in the area of microarray technology, assisting qualified investigators in the collection and analysis of microarray gene expression data.

Dr. Robin Knight
http://www.colorado.edu/chem/people/knightr.html
Identifying Secreted Bacterial Proteins That Act on Host Cells With Bioinformatics and Genetics
Butcher Foundation (Co-Principal Investigator)
The goal of this project is to develop novel methods for identifying Type III secreted effectors in Salmonella, and to test these predictions in vitro.

Improving Motif-Based Alignment Strategies
W.M. Keck Foundation, Keck RNA Bioinformatics Initiative (Principal Investigator)
The goal of this project is to develop better methods for aligning unaligned RNA sequences, based on alignment ‘seeds.’

Dr. Dennis Lezotte
http://pmb.uchsc.edu/faculty/Lezotte
National Database Coordinating Center for Burn Model Systems
(BMS/DCC) (Center Director and Principal Investigator)
Department of Education/NIDDR H133A30015.
The goal of this project is to:
• Maintain a four–center longtitudinal database of patients seen and treated at
   one of the Model Systems For Burn Injury Care and Rehabilitation
• To provide study design and analytical support for conducting collaborative
   clinical and outcomes research at these model systems supported by
   NIDRR research grants

Dr. David Osguthorpe

Dr. David Pollock
http://pmb.uchsc.edu/faculty/pollock
Protein Sequence, Structure and Computational Analysis
NIH 1R21GM065612-01. (Principal Investigator)
This study developed fundamental understanding of the relationship between protein sequence, structure, and function. The understanding was achieved through development of innovative computational and statistical technologies to analyze patterns of protein evolution and co-evolution. Researchers also developed methods to manage and visualize sequence, structure, function and phylogenies for large, taxonomically diverse datasets.

Louisiana’s Strategic Infrastructure Improvement
National Science Foundation EPSCOR. (Co-Investigator)
The major goal of this project is to advance BioMems research in the State of Louisiana.