Daniel Quest
Department of Pathology and Microbiology
University of Nebraska Medical Center
Omaha, NE 68198
(402)554-6004
djquest nospam [at] unmc dot edu
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Daniel Quest Department of Pathology and Microbiology University of Nebraska Medical Center Omaha, NE 68198 (402)554-6004 djquest nospam [at] unmc dot edu |
Research Interests:
Bioinformatics, Algorithms, Machine Learning, Data Mining, High Performance Computing, Gene Regulatory Circuits, Software Engineering, Ontologies and Semantic Knowledge Representation, RNA structure prediction.
Valuable Websites:
Bioinformatics Lab internal BLOG: Blog
Collaborators:
Alexander Churbanov Website,
Kiran Bastola
Steve Hinrichs
Hesham Ali
Software:
GIGO gene is a RNA-DNA homology based annotation system for Human, Mouse, Rat, and other higher eukaryotes. The most recient version of GIGO gene is availible here: Alexander's Website or here: Alexander's Website
AGAST: The Advanced Gramar Alignment Search Tool (Please e-mail me software requests)
MTAP: The Motif Assessment Tool Pipeline pre-Alpha Release from the CSB 2006 Poster is availible here: motif pipeline
Our Motif Tool Encyclopedia is availible here: Motif Encyclopedia
List of Publications:
Books:
1. Deitel & Assoiciates, Inc., Mark A. Pauley and Daniel Quest, Laboratory Manual to Accompany
C++ How to Program, 2nd Edition, Pearson Custom Publishing, Boston (2002) (ISBN 0-536-66753- 5).
2. Deitel & Assoiciates, Inc., Mark A. Pauley and Daniel Quest, Laboratory Manual to Accompany
C++ How to Program, Pearson Custom Publishing, Boston (2000) (ISBN 0-536-62095-4).
Journal and Conference Articles:
1. Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, and Hesham Ali. MTAP: A Motif Tool Assessment Pipeline for Automated Assessment of De Novo Regulatory Motif Discovery Tool. BMC Bioinformatics (In Press). Expected 2008.
2. Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, and Hesham Ali. A Parallel Architecture for Regulatory Motif Algorithm Assessment. HiCOMB 2008: Seventh IEEE International Workshop on High Performance Computational Biology. April 14th 2008. [ PREPRINT (MOST COMPLETE)] [ CAMERA READY] [ SUPLEMENTAL]
3. Daniel Quest, William Tapprich, Hesham Ali. A Robust Grammar Based Methodology for RNA Database Search and Analysis. Computational Systems Bioinformatics (CSB) 2007.
4. Alexander Churbanov, Mark Pauley, Daniel Quest, Hesham Ali. A Method of Precise mRNA/DNA Homology-Based Gene Structure Prediction. BMC Bioinformatics,6:1 p 261. 2005.
5. Daniel Quest, Hesham H. Ali. A Grammar Based Approach for Mining Bioinformatics Databases. Proceedings of the 38th Annual Hawaii International Conference on System Sciences (HICSS'05) Track 9, p 280b. January 03-06, 2005.
6. Alexandre Tchourbanov, Daniel Quest, Hesham H. Ali, Mark Pauley, Robert Norgren. A New Approach for Gene Annotation Using Unambiguous Sequence Joining. Computational Systems Bioinformatics (CSB), p 353-362. 2003.
Short Papers, Abstracts, and Posters:
1. D. Quest, K. Dempsey, M. Shafiullah, D. Bastola, and H. Ali. An Automated Assessment of Regulatory Motif Detection Tools. A poster presentation at the New Mexico Bioinformatics Symposium, Santa Fe, NM. March 9, 2007.
2. D. Quest, K. Dempsey, M. Shafiullah, D. Bastola, and H. Ali. An Assessment of Regulatory Motif Discovery Tools on Prokaryote Genomes. Pacific Symposium on Biocomputing (PSB). 2007.
3. D Quest, K. Dempsey, D. Bastola, and H. Ali. An Automated Pipeline for Regulatory Motif Tool Assessment. Computational Systems Bioinformatics (CSB). 2006.
4. Daniel Quest, Hesham H. Ali. AGAST: Advanced Grammar Alignment Search Tool. Pacific Symposium on Biocomputing (PSB), p 118. 2005.
5. Daniel Quest, Hesham H. Ali. Ontology Specific Data Mining, Based on Dynamic Grammars. Computational Systems Bioinformatics (CSB), p 495-496. 2004.
Presentations:
1. D. Quest. Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations. Presented to the University of Nebraska Medical Center Department of Pathology Microbiology. April 24, 2007.
2. K. Dempsey, D. Quest. On the Development of an Automated Assessment Approach of Motif Detection Tools. Presented at the Nebraska Academy of Sciences Meeting, Lincoln, NE. March 2007.
3. D. Quest. The Motif Assessment Tool Platform and The Motif Tool Encyclopedia. Defended as a comprehensive examination and presented to the University of Nebraska Medical Center Department of Pathology and Microbiology. May 2007.
4. D. Quest. Towards A Computational Method for de novo Prokaryote Regulatory Motif Discovery. Presented to the University of Nebraska Medical Center Department of Pathology and Microbiology Research Seminar. January 31, 2007.
5. D. Quest. A Sequence-Based Filtering Method for ncRNA Identification and its Application to Searching for Riboswitch Elements. Presented to the University of Nebraska Bioinformatics Researchers. March 21 2007.
6. D. Quest. Fundemental Issues of Systems Biology. Presented to the University of Nebraska Bioinformatics Researchers. November 27, 2006.
7. D. Quest and K. Dempsey. Automated Regulatory Motif Assessment. A poster presentation at the 4th Annual Nebraska Idea Networks of Biomedical Research Excellence (INBRE) Meeting. Grand Island, NE. August 10, 2006.
8. K. Dempsey, D. Quest, D. Bastola, and H. Ali. Motif Detection in Staphylococcus Aureus. An abstract and oral presentation for the Nebraska Academy of Sciences Meeting. Lincoln, NE. April 21, 2006.
9. D. Quest. Short Tandem Repeat Repeat Profiling Provides an International Reference Standard for Human Cell Lines. Presented to the University of Nebraska Medical Center Department of Pathology and Microbiology. March 2006.
10. D. Quest. A Grammar Based Filtering and Searching Tool for Sequence Data. Presented to the University of Nebraska Medical Center Department of Pathology and Microbiology Research Seminar. October 2005.
11. D. Quest. Biomedical Ontologies. Presented to the University of Nebraska Medical Center Department of Pathology and Microbiology. February 2005.
12. D. Quest. Genbank Data Mining Based on Dynamic Grammars. A poster presentation at the 2nd Annual Nebraska Idea Networks of Biomedical Research Excellence (INBRE) Meeting. Grand Island, NE. August 2004.
13. D. Quest. Phylogeny and Conservation of Amino Acids in Invertase, A Bioinformatics Approach. Presented to the Department of Arts and Sciences of the University of Nebraska at Omaha. December, 2004.
14. D. Quest. Solving the Gene Duplication and Loss Problem with Simulated Annealing. Presented to the Department of Computer Science at Iowa State University, Ames Iowa. May 2003.