BiRG publications and funding (in reverse chronological order)

More current publications may be listed on Dr. Doom's or Dr. Raymer's on-line CVs.

To appear soon

  • J. Gilder, T. Doom, K. Inman, and D. Krane. "Run-specific limits of detection and quantitation for STR-based DNA testing." To appear in the Journal of Forensic Sciences, January 2007.

  • S. Ramachandran, T. Doom, M. Raymer, and D. Krane. "Parsimony based approach to test the Evolving Master Gene hypothesis for human ALU repeats." Accepted for the Proceedings of the 6th IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2006), August 2006.

  • E. Heizer, D. Raiford, M. Raymer, T. Doom, R. Miller, and D. Krane. "Amino acid cost and codon usage biases in six prokaryotic genomes: A whole genome analysis." Journal of Molecular Biology and Evolution, accepted and in press.

    2006 (partial)

  • D. Raiford, T. Doom, D. Krane, and M. Raymer. "An Investigation of Codon Usage Bias Including Visualization and Quantification in Organisms Exhibiting Multiple Biases". In Proceedings of the Ohio Collaborative Conference on Bioinformatics (OCCBIO) 2006, Athens (OH), June 2006.

  • S. Ramachandran, T. Doom, M. Raymer, and D. Krane. "ALU elements as time series genomic data." In Proceedings of the Ohio Collaborative Conference on Bioinformatics (OCCBIO) 2006, Athens (OH), June 2006.

  • D. Paoletti, T. Doom, M. Raymer, and D. Krane. "Assesing the implications for close relatives in the event of similar but non-matching DNA profiles." Jurimetrics , Vol. 46, No. 2, pp. 161-175, Winter 2006.

    2005

  • P. Anderson, D. Raiford, D. Sweeney, T. Doom, and M. Raymer. "Stochastic model of protease-ligand reactions." Proceedings of the 5th IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2005), Minneapolis, Minnesota, pp 306-310, October 2005.

  • D. Paoletti, T. Doom, C. Krane, M. Raymer, and D. Krane. "Empirical Analysis of the STR profiles resulting from conceptual mixtures." Journal of Forensic Sciences, Vol. 50, No. 6, pp. 1361-1366, November 2005.

  • M. Peterson, T. Doom, and M. Raymer. "GA-facilitated KNN classifier optimization with varying similarity measures." Proceedings of the 2005 IEEE Congress on Evolutionary Computation, vol 3, pp. 2514-2521, 2005.

    2004

  • M. Peterson, T. Doom, and M. Raymer. ``GA-facilitated knowledge discovery and pattern recognition optimization applied to the biochemistry of protein solvation.'' Proceedings of ACM Genetic and Evolutionary Computation Conference (GECCO) 2004, Seattle (WA), pp. 426-437, June 2004.

  • M. Raymer, M. Peterson and T. Doom. ``Knowledge discovery in large biological data sets using hybrid classifier/evolutionary algorithms", Proceedings the 36th Symposium on the Interface: Computational Biology and Bioinformatics , Baltimore, MD, May 26 - 29, 2004.

  • G. Cooper, M. Raymer, T. Doom, D. Krane, and N. Futamura. ``Indexing genomic databases''. Proceedings of 2004 IEEE international symposium on Bioinformatics and Bioengineering (BIBE) , Taichung (Taiwan), pp. 587-591, May 2004.

  • D. Burhans, M. DeJohgh, T. Doom, and M. LeBlanc. ``Bioinformatics in the undergraduate curriculum: Opportunities for computer science educators.'' Proceedings of the ACM Special Interest Group on Computer Science Education (SIGCSE) 2004, Norfolk (VA), March 2004.

  • T. Doom, M. Raymer, and D. Krane. ``Bioinformatics: Where Biology meets Computer Science.'' IEEE Potentials, pgs. 24-28, Vol. 23, No. 1, Feb/March 2004.

  • J. Gilder, S. Ford, T. Doom, M. Raymer, and D. Krane. ``Systematic differences in electropherogram peak heights reported by different version of the Genescan (R) software.'' Journal of Forensic Science, pgs. 92-85, Vol 49, No. 1, January 2004.

    2003

  • M. Raymer, T. Doom, L. Kuhn, and W. Punch. ``Knowledge Discovery in Medical and Biological Datasets Using a Hybrid Bayes Classifier/Evolutionary Algorithm.'' IEEE Transactions on Systems, Man, and Cybernetics, Vol. 33, No. 5, October 2003.

  • J. Gilder, S. Ford, M. Raymer, T. Doom, D. Krane. ``Differences in electropherogram peak heights reported by different versions of the Genescan(R) software.'' 14th International Symposium on Human Identification (Promega), Phoenix (AZ), September, 2003.

  • T. Doom, M. Raymer, D. Krane, and O. Garcia. ``Crossing the interdisciplinary barrier: A baccalaureate computer science option in bioinformatics.'' IEEE Transactions on Education, Volume 46, No. 3, pp 387-393, August 2003.

  • D. Sweeney, M. Raymer, and T. Lockwood, ``Antidiabetic and antimalarial biguanide drugs are metal-interactive antiproteolytic agents,'' Biochemical Pharmacology, In press.

  • W. Thompson, S. Ford, T. Doom, M. Raymer, and D. Krane, ``Evaluating forensic DNA evidence: Breaking open the black box (how to review electronic data).'' The Champion , pgs. 25-28, Vol. XXVII, No. 3, May 2003.

  • J. Gilder, D. Krane, T. Doom and M. Raymer, ``Identifing patterns in DNA change.'' Proceedings of the 2003 Midwest Artificial Intelligence and Cognitive Science Conference, Vol. 34, pgs. 78-84. Columbus OH, April 2003. MS-Word Download. Powerpoint Download.

  • J. Gilder, S. Ford, T. Doom, M. Raymer, and D. Krane, ``Differences in electropherogram peak heights reported by different version of the Genescan software.'' Journal of Forensic Science, submitted for review.

  • W. Thompson, S. Ford, T. Doom, M. Raymer, and D. Krane, ``Evaluating forensic DNA evidence: Essential elements of a competent defense review.'' The Champion, pgs. 16-25 (Cover Story), Vol. XXVII, No. 3, April 2003.

  • D. Millhorn, R. Fyffe, O. Garcia, M. Raymer, T. Doom, D. Krane, et al., ``A genome research institute in Ohio,'' Ohio BRTT Grant, $1,700,000, Period January 2003 - 2005.

    2002

  • M. Peterson, T. Doom, and M. Raymer, ``GA-facilitated cosine classifer optimization with application to the biochemistry of protien-water interactions.'' Bioinformatics Workshop, 6th International Conference/Exhibition on High Performance Computing (HPC-Asia 2002) , Banglore (India), December, 2002.

  • D. Krane, T. Doom, M. Raymer, and O. Garcia, ``An interdisciplinary undergraduate bioinformatics curriculum for biological scientists.'' Journal of College teaching , submitted for review.

  • T. Doom, M. Raymer, D. Krane, and O. Garcia, ``Crossing the interdisciplinary barrier: A baccalaureate computer science option in bioinformatics.'' IEEE Transactions on Education , in press Vol. 46, Num. 3. PDF Download

  • Raymer, M., T. Doom, L. Kuhn, and W. Punch, ``Knowledge Discovery in Medical and Biological Datasets Using a Hybrid Bayes Classifier/Evolutionary Algorithm.'' IEEE Transactions on System, Man, and Cybernetics , accepted.

  • T. Doom, M. Raymer, D. Krane, and O. Garcia, ``A proposed undergraduate bioinformatics curriculum for computer scientists.'' Proceedings of the 2002 ACM Special Interest Group on Computer Science Education (SIGCSE 2002), Convington (KY), February, 2002, 34:78-84. PDF Download

    2001

  • J. Gilder, M. Raymer, T. Doom, ``PocketMol: A Molecular Visualization Program for the Pocket PC.'' poster at the Symposium on Bioinformatics for Drug-Development, Toledo (OH), November, 2001. Powerpoint Download

  • M. Peterson, M. Raymer, T. Doom, ``Prediction Enhancement of Protein-Water Binding Conservation through Evolutionary Computation.'' poster at the Symposium on Bioinformatics for Drug-Development, Toledo (OH), November, 2001. Powerpoint Download

  • D. Sweeney, T. Doom, M. Raymer, ``Profile Combinatorics for Fragment Selection in Comparative Protein Structure Modeling.'' poster at the Symposium on Bioinformatics for Drug-Development, Toledo (OH), November, 2001.

  • J. Gilder, M. Raymer, T. Doom, ``PocketMol: A Molecular Visualization Tool for the PocketPC.'' 2001 IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001), November, 2001. PDF Download

  • D. Sweeney, J. Alter, M. Raymer, T. Doom, ``Profile Combinatorics for Fragment Selection in Comparative Modeling.'' 2001 IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001), November, 2001. Postscript Download

  • T. Doom and O. Garcia, ``Bioinformatics: An option in computer science.'' Proceedings of the 2001 Midwest Artificial Intelligence and Cognitive Science Conference, March, 2001.

  • M. Raymer, T. Doom, and D. Krane (co-P.I.s), ``Crossing the interdisciplinary barrier: An integrated undergraduate program in bioinformatics,'' NSF CISE Educational Innovation Grant #EIA-0122582, $840,300, Period: September 2001 - August 2004.

  • D. Krane, M. Raymer, T. Doom, and O. Garcia (co-P.I.s), ``Commercialization of forensic DNA typing expertise,'' Wright State University Technology Commercialization Grant #664723, $99,951, Period: September 2001 - August 2002.

  • T. Doom, J. Gallager, M. Raymer (co-P.I.s), ``Cluster Computing for Bioinformatics and Biocontrol,'' Ohio Shared Computing Center Resourses Grant.

  • T. Doom (P.I.), ``Development of a bioinformatics option in computer science and engineering,'' Research Initiation Grant, Wright State University, #241656, $8,000, Period: 15 April 2001 - 31 May 2002.
    • Designed by Paul Anderson and Matthew Gerald
    Last modified: Tuesday, 15-Aug-2006 14:35:18 EDT