Education

Computer Science and Engineering, Ph.D. (1998)


Computer Science and Engineering, M.S. (1994)

Michigan State University, East Lansing, MI.
Thesis: Design Recovery for Combinational Logic Exploiting Boolean Relationships.
Advisor: Professor Anthony S. Wojcik
Focus: Design automation, Formal Analysis of Digital Systems, Computer Architecture/Systems, Distrubuted Computing, and Computational Mathematics.

Computer Science, B.S. (1992)
Mathematics & Statistics, B.S. (1992)

Bowling Green State University, Bowling Green, OH.
Minor Cognate: Microcomputer Electronics
Magna Cum Laude with University Honors and Thesis
Focus: Computer Engineering, Digital Systems, Computational Mathematics.

Work Experience

Wright State University, Dayton, OH.

Associate Professor of Computer Science and Engineering [with Tenure] (2004+)
Associate Professor of Electrical Engineering (by courtesy, 2004+)
Faculty member of Biomedical Sciences Ph.D. Program (2003+)
Faculty member of WSU Graduate Program (2000+)
Assistant Professor of Electrical Engineering (by courtesy, 1999-promotion)
Assistant Professor of Computer Science and Engineering (1998-promotion)

Argonne National Laboratory, Argonne, IL.

Research Scientist (STA) (1997-1998)

Intel Corporation, Hillsboro, OR.

Performance Engineer (STA) (1996)

Michigan State University, East Lansing, MI.

Instructor (1998)
System Administrator (1994-1997)
Lead Teaching Assistant (1993-1994)
Teaching Assistant (1992-1993)

Research Interests

Research interests include design automation, computational biology, high-performance computer architecture and systems, performance evaluation/operational analysis, distributed/parallel systems, and computational theory.

An undergraduate program in bioinformatics: Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of experimental molecular biology and biochemistry, and from the the artificial intelligence, database, and algorithms disciplines of computer science. Largely because of the inherently interdisciplinary nature of bioinformatics research, academia has been slow to respond to strong industry and government demands for trained scientists to develop and apply novel bioinformatics techniques to the rapidly-growing, freely-available repositories of genetic and proteomic data. This research is focused on the creation of a complete and cohesive program of study to allow baccalaureate degree program students opportunities to prepare themselves to take part in the basic research of this emerging discipline and be immediately available to meet the workforce needs of the nation.

Automation of forensic DNA evidence analysis: Forensic DNA evidence is typically generated and interpreted by state or federal crime laboratories who assist prosecutors both before and during trial. This research investigates the automation of the analysis of this data to allow attorneys and experts to more affordabily and objectively determine if forensic DNA evidence has been reliably generated and interpreted. The development of an automated and objective system for such analysis has the potential to facilitate such screenings on a large scale and to help objectively standardize significance for forensic DNA testing results.

Design recovery for digital systems: The goal of digital reengineering is to respecify or remanufacture an electronic part, board, or system without resorting to a complete redesign of the system. Reengineering techniques reported in the literature make the simplifying assumption that complete design information is available at some level of description. In practice, the recovery of design is exceptionally challenging since often only partial information about the design is available. In this project we attempt to provide a systematic methodology for representing full or partial functionality, reconstructing missing information, detecting conflicts, and identifying high-level functionality of known or recovered components. We also attempt to produce behavioral-level descriptions from structural-level information obtained from digital components. Existing syntactic techniques that attempt this task depend upon exact structural matching of components and are thus subject to failure in the presence of optimizations or intentional obfuscation. Our semantic approach attempts to identify behavioral-level modules by finding component matchings for subcircuit functionality.

Teaching Interests

Teaching interests include both undergraduate and graduate computer science, computer engineering, and electrical engineering courses. Particular areas of teaching interest include bioinformatics, digital systems design, computer architecture, design automation, operating systems, telecommunications/data networks, parallel/distributed systems, and theoretical computer science.

Grants

• D. Millhorn, T. Boat, R. Fyffe, et al, "A genome research institute in Ohio," Ohio BRTT Grant. Award amount: $1,700,000. Raymer, Doom, Krane (co-PIs) on subcomponent grant under this award. Subcomponent award amount: $427,642. Period: January 2003 - January 2005.
  
• M. Raymer, T. Doom, and D. Krane (co-PIs), "Crossing the interdisciplinary barrier: An integrated undergraduate program in bioinformatics," NSF CISE Research Infrastructure Grant #EIA-0122582, Award amount: $552,056. Period: September 2001 - August 2004.
  
• D. Krane, M. Raymer, T. Doom, and O. Garcia (co-PIs), "Commercialization of forensic DNA typing expertise," Wright State University Technology Commercialization Grant #664723. Award amount: $99,951. Period: September 2001 - August 2002.
  
• T. Doom, J. Gallager, M. Raymer (co-PIs), "Cluster Computing for Bioinformatics and Biocontrol," Ohio Shared Computing Center Resources Grant. Award: A cluster of eight two-processor systems with a value of approximately $50,000. Sept 2001.
  
• T. Doom (PI), "Development of a bioinformatics option in computer science and engineering," Research Initiation Grant, Wright State University, #241656. Award amount: $8,000. Period: April 2001 - May 2002.
  
• T. Doom (PI), "Algorithms for functional identification in the reengineering of digital systems," Research Challenge Grant, Wright State University, #663641. Award amount: $25,000. Period: February 1999 - August 2000.
  

Scholarship

Peer-reviewed articles and papers
D. Raiford, D. Krane, T. Doom, and M. Raymer. "Direct search-based approach for isolating translational efficiency bias." Submitted to IEEE/ACM Trans. on Bioinformatics and Computational Biology (TCBB).
P. Anderson, N. Reo, N. DelRaso, T. Doom, and M. Raymer. "Gaussian binning: A new kernel-based method for processing NMR spectroscopic data for metabolomics." To appear in Metabolomics.
D. Raiford, D. Krane, T. Doom, and M. Raymer. "Automated isolation of translational efficiency biases that resists the confounding effect of GC(AT)-content." IEEE/ACM Trans. on Bioinformatics and Computational Biology (TCBB), June 2008.
D. Raiford, D. Krane, T. Doom, and M. Raymer. "A multi-objective genetic algorithms that employs a hybrid approach for isolating codon usage bias indicative of translational efficiency." Proceedings of the Seventh IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2007), pages 278-285, Cambridge (MA), October 2007.
B. Kelly, P. Anderson, N. Reo, N. DelRaso, T. Doom, and M. Raymer. "A proposed statistical protocol for the analysis of metabolic toxicological data derived from NMR spectroscopy." Proceedings of the Seveth IEEE Symposum on Bioinformatics and Bioengineering (BIBE 2007), pages 1414-1418, Cambridge (MA), October 2007.
J. Gilder, T. Doom, K. Inman, and D. Krane. "Run-specific limits of detection and quantitation for STR-based DNA testing." 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." Proceedings of the 6th IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2006), Washington D.C., October 2006. (Best Original Research Paper Award, also Best Student Paper Award).
D. Raiford, D. Krane, T. Doom, and M. Raymer. "Isolation and visualization of codon usage biases." Proceedings of the 6th IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2006), pages 179-182, Washington D.C., October 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, Vol. 23, No. 9, pp, 1670-1680, September 2006.
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.
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.
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.
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.
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.
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 Sciences, pgs. 92-95, Vol 49, No. 1, January 2004.
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.
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.
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, Columbus OH, April 2003.
W. Thompson, S. Ford, T. Doom, M. Raymer, and D. Krane. "Evaluating forensic DNA evidence: Essential elements of a competent defense review." The Champion, (cover) pgs. 16-25, Vol. XXVII, No. 3, April 2003.
J. Gilder, M. Peterson, J. Wright, and T. Doom. "A versatile tool for student projects: An ASM programming language for the LEGO mindstorm." ACM Journal on Educational Resources in Computing (JERIC), III:1, ISSN: 1531-4278, March 2003.
M. Peterson, T. Doom, and M. Raymer. "GA-facilitated cosine classifer optimization with application to the biochemistry of protein-water interactions." Proceedings of the 6th International Conference/Exhibition on High Performance Computing (HPC-Asia 2002), Banglore (India), December 2002.
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), Covington (KY), February 2002.
J. Gilder, M. Raymer, and T. Doom. "PocketMol: A Molecular Visualization Tool for the PocketPC." 2001 IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001), November 2001.
D. Sweeney, J. Alter, M. Raymer, and T. Doom. "Profile Combinatorics for Fragment Selection in Comparative Modeling." 2001 IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001), November 2001.
J. White, M.C. Chung, A. Wojcik, and T. Doom. "Efficient algorithms for subcircuit enumeration and classification." Proceedings of the 2001 IEEE Conference on Computer Design, Austin (TX), September 2001.
C. Leighber and T. Doom. "Using output signatures to enhance semantic matching." Proceedings of the 44th IEEE Midwest Symposium on Circuits and Systems , Dayton (OH), August 2001.
T. Doom and O. Garcia. "Bioinformatics: An option in computer science." Proceedings of the 2001 Midwest Artificial Intelligence and Cognitive Science Conference, March 2001.
J. White, A. S. Wojcik, M. Chung, and T. Doom. "Candidate subcircuits for functional module identification in logic circuits." Proceedings of the 2000 Great Lakes Symposium on VLSI, March, 2000.
T. Doom, A. S. Wojcik, and M. Chung. "Design recovery for incomplete combinational logic." Proceedings of the IEEE 1999 Great Lakes Symposium on VLSI, March, 1999.
T. Doom, J. White, A. S. Wojcik, and G. Chisholm. "Identifying high-level components in combinational circuits." in Proceedings of the IEEE 1998 Great Lakes Symposium on VLSI, February, 1998.
Book chapters, letters, abstracts, and other non peer-reviewed technical communications
M. Peterson, T. Doom, and M. Raymer. "GA-facilitated classifier optimization with varying similarity measures." Abstract and poster at the ACM Genetic and Evolutionary Computation Conference (GECCO) 2005, April 2005.
S. Ramachandran, N. Futamura and T. Doom. "Hardware Implementation of a Scalable, Efficient and High Speed lookup Algorithm for IP Routing." Proceedings of the First Annual Ohio Graduate Student Symposium on Computer and Information Science & Engineering (OGSS 2004), June 10, 2004.
S. Khetarpal, S. Ramachandran, and T. Doom. "A survey of hardware description languages for high level synthesis." Proceedings of the First Annual Ohio Graduate Student Symposium on Computer and Information Science & Engineering (OGSS-CISE 2005), June 10, 2005.
D. Krane, T. Doom, L. Mueller, M. Raymer, W. Shields, and W. Thompson. "Commentary on: Budowle B, Shea B, Niezgoda S, Chakraborty R. CODIS STR loci data from 41 sample populations. J Forensic Sci 2001; 46:453-489." Journal of Forensic Sciences, Vol. 49, No. 6, pgs. 1388-1389, November 2004.
D. Krane, M. Raymer, and T. Doom. "An interdisciplinary undergraduate bioinformatics curriculum for biological scientists." Journal of College Science Teaching, XXXII:296.
T. Doom. Appendix Chapter B.1 "Introduction to Altera MAX+plus II" of D. Givone's Digital Principles and Design, McGraw-Hill, 2002.
J. Gilder, M. Raymer, and T. Doom. "PocketMol: A Molecular Visualization Program for the Pocket PC." Abstract and poster at the Symposium on Bioinformatics for Drug-Development, Toledo (OH), November 2001.
M. Peterson, M. Raymer, and T. Doom. "Prediction Enhancement of Protein-Water Binding Conservation through Evolutionary Computation." Abstract and poster at the Symposium on Bioinformatics for Drug-Development, Toledo (OH), November 2001.
D. Sweeney, T. Doom, and M. Raymer. "Profile Combinatorics for Fragment Selection in Comparative Protein Structure Modeling." Abstract and poster at the Symposium on Bioinformatics for Drug-Development, Toledo (OH), November 2001.
K. Velichetii and T. Doom. "A framework for design recovery of digital systems." Proceedings of the On-line Symposium for Electronics Engineers, November 28, 2000.
K. Dowd and C. Severance. High Performance Computing. 2nd Edition, O'Riley & Associates, Inc., 1999. [Dr. Doom is acknowledged for contributions to the technical content of this book].
T. Doom, J. White, and A. S. Wojcik. "Design recovery for incomplete combinational Logic." Record of the Argonne/DoD Workshop on Reverse Engineering of Digital Systems , January 1998.
J. White, T. Doom, and A. S. Wojcik. "Candidate subgraph enumeration to facilitate design recovery." Record of the Argonne/DoD Workshop on Reverse Engineering of Digital Systems , January 1998.
T. Doom, J. White, G. Chisholm, and A. S. Wojcik. "The identification of functional components in combinational circuits." Tech. Rep. ANL/DIS/TM-47, Division of Information Science, Argonne National Laboratory, January 1998.
J. White, T. Doom, A. Wojcik, M. Chung, and G. Chisholm. "Candidate subcircuit generation to facilitate identification of high-level components in logic circuits." Tech. Rep. MSUCPS:TR97-48 Department of Computer Science, Michigan State University, December 1997.
A. Wojcik, C. Wey, T. Doom, and J. Samarziya. "An approach to the redesign of digital circuits from partial information." Tech. Rep. MSUCPS:TR97-47 Department of Computer Science, Michigan State University, December 1997.
T. Doom and A. S. Wojcik. "Reengineering from partial specifications through BDD representation of functional constraint." Tech. Rep. MSUCPS:TR97-3, Department of Computer Science, Michigan State University, February 1997.
M. Brehob, T. Doom, R. J. Enbody, S. Moore, W. Moore, R. Sass, and C. Severance. "Beyond RISC - The Post-RISC Architecture." Tech. Rep. MSUCPS:TR96-11, Department of Computer Science, Michigan State University, March 1996.

Awards and Honors

• Senior Member, IEEE Computer Society (inducted as Senior Member, 2003).
• College of Engineering and Computer Science Excellence in Teaching Award (1998-1999 (top 5), 1999-2000 (co-winner), 2000-2003 (ineligible), 2004 (top 5), 2005 (winner), 2006-2009 (ineligible).
• Tau Beta Pi (2007+).
• University honors, Bowling Green State University (1992).
• Top graduating student in Department of Computer Science, Bowling Green State University (1991).
• Academic Achievement Award, Bowling Green State University (1988-1992).
• National Merit Scholar (1988-1992).

Service

University service
• ad-hoc Academic Integrity Committee, College of Engineering and Computer Science, Wright State University (Chair, 2007-).
• Faculty Governance Committee, Wright State University, (2007-).
• Steering Committee, Department of Computer Science and Engineering, Wright State Univeristy (2007-2009).
• Enrollment/Recruitment Committee, Department of Computer Science and Engineering, Wright State University (2006-).
• Center for Teaching and Learning Advisory Council, Wright State University (2005-2006).
• WSU Banner Self-Service Advisory Team (2005-2006).
• Graduate Studies Committee, Department of Computer Science and Engineering, Wright State University (2005-2006).
• Executive Committee, Wright State University chapter of the American Association of University Professors (Member-at-large, 2005-2006; Treasurer 2006+).
• Ad-hoc Program Assessement and Planning Committee, Department of Computer Science and Engineering, Wright State University (Chair, 2004-2005).
• Faculty Development Committee, Department of Computer Science and Engineering, Wright State University (2004+).
• Faculty Search Committee, Department of Computer Science and Engineering, Wright State University (2004).
• Academic Computing Committee, College of Engineering and Computer Science, Wright State University (2004-2005).
• Petitions Committee, Wright State University, Wright State University (2004-2006).
• Petitions Committee, College of Engineering and Computer Science, Wright State University (2004-2006).
• Ad-hoc Engineering Math Committee, College of Engineering and Computer Science, Wright State University (2001-2002).
• College Representative to the University Athletic Council, Wright State University (2001-2002).
• Ph.D. Qualifiers Committee, Department of Computer Science and Engineering, Wright State University (2001+).
• By-laws Committee, Department of Computer Science and Engineering, Wright State University (2000-2003).
• Teaching Awards Committee, College of Engineering and Computer Science, Wright State University (2000-2003, 2006-2009).
• University Academic Integrity Hearing Panel, Wright State University (2000+; Chair (acting), Summer 2004; Chair, 2006-).
• Instructor for the College of Engineering Academic Advantage Program (2000+).
• Alternate College Representative to the University Athletic Council, Wright State University (2000-2001).
• Undergraduate Curriculum Committee, Department of Computer Science and Engineering, Wright State University (1998-2005, 2006-).
• Selection Committee for Withrow Award for Teaching Excellence, Michigan State University (1996).
• Advisory Committee, Graduate Student Representative, Department of Computer Science, Michigan State University (1995-1996).
• Computing Environment Committee, Graduate Student Representative, Department of Computer Science, Michigan State University (1994-1995).

Professional service
• Task Force (Technical Committee) on Bioinformatics, IEEE Computer Society, Chair (2007+).
• Program committee, IEEE Bioinformatics and Bioengineering (2006, 2007).
• Reviewer for Academic Texts: Peterson (2005), John Wiley and Sons (2004+), Oxford Press (2004), Brooks/Cole (2002,2004), McGraw-Hill (2001+).
• Reviewer for NSF Pathways to Revitilized Undergraduate Computing Education panel (2007).
• Reviewer for NSF Dynamic Data Driven Applications Systems panel (2005).
• Reviewer for NSF Educational Innovation panel (2003, 2004).
• Reviewer for IEEE Bioinformatics and Bioengineering (2002, 2005, 2006).
• Reviewer for IEEE Transactions on Computer-aided Design (1998).
• Reviewer for IEEE Transactions on Education (1998+).
• Reviewer for IEEE Great Lakes Symposium on VLSI (1997-1998).
• Reviewer for IEEE Design Automation Conference (1997-2000).

Professional membership
• Member, Association for Computing Machinary, Special Interest Group on Computer Science Education (ACM SIGCSE) (inducted 2002).
• Member, American Society for Engineering Education (inducted 2001).
• Senior Member, IEEE Computer Society (inducted as Member, 1998; inducted as Senior Member, 2003).
• Member, Golden Key Honor Society (inducted 1992).
• Member, Kappa Mu Epsilon, Mathematics Honor Society (inducted 1991).

Other synergistic activities
• Technical judge for regional and state FIRST LEGO mindstorm competitions (grades 4-8 engineering competition)
• Instructor, Honors Seminars of Metropolitan Dayton (2005, 2006)
• Expert witness in computational aspects of the analysis of Forensic DNA evidence (2003+).
• Consulting senior systems engineer and co-founder, Forensic Bioinformatic Services (http://www.bioforensics.com), (2002+).
• Expert witness in Digital Reverse Engineering (2001+).
• Ohio Teaching Excellence Program Invitee (2001-2002).

Last modified: 08/07/08