Selected Recent Publications

Copies available upon request.

``Kernelization Algorithms for the Vertex Cover Problem: Theory and Experiments,'' Proceedings, Workshop on Algorithm Engineering and Experiments, New Orleans, Louisiana, January, 2004, with F. N. Abu-Khzam, R. L. Collins, M. R. Fellows, W. H. Suters and C. T. Symons.
``High Performance Computational Tools for Motif Discovery,'' Proceedings, IEEE International Workshop on High Performance Computational Biology, Santa Fe, New Mexico, April, 2004, with N. E. Baldwin, R. L. Collins, M. R. Leuze, C. T. Symons and B. H. Voy.
``A Direct Algorithm for the Parameterized Face Cover Problem,'' Proceedings, International Workshop on Parameterized and Exact Computation, Bergen, Norway, September, 2004, with F. N. Abu-Khzam.
``Detecting Network Motifs in Gene Co-expression Networks,'' Proceedings, International Conference for the Critical Assessment of Microarray Data Analysis, Durham, North Carolina, November, 2004, with N. E. Baldwin, X. Peng, A. M. Saxton and J. R. Snoddy.
``Fast, Effective Vertex Cover Kernelization: A Tale of Two Algorithms,'' Proceedings, ACS/IEEE International Conference on Computer Systems and Applications, Cairo, Egypt, January, 2005, with F. N. Abu-Khzam and W. H. Suters.
``On the Relative Efficiency of Maximal Clique Enumeration Algorithms, with Application to High-Throughput Computational Biology,'' Proceedings, International Conference on Research Trends in Science and Technology, Beirut, Lebanon, March, 2005, with F. N. Abu-Khzam, N. E. Baldwin and N. F. Samatova.
``Complex Trait Analysis of Gene Expression Uncovers Polygenic and Pleiotropic Networks that Modulate Nervous System Function,'' Nature Genetics 37 (2005), 233-242, with N. E. Baldwin, E. J. Chesler, J. Gu, H. C. Hsu, L. Lu, K. F. Manly, J. D. Mountz, Y. Qu, S. Shou, D. W. Threadgill, J. Wang and R. W. Williams.
``Computational, Integrative and Comparative Methods for the Elucidation of Genetic Co-Expression Networks,'' Journal of Biomedicine and Biotechnology 2 (2005) 172-180, with N. E. Baldwin, E. J. Chesler, S. Kirov, J. R. Snoddy, R. W. Williams and B. Zhang.
``Asymptotically Faster Algorithms for the Parameterized Face Cover Problem,'' Proceedings, International Workshop on Algorithms and Complexity in Durham, Durham, England, July, 2005, with F. N. Abu-Khzam and H. Fernau.
``A New Approach and Faster Exact Methods for the Maximum Common Subgraph Problem,'' Proceedings, International Computing and Combinatorics Conference, Kunming, China, August, 2005, with F. N. Abu-Khzam, N. F. Samatova, W. Henry Suters, C. T. Symons and Y. Zhang.
``Genome-Scale Computational Approaches to Memory-Intensive Applications in Systems Biology,'' Proceedings, SuperComputing 2005, Seattle, Washington, November, 2005, with F. N. Abu-Khzam, N. E. Baldwin, E. J. Chesler, N. F. Samatova and Y. Zhang.
``Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data,'' Proceedings, RECOMB Satellite Workshop on Systems Biology and Regulatory Genomics, San Diego, California, December, 2005, with E. J. Chesler.
``Computational Analysis of Mass Spectrometry Data Using Novel Combinatorial Methods,'' Proceedings, ACS/IEEE International Conference on Computer Systems and Applications, Dubai, United Arab Emirates, March, 2006, with A. Fadiel, F. Naftolin, X. Peng, A. D. Perkins, P. Pevsner, H. S. Taylor, O. Tuncalp and D. Vitello.
``Innovative Computational Methods for Transcriptomic Data Analysis,'' Proceedings, ACM Symposium on Applied Computing, Dijon, France, April, 2006, with A. D. Perkins, A. M. Saxton, J. A. Scharff and B. H. Voy.
``Combinatorial Algorithms and High Performance Implementations for Elucidating Complex Ecosystem Relationships from North Sea Historical Data,'' Proceedings, International Council for the Exploration of the Sea Annual Science Conference, Maastricht, The Netherlands, September, 2006, with D. J. Beare, R. W. Gauldie, A. J. Kenny, P. J. Kershaw, A. D. Perkins, J. Reid and K. Winpenny.
``North Sea Integrated Assessment - Implications for Marine Management,'' Proceedings, International Council for the Exploration of the Sea Annual Science Conference, Maastricht, The Netherlands, September, 2006, with D. J. Beare, M. Devlin, A. Gallego, R. W. Gauldie, C. Haughton, A. J. Kenny, P. J. Kershaw, P. Licandro, A. D. Perkins, J. Reid, H. R. Skjoldal and K. Winpenny.
``The Cluster Editing Problem: Implementations and Experiments,'' Proceedings, International Workshop on Parameterized and Exact Computation, Zürich, Switzerland, September, 2006, with F. Dehne, X. Luo, S. Pitre, P. Shaw and Y. Zhang.
``The Undirected Feedback Vertex Set Problem Has a Poly(k) Kernel,'' Proceedings, International Workshop on Parameterized and Exact Computation, Zürich, Switzerland, September, 2006, with K. Burrage, V. Estivill-Castro, M. R. Fellows, S. Mac and F. A. Rosamond.
``A Network-Based Analysis of the Late Phase Reaction of the Skin,'' Journal of Allergy and Clinical Immunology 118 (2006), 220-225, with M. Adner, B. Andersson, M. Benson, L. O. Cardell and A. Torinssson-Naluai.
``Extracting Gene Networks for Low Dose Radiation using Graph Theoretical Algorithms,'' PLoS Computational Biology 2 (2006), e89, with B. Borate, L. K. Branstetter, E. J. Chesler, A. D. Perkins, A. M. Saxton, J. A. Scharff and B. H. Voy.
``Scalable Parallel Algorithms for FPT Problems,'' Algorithmica 45 (2006), 269-284, with F. N. Abu-Khzam, P. Shanbhag and C. T. Symons.
``Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics,'' Journal of Proteome Research 5 (2006), 2909-2918, with R. L. Hettich, N. F. Samatova, E. Uberbacher, N. C. VerBerkmoes and B. Zhang.
``A Network-Based Analysis of Allergen-Challenged CD4+ T Cells from Patients with Allergic Rhinitis,'' Genes and Immunity 7 (2006), 514-521, with B. Andersson, M. Benson, L. Carlsson, G. Guillot, M. Jernas and M. Rudemo.
``Efficient Parameterized Preprocessing for Cluster Editing,'' Proceedings, International Symposium on Fundamentals of Computation Theory, Budapest, Hungary, August, 2007, with M. R. Fellows, F. A. Rosamond and P. Shaw.
``Statistical Tools are Needed for Microarray Expression and Co-Expression,'' in Prediction with Regression: A Comparison of Methods (R. J. Freund, editor), American Statistical Association, 2007, 4381-4386, with A. M. Saxton and B. H. Voy.
``Combinatorial and Algorithmic Issues for Microarray Analysis,'' in Approximation Algorithms and Metaheuristics (T. F. Gonzales, editor), Taylor & Francis, 2007, 74.1-74.14, with C. Cotta and P. Moscato.
``Linear-Time Algorithms for Planar Graphs of Fixed Disk Dimension,'' Information Processing Letters 101 (2007), 36-40, with F. N. Abu-Khzam.
``Crown Structures for Vertex Cover Kernelization,'' Theory of Computing Systems 41 (2007), 411-430, with F. N. Abu-Khzam, M. R. Fellows and W. H. Suters.
``An O*(2^O(k)) FPT Algorithm for the Undirected Feedback Vertex Set Problem,'' Theory of Computing Systems 41 (2007), 479-492, with F. Dehne, M. R. Fellows, F. A. Rosamond and K. Stevens.
``Genome-Level Analysis of Genetic Regulation of Liver Gene Expression Networks,'' Hepatology 46 (2007), 548-557, with E. J. Chesler, D. Gatti, R. Kirova, O. Kosyk, L. Lu, A. Maki, K. Manly, A. D. Perkins, Y. Qu, I. Rusyn, R. W. Williams and D. Threadgill.
``On Finding Bicliques in Bipartite Graphs: a Novel Algorithm with Application to the Integration of Diverse Biological Data Types,'' Proceedings, Hawaii International Conference on System Sciences (HICSS), Big Island, Hawaii, January, 2008, with E. J. Chesler and Y. Zhang.
``Parameterized Complexity, An Introduction to the Special Issue,'' The Computer Journal 51 (2008), 1-6, with R. G. Downey and M. R. Fellows.
``Innovative Computational Methods for Transcriptomic Data Analysis: A Case Study in the Use of FPT for Practical Algorithm Design and Implementation,'' The Computer Journal 51 (2008), 26-38, with A. D. Perkins, A. M. Saxton, J. A. Scharff and B. H. Voy,
``A Bounded Search Tree Algorithm for Parameterized Face Cover,'' Journal of Discrete Algorithms 6 (2008), 541-552, with F. N. Abu-Khzam and H. Fernau.
``Graph Algorithms for Integrated Biological Analysis, with Applications to Type 1 Diabetes Data,'' in Clustering Challenges in Biological Networks (S. Butenko, W. A. Chaovalitwongse and P. Pardalos, editors), World Scientific, 2009, 207-222, with J. D. Eblen, I. C. Gerling, A. M. Saxton, J. R. Snoddy and J. Wu.
``A Module-Based Analytical Strategy to Identify Novel Disease-Associated Genes Shows an Inhibitory Role for Interleukin 7 Receptor in Allergic Inflammation,'' BMC Systems Biology 3:19 (2009), with B. Andersson, M. Benson, L. O. Cardell, J. Erjefael, M. Hahn-Zoric, R. Mobini and A. D. Perkins.
``Bridging the Gap between Systems Biology and Medicine,''Genome Medicine 1:9 (2009), with B. J. Aronow, C. Auffray, M. Benson, G. Clermont, D. Dalevi, F. Dehne, D. Dubhashi, D. R. Marshall, Y. Moreau, P. Provero, P. Raasch, D. M. Rock and J. Tegner.
``Threshold Selection in Gene Co-Expression Networks Using Spectral Graph Theory Techniques,'' BMC Bioinformatics 10 (2009), with A. D. Perkins.
``Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data,'' EURASIP Journal on Bioinformatics and Systems Biology (2009), with S. E. Bergeson, E. J. Chesler, R. Kirova, E. R. Lance, C. K. Lewis, K. H. Lodowski and J. Song.
``A Systems Genetic Analysis of Chronic Fatigue Syndrome: Combinatorial Data Integration from SNPs to Differential Diagnosis of Disease,'' in Methods of Microarray Data Analysis VI (J. Cuticchia and S. M. Lin, editors), CreateSpace Publishing, 2009, 81-98, with E. J. Chesler, R. Kirova, X. Peng and A. D. Perkins.
``Using Out-of-Core Techniques to Produce Exact Solutions to the Maximum Clique Problem on Extremely Large Graphs,'' Proceedings, ACS/IEEE International Conference on Computer Systems and Applications (AICCSA), Rabat, Morocco, May, 2009, with F. N. Abu-Khzam, J. D. Eblen, A.D. Perkins, C.A. Phillips and G. L. Rogers.
``Ontological Discovery Environment: A System for Integrating Gene-Phenotype Associations,'' Genomics 94 (2009), 377-387, with E. J. Baker, E. J. Chesler, J. J. Jay; R. Kirova, Z. Li, V. M. Philip, and Y. Zhang.
``Comparison of Thresholding Approaches for Microarray Gene Co-Expression Matrices,'' BMC Research Notes 2 (2009), with B. R. Borate, E. J. Chesler, A. M. Saxton and B. H. Voy.
``Identifying Genetic Loci and Spleen Gene Coexpression Networks Underlying Immunophenotypes in BXD Recombinant Inbred Mice,'' Physiological Genomics 41 (2010), 244-253, with E. J. Chesler, S. Das, S. A. Kania, R. M. Lynch, S. Naswa, G. L. Rogers, A. M. Saxton and B. H. Voy.
``A Fixed-Parameter Algorithm for String-to-String Correction,'' Proceedings, Computing: the Australasian Theory Symposium (CATS), Brisbane, Australia, January, 2010, with F. N. Abu-Khzam, H. Fernau, S. Lee-Cultura and U. Stege.
``Genetic Analysis of BDNF Expression Cliques and Adult Neurogenesis in the Hippocampus,'' Proceedings, ORNL Biomedical Science and Engineering Conference: Biomedical Sciences Research and Analysis in Neurosciences, Oak Ridge, Tennessee, May, 2010, with G. Kempermann, L. Lu, M. K. Mulligan, R. W. Overall, G. L. Rogers Jr. and R. W. Williams.
``A Hybrid Graph Representation for Recursive Backtracking Algorithms,'' Proceedings, International Frontiers of Algorithmics Workshop, Wuhan, China, August, 2010, with F. N. Abu-Khzam, A. E. Mouawad and C. P. Nolan.
``Charge and Reduce: A Fixed-Parameter Algorithm for String-to-String Correction,'' Discrete Optimization 8 (2011), 41-49, with F. N. Abu-Khzam, H. Fernau, S. Lee-Cultura and U. Stege.
``Quadratic Kernelization for Convex Recoloring of Trees,'' Algorithmica 61 (2011), 362-388, with H. L. Bodlaender, M. R. Fellows, M. A. Ragan, F. A. Rosamond and M. Weyer.
``Parallel Vertex Cover: A Case Study in Dynamic Load Balancing,'' Proceedings, Australasian Symposium on Parallel and Distributed Computing, Perth, Australia, January, 2011, with J. D. Eblen, G. L. Rogers and D. P. Weerapurage.
``A Complete Resolution of the Keller Maximum Clique Problem,'' Proceedings, ACM-SIAM Symposium on Discrete Algorithms, San Francisco, California, January, 2011, with J. Debroni, J. D. Eblen, W. Myrvold, P. Shor and D. P. Weerapurage.
``The Use of Fast Approximate Graph Coloring to Enhance Exact Parallel Algorithm Performance,'' Proceedings, Australasian Symposium on Parallel and Distributed Computing, Melbourne, Australia, February, 2012, with J. D. Eblen, G. L. Rogers and C. A. Phillips.
``GeneWeaver: a Web-based System for Integrative Functional Genomics,'' Nucleic Acids Research, with E. J. Baker, J. A. Bubier, E. J. Chesler and J. J. Jay, accepted for publication.
``Inferring Networks for Disease,'' Systems Biology (R.A. Meyers, editor), Wiley-VCH, with M. Benson, accepted for publication.
``Effects of Edge Lifting on Domination in Graphs,'' Bulletin of the Institute of Combinatorics and its Applications, with W. J. Desormeaux, A. J. Hall, T. W. Haynes, D. Koessler, S. Rickett and H. Scott, accepted for publication.
``Increased Expression of IRF4 in Allergen-Challenged CD4+ Cells from Patients with Intermittent Allergic Rhinitis,'' Allergy, the European Journal of Allergy and Clinical Immunology, with B. A. Andersson, F. Barren╝s, M. Benson, S. Bruhn, S. Chavali, B. S. Egan, E. Hovig, R. Mobini, G. L. Rogers, G. K. Sandve and H. Wang, accepted for publication.
``The Maximum Clique Enumeration Problem: Algorithms, Applications and Implementations,'' BMC Bioinformatics, with J. D. Eblen, C. A. Phillips and G. L. Rogers, accepted for publication. A preliminary version of a portion of this paper appeared in Lecture Notes in Bioinformatics 6674 (J. Chen, J. Wang and A. Zelikovsky, editors), Springer, 306-319.
``A Systematic Comparison of Genome Scale Clustering Algorithms,'' BMC Bioinformatics, with M. Benson, E. J. Chesler, J. D. Eblen, J. J. Jay, A. D. Perkins, A. M. Saxton, B. H. Voy and Y. Zhang, accepted for publication. A preliminary version of a portion of this paper appeared in Lecture Notes in Bioinformatics 6674 (J. Chen, J. Wang and A. Zelikovsky, editors), Springer, 416-427.