Links to pdf preprints of some of these documents are given below; the rest may be obtained by contacting the author (fernande@cs.iastate.edu).
Copyright notice: The material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.
Acknowledgement and disclaimer: Most of this material is based upon work supported by the National Science Foundation over the last 18 years, most recently under grant 0334832. Any opinions, findings, and conclusions, or recommendations expressed in this material are those of the author (s) and do not necessarily reflect the views of the National Science Foundation.
D. Fernández-Baca and B. Venkatachalam. Parametric analysis for ungapped Markov models of evolution. To appear in ACM Transactions on Algorithms. A preliminary version appeared in Combinatorial Pattern Matching 2005.
M. S. Bansal, J. Dong, and D. Fernández-Baca. Aggregating partially resolved trees. To appear in Proceedings of the 8th Latin American Theoretical Informatics Symposium, Springer Lecture Notes in Computer Science, 2008.
D. Chen, J. G. Burleigh, M. S. Bansal, and D. Fernández-Baca. PhyloFinder: An intelligent search engine for phylogenetic tree databases. BMC Evolutionary Biology 8:90.
D. Fernández-Baca and B. Venkatachalam. Sensitivity Analysis in Combinatorial Optimization. In Handbook of Approximation Algorithms and Metaheuristics (T. Gonzalez, ed.), Chapman and Hall/CRC Press Computer and Information Science Series, 2007.
D. Chen, Gordon J. Burleigh, and David Fernández-Baca. Spectral partitioning of phylogenetic data sets based on compatibility. Systematic Biology 56(4): 623 – 632 (2007).
D. Chen, O. Eulenstein, David Fernández-Baca and J.Gordon Burleigh. Improved Heuristics for Minimum-Flip Supertree Construction. Evolutionary Bioinformatics 2: 401–410 (2006).
D. Chen, O. Eulenstein, D. Fernández-Baca, and M.J. Sanderson. Minimum flip supertrees: Complexity and algorithms. IEEE/ACM Trans. Comput. Biology Bioinform. 3(2): 165-173 (2006).
D. Fernández-Baca and B. Venkatachalam. Parametric sequence alignment. In Handbook of Computational Molecular Biology (S. Aluru, ed.), Chapman and Hall/CRC Press Computer and Information Science Series, 2006.
F. Sun, D. Fernández-Baca, and W. Yu. Inverse parametric sequence alignment. Journal of Algorithms, 53(1):36--54 (2004).
D. Chen, O. Eulenstein, and D. Fernández-Baca. Rainbow: A toolbox for phylogenetic supertree construction and analysis. Bioinformatics 20(16):2872--2873 (2004).
D. Fernández-Baca, T. Seppäläinen, and G. Slutzki. Parametric multiple sequence alignment and phylogeny construction. Journal of Discrete Algorithms, 2(2):271--287 (2004), special issue on Combinatorial Pattern Matching, edited by R. Giancarlo and D. Sankoff.
O. Eulenstein, D. Chen, J.G. Burleigh, D. Fernández-Baca, and M.J. Sanderson. Performance of flip supertrees with a heuristic algorithm. Systematic Biology, 53(2):299--308 (2004).
D. Fernández-Baca and J. Lagergren. A polynomial-time algorithm for near-perfect phylogeny. SIAM J. Computing, 32(5):1115--1127 (2003).
D. Chen, L. Diao, O. Eulenstein, D. Fernández-Baca, and M.J. Sanderson. Flipping: A supertree construction method. In Bioconsensus, M. Janowitz et al. (eds), DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 61, pp. 135--160, American Mathematical Society, 2003.
D. Fernández-Baca. Decomposable multiparameter matroidal knapsack problems. Theoretical Computer Science, 297:183--198 (2003).
D. Fernández-Baca, T. Seppäläinen, and G. Slutzki. Bounds for parametric sequence comparison. Discrete Applied Mathematics, 118:181--198 (2002).
D. Fernández-Baca. The perfect phylogeny problem. In Steiner Trees in Industry, X. Cheng and D.-Z. Du (eds.), pp. 203--234, Kluwer, 2001.
D. Fernández-Baca. On nonlinear parametric search. Algorithmica, 30:1--11, 2001.
D. Fernández-Baca and J. Lagergren. On the approximability of the Steiner tree problem in phylogeny. Discrete Applied Mathematics 88:129--145 (1998).
D. Fernández-Baca and G. Slutzki. Linear-time algorithms for parametric minimum spanning tree problems on planar graphs. Theoretical Computer Science, 181:57--74 (1997)
D. Fernández-Baca and G. Slutzki. Optimal parametric search on graphs of bounded tree-width. Journal of Algorithms 22:212--240, 1997.
D. Fernández-Baca, G. Slutzki, and D. Eppstein. Using sparsification for parametric minimum spanning tree problems. Nordic Journal of Computing, 3(4):352--366 (1996).
R. Agarwala and D. Fernández-Baca. Weighted multidimensional search and its application to convex optimization. SIAM J. Computing, 25:83--99 (1996).
R. Agarwala and D. Fernández-Baca. Simple algorithms for perfect phylogeny and triangulating colored graphs. International Journal of Foundations of Computer Science, 7(1):11--21 (1996).
R. Agarwala, D. Fernández-Baca, and G. Slutzki. Fast algorithms for inferring evolutionary trees. Journal of Computational Biology, 2(3):397--408 (1995).
R. Agarwala and D. Fernández-Baca. A polynomial-time algorithm for the perfect phylogeny problem when the number of character states is fixed. SIAM J. Computing, 23:1216--1224 (1994).
D. Fernández-Baca and G. Slutzki. Parametric problems on graphs of bounded tree-width. J. Algorithms, 16:408--430 (1994).
D. Fernández-Baca and A. Medepalli. Parametric module allocation on partial k-trees. IEEE Transactions on Computers 42:738--742 (1993).
D. Fernández-Baca and S. Srinivasan Constructing the minimization diagram of a two-parameter problem. Operations Research Letters 10:87--93 (1991).
D. Fernández-Baca. Allocating modules to processors in a distributed system. IEEE Transactions on Software Engineering 15(11):1427--1436 (1989).
D. Fernández-Baca and G. Slutzki. Solving parametric problems on trees. J. Algorithms 10:381--402 (1989).
D. Gusfield, C. Martel, and D. Fernández-Baca. Fast algorithms for bipartite network flow. SIAM J. Computing, 16(2):237--251 (1987).
Last modified on 1 February 2008