Publications

2008

• Mukul S. Bansal and Oliver Eulenstein. The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches. To appear in ISBRA 2008.
• J. G. Burleigh, Mukul S. Bansal, Andre Wehe, and Oliver Eulenstein. Locating Multiple Gene Duplications Through Reconciled Trees. To appear in RECOMB 2008.
• D. Chen, J. G. Burleigh, M. S. Bansal, and D. Fernández-Baca. PhyloFinder: An intelligent search engine for phylogenetic tree databases. To appear in BMC Evolutionary Biology.
• M. S. Bansal, J. Dong, and D. Fernández-Baca. Comparing and aggregating partially resolved trees. To appear in LATIN 2008.
• 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.
• C. Ane, O. Eulenstein, R. Piaggio-Talice, and M. J. Sanderson. Groves of phylogenetic trees. To appear in Annals of Combinatorics.

2007

• Mukul S. Bansal and Oliver Eulenstein. An Ω(n²/ log n) speed-up of TBR heuristics for the gene-duplication problem. WABI, LNCS/LNBI 4645: 124-135, 2007.
• M. Sanderson, C. Ané, O. Eulenstein, D. Fernández-Baca, J. Kim, M. McMahon, R. Piaggio-Talice. Fragmentation of large data sets in phylogenetic analyses. Reconstructing Evolution: New Mathematical and Computational Advances, Oxford University Press, 199--244, 2007.
• D. Chen, Gordon J. Burleigh, and David Fernández-Baca. Spectral partitioning of phylogenetic data dets based on compatibility. Systematic Biology 56(4): 623--632, 2007.
• 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.
• Mukul S. Bansal, J. G. Burleigh, O. Eulenstein, and A. Wehe. Heuristics for the gene-duplication problem: A Q(n) speed-up for the local search. RECOMB, Lecture Notes in Bioinformatics (LNBI), 4453: 238-252 , 2007.
• Sanderson, M. J., C. Ane, O. Eulenstein, D. Fernandez-Baca, J. Kim, M. M. McMahon, and R. Piaggio-Talice. 2007. Fragmentation of large data sets in phylogenetic analyses. In Reconstructing Evolution: New Mathematical and Computational Advances (M. Steel and O. Gascuel, eds). pp. 199--216, Oxford University Press.

2006

• D. Chen, J. G. Burleigh, O. Eulenstein, and D. Fernández-Baca. Improved heurisitcs for minimum-Flip supertree construction. Evolutionary Bioinformatics, 2006.
• D. Chen, O. Eulenstein, D. Fernández-Baca, and M. J. Sanderson. Minimum-Flip supertrees. IEEE Transactions on Computational Biology and Bioinformatics, 3(2):165--173, 2006.
• W. Chang and O. Eulenstein. Reconciling trees with apparent polytomies. COCOON, Lecture Notes in Computer Science, 4112, pages 235--244. Springer, 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.

2005

• M. Wilkinson, J. A. Cotton, C. Creevey, O. Eulenstein, S. R. Harris, F. Lapointe, C. Levasseur, J. O. Mcinerney, D. Pisani, and J. L. Thorley. The shape of supertrees to come: Tree shape related properties of fourteen supertree methods. Systematic Biology, 54(3):419--431, 2005.
• C. Yan, J. G. Burleigh, and O. Eulenstein. Identifying optimal incomplete phylogenetic data sets from sequence databases. Molecular Phylogenetics and Evolution, 35:528--535, 2005.
• D. Fernández-Baca and B. Venkatachalam. Parametric analysis for ungapped Markov models of evolution. Combinatorial Pattern Matching 2005.
• O. Eulenstein. Consensus Trees and Supertrees. Handbook of Computational Molecular Biology (S. Aluru, ed.), Chapman and Hall/CRC Press Computer and Information Science Series, 2005.
• C. Ane, O. Eulenstein, and R. Piaggio-Tallice. Model selection via improved phylogenetic compression. Mathematics of Evolution and Phylogeny conference, 2005.
• C. Ane, O. Eulenstein, R. Piaggio-Tallice, and M. J. Sanderson. Groves clustering phylogenetic databases. Mathematics of Evolution and Phylogeny conference, 2005.
• W. Chang and O. Eulenstein. Gene-tree reconciliation with soft multifurcations. Mathematics of Evolution and Phylogeny conference, 2005.

2004

• O. Eulenstein, D. Chen, J. G. Burleigh, D. Fernández-Baca, and M. J. Sanderson. Performance of flip-supertree construction. Systematic Biology, 53(2):1--10, 2004.
• 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). Software can be obtained from http://genome.cs.iastate.edu/CBL/download/.
• 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.
• R. Piaggio-Talice, G. Burleigh, and O. Eulenstein. Quartet Supertrees, Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pages 173--192. Springer, 2004.
• G. Burleigh, O. Eulenstein, D. Fernández-Baca, and M. J. Sanderson. MRF Supertrees, Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pages 65--86. Springer, 2004.

2003

• M. J. Sanderson, A. C. Driskell, R. H. Ree, O. Eulenstein, and S. Langley. Obtaining maximal concatenated phylogenetic data-sets from large sequence databases. Molecular Biology Evolution, 20:1028--1035, 2003.
• 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.

2002

• D. Fernández-Baca, T. Seppäläinen, and G. Slutzki. Bounds for parametric sequence comparison. Discrete Applied Mathematics, 118:181--198, 2002.
• D. Chen, O. Eulenstein, D. Fernández-Baca, and M.J. Sanderson. Supertrees by flipping. In Proceedings of COCOON 2002, Springer-Verlag LNCS.
• F. Sun, D. Fernández-Baca, and W. Yu. Inverse parametric sequence alignment. In Proceedings of COCOON 2002, Springer-Verlag LNCS.

2001

• 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.

2000

• D. Fernández-Baca, T. Seppäläinen, and G. Slutzki. Parametric multiple sequence alignment and phylogeny construction. To appear in J. Disc. Algorithms. An earlier version appeared in Proc. Combinatorial Pattern Matching 2000, Springer-Verlag LNCS, Vol. 1848, pp. 69--83.