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Publications

2008

  • Mukul S. Bansal and Oliver Eulenstein. An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem. To appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).
  • Mukul S. Bansal and Oliver Eulenstein. The Multiple Gene Duplication Problem Revisited. ISMB 2008, Bioinformatics, 24(13): i132-i138, 2008.
  • Andre Wehe, Mukul S. Bansal, J. G. Burleigh, and Oliver Eulenstein. DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics, 24(13): 1540-1541, 2008.
  • Mukul S. Bansal and Oliver Eulenstein. The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches. ISBRA, LNCS 4983: 14-25, 2008.
  • J. G. Burleigh, Mukul S. Bansal, Andre Wehe, and Oliver Eulenstein. Locating Multiple Gene Duplications Through Reconciled Trees. RECOMB, LNCS 4955: 273-284, 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 2008, 8:90.
  • M. S. Bansal, J. Dong, and D. Fernández-Baca. Comparing and aggregating partially resolved trees. LATIN, LNCS 4957: 72-83, 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. Fernández-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, 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

2001

2000

Computational Biology Laboratory
Department of Computer Science
Iowa State University
Ames, IA 50011-1040
phone: +1-515-294-2597