Publications

    Updated: 25 February 2011

    Acknowledgement and disclaimer: Most of this material is based upon work supported by the National Science Foundation over the last decade, most recently under grants CCF-106029, DEB-0830012, DEB-0334832, and DEB-0075319. 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.

    2011

  1. Pawel Górecki and Oliver Eulenstein. A linear time algorithm for error-corrected reconciliation of unrooted gene trees, ISBRA 2011, (accepted).
  2. Wen-Chieh Chang, Sudheer Vakati, Roland Krause and Oliver Eulenstein. Mining Biological Interaction Networks using Weighted Quasi-Bicliques. ISBRA 2011, (accepted).
  3. Ruchi Chaudhary, J. Gordon Burleigh and Oliver Eulenstein. Algorithms for Rapid Error Correction for the Gene Duplication Problem. ISBRA 2011, (accepted).
  4. Harris T. Lin, J. Gordon Burleigh and Oliver Eulenstein. The Deep Coalescence Consensus Tree Problem is Pareto on Clusters. ISBRA 2011, (accepted).
  5. John Wiedenhoeft, Roland Krause, and Oliver Eulenstein. The Plexus Model for the Inference of Ancestral Multi-Domain Proteins, IEEE/ACM Trans. Comput. Biology Bioinform, (to appear). A preliminary version of this paper appeared in ISBRA 2010.
  6. Pawel Górecki and Oliver Eulenstein. Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. APBC 2011; BMC Bioinformatics, 12(Suppl 1):S15, 2011. [full text]
  7. Wen-Chieh Chang, Gordon J Burleigh, David F. Fernández-Baca, and Oliver Eulenstein An ILP solution for the gene duplication problem. APBC 2011; BMC Bioinformatics, 12(Suppl 1):S14, 2011. [full text]
  8. J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Stephanie Hartmann, André Wehe, and Todd J. Vision. Genome-scale phylogenetics: Inferring the plant tree of life from 18,896 discordant gene trees. Systematic Biology, 60(2):117-125, 2011.
  9. 2010

  10. J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, and Todd J. Vision. Inferring Species Trees From Gene Duplication Episodes. In Proc. of ACM Conf. on Bioinformatics and Computational Biology (ACM-BCB), pages 198-203, 2010.
  11. Oliver Eulenstein, S. Huzurbazar, and David Liberles. Reconciling phylogenetic trees. In Evolution after gene duplication (S. Huzurbazar and D. Liberles, ed.), Wiley, New York, pages 185-206, 2010.
  12. Homilius Max, J. Gordon Burleigh, and Oliver Eulenstein. Triplet-supertrees constructed from minimum triplet presentations. In Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology, BICoB (Al-Mubaid Hisham, ed.), pages 127-132, 2010.
  13. John Wiedenhoeft, Roland Krause, and Oliver Eulenstein. Inferring Evolutionary Scenarios for Protein Domain Compositions. Lecture Notes in Computer Science, 6053:179-190, 2010. [link]
  14. Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, and Oliver Eulenstein. iGTP: A software package for large-scale gene tree parsimony analysis. BMC Bioinformatics, 11:574, 2010. [full text]
  15. Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, and David Fernández-Baca. Robinsonfoulds supertrees. Algorithms in Molecular Biology, 5(1):18, 2010. [full text]
  16. André Wehe, Wen-Chieh Chang, Oliver Eulenstein, and Srinivas Aluru. A scalable parallelization of the gene duplication problem. Journal of Parallel and Distributed Computing, 70:237-244, 2010.
  17. Mukul S. Bansal, J. Gordon Burleigh, and Oliver Eulenstein. Efficient genome-scale phylogenetican alysis under the duplication-loss and deep coalescence cost models. APBC 2010; BMC Bioinformatics,11(Suppl 1):S42, 2010. [full text]
  18. 2009

  19. Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, and David Fernández-Baca. Generalized binary tanglegrams: Algorithms and applications. In BICoB; Lecture Notes in Computer Science (Sanguthevar Rajasekaran, ed.), 5462:114-125, 2009. Awarded 'Best Paper'.
  20. Mukul S. Bansal, Oliver Eulenstein, and André Wehe. The gene-duplication problem: Near linear time algorithms for NNI-based local searches. IEEE/ACM Trans. Comput. Biology Bioinform., 6(2):221-231, 2009. A preliminary version of this paper appeared in ISBRA 2008.
  21. Harris T. Lin, J. Gordon Burleigh, and Oliver Eulenstein. Triplet supertree heuristics for the tree of life. APBC 2011; BMC Bioinformatics, 10(S-1), 2009. [full text]
  22. J. Gordon Burleigh, Mukul S. Bansal, Andre Wehe, and Oliver Eulenstein. Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants. J Comput Biol, 16(8):1071-83, 2009. A preliminary version of this paper appeared in RECOMB 2008.
  23. Cécile Ané, Oliver Eulenstein, Raul Piaggio-Talice, and Michael Sanderson. Groves of phylogenetic trees. Annals of Combinatorics, 13(2):139-167, 2009.
  24. 2008

  25. J. Gordon Burleigh, Mukul S. Bansal, André Wehe, and Oliver Eulenstein. Locating multiple gene duplications through reconciled trees. In RECOMB, Lecture Notes in Computer Science (Martin Vingron and Limsoon Wong, ed.), 4955:273-284, 2008.
  26. Mukul S. Bansal and Oliver Eulenstein. An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem. IEEE/ACM Trans. Comput. Biology Bioinform., 5(4):514-524, 2008. A preliminary version of this paper appeared in WABI 2007.
  27. Mukul S. Bansal and Oliver Eulenstein. The gene-duplication problem: Near-linear time algorithms for NNI based local searches. In ISBRA; Lecture Notes in Computer Science (Ion I. Mandoiu, Raj Sunderraman, and Alexander Zelikovsky, ed.), 4983:14-25. Springer, 2008.
  28. André Wehe, Mukul S. Bansal, J. Gordon Burleigh, and Oliver Eulenstein. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics, 24(13):1540-1541, 2008.
  29. Mukul S. Bansal and Oliver Eulenstein. The multiple gene duplication problem revisited. ISMB; Bioinformatics, 24(13):i132-8, 2008.
  30. 2007

  31. Oliver Eulenstein. Consensus trees and supertrees. In Handbook of Computational Molecular Biology (Srinivas Aluru, ed.), Hall/CRC, 2005.
  32. Michael J. Sanderson, Cécile Ané, Oliver Eulenstein, David Fernández-Baca, Kim Junhyong, Michelle M. McMahon, and Raul Piaggio-Talice. Fragmentation of large data sets in phylogenetic analyse. In Reconstructing Evolution (Olivier Gascuel and Mike Steel, ed.), Oxford Universtiy Press, 2007.
  33. Mukul S. Bansal, Oliver Eulenstein. An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem. In WABI 2007; Lecture Notes in Computer Science (Raaele Giancarlo and Sridhar Hannenhalli, ed.), 4645:124-135, 2007.
  34. Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, and André Wehe. Heuristics for the gene-duplication problem: An O(n) speed-up for the local search. In Recomb; Lecture Notes in Computer Science (Terence P. Speed and Haiyan Huang, ed.), 4453:238-252. Springer, 2007.
  35. 2006

  36. Duhong Chen, Oliver Eulenstein, David Fernández-Baca, and J. Gordon Burleigh. Improved heuristics for minimum-flip supertree construction. Evol Bioinform Online, 2:391-400, 2006.
  37. Duhong Chen, Oliver Eulenstein, David Fernández-Baca, and Michael J. Sanderson. Minimum-flip supertrees: Complexity and algorithms. IEEE/ACM Trans. Comput. Biology Bioinform., 3(2):165-173, 2006.
  38. Wen-Chieh Chang and Oliver Eulenstein. Reconciling gene trees with apparent polytomies. In COCOON; Lecture Notes in Computer Science (Danny Z. Chen and D. T. Lee, ed.), 4112:235-244, 2006.
  39. 2005

  40. Changhui Yan, J. Gordon Burleigh, and Oliver Eulenstein. Identifying optimal incomplete phylogenetic data sets from sequence databases. Mol Phylogenet Evol, 35(3):528-35, Jun 2005.
  41. Mark Wilkinson, James A. Cotton, Chris Creevey, Oliver Eulenstein, Simon R. Harris, Francois-Joseph Lapointe, Claudine Levasseur, James O. McInerney, Davide Pisani, and Joseph L. Thorley. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol, 54(3):419-31, 2005.
  42. 2004

  43. Oliver Eulenstein, Duhong Chen, J. Gordon Burleigh, David Fernández-Baca, and Michael J. Sanderson. Performance of flip supertree construction with a heuristic algorithm. Syst Biol, 53(2):299-308, 2004.
  44. Duhong Chen, Oliver Eulenstein, and David Fernández-Baca. Rainbow: a toolbox for phylogenetic supertree construction and analysis. Bioinformatics, 20(16):2872-2873, 2004.
  45. J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca, and Michael J. Sanderson. MRF supertrees. In Phylogenetic supertrees: combining information to reveal the tree of life (Olaf Bininda-Emonds, ed.), pages 65-86, Kluwer, 2004.
  46. Raul Piaggio-Talice, J. Gordon Burleigh, and Oliver Eulenstein. Quartet supertrees. In Phylogenetic supertrees: combining information to reveal the Tree of Life (Olaf Bininda-Emonds, ed.), pages 173-192, Kluwer, 2004.
  47. 2003

  48. Michael J. Sanderson, Amy C Driskell, Richard H Ree, Oliver Eulenstein, and Sasha Langley. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol Biol Evol, 20(7):1036-42, Jul 2003.
  49. Duhong Chen, Lixia Diao, Oliver Eulenstein, David Fernández-Baca, and Michael J. Sanderson. Flipping: A supertree construction method. In Bioconsensus, DIMACS Series in Discrete Mathematics and Theoretical Computer Science (M. F. Janowitz, ed.), 37:135-169, American Mathematical Society, Providence, RI, 2003.
  50. 2002

  51. J. Schonfeld, Oliver Eulenstein, Kent Vander Velden, and Gavin J. P. Naylor. Investigating evolutionary lines of least resistance using the inverse protein-folding problem. In Pacic Symposium on Biocomputing, pages 613-624, 2002.
  52. Duhong Chen, Oliver Eulenstein, David Fernández-Baca, and Michael Sanderson. Supertrees by flipping. In COCOON; Lecture Notes in Computer Science (Oscar H. Ibarra and Louxin Zhang, editors), 2387:391-400, 2002.
  53. 1998

  54. Oliver Eulenstein, Boris Mirkin, and Martin Vingron. Duplication-based measures of dierence between gene and species trees. Journal of Computational Biology, 5(1):135-148, 1998.
  55. Oliver Eulenstein and Martin Vingron. On the equivalence of two tree mapping measures. Discrete Applied Mathematics, 88(1-3):103-128, 1998.
  56. Yan P. Yuan, Oliver Eulenstein, Martin Vingron, and Peer Bork. Towards detection of orthologues in sequence databases. Bioinformatics, 14(3):285-289, 1998.
  57. 1997

  58. Oliver Eulenstein, Boris Mirkin, and Martin Vingron. Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees. In Mathematical Hierarchies and Biology, DIMACS Series in Discrete Mathematics and Theoretical Computer Science (Boris Mirkin, Fed R. McMorris, Fred S. Roberts, and Andrey Rzhetsky, ed.), 37:71-94, American Mathematical Society, Providence, RI, 1997.
  59. Yan P. Yuan, Oliver Eulenstein, Martin Vingron, and Peer Bork. Towards detection of sequence orthologs. In German Conference on Bioinformatics, pages 25-30, 1997.