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Collaborations
Presentations Publications
Community Software Morphology Databases Sequence Databases ATol

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Publications

  1. Alfaro, M. E. and Holder, M. T. (2006) "The prior and the posterior in Bayesian phylogenetics." Annual Review of Ecology, Evolution, and Systematics 37:19-42.
  2. Alfaro, M. E. and Huelsenbeck, J. P. (2006) "Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty." Systematic Biology  55:89-96. 
  3. Altekar, G., Dwarkadas, S., Huelsenbeck, J. P. and Ronquist, F. (2004) "Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference." Bioinformatics  20:407-415.
  4. Angelov, S., Harb, B., Kannan, S., Khanna, S. and Kim, J. (2006) "Efficient enumeration of phylogenetically informative substrings." Lecture Notes in Computer Science 3909:248-264.
  5. Angelov, S., Harb, B., Khanna, S., Khanna, S., Kim, J. and Wang, L.-S. (2004) "Genome identification and classification by short oligo arrays." Lecture Notes in Computer Science. 3240: 400-411.
  6. Bachrach, A., Chen, K., Harrelson, C., Mihaescu, R., Rao, S. and Shah, A. (2005) "Lower bounds for maximum parsimony with gene order data." Lecture Notes in Computer Science  3678:1-10.
  7. Bader, D. A. (2004) "Computational biology and high-performance computing." Communications of the ACM, Special Issue on Bioinformatics  47(11):34-41.
  8. Bader, D. A. (2004) "An improved, randomized algorithm for parallel selection with an experimental study." Journal of Parallel and Distributed Computing  64(9):1051-1059.
  9. Bader, D. A. (2005) "High-performance algorithm engineering for large-scale graph problems and computational biology." Experimental and Efficient Algorithms, Proceedings  3503:16-21.
  10. Bader, D. A., Chandu, V. and Yan, M. (2006) "ExactMP: An efficient parallel exact solver for phylogenetic tree reconstruction using maximum parsimony." 35th Int’l Conf. on Parallel Processing ICPP’06 pp.65-73.
  11. Bader, D. A. and Cong, G. (2004) "Fast shared memory algorithms for computing the minimum spanning forest of sparse graphs." Proc. 18th IEEE Int'l Parallel and Distributed Processing Symp. (IPDPS'04)
  12. Bader, D. A. and Cong, G. (2006) "Fast shared-memory algorithms for graph theoretic problems." Journal of Parallel and Distributed Computing  66(11):1366-1378.
  13. Bader, D. A. and Cong, G. (2007) "Efficient parallel graph algorithms for shared-memory multiprocessors." Handbook of Parallel Computing: Models, Algorithms, and Applications In Press.  CRC Press.
  14. Bader, D. A., Cong, G. and Feo, J. (2005) "On the Architectural Requirements for Efficient Execution of Graph Algorithms." The 34th International Conference on Parallel Processing (ICPP 2005) pp.547-556.
  15. Bader, D. A. and G. J. Cong 2005. "A fast, parallel spanning tree algorithm for symmetric multiprocessors (SMPS)." Journal of Parallel and Distributed Computing 65(9): 994-1006.
  16. Bader, D. A. and Cong, G. (2006) "Fast shared-memory algorithms for graph theoretic problems." Journal of Parallel and Distributed Computing  66(11):1366-1378.
  17. Bader, D. A. and Cong, G. (2007) "Effcient parallel graph algorithms for shared-memory multiprocessors." Handbook of Parallel Computing: Models, Algorithms, and Applications In Press. CRC Press. 
  18. Bader, D. A., Hart, W. E. and Phillips, C. A. (2004) "Parallel algorithm design for branch and bound." Tutorials on Emerging Methodologies and Applications in Operations Research pp.1-44, Kluwer Academic Press.
  19. Bader, D. A., Li, Y., Li, T. and Sachdeva, V. (2005) "BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications." The IEEE International Symposium on Workload Characterization (IISWC 2005).
  20. Bader, D. A. and Madduri, K. (2004) "A parallel state assignment algorithm for finite state machines." The 11th International Conference on High Performance Computing (HiPC 2004)  3296: 297-308. 
  21. Bader, D. A. and Madduri, K. (2005) "Design and implementation of the HPCS graph analysis benchmark on symmetric multiprocessors." 12th Conf. on High Performance Computing HiPC’05, Lecture Notes in Computer Science 3769:465-476. 
  22. Bader, D. A. and Madduri, K. (2006) "Designing Multithreaded Algorithms for Breadth-First Search and st-connectivity on the Cray MTA-2." 35th International Conference on Parallel Processing (ICPP 2006). 
  23. Bader, D. A. and Madduri, K. (2006) "Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks." The 35th International Conference on Parallel Processing (ICPP 2006).
  24. Bader, D. A., Madduri, K., Cong, G. and Feo, J. (2007) "Design of multithreaded algorithms for combinatorial problems." Handbook of Parallel Computing: Models, Algorithms, and Applications, CRC Press.  
  25. Bader, D. A., Roshan, U. and Stamatakis, A. (2005) "Computational grand challenges in assembling the tree of life: Problems & solutions." IEEE/ACM Supercomputing SC’2005.
  26. Bader, D. A., Roshan, U. and Stamatakis, A. (2006) "Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions. Advances in Computing, in Computational Biology and Bioinformatics  68:127-176.
  27. Bader, D. A. and Sachdeva, V. (2005) "A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic." The 18th ISCA International Conference on Parallel and Distributed Computing Systems (PDCS 2005). 
  28. Bader, D. A. and Yan, M. (2006) "High Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony." Handbook of Computational Molecular Biology pp1-19. Chapman & Hall.
  29. Batu, T., Kannan, S., Khanna, S. and McGregor, A. (2004) "Reconstructing strings from random traces." Proc. Symp. Discrete Algorithms, SODA ’04 pp.910-918.
  30. Bell, C. D. and M. J. Donoghue (2005) "Dating the dipsacales: Comparing models, genes, and evolutionary implications." American Journal of Botany 92(2):284-296.
  31. Bell, C. D. and M. J. Donoghue (2005) "Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians."Organisms Diversity & Evolution 5(2):147-159.
  32. Berger-Wolf, T. Y. and Warnow, T. (2004) "Online consensus of phylogenetic trees." Proc. 4th Workshop on Algorithms in Bioinformatics (WABI'04)  3240:350-361.  http://www.ii.uib.no/algo2004/wabi2004/
  33. Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L. and Purvis, A. (2007) The delayed rise of present-day mammals. Nature  446:507-512. 
  34. Bowers, S., McPhillips, T., Ludascher, B., Cohen, S. and Davidson, S. B. (2006) "A model for user-oriented data provenance in pipelined scientific workflows." Proc. Int’l Provenance and Annotation Workshop PAW’06  4145:133-147.  
  35. Boyer, R. S., Hunt, W. A. J. and Nielesen, S. M. (2005) "A compressed format for collections of phylogenetic trees and improved consensus performance." Proc. 5th Workshop Algorithms in Bioinformatics (WABI’05), Lecture Notes in Computer Science  3692:353-364.
  36. Bray, N. and Pachter, L. (2004) "MAVID: constrained ancestral alignment of multiple sequences." Genome Research  14:693-699.
  37. Chaudhuri, K., Chen, K., Mihaescu, R. and Rao, S. (2006) "On the tandem duplication-random loss model of genome rearrangement." 17th ACM-SIAM Symp. on Discrete Algorithms SODA’06 pp.564-570.
  38. Chen, B., Piel, W. H., Gui, L., Bruford, E. and Monteiro, A. (2005) "HSP90 family of genes in the human genome: insights into their divergence and evolution." Genomics  86:627-637.
  39. Chen, K. and Pachter, L. (2005) "Bioinformatics for whole-genome shotgun sequencing of microbial communities." PLoS Comput Biol. 1(2):e24. 
  40. Chor, B., Hendy, M. D. and Snir, S. (2006) "Maximum likelihood Jukes-Cantor triples: Analytical solutions." Mol. Biol. Evol.  23(3):626-632. 
  41. Chor, B. and Snir, S. (2007)"Molecular clock forks: Symbolic mathematical analysis." Mathematical Biosciences  208(2):347-358
  42. Clark, L. G. and Donoghue, M. J. (2005) "John H. Beaman - Recipient of the 2004 Asa Gray Award."Systematic Botany  30(1):1-6.
  43. Coarfa, C., Dotsenko, Y., Mellor-Crummey, J., Nakhleh, L. and Roshan, U.(2005) "PRec-I-DCM3: A parallel for fast and accurate large scale phylogeny reconstruction." 1st IEEE Workshop on High-Performance Computing in Medicine and Biology (HiPCoMB2005)  2:346-350. 
  44. Cohen, S., Cohen-Boulakia, S. and Davidson, S. B. (2006) "Towards a model of provenance and user views in scientific workflows." Data Integration for the Life Sciences DILS’06 in Lecture Notes in Computer Science 4076:264-279.
  45. Cohen-Boulakia, S., Davidson, S. and Froidevaux, C. (2005) "A user-centric framework for accessing biological sources and tools."Data Integration in the Life Sciences, in Lecture Notes in Computer Science 3615:3-18.
  46. Cong, G. and Bader, D. A. (2004) "The Euler tour technique and parallel rooted spanning tree." 33rd International Conference on Parallel Processing (ICPP). pp.448-457.
  47. Cong, G. and Bader, D. A. (2004) "Lock-free parallel algorithms: an experimental study." The 11th International Conference on High Performance Computing (HiPC 2004)  3296:516-527.
  48. Cong, G. and Bader, D. A. (2005) "An empirical analysis of parallel random permutation algorithms on SMPs." 18th ISCA Conf. on Parallel and Distributed Computing Systems PDCS’05. pp.27-34. 
  49. Cong, G. and Bader, D. A. (2006) (abstract) "Designing irregular parallel algorithms with mutual exclusion and lock-free protocols." Journal of Parallel and Distributed Computing  66(6):854-866. 
  50. Cracraft, J. and Donoghue, M. J. (2004) "Assembling the Tree of Life." Oxford University Press 592 pp. 
  51. Cui, L., Leebens-Mack, J. H., Wang, L.-S., Tang, J., Rymarquis, L., Stern, D. B. and dePamphilis, C. W. (2006) "Adaptive evolution of chloroplast genome structure." BMC Evolutionary Biology  6:13. 
  52. Daskalakis, C., Hill, C., Jaffe, A., Mihaescu, R., Mossel, E. and Rao, S. (2006) "Maximal accurate forests from distance matrices." 10th Ann. Int’l Conf. Comput. Mol. Biol. (RECOMB’06)  in Lecture Notes in Computer Science 3909:281-295, Springer-Verlag.  
  53. Daskalakis, C., Mossel, E. and Roch, S. (2006) "Optimal Phylogenetic Reconstruction." Thirty-eighth annual ACM Symposium on Theory of Computing (STOC '06). pp159-168.
  54. Davidson, S. B., Kim, J. and Zheng, Y. (2005) "Efficiently supporting structure queries on phylogenetic trees." 7th Int’l Conf. Scientific & Statistical Database Management SSDBM’05 pp.93-102.
  55. Davis, C. C., Webb, C. O., Wurdack, K. J., Jaramillo, C. A. and Donoghue, M. J. (2005) (abstract) "Explosive radiation of malpighiales supports a mid-Cretaceous origin of modern tropical rain forests." American Naturalist  165(3):E36-E65.
  56. Donoghue, M. J. (2005) "Comparisons, phylogeny, and teaching evolution." in Evolutionary Science and Society: Educating a New Generation, pp.69-77.
  57. Donoghue, M. J. (2005) (abstract only) "Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny." Paleobiology  31(2):77-93.
  58. Donoghue, M. J., Baldwin, B. G., Li, J. and Winkworth, R. C. (2004) "Viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences." Syst. Bot.  29(1):188-198.
  59. Donoghue, M. J. and Gauthier, J. A. (2004) "Implementing the PhyloCode." Trends in Ecol. and Evol. 19:281-282.
  60. Donoghue, M. J. and Smith, M. (2005) "Biodiversity inventory: Reflections on preparedness and efficiency." Biodiversity: Science and Governance.pp 79-86. Musee National d’Histoire Naturelle.
  61. Dotsenko, Y., Coarfa, C., Mellor-Crummey, J., Nakhleh, L. and Roshan, U. (2006)"PRec-I-DCM3:A parallel framework for fast and accurate large scale phylogeny reconstruction." Intl J. Bioinformatics Research and Applications 2(4):407-419.
  62. Du, Z., Stamatakis, A., Lin, F., Roshan, U. and Nakhleh, L. (2005) "Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood." Conf. on High-Performance Computing and Communications (HPCC’05) 2:346-350.
  63. Du, Z. H., Lin, F. and Roshan, U. W. (2005) "Reconstruction of large phylogenetic trees: A parallel approach." Computational Biology and Chemistry  29(4):273-280.
  64. Duran, K. L., Lowrey, T. K., Parmenter, R. R. and Lewis, P. O. (2005) "Genetic diversity in Chihuahuan Desert populations of creosotebush (Zygophyllaceae : Larrea tridentata)." American Journal of Botany  92(4):722-729.
  65. Earnest-DeYoung, J. V., Lerat, E. and Moret, B. M. E. (2004) "Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data." Proc. 4th Workshop on Algorithms in Bioinformatics (WABI'04) in Lecture Notes in Computer Science 3240:1-13.  compbio.unm.edu/~joeled/Ancestral.pdf
  66. Edgar, R. and Myers, E. (2005) "PILER: Identification and classification of repeated genomic elements." 13th Conf. on Intelligent Systems for Molecular Biology (ISMB’05)  21:i152-i158.
  67. Erika, J. E., R. Nyffeler, et al. (2005) "Basal cactus phylogeny: Implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form." American Journal of Botany 92(7): 1177-1188.
  68. Eriksson, N. (2005) "Tree construction using singular value decomposition." in Algebraic Statistics for Computational Biology pp.347-358, Cambridge University Press.
  69. Eskin, E. and Snir, S. (2005) "The homology kernel: A biologically motivated sequence embedding into Euclidean space." 3rd IEEE Symp. on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB’05) pp.179-186. 
  70. Eskin, E. and Snir, S. (2006) "Incorporating homologues into sequence embeddings for protein analysis." J. Bioinformatics and Comput. Biology  5(3):717-38.
  71. Evans, S. N. and Warnow, T. (2004) "Unidentifiable divergence times in rates-across-sites models." IEEE/ACM Transactions Computational Biology and Bioinformatics 1:130-134.
  72. Evans, S. N., Warnow, T. and Ringe, D. (2004) "Inference of divergence times as a statistical inverse problem." Phylogenetic Methods and the Prehistory of Languages pp.119-129. Cambridge University Press.
  73. Feild, T. S., Arens, N. C., Doyle, J. A., Dawson, T. E. and Donoghue, M. J. (2004) (abstract) "Dark and disturbed: a new image of early angiosperm ecology." Paleobiology  30:82-107.
  74. Ganapathy, G., Goodson, B., Jansen, R., Ramachandran, V. and Warnow, T. (2005) "Pattern identification in biogeography: metrics and algorithms for comparing area cladograms." 5th Workshop Algorithms in Bioinformatics (WABI’05), in Lecture Notes in Computer Science 3692:116-127. Springer-Verlag.  
  75. G. Ganapathy, V. Ramachandran, and T. Warnow 2003. "Better Hill-Climbing Seaches for Parsimony." In Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI), pp. 245--258.
  76. G. Ganapathy, V. Ramachandran, and T. Warnow 2004. "On Contract-and-Refine-Transformations Between Phylogenetic Trees." In Proceedings of the Fifteenth ACM-SIAM Symposium on Discrete Algorithms (SODA).
  77. Ge, F., Wang, L.-S. and Kim, J. (2005) "The cobweb of life revealed by genome-scale estimates of horizontal gene transfer." PLoS Biology  3(10):e316. 
  78. Glenner, H., Hansen, A. J., Sorensen, M. V., Ronquist, F., Huelsenbeck, J. P. and Willerslev, E. (2004) "Bayesian inference of the metazoan phylogeny: A combined analysis." Curr. Biol.  14:1644-1649.
  79. Grebennikov, V. V. and D. R. Maddison (2005) (abstract only) "Phylogenetic analysis of Trechitae (Coleoptera : Carabidae) based on larval morphology, with a description of first-instar Phrypeus and a key to genera." Systematic Entomology 30(1):38-59.
  80. Guan, Z., Miller, M. A. and Altintas, I. (2006) "Authentication framework in the Kepler workflow system." 1st TeraGrid Conf.
  81. Guindon, S., Rodrigo, A. G., K., D. and Huelsenbeck, J. P. (2004) "Modeling the site-specific variation of selection patterns along lineages." Proc. Nat’l Acad. Sci., USA  101(35):12957-12962.
  82. Harb, B., Kannan, S. and McGregor, A. (2005) "Approximating the best-fit tree under Lp norms." 8th Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX’05) pp.123-133.
  83. Herbert, K. G., Gehani, N. J., Piel, W. H., Wang, J. T. L. and Wu, C. H. (2004) "BIO-AJAX: An extensible framework for biological data cleaning." SIGMOD Record,  33(2):51-57.
  84. Herbert, K. G., Wang, J. T. L., Pusapati, S. and Piel, W. H. (2005) "Lineage path integration for phylogenetic resources." 17th Int’l Conf. Scientific & Statistical Database Management SSDBM’05 pp.117-120.
  85. Hillis, D. M., Heath, T. A. and St John, K. (2005) "Analysis and visualization of tree space." Systematic Biology 54(3):471-482.
  86. Hillis, D. M. and Wilcox, T. P. (2005). "Phylogeny of the New World true frogs (Rana)." Molecular Phylogenetics and Evolution 34(2):299-314.
  87. Holder, M. T., Lewis, P. O., Swofford, D. L. and Larget, B. (2006) "Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics." Syst. Biol.  54:961-965. 
  88. Howarth, D. G. and Donoghue, M. J. (2005) "Duplications in CYC-like genes from dipsacales correlate with floral form." International Journal of Plant Sciences  166(3):357-370.
  89. Huelsenbeck, J. P., Larget, B. and Alfaro, M. E. (2004) "Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo". Mol. Biol. Evol. 21(6):1123-1133. 
  90. Huelsenbeck, J. P. and Rannala, B. (2004) "Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models." Syst. Biol.  53(6):904-913
  91. Huelsenbeck, J. P. and Ronquist, F. (2005) "Bayesian analysis of molecular evolution using MrBayes." Statistical Methods in Molecular Evolution  Vol XII in Statistics for Biology and Health; Springer-Verlag.
  92. Janson, S. and Mossel, E. (2004) "Robust reconstruction on trees is determined by the second eigenvalue." Ann. Probab. 32:2630-2649.
  93. Jin, G., Nakhleh, L., Snir, S. and Tuller, T. (2006) "Efficient parsimony-based methods for phylogenetic network reconstruction." European Conference on Computational Biology  23:e123-e128.
  94. Jin, G., Nakhleh, L., Snir, S. and Tuller, T. (2006) "Maximum Likelihood of Phylogenetic Networks." Bioinformatics  22(21):2604-2611. 
  95. Kanj, I., Nakhleh, L. and Xia, G. (2006) "Reconstructing evolution of natural languages: Complexity and parameterized algorithms." 12th Annual International Computing and Combinatorics Conference (COCOON 06) in Lecture Notes in Computer Science 4112:299-308.
  96. Kannan, S. and McGregor, A. (2005) "More on reconstructing strings from random traces: Insertions and deletions." Intl. Symp. Information Theory, (ISIT’05)_ pp.297-301.
  97. Kelch, D. G., Driskell, A., and Mishler, B. D. (2004) "Inferring phylogeny using genomic characters: A case study using land plant plastomes." in Molecular systematics of bryophytes, B. Goffinet, V. H., and R. Magill (eds.), Missouri Botanical Garden Press: St. Louis. p. 3-12 .
  98. Khetan, A., Chor, B. and Snir, S. (2006) "Maximum likelihood on molecular clock comb: Analytic solutions." Journal of Computational Biology 13(3):819-837
  99. Kosakovsky-Pond, S. L., Frost, S. D. and Muse, S. V. (2005) "Hyphy: A platform for molecular evolutionary analysis." Bioinformatics  21:676-679. 
  100. Kosakovsky-Pond, S. L., and Muse, S. V. (2005) "Modeling heterogeneity of synonymous and nonsynonymous substitution rates across sites." Mol. Biol. Evol. 22(12):2375-2385.
  101. Lapp, H., Bala, S., Balhoff, J. P., Bouck, A., Goto, N., Holder, M. T., Holland, R., Holloway, A., Katayama, T., Lewis, P. O., Mackey, A., Osbourne, B. I., Piel, W. H., Kosakovsky-Pond, S. L., Poon, A., Qui, W.-G., Stajich, J. E., Stoltzfus, A., Thierer, T., Vilella, A. J., Vos, R. A., Zmasek, C. M., Zwickl, D. and Vision, T. J. (2007) The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics  In Press. 
  102. Lewis, P. O., Holder, M. T. and Holsinger, K. E. (2005) "Polytomies and Bayesian phylogenetic inference." Systematic Biology 54(2):241-253.
  103. Linder, C. R., Moret, B. M. E., Nakhleh, L. and Warnow, T. (2004) "Network (reticulated) evolution: Biology, models, and algorithms." 
  104. Linder, C. R. and Riesenberg, L. (2004) "Reconstructing patterns of reticulate evolution in plants." Am. J. Botany  91(10):1700-1708. 
  105. Linder, C. R. and Warnow, T. (2006) "An overview of phylogeny reconstruction." Handbook of Computational Molecular Biology. Chapman & Hall.
  106. Liu, T., Tang, J. and Moret, B. M. E. (2005) "Quartet methods for phylogeny reconstruction from gene orders." 11th Conf. Computing and Combinatorics (COCOON’05) in Lecture Notes in Computer Science 3595:63-73, Springer-Verlag.
  107. Mannino, F. V. and Muse, S. V. (2006) "Extensive site-to-site variability of synonymous substitution rates in mitochondrial genomes." Genetics. 
  108. Mao, R., Xu, W., Ramakrishnan, S., Nuckolls, G. and Miranker, D. P. (2005) "On optimizing distance-based similarity search for biological databases." 4th Computational Systems Biology Conf. (CSB’05) pp.351-361. 
  109. Marron, M., Swenson, K. M., and Moret, B. M. E. (2004) "Genomic distances under deletions and insertions." Theoretical Computer Science. 325(3):347-360.
  110. Mihaescu, R. (2005) "Parametric inference." Algebraic Statistics for Computational Biology pp.165-180, Cambridge University Press.  
  111. Mihaescu, R., Levy, D. and Pachter, L. (2006) "Why neighbor-joining works." 3rd International Conf. in Phylogenomics. 
  112. Milch, B., Marthi, B., and Russell, S. (2004) "Blog: Relational modeling with unknown objects." in Proc. ICML-04 Workshop on Statistical Relational Learning. Banff, Canada.
  113. Milch, B., Marthi, B., Sontag, D., Russell, S., Ong, D. L., and Kolobov, A. (2005) "Approximate inference for infinite contingent bayesian networks." in Proc. Tenth International Workshop on Artificial Intelligence and Statistics. Barbados.
  114. Miranker, D. P., Xu, W. and Mao, R. (2004) "MoBIoS: A metric-space DBMS to support biological discovery." 16th Intl Conf. Scientific & Statistical Database Management SSDBM’04 pp.241-244.
  115. Mishler, B. (2004) "The evolution and ecology of desiccation tolerance in mosses." Integrative and Comparative Biology  44(6):608-608.
  116. Mishler, B. D. (2005) "The logic of the data matrix in phylogenetic analysis." in Parsimony, Phylogeny, and Genomics pp.57-70, Oxford University Press.
  117. Moore, B. R., Chan, K. M. A. and Donoghue, M. J. (2004) "Detecting diversification rate variation in supertrees." Phylogenetic Supertrees: Combining information to reveal the Tree of Life pp.487-533, Kluwer Academic Publishers.
  118. Moore, B. R., Smith, R. S. and Donoghue, M. J. (2006) (abstract) "Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping." Syst. Biol. 55(4):662-676.
  119. Moore, B. R., Smith, S. A., Ree, H. R. and Donoghue, M. J. (2007) "Incorporating fossil data in biogeographic inference: a likelihood approach." Evolution  In press.
  120. Moran, S., Rao, S. and Snir, S. (2005) "Using semi-definite programming to enhance supertree resolvability." 5th Workshop Algorithms in Bioinformatics (WABI’05) in Lecture Notes in Computer Science 3692:89-103.
  121. Moran, S. and Snir, S. (2005) "Convex recolorings of strings and trees: Definitions, hardness results and algorithms." 9th Int’l. Workshop on Algs. and Data Structures (WADS’05) pp.218 - 232.
  122. Moret, B. M. E. 2005. "Computational challenges from the tree of life." in Proc. 7th Workshop on Algorithm Engineering & Experiments  (ALENEX '05). Vancouver.  SIAM Press.
  123. Moret, B. M. E., Bader, D. A. and Warnow, T. (2001) "High-performance algorithm engineering for computational phylogenetics." Computational Science -- ICCS 2001, Proceedings Pt 2  2074:1012-1021.
  124. Moret, B. M. E., Nakhleh, L., Warnow, T., et. al. (2004) "Phylogenetic networks: modeling, reconstructibility, and accuracy." IEEE/ACM Trans. on Computational Biology and Biocomputing. 1(1):13-23
  125. Moret, B. M. E., Tang, J., and Warnow, T. (2005)  "Reconstructing phylogenies from gene-content and gene-order data." in Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford Univ. Press. pp.321-352.
  126. Moret, B.M.E. and Warnow, T. "Advances in phylogeny reconstruction from gene order and content data." in Molecular Evolution: Producing the Biochemical Data, Part B, E.A. Zimmer and E.H. Roalson, eds., Meth. Enzymol.395:673-683.
  127. Morin, M. M. and Moret, B. M. E. (2006) "NetGen: Generating phylogenetic networks with diploid hybrids." Bioinformatics  22:1921-1923. 
  128. Mossel, E. (2004) "Phase transitions in phylogeny." Trans. Amer. Math. Soc. 356(6):2379-2404. 
  129. Mossel, E. (2004) "Survey: Information flow on trees." Graphs, Morphisms and Statistical Physics. DIMACS  in discrete mathematics and theoretical computer science,  63:155-170, AMS Press.
  130. Mossel, E. (2006) "Distorted metrics on trees and phylogenetic forests." IEEE/ACM Trans. on Computational Biology and Bioinformatics  4(1):108-116.
  131. Mossel, E. and M., S. (2004) "A phase transition for a random cluster model on phylogenetic trees." Math. Biosci. 187(2):189-203. 
  132. Mossel, E. and Roch, S. (2005) "Learning Nonsingular Phylogenies and Hidden Markov Models." 37th Symp. on the Theory of Computing (STOC’05) pp.366-376. 
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