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@article{111,
        author = "M. E. Alfaro and M. T. Holder",
        title = "The prior and the posterior in Bayesian phylogenetics",
        journal = "Annual Review of Ecology, Evolution, and Systematics",
        pages = "19-42",
        volume = "37",
        year = "2006"
}

@article{112,
        author = "M. E. Alfaro and J. P. Huelsenbeck",
        title = "Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty",
        journal = "Systematic Biology",
        pages = "89 -- 96",
        volume = "55",
        year = "2006"
}

@article{113,
        author = "G. Altekar and S. Dwarkadas and J. P. Huelsenbeck and F. Ronquist",
        title = "Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference",
        journal = "Bioinformatics",
        pages = "407 -- 415",
        volume = "20",
        year = "2004"
}

@article{114,
        author = "S. Angelov and B. Harb and S. Kannan and S. Khanna and J. Kim",
        title = "Efficient enumeration of phylogenetically informative substrings",
        journal = "Lecture Notes in Computer Science",
        pages = "248-264",
        volume = "3909",
        year = "2006"
}

@article{115,
        author = "S. Angelov and B. Harb and S. Khanna and S. Khanna and J. Kim and L.-S. Wang",
        title = "Genome identification and classification by short oligo arrays",
        journal = "Lecture Notes in Computer Science.",
        pages = "400--411.",
        volume = "3240",
        year = "2004"
}

@article{117,
        author = "A. Bachrach and K. Chen and C. Harrelson and R. Mihaescu and S. Rao and A. Shah",
        title = "Lower bounds for maximum parsimony with gene order data",
        journal = "Lecture Notes in Computer Science",
        pages = "1-10",
        volume = "3678",
        year = "2005"
}

@article{7,
        author = "D. A. Bader",
        editor = "C. Stewart",
        title = "Computational biology and high-performance computing",
        journal = "Communications of the ACM, Special Issue on Bioinformatics",
        pages = "34-41",
        volume = "47",
        number = "11",
        year = "2004",
        uri = "http://portal.acm.org/citation.cfm?id=1029496.1029523&coll=ACM&dl=ACM&idx=1029496&part=periodical&WantType=periodical&title=Communications%20of%20the%20ACM&CFID=30617240&CFTOKEN=22560579"
}

@article{5,
        author = "D. A. Bader",
        title = "An improved, randomized algorithm for parallel selection with an experimental study",
        journal = "Journal of Parallel and Distributed Computing",
        pages = "1051-1059",
        volume = "64",
        number = "9",
        year = "2004",
        uri = "www.eece.unm.edu/~dbader/papers/ALENEX00-select.pdf",
        uri = "www.eece.unm.edu/~dbader/papers/ALENEX00-select.pdf"
}

@inbook{110,
        author = "D. A. Bader",
        title = "High-performance algorithm engineering for large-scale graph problems and computational biology",
        booktitle = "Experimental and Efficient Algorithms, Proceedings",
        series = "Lecture Notes in Computer Science",
        pages = "16-21",
        volume = "3503",
        year = "2005",
        issn = "0302-9743",
        abstract = "Many large-scale optimization problems rely on graph theoretic solutions; yet high-performance computing has traditionally focused on regular applications with high degrees of locality. We describe our novel methodology for designing and implementing irregular parallel algorithms that attain significant performance on high-end computer systems. Our results for several fundamental graph theory problems are the first ever to achieve parallel speedups. Specifically, we have demonstrated for the first time that significant parallel speedups are attainable for arbitrary instances of a variety of graph problems and are developing a library of fundamental routines for discrete optimization (especially in computational biology) on shared-memory systems. Phylogenies derived from gene order data may prove crucial in answering some fundamental questions in biomolecular evolution. High-performance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing approaches. We discuss one such such application, GRAPPA, that demonstrated over a billion-fold speedup in running time (on a variety of real and simulated datasets), by combining low-level algorithmic improvements, cache-aware programming, careful performance tuning, and massive parallelism. We show how these techniques are directly applicable to a large variety of problems in computational biology.",
        annote = "ISI Document Delivery No.: BCL08 Article"
}

@inproceedings{118,
        author = "D.A. Bader and V. Chandu and M. Yan",
        title = "ExactMP: An efficient parallel exact solver for phylogenetic tree reconstruction using maximum parsimony.",
        pages = "65-73",
        year = "2006"
}

@inproceedings{30,
        author = "D. A. Bader and G. Cong",
        title = "Fast shared memory algorithms for computing the minimum spanning forest of sparse graphs",
        year = "2004",
        publisher = "IEEE Press",
        uri = "www.ece.unm.edu/~dbader/papers/MST-IPDPS2004-BC04b.pdf",
        uri = "www.ece.unm.edu/~dbader/papers/MST-IPDPS2004-BC04b.pdf"
}

@article{120,
        author = "D.A. Bader and G. Cong",
        title = "Fast shared-memory algorithms for graph theoretic problems",
        journal = "Journal of Parallel and Distributed Computing",
        pages = "1366 -1378",
        volume = "66",
        number = "11",
        year = "2006"
}

@inbook{119,
        author = "D.A. Bader and G. Cong",
        editor = "S. Rajasekaran and J. Reif",
        title = "Efficient parallel graph algorithms for shared-memory multiprocessors.",
        booktitle = "Handbook of Parallel Computing: Models, Algorithms, and Applications",
        pages = "In Press",
        year = "2007",
        publisher = "CRC Press"
}

@inproceedings{121,
        author = "D.A. Bader and G. Cong and J. Feo",
        title = "On the Architectural Requirements for Efficient Execution of Graph Algorithms",
        pages = "547-556",
        year = "2005",
        month = "June 14-17,"
}

@article{106,
        author = "D. A. Bader and G. J. Cong",
        title = "A fast, parallel spanning tree algorithm for symmetric multiprocessors (SMPS)",
        journal = "Journal of Parallel and Distributed Computing",
        pages = "994-1006",
        volume = "65",
        number = "9",
        year = "2005",
        month = "Sep",
        issn = "0743-7315",
        abstract = "The ability to provide uniform shared-memory access to a significant number of processors in a single SMP node brings us much closer to the ideal PRAM parallel computer. Many PRAM algorithms can be adapted to SMPs with few modifications. Yet there are few studies that deal with the implementation and performance issues of running PRAM-style algorithms on SMPs. Our study in this paper focuses on implementing parallel spanning tree algorithms on SMPs. Spanning tree is an important problem in the sense that it is the building block for many other parallel graph algorithms and also because it is representative of a large class of irregular combinatorial problems that have simple and efficient sequential implementations and fast PRAM algorithms, but these irregular problems often have no known efficient parallel implementations. Experimental studies have been conducted on related problems (minimum spanning tree and connected components) using parallel computers, but only achieved reasonable speedup on regular graph topologies that can be implicitly partitioned with good locality features or on very dense graphs with limited numbers of vertices. In this paper we present a new randomized algorithm and implementation with superior performance that for the first time achieves parallel speedup on arbitrary graphs (both regular and irregular topologies) when compared with the best sequential implementation for finding a spanning tree. This new algorithm uses several techniques to give an expected running time that scales linearly with the number p of processors for suitably large inputs (n > p(2)). As the spanning tree problem is notoriously hard for any parallel implementation to achieve reasonable speedup, our study may shed new light on implementing PRAM algorithms for shared-memory parallel computers. The main results of this paper are 1. A new and practical spanning tree algorithm for symmetric multiprocessors that exhibits parallel speedups on graphs with regular and irregular topologies; and 2. an experimental study of parallel spanning tree algorithms that reveals the superior performance of our new approach compared with the previous algorithms. The source code for these algorithms is freely-available from our web site. (c) 2005 Elsevier Inc. All rights reserved.",
        annote = "ISI Document Delivery No.: 959KK",
        howpublished = "Article",
        uri = "<Go to ISI>://000231516400002"
}

@inbook{52,
        author = "D. A. Bader and W. E. Hart and C. A. Phillips",
        editor = "H. J. Greenberg",
        title = "Parallel algorithm design for branch and bound",
        booktitle = "Tutorials on Emerging Methodologies and Applications in Operations Research",
        pages = "1-44",
        year = "2004",
        publisher = "Kluwer Academic Press",
        uri = "http://www.eece.unm.edu/~dbader/papers/ParallelBranchBound.pdf",
        uri = "http://www.eece.unm.edu/~dbader/papers/ParallelBranchBound.pdf"
}

@inproceedings{244,
        author = "D.A. Bader and Y. Li and T. Li and V. Sachdeva",
        title = "BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications",
        year = "2005",
        month = "October 6-8,"
}

@inproceedings{50,
        author = "D. A. Bader and K. Madduri",
        title = "A parallel state assignment algorithm for finite state machines",
        series = "Lecture Notes in Computer Science",
        pages = "297-308",
        volume = "3296",
        year = "2004",
        publisher = "Springer-Verlag",
        uri = "http://www.ece.unm.edu/~dbader/papers/parjedi-HiPC2004.pdf",
        uri = "http://www.ece.unm.edu/~dbader/papers/parjedi-HiPC2004.pdf"
}

@inproceedings{122,
        author = "D.A. Bader and K. Madduri",
        title = "Design and implementation of the HPCS graph analysis benchmark on symmetric multiprocessors.",
        series = "Lecture Notes in Computer Science",
        pages = "465-476",
        volume = "3769",
        year = "2005"
}

@inproceedings{123,
        author = "D.A. Bader and K. Madduri",
        title = "Designing Multithreaded Algorithms for Breadth-First Search and st-connectivity on the Cray MTA-2",
        year = "2006",
        month = "August 14-18,"
}

@inproceedings{124,
        author = "D.A. Bader and K. Madduri",
        title = "Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks",
        year = "2006",
        month = "August 14-18,"
}

@inbook{125,
        author = "D.A. Bader and K. Madduri and G. Cong and J. Feo",
        editor = "S. Rajasekaran and J. Reif",
        title = "Design of multithreaded algorithms for combinatorial problems",
        booktitle = "Handbook of Parallel Computing: Models, Algorithms, and Applications",
        year = "2007",
        publisher = "CRC Press"
}

@inproceedings{126,
        author = "D.A. Bader and U. Roshan and A. Stamatakis",
        title = "Computational grand challenges in assembling the tree of life: Problems & solutions",
        year = "2005",
        month = "November 13,"
}

@inbook{127,
        author = "D.A. Bader and U. Roshan and A. Stamatakis",
        editor = "T S Tseng",
        title = "Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions",
        booktitle = "Computational Biology and Bioinformatics",
        series = "Advances in Computing",
        pages = "127 -176",
        volume = "68",
        year = "2006",
        publisher = "Elsevier"
}

@inproceedings{128,
        author = "D.A. Bader and V. Sachdeva",
        title = "A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic",
        year = "2005",
        month = "September 12-14,"
}

@inbook{129,
        author = "D.A. Bader and M. Yan",
        editor = "S. Aluru",
        title = "High Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony",
        booktitle = "Handbook of Computational Molecular Biology",
        series = "CRC Computer and Information Science Series",
        pages = "1-19",
        year = "2006",
        publisher = "Chapman & Hall"
}

@inproceedings{130,
        author = "T. Batu and S. Kannan and S. Khanna and A. McGregor",
        title = "Reconstructing strings from random traces",
        pages = "910 - 918",
        year = "2004"
}

@article{100,
        author = "C. D. Bell and M. J. Donoghue",
        title = "Dating the dipsacales: Comparing models, genes, and evolutionary implications",
        journal = "American Journal of Botany",
        pages = "284-296",
        volume = "92",
        number = "2",
        year = "2005",
        month = "Feb",
        issn = "0002-9122",
        abstract = "Dipsacales is an asterid angiosperm clade of ca. 1100 species, with most of its lineages occupying temperate regions of the Northern Hemisphere. A recent phylogenetic analysis based on 7593 nucleotides of chloroplast DNA recovered a well-resolved and strongly supported phylogenetic hypothesis, which we use here to estimate divergence times within the group. A molecular clock is strongly rejected, regardless of data partition. We used recently proposed methods that relax the assumption of rate constancy among lineages (local clocks, nonparametric rate smoothing, penalized likelihood, and Bayesian relaxed clock) to estimate the ages of major lineages. Age estimates for Dipsacales varied widely among markers and codon positions, and depended on the fossils used for calibration and method of analysis. Some methods yielded dates for the Dipsacales diversification that appear to be too old (prior to the presumed 125 my [million years] age of eudicots), and others suggested ages that are too young based on well-documented Dipsacales fossils. Concordant penalized likelihood and Bayesian studies imply that Dipsacales originated in the Cretaceous, as did its two major lineages, Adoxaceae and Caprifoliaceae. However, diversification of crown Adoxaceae and Caprifoliaceae mainly occurred in the Tertiary, with the origin of major lineages within these clades mainly occurring during the Eocene. Another round of diversification appears to have occurred in the Miocene. Several radiations, such as Valerianaceae in South America and Dipsacaceae around the Mediterranean, are even more recent. This study demonstrates the wide range of divergence times that can be obtained using different methods and data sets, and cautions against reliance on age estimates based on only a single gene or methodology. Despite this variance, significant conclusions can be made about the timing of Dipsacales evolution.",
        annote = "ISI Document Delivery No.: 897RB",
        howpublished = "Article",
        uri = "<Go to ISI>://000227021400010"
}

@article{88,
        author = "C. D. Bell and M. J. Donoghue",
        title = "Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians",
        journal = "Organisms Diversity & Evolution",
        pages = "147-159",
        volume = "5",
        number = "2",
        year = "2005",
        issn = "1439-6092",
        abstract = "Species of Valerianaceae are a common component of the alpine flora throughout the Northern Hemisphere as well as the Andes of South America. Sequence data from three chloroplast markers (psbA-trnH intron, trnK-matK intron, and the trnL-F region) along with the internal transcribed spacer region (ITS) of nuclear ribosomal DNA were used to infer relationships within Valerianaceae. Both genomes, as well as a combined data set, provide support for the major clades within the group and do not support a monophyletic Valeriana. In addition, these data indicate that Plectritis is nested within South American Valeriana, as opposed to being sister to Centhranthus as previously hypothesized. Valerianaceae appear to have originated in Asia, probably in the Himalayas, and subsequently to have dispersed several times to Europe and to the New World. Our results imply that Valerianaceae colonized South America on multiple occasions from the north. In one of these cases there appears to have been a substantial and rapid radiation, primarily in the high elevation paramo habitat. A variety of methods were used to estimate divergence times to determine when Valerianaceae might have colonized South America. Regardless of the method and fossil constraints applied, our estimates suggest that Valerianaceae colonized South America prior to the formation of the Isthmus of Panama. (c) 2005 Gesellschaft fur Biologische Systematik. Published by Elsevier GmbH. All rights reserved.",
        annote = "ISI Document Delivery No.: 941FQ",
        howpublished = "Article",
        uri = "<Go to ISI>://000230201100006"
}

@misc{14,
        author = "T.Y. Berger-Wolf",
        title = "Properties of compatibility and consensus sets of phylogenetic trees",
        booktitle = "Technical Report",
        volume = "TR-CS-2004-24",
        year = "2004",
        address = "U. New Mexico",
        uri = "http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-24"
}

@inproceedings{22,
        author = "T.Y. Berger-Wolf and T. Warnow",
        editor = "J. Kim and I. Jonassen",
        title = "Online consensus of phylogenetic trees",
        series = "Lecture Notes in Computer Science",
        pages = "3240, 350-361",
        volume = "3240",
        edition = "TR-CS-2003-34",
        year = "2004",
        publisher = "Springer-Verlag",
        uri = "http://www.ii.uib.no/algo2004/wabi2004/"
}

@article{243,
        author = "O. R. P. Bininda-Emonds and M. Cardillo and K. E. Jones and R. D. E. MacPhee and R. M. D. Beck and R. Grenyer and S. A. Price and R. A. Vos and J. L. Gittleman and A. Purvis",
        title = "The delayed rise of present-day mammals",
        journal = "Nature",
        pages = "507-512",
        volume = "446",
        year = "2007"
}

@inbook{131,
        author = "S. Bowers and T. McPhillips and B. Ludascher and S. Cohen and S. B. Davidson",
        title = "A model for user-oriented data provenance in pipelined scientific workflows",
        booktitle = "Proc. Int'l Provenance and Annotation Workshop PAW'06",
        series = "Lecture Notes in computer Science",
        pages = "133-147",
        volume = "4145",
        year = "2006"
}

@inproceedings{132,
        author = "R. S. Boyer and W. A. Jr. Hunt and S. M. Nielesen",
        title = "A compressed format for collections of phylogenetic trees and improved consensus performance.",
        pages = "353 -364",
        volume = "3692",
        year = "2005",
        publisher = "Springer-Verlag"
}

@article{133,
        author = "N. Bray and L. Pachter",
        title = "MAVID: constrained ancestral alignment of multiple sequences",
        journal = "Genome Research",
        pages = "693 - 699",
        volume = "14",
        year = "2004"
}

@inproceedings{134,
        author = "K. Chaudhuri and K. Chen and R. Mihaescu and S. Rao",
        title = "On the tandem duplication-random loss model of genome rearrangement.",
        pages = "564--570",
        year = "2006",
        publisher = "SIAM Press"
}

@article{135,
        author = "B. Chen and W. H. Piel and L. Gui and E. Bruford and A. Monteiro",
        title = "HSP90 family of genes in the human genome: insights into their divergence and evolution",
        journal = "Genomics",
        pages = "627--637",
        volume = "86",
        year = "2005"
}

@article{136,
        author = "K. Chen and L. Pachter",
        title = "Bioinformatics for whole-genome shotgun sequencing of microbial communities",
        journal = "PLoS Comput Biol.",
        pages = "e24",
        volume = "1",
        number = "2",
        year = "2005"
}

@article{137,
        author = "B. Chor and M.D. Hendy and S. Snir",
        title = "Maximum likelihood Jukes-Cantor triples: Analytical solutions.",
        journal = "Mol. Biol. Evol.",
        pages = "626-632",
        volume = "23",
        number = "3",
        year = "2006"
}

@article{138,
        author = "B. Chor and S. Snir",
        title = "Molecular clock forks: Symbolic mathematical analysis.",
        journal = "Mathematical Biosciences",
        pages = "347 - 358",
        volume = "208",
        number = "2",
        year = "2007",
        uri = "doi:10.1016/j.mbs.2006.04.001"
}

@article{99,
        author = "L. G. Clark and M. J. Donoghue",
        title = "John H. Beaman - Recipient of the 2004 Asa Gray Award",
        journal = "Systematic Botany",
        pages = "1-6",
        volume = "30",
        number = "1",
        year = "2005",
        month = "Jan-Mar",
        issn = "0363-6445",
        annote = "ISI Document Delivery No.: 901PA",
        howpublished = "Biographical-Item",
        uri = "<Go to ISI>://000227293200001"
}

@inproceedings{139,
        author = "C. Coarfa and Y. Dotsenko and J. Mellor-Crummey and L. Nakhleh and U. Roshan",
        title = "PRec-I-DCM3: A parallel framework for fast and accurate large scale phylogeny reconstruction.",
        pages = "346--350",
        volume = "2",
        year = "2005"
}

@inbook{140,
        author = "S. Cohen and S. Cohen-Boulakia and S.B. Davidson",
        title = "Towards a model of provenance and user views in scientific workflows.",
        booktitle = "Data Integration for the Life Sciences DILS'06",
        series = "Lecture Notes in Computer Science",
        pages = "264-279",
        volume = "4076",
        year = "2006"
}

@inbook{105,
        author = "S. Cohen-Boulakia and S. Davidson and C. Froidevaux",
        title = "A user-centric framework for accessing biological sources and tools",
        booktitle = "Data Integration in the Life Sciences, Proceedings",
        series = "Lecture Notes in Computer Science",
        pages = "3-18",
        volume = "3615",
        year = "2005",
        issn = "0302-9743",
        abstract = "Biologists face two problems in interpreting their experiments: the integration of their data with information from multiple heterogeneous sources and data analysis with bioinformatics tools. It is difficult for scientists to choose between the numerous sources and tools without assistance. Following a thorough analysis of scientists' needs during the querying process, we found that biologists express preferences concerning the sources to be queried and the tools to be used. Interviews also showed that the querying process itself - the strategy followed - differs between scientists. In response to these findings, we have introduced a user-centric framework allowing to specify various querying processes. Then we have developed the BioGuide system which helps the scientists to choose suitable sources and tools, find complementary information in sources, and deal with divergent data. It is generic in that it can be adapted by each user to provide answers respecting his/her preferences, and obtained following his/her strategies.",
        annote = "ISI Document Delivery No.: BCT88 Article",
        uri = "<Go to ISI>://000231195100001"
}

@inproceedings{8,
        author = "G. Cong and D. A. Bader",
        title = "The Euler tour technique and parallel rooted spanning tree",
        pages = "448-457",
        year = "2004",
        uri = "http://www.eece.unm.edu/~dbader/papers/RootedSpanningTree.pdf",
        uri = "http://www.eece.unm.edu/~dbader/papers/RootedSpanningTree.pdf"
}

@inproceedings{51,
        author = "G. Cong and D. A. Bader",
        editor = "L. Boug\'e and V.K. Prasanna",
        title = "Lock-free parallel algorithms: an experimental study",
        series = "Lecture Notes in Computer Science",
        pages = "516-527",
        volume = "3296",
        year = "2004",
        publisher = "Springer-Verlag LNCS",
        uri = "http://www.eece.unm.edu/~dbader/papers/lockfree-HiPC2004.pdf",
        uri = "http://www.eece.unm.edu/~dbader/papers/lockfree-HiPC2004.pdf"
}

@inproceedings{141,
        author = "G. Cong and D.A. Bader",
        title = "An empirical analysis of parallel random permutation algorithms on smps.",
        pages = "27-34",
        year = "2005"
}

@article{142,
        author = "G. Cong and D.A. Bader",
        title = "Designing irregular parallel algorithms with mutual exclusion and lock-free protocols.",
        journal = "Journal of Parallel and Distributed Computing",
        pages = "854--866",
        volume = "66",
        number = "6",
        year = "2006",
        uri = "http://dx.doi.org/10.1016/j.jpdc.2005.12.004"
}

@book{143,
        author = "J. Cracraft and M.J. Donoghue",
        title = "Assembling the Tree of Life",
        booktitle = "Assembling the Tree of Life",
        year = "2004",
        publisher = "Oxford University Press"
}

@article{144,
        author = "L. Cui and J.H. Leebens-Mack and L.-S. Wang and J. Tang and L. Rymarquis and D.B. Stern and C.W. dePamphilis",
        title = "Adaptive evolution of chloroplast genome structure.",
        journal = "BMC Evolutionary Biology",
        pages = "13",
        volume = "6",
        year = "2006"
}

@inbook{145,
        author = "C. Daskalakis and C. Hill and A. Jaffe and R. Mihaescu and E. Mossel and S. Rao",
        title = "Maximal accurate forests from distance matrices.",
        booktitle = "10th Ann. Int'l Conf. Comput. Mol. Biol. (RECOMB'06)",
        series = "Lecture Notes in Computer Science",
        pages = "281 - 295",
        volume = "3909",
        year = "2006",
        publisher = "Springer-Verlag"
}

@inproceedings{146,
        author = "C. Daskalakis and E. Mossel and S. Roch",
        title = "Optimal Phylogenetic Reconstruction",
        pages = "159 - 168",
        year = "2006",
        uri = "http://portal.acm.org/citation.cfm?id=1132540"
}

@inproceedings{147,
        author = "S. B. Davidson and J. Kim and Y. Zheng",
        title = "Efficiently supporting structure queries on phylogenetic trees",
        pages = "93-102",
        year = "2005",
        uri = "http://portal.acm.org/citation.cfm?id=1116891"
}

@article{97,
        author = "C. C. Davis and C. O. Webb and K. J. Wurdack and C. A. Jaramillo and M. J. Donoghue",
        title = "Explosive radiation of malpighiales supports a mid-Cretaceous origin of modern tropical rain forests",
        journal = "American Naturalist",
        pages = "E36-E65",
        volume = "165",
        number = "3",
        year = "2005",
        month = "Mar",
        issn = "0003-0147",
        abstract = "Fossil data have been interpreted as indicating that Late Cretaceous tropical forests were open and dry adapted and that modern closed-canopy rain forest did not originate until after the Cretaceous-Tertiary (K/T) boundary. However, some mid-Cretaceous leaf floras have been interpreted as rain forest. Molecular divergence-time estimates within the clade Malpighiales, which constitute a large percentage of species in the shaded, shrub, and small tree layer in tropical rain forests worldwide, provide new tests of these hypotheses. We estimate that all 28 major lineages (i.e., traditionally recognized families) within this clade originated in tropical rain forest well before the Tertiary, mostly during the Albian and Cenomanian ( 112 - 94 Ma). Their rapid rise in the mid-Cretaceous may have resulted from the origin of adaptations to survive and reproduce under a closed forest canopy. This pattern may also be paralleled by other similarly diverse lineages and supports fossil indications that closed-canopy tropical rain forests existed well before the K/T boundary. This case illustrates that dated phylogenies can provide an important new source of evidence bearing on the timing of major environmental changes, which may be especially useful when fossil evidence is limited or controversial.",
        annote = "ISI Document Delivery No.: 904RY",
        howpublished = "Review",
        uri = "<Go to ISI>://000227516600001"
}

@inbook{148,
        author = "M.J. Donoghue",
        editor = "J. Cracraft and R. Bybee",
        title = "Comparisons, phylogeny, and teaching evolution",
        booktitle = "Evolutionary Science and Society: Educating a New Generation",
        pages = "69-77",
        year = "2005"
}

@article{89,
        author = "M. J. Donoghue",
        title = "Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny",
        journal = "Paleobiology",
        pages = "77-93",
        volume = "31",
        number = "2",
        year = "2005",
        issn = "0094-8373",
        abstract = "Improvements in our understanding of green plant phylogeny are casting new light on the connection between character evolution and diversification. The repeated discovery of paraphyly has helped disentangle what once appeared to be phylogenetically coincident character changes, but this has also highlighted the existence of sequences of character change, no one element of which can cleanly be identified as the "key innovations" responsible for shifting diversification rate. In effect, the cause becomes distributed across a nested series of nodes in the tree. Many of the most conspicuous plant "innovations" (such as macrophyllous leaves) are underlain by earlier, more subtle shifts in development (such as overtopping growth), which appear to have enabled the exploration of a greater range of morphological designs. Often it appears that these underlying changes have been brought about at the level of cell interactions within meristems, highlighting the need for developmental models and experiments focused at this level. The standard practice of attempting to identify correlations between recurrent character change (such as the tree growth habit) and clade diversity is complicated by the observation that the "same" trait may be constructed quite differently in different lineages (e.g., different forms of cambial activity), with some solutions imposing more architectural limitations than others. These thoughts highlight the need for a more nuanced view, which has implications for comparative methods. They also bear on issues central to Stephen Jay Gould ' s vision of macroevolution, including exaptation and evolutionary recurrence in relation to constraint and the repeatability of evolution.",
        annote = "ISI Document Delivery No.: 938BB Suppl. S",
        howpublished = "Article",
        uri = "<Go to ISI>://000229973800007"
}

@article{150,
        author = "M. J. Donoghue and B.G. Baldwin and J. Li and R.C. Winkworth",
        title = "Viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences",
        journal = "Syst. Bot.",
        pages = "188--198",
        volume = "29",
        number = "1",
        year = "2004"
}

@article{149,
        author = "M. J. Donoghue and J. A. Gauthier",
        title = "Implementing the PhyloCode",
        journal = "Trends in Ecol. and Evol.",
        pages = "281--282",
        volume = "19",
        year = "2004"
}

@inbook{151,
        author = "M. J. Donoghue and M. Smith",
        editor = "J.-P. {Le Duc}",
        title = "Biodiversity inventory: Reflections on preparedness and efficiency",
        booktitle = "Biodiversity: Science and Governance",
        pages = "79-86",
        year = "2005",
        publisher = "Mus\'{}ee National d'Histore Naturelle"
}

@article{152,
        author = "Y. Dotsenko and C. Coarfa and J. Mellor-Crummey and L. Nakhleh and U. Roshan",
        title = "PRec-I-DCM3: A parallel framework for fast and accurate large scale phylogeny reconstruction",
        journal = "Int'l J. on Bioinformatics Research and Applications",
        pages = "407-419",
        volume = "2",
        number = "4",
        year = "2006"
}

@inproceedings{153,
        author = "Z. Du and A. Stamatakis and F. Lin and U. Roshan and L. Nakhleh",
        title = "Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood.",
        pages = "346--350",
        volume = "2",
        year = "2005"
}

@article{108,
        author = "Z. H. Du and F. Lin and U. W. Roshan",
        title = "Reconstruction of large phylogenetic trees: A parallel approach",
        journal = "Computational Biology and Chemistry",
        pages = "273-280",
        volume = "29",
        number = "4",
        year = "2005",
        month = "Aug",
        issn = "1476-9271",
        abstract = "Reconstruction of phylogenetic trees for very large datasets is a known example of a computationally hard problem. In this paper, we present a parallel computing model for the widely used Multiple Instruction Multiple Data (MIMD) architecture. Following the idea of divide-and-conquer, our model adapts the recursive-DCM3 decomposition method [Roshan, U., Moret, B.M.E., Williams, T.L., Wainow, T, 2004a. Performance of suptertree methods on various dtaset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] to divide datasets into smaller subproblems. It distributes computation load over multiple processors so that each processor constructs subtrees on each subproblem within a batch in parallel. It finally collects the resulting trees and merges them into a supertree. The proposed model is flexible as far as methods for dividing and merging datasets are concerned. We show that our method greatly reduces the computational time of the sequential version of the program. As a case study, our parallel approach only takes 22.1 h on four processors to outperform the best score to date (Found at 123.7 h by the Rec-I-DCM3 program [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dtaset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Morel, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] on one dataset. Developed with the standard message-passing library, MPI, the program can be recompiled and run on any MIMD systems. (c) 2005 Elsevier Ltd. All rights reserved.",
        annote = "ISI Document Delivery No.: 956XI",
        howpublished = "Article",
        uri = "<Go to ISI>://000231333000002"
}

@article{95,
        author = "K. L. Duran and T. K. Lowrey and R. R. Parmenter and P. O. Lewis",
        title = "Genetic diversity in Chihuahuan Desert populations of creosotebush (Zygophyllaceae : Larrea tridentata)",
        journal = "American Journal of Botany",
        pages = "722-729",
        volume = "92",
        number = "4",
        year = "2005",
        month = "Apr",
        issn = "0002-9122",
        abstract = "We examined isozyme variation in the dominant Chihuahuan Desert shrub, Larrea tridentata (creosotebush), to determine the genetic variation within and among populations, the biogeographic relationships of populations, and the potential inbreeding in the species. We surveyed 17 populations consisting of 20 to 50 individuals per Population along a 1600-km north-south transect across the Chihuahuan Desert. The southernmost population was near Villa Hidalgo, Mexico, and the northernmost near Isleta Pueblo, New Mexico. All 12 isozyme loci examined were polymorphic (H-t = 0.416), with up to nine alleles per locus. Despite high levels of variation, we detected moderate inbreeding in L. tridentata populations. Most variation was found within rather than among populations (G(ST) = 0.118). Furthermore, recently established populations in the northern limits of the Chihuahuan Desert did not show decreased levels of genetic variation (H-o = 0.336). A significant correlation was found between pairwise genetic and geographic distances (r = 0.305). Larrea tridentata showed and continues to show a massive range expansion into the and and semi-arid regions of the American Southwest, but as shown by the high genetic variation, this expansion took place as a wave, rather than a series of founder events.",
        annote = "ISI Document Delivery No.: 913CB",
        howpublished = "Article",
        uri = "<Go to ISI>://000228126800017"
}

@inproceedings{24,
        author = "J. V. Earnest-DeYoung and E. Lerat and B. M. E. Moret",
        title = "Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data",
        series = "Lecture Notes in Computer Science",
        pages = "1-13",
        volume = "3240",
        year = "2004",
        publisher = "Springer-Verlag",
        uri = "compbio.unm.edu/~joeled/Ancestral.pdf",
        uri = "compbio.unm.edu/~joeled/Ancestral.pdf"
}

@inproceedings{154,
        author = "R. Edgar and E. Myers",
        title = "PILER: Identification and classification of repeated genomic elements.",
        pages = "i152--i158",
        volume = "21",
        year = "2005"
}

@article{87,
        author = "J. E. Erika and R. Nyffeler and M. J. Donoghue",
        title = "Basal cactus phylogeny: Implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form",
        journal = "American Journal of Botany",
        pages = "1177-1188",
        volume = "92",
        number = "7",
        year = "2005",
        month = "Jul",
        issn = "0002-9122",
        abstract = "The cacti are well-known desert plants, widely recognized by their specialized growth form and essentially leafless condition. Pereskia, a group of 17 species with regular leaf development and function, is generally viewed as representing the "ancestral cactus," although its placement within Cactaceae has remained uncertain. Here we present a new hypothesis of phylogenetic relationships at the base of the Cactaceae, inferred from DNA sequence data from five gene regions representing all three plant genomes. Our data support a basal split in Cactaceae between a clade of eight Pereskia species, centered around the Caribbean basin, and all other cacti. Two other Pereskia clades, distributed mostly in the southern half of South America, are part of a major clade comprising Maihuenia plus Cactoideae, and Opuntioideae. This result highlights several events in the early evolution of the cacti. First, during the transition to stem-based photosynthesis, the evolution of stem stomata and delayed bark formation preceded the evolution of the stem cortex into a specialized photosynthetic tissue system. Second, the basal split in cacti separates a northern from an initially southern cactus clade, and the major cactus lineages probably originated in southern or west-central South America.",
        annote = "ISI Document Delivery No.: 942CP",
        howpublished = "Article",
        uri = "<Go to ISI>://000230260800015"
}

@inbook{245,
        author = "N. Eriksson",
        editor = "L. Pachter and B. Sturmfels",
        title = "Tree construction using singular value decomposition",
        booktitle = "Algebraic Statistics for Computational Biology",
        pages = "347-358",
        year = "2005",
        publisher = "Cambridge University Press"
}

@inproceedings{155,
        author = "E. Eskin and S. Snir",
        title = "The homology kernel: A biologically motivated sequence embedding into Euclidean space",
        pages = "179--186",
        year = "2005",
        publisher = "IEEE Press"
}

@article{156,
        author = "E. Eskin and S. Snir",
        title = "Incorporating homologues into sequence embeddings for protein analysis.",
        journal = "J. of Bioinformatics and Comput. Biology",
        pages = "717-38",
        volume = "5",
        number = "3",
        year = "2006"
}

@article{78,
        author = "S. N. Evans and T. Warnow",
        title = "Unidentifiable divergence times in rates-across-sites models",
        journal = "IEEE/ACM Transactions on Computational Biology and Bioinformatics",
        pages = "130-134",
        volume = "1",
        year = "2005",
        uri = "http://www.stat.berkeley.edu/users/evans/668.pdf",
        uri = "http://www.stat.berkeley.edu/users/evans/668.pdf"
}

@inbook{157,
        author = "S.N. Evans and T. Warnow and D. Ringe",
        editor = "P. Foster and C. Renfrew",
        title = "Inference of divergence times as a statistical inverse problem",
        booktitle = "Phylogenetic Methods and the Prehistory of Languages",
        pages = "119--129",
        year = "2004",
        publisher = "Cambridge University Press"
}

@article{158,
        author = "T. S. Feild and N. C. Arens and J. A. Doyle and T. E. Dawson and M. J. Donoghue",
        title = "Dark and disturbed: a new image of early angiosperm ecology",
        journal = "Paleobiology",
        pages = "82--107",
        volume = "30",
        year = "2004",
        uri = "http://paleobiol.geoscienceworld.org/cgi/content/abstract/30/1/82"
}

@inbook{159,
        author = "G. Ganapathy and B. Goodson and R. Jansen and V. Ramachandran and T. Warnow",
        title = "Pattern identification in biogeography: metrics and algorithms for comparing area cladograms",
        booktitle = "5th Workshop Algorithms in Bioinformatics (WABI'05),",
        series = "Lecture Notes in Computer Science",
        pages = "116--127",
        volume = "3692",
        year = "2005",
        publisher = "Springer-Verlag"
}

@inproceedings{72,
        author = "G. Ganapathy and V. Ramachandran and T. Warnow",
        title = "Better Hill-Climbing Seaches for Parsimony",
        pages = "245-258",
        volume = "WABI 2003:",
        year = "2003",
        uri = "http://www.cs.utexas.edu/~gsgk/papers/bn-ver7.pdf",
        uri = "http://www.cs.utexas.edu/~gsgk/papers/bn-ver7.pdf"
}

@inproceedings{74,
        author = "G. Ganapathy and V. Ramachandran and T. Warnow",
        editor = "J. Ian Munro",
        title = "On Contract-and-Refine-Transformations Between Phylogenetic Trees",
        pages = "900-909",
        volume = "SODA 2004:",
        year = "2004",
        month = "January 11-14,",
        uri = "http://www.cs.utexas.edu/~vlr/papers/soda04.pdf",
        uri = "http://www.cs.utexas.edu/~vlr/papers/soda04.pdf"
}

@article{160,
        author = "F. Ge and L.-S. Wang and J. Kim",
        title = "The cobweb of life revealed by genome-scale estimates of horizontal gene transfer",
        journal = "PLoS Biology",
        pages = "e316",
        volume = "3",
        number = "10",
        year = "2005"
}

@article{161,
        author = "H. Glenner and A. J. Hansen and M. V. Sorensen and F. Ronquist and J. P. Huelsenbeck and E. Willerslev",
        title = "Bayesian inference of the metazoan phylogeny: A combined analysis.",
        journal = "Curr. Biol.",
        pages = "1644--1649",
        volume = "14",
        year = "2004"
}

@article{101,
        author = "V. V. Grebennikov and D. R. Maddison",
        title = "Phylogenetic analysis of Trechitae (Coleoptera : Carabidae) based on larval morphology, with a description of first-instar Phrypeus and a key to genera",
        journal = "Systematic Entomology",
        pages = "38-59",
        volume = "30",
        number = "1",
        year = "2005",
        month = "Jan",
        issn = "0307-6970",
        abstract = "Sixty-nine characters of larval structure of twenty-eight genera of the supertribe Trechitae (Coleoptera: Carabidae) were analysed phylogenetically. The monophyly of Trechitae is strongly supported with five unique synapomorphies. The monophyly of Zolini + Bembidiini + Pogonini is supported with two synapomorphies. We propose that the tribe Trechini is a sister group to them and its monophyly is supported with two unique synapomorphies. The inferred branching pattern of Trechini genera is (Perileptus + Thalassophilus) + (Amblystogenium + (Trechimorphus + (Trechus + Epaphius + Aepopsis + Trechisibus))); Perileptus is a member of Trechodina rather than Trechina. The monophyly of Zolini is not supported. The monophyly of Pogonini is supported with two unique synapomorphies; its sister group relationships remain obscure; the branching pattern of pogonine genera is (((Pogonus + Pogonistes) + Cardiaderus) + Thalassotrechus). No evidence for monophyly of the tribe Bembidiini (s. lato; including subtribes Bembidiina, Tachyina, Xystosomina, and Anillina) was found. The relationships of Phrypeus are obscure; no evidence could be found linking it with Bembidiina. Without Phrypeus, Bembidiina might be a monophylum with a single synapomorphy. Sinechostictus branches basal of (Bembidion + Asaphidion) and therefore should be treated as a separate genus. Tachyina and Xystosomina form a monophylum based on two unique synapomorphies; a close relationship with a monophyletic Anillina is suggested. Reduction of the number of claws from two to one in Trechitae has taken place twice: within Trechina (Trechus, Epaphius, Aepopsis and Trechisibus) and in (Zolini + Bembidiini + Pogonini). The previously unknown larvae of the isolated genus Phrypeus are described and illustrated. A key to all twenty-eight analysed Trechitae genera based on characters of larvae and a list of larval autapomorphies for each genus are provided.",
        annote = "ISI Document Delivery No.: 888ML",
        howpublished = "Article",
        uri = "<Go to ISI>://000226378400003"
}

@inproceedings{162,
        author = "Z. Guan and M. A. Miller and I. Altintas",
        title = "Authentication framework in the Kepler workflow system.",
        year = "2006"
}

@article{163,
        author = "S. Guindon and A. G. Rodrigo and Dyer K. and J. P. Huelsenbeck",
        title = "Modeling the site-specific variation of selection patterns along lineages",
        journal = "Proc. Nat'l Acad. Sci., USA",
        pages = "12957--12962",
        volume = "101",
        number = "35",
        year = "2004"
}

@inproceedings{164,
        author = "B. Harb and S. Kannan and A. McGregor",
        title = "Approximating the best-fit tree under Lp norms",
        pages = "123--133",
        year = "2005"
}

@article{165,
        author = "K.G. Herbert and N. J. Gehani and W. H. Piel and J.T.L. Wang and C.H. Wu",
        title = "BIO-AJAX: An extensible framework for biological data cleaning.",
        journal = "SIGMOD Record,",
        pages = "51--57",
        volume = "33",
        number = "2",
        year = "2004"
}

@inproceedings{166,
        author = "K.G. Herbert and J.T.L. Wang and S. Pusapati and W. H. Piel",
        title = "Lineage path integration for phylogenetic resources",
        pages = "117 - 120",
        year = "2005"
}

@article{86,
        author = "D. M. Hillis and T. A. Heath and K. {St John}",
        title = "Analysis and visualization of tree space",
        journal = "Systematic Biology",
        pages = "471-482",
        volume = "54",
        number = "3",
        year = "2005",
        month = "Jun",
        issn = "1063-5157",
        abstract = "We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring "tree islands" ( sets of topologically related trees among larger sets of near-optimal trees), for comparing sets of trees obtained from bootstrapping and Bayesian sampling, for comparing trees obtained from the analysis of several different genes, and for comparing multiple Bayesian analyses. The technique was also useful as a teaching aid for illustrating the progress of a Bayesian analysis and as an exploratory tool for examining large sets of phylogenetic trees. We also identified some limitations to the method, including distortions of the multidimensional tree space into two dimensions through the MDS technique, and the definition of the MDS-defined space based on a limited sample of trees. Nonetheless, the technique is a useful approach for the analysis of large sets of phylogenetic trees.",
        annote = "ISI Document Delivery No.: 942SL",
        howpublished = "Article",
        uri = "<Go to ISI>://000230302500010"
}

@article{103,
        author = "D. M. Hillis and T. P. Wilcox",
        title = "Phylogeny of the New World true frogs (Rana)",
        journal = "Molecular Phylogenetics and Evolution",
        pages = "299-314",
        volume = "34",
        number = "2",
        year = "2005",
        month = "Feb",
        issn = "1055-7903",
        abstract = "Phylogenetic relationships among the species of true frogs (Rana) from North, South, and Central America were investigated based on the sequences of approximately 2 kb from the mitochondrial genome, sampled from most of the described species, as well as eight undescribed species. This analysis, combined with previous studies of the phylogeny of New World Rana, served as the basis for a revised classification of the group. The American species of Rana are not monophyletic; the western North American Amerana is more closely related to the R. temporaria group of Eurasia (together, these frogs form the group Laurasiarana). The remaining species from the Americas form the monophyletic group Novirana, which includes: R. sylvatica; Aquarana (the R. catesbeiana group); Ranula (the R. palmipes group, including the mostly upland Levirana species and the mostly lowland Lithobates species); Torrentirana (the R. tarahumarae group, or Zweifelia, plus R. sierramadrensis), Stertirana (the R. montezumae group, or Lacusirana, plus R. pipiens), Nenirana (the R. areolata group), and Scurrilirana (most of the southern and tropical leopard frogs). The mitochondrial sequences supported many of the previous hypotheses of relationships of New World Rana, although there were some differences involving the placement of the species R. pipiens, R. sierramadrensis, and R. sylvatica. Parametric bootstrap analyses indicated significant support for the relationships inferred from the mtDNA sequences, and rejected the previous hypotheses of relationships for these three species. (C) 2004 Elsevier Inc. All rights reserved.",
        annote = "ISI Document Delivery No.: 886UQ",
        howpublished = "Article",
        uri = "<Go to ISI>://000226258600005"
}

@article{167,
        author = "M. T. Holder and P. O. Lewis and D. L. Swofford and B. Larget",
        title = "Hastings ratio of the LOCAL proposal used in Bayesian phylogenet¬ics",
        journal = "Syst. Biol.",
        pages = "961-965",
        volume = "54",
        year = "2006"
}

@article{92,
        author = "D. G. Howarth and M. J. Donoghue",
        title = "Duplications in CYC-like genes from dipsacales correlate with floral form",
        journal = "International Journal of Plant Sciences",
        pages = "357-370",
        volume = "166",
        number = "3",
        year = "2005",
        month = "may",
        issn = "1058-5893",
        abstract = "Flower symmetry is of special interest in understanding the evolution and ecology of angiosperms. Evidence from the Antirrhineae (within the lamiid clade of Asteridae) indicates that several TCP gene family transcription factors, especially CYCLOIDEA (CYC), play a role in specifying dorsal identity in the corolla and androecium of monosymmetric (bilateral) flowers. We examine the evolution of this gene family in Dipsacales, representing the campanulid clade of Asteridae, in relation to evolutionary shifts in floral symmetry and stamen abortion. We identify three major forms of CYC-like genes in Dipsacales. We identify the position of additional gene duplications by comparing each of the three gene trees to a well-supported Dipsacales phylogeny. We infer duplications in two of the major gene lineages along the line leading to the Caprifoliaceae correlated with the origin of monosymmetric flowers. There are no duplications or losses associated with major shifts in stamen number. However, there are several additional duplications within the Caprifoliaceae, especially in the Morinaceae, possibly related to calyx monosymmetry and/or stamen reduction. Within the protein-coding sequences, we identify a new conserved region - the ECE region - that appears to be present across known angiosperm sequences. There are major changes in length and in the presence or absence of the ECE region in the Dipsacales, indicating changes in gene function. These studies expand our understanding of the evolution of CYC-like genes in angiosperms and provide a new system for studying the role of this gene family in determining floral form.",
        annote = "ISI Document Delivery No.: 916KP",
        howpublished = "Article",
        uri = "<Go to ISI>://000228384100001"
}

@article{168,
        author = "J. P. Huelsenbeck and B. Larget and M. E. Alfaro",
        title = "Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo.",
        journal = "Mol. Biol. Evol.",
        pages = "1123--1133",
        volume = "21",
        number = "6",
        year = "2004"
}

@article{169,
        author = "J. P. Huelsenbeck and B. Rannala",
        title = "Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models.",
        journal = "Syst. Biol.",
        pages = "904--913",
        volume = "53",
        number = "6",
        year = "2004"
}

@inbook{170,
        author = "J. P. Huelsenbeck and F. Ronquist",
        editor = "R. Nielsen",
        title = "Bayesian analysis of molecular evolution using MrBayes",
        booktitle = "Statistical Methods in Molecular Evolution",
        series = "Statistics for Biology and Health",
        volume = "XII",
        year = "2005",
        publisher = "Springer-Verlag"
}

@article{171,
        author = "S. Janson and E. Mossel",
        title = "Robust reconstruction on trees is determined by the second eigenvalue.",
        journal = "Ann. Probab.",
        pages = "2630--2649",
        volume = "32",
        year = "2004"
}

@inproceedings{172,
        author = "G. Jin and L. Nakhleh and S. Snir and T. Tuller",
        title = "Efficient parsimony-based methods for phylogenetic network reconstruction",
        pages = "e123-e128,",
        volume = "23",
        year = "2006"
}

@article{240,
        author = "G. Jin and L. Nakhleh and S. Snir and T. Tuller",
        title = "Maximum Likelihood of Phylogenetic Networks",
        journal = "Bioinformatics",
        pages = "2604-2611",
        volume = "22",
        number = "21",
        year = "2006"
}

@inbook{173,
        author = "I. Kanj and L. Nakhleh and G. Xia",
        title = "Reconstructing evolution of natural languages: Complexity and parameterized algorithms",
        booktitle = "12th Annual International Computing and Combinatorics Conference (COCOON 06)",
        series = "Lecture Notes in Computer Science",
        pages = "299-308",
        volume = "4112",
        year = "2006"
}

@inproceedings{174,
        author = "S. Kannan and A. McGregor",
        title = "More on reconstructing strings from random traces: Insertions and deletions",
        pages = "297--301",
        year = "2005"
}

@inbook{43,
        author = "D. G. Kelch and A. Driskell and B. D. Mishler",
        editor = "V. Hollowell, and R. Magill (eds.) {In B. Goffinet}",
        title = "Inferring phylogeny using genomic characters: a case study using land plant plastomes",
        booktitle = "Molecular Systematics of Bryophytes",
        series = "Monographs in Systematic Botany",
        pages = "3-12",
        volume = "98",
        year = "2004",
        publisher = "Missouri Botanical Garden Press"
}

@article{116,
        author = "A. Khetan and B. Chor and S. Snir",
        title = "Maximum likelihood on molecular clock comb: Analytic solutions.",
        journal = "Journal of Computational Biology",
        pages = "819 -- 837",
        volume = "13",
        number = "3",
        year = "2006"
}

@article{175,
        author = "S.L. Kosakovsky-Pond and S.D. Frost and S. V. Muse",
        title = "Hyphy: A platform for molecular evolutionary analysis.",
        journal = "Bioinformatics",
        pages = "676--679",
        volume = "21",
        year = "2005"
}

@article{176,
        author = "S.L. Kosakovsky-Pond and S. V. Muse",
        title = "Modeling heterogeneity of synonymous and nonsynonymous substitution rates across sites",
        journal = "Mol. Biol. Evol.",
        pages = "2375--2385",
        volume = "22",
        number = "12",
        year = "2005"
}

@article{239,
        author = "H. Lapp and S. Bala and J. P. Balhoff and A. Bouck and N. Goto and M. T. Holder and R. Holland and A. Holloway and T. Katayama and P. O. Lewis and A. Mackey and B. I. Osbourne and W. H. Piel and S.L. Kosakovsky-Pond and A. Poon and W.-G. Qui and J. E. Stajich and A. Stoltzfus and T. Thierer and A.J. Vilella and R. A. Vos and C. M. Zmasek and D. Zwickl and T. J. Vision",
        title = "The 2006 NESCent Phyloinformatics Hackathon: A Field Report",
        journal = "Evolutionary Bioinformatics",
        volume = "In Press",
        year = "2007"
}

@article{91,
        author = "P. O. Lewis and M. T. Holder and K. E. Holsinger",
        title = "Polytomies and Bayesian phylogenetic inference",
        journal = "Systematic Biology",
        pages = "241-253",
        volume = "54",
        number = "2",
        year = "2005",
        month = "Apr",
        issn = "1063-5157",
        abstract = "Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short edge lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard ( or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible- jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.",
        annote = "ISI Document Delivery No.: 921ZP",
        howpublished = "Article",
        uri = "<Go to ISI>://000228805100005"
}

@article{177,
        author = "C. R. Linder and B. M. E. Moret and L. Nakhleh and T. Warnow",
        title = "Network (reticulated) evolution: Biology, models, and algorithms",
        year = "2004",
        uri = "www.compbio.unm.edu/papers.html"
}

@article{178,
        author = "C. R. Linder and L. Riesenberg",
        title = "Reconstructing patterns of reticulate evolution in plants.",
        journal = "Am. J. Botany",
        pages = "1700-- 1708",
        volume = "91",
        number = "10",
        year = "2004"
}

@inbook{179,
        author = "C. R. Linder and T. Warnow",
        editor = "S. Aluru",
        title = "An overview of phylogeny reconstruction.",
        booktitle = "Handbook of Computational Molecular Biology",
        year = "2006",
        publisher = "Chapman & Hall"
}

@inbook{180,
        author = "T. Liu and J. Tang and B. M. E. Moret",
        title = "Quartet methods for phylogeny reconstruction from gene orders.",
        booktitle = "11th Conf. Computing and Combinatorics (COCOON'05)",
        series = "Lecture Notes in Computer Science",
        pages = "63-73",
        volume = "3595",
        year = "2005",
        publisher = "Springer-Verlag"
}

@article{181,
        author = "F. V. Mannino and S. V. Muse",
        title = "Extensive site-to-site variability of synonymous substitution rates in mitochondrial genomes",
        journal = "Genetics",
        year = "2006"
}

@inproceedings{182,
        author = "R. Mao and W. Xu and S. Ramakrishnan and G. Nuckolls and D.P. Miranker",
        title = "On optimizing distance-based similarity search for biological databases",
        pages = "351--361",
        year = "2005",
        publisher = "IEEE Press"
}

@article{25,
        author = "M. Marron and K.M. Swenson and B.M.E. Moret",
        title = "Genomic distances under deletions and insertions",
        journal = "Theoretical Computer Science",
        pages = "347-360",
        volume = "325",
        number = "3",
        year = "2004",
        uri = "www.cs.unm.edu/~moret/cocoon03.pdf",
        uri = "www.cs.unm.edu/~moret/cocoon03.pdf"
}

@inbook{183,
        author = "R. Mihaescu",
        editor = "L. Pachter and B. Sturmfels",
        title = "Parametric inference",
        booktitle = "Algebraic Statistics for Computational Biology",
        pages = "165--180",
        year = "2005",
        publisher = "Cambridge University Press"
}

@inproceedings{184,
        author = "R. Mihaescu and D. Levy and L. Pachter",
        title = "Why neighbor-joining works",
        year = "2006",
        uri = "http://lanl.arxiv.org/abs/cs.DS/0602041"
}

@inproceedings{4,
        author = "B. Milch and B. Marthi and S. Russell",
        title = "BLOG: Relational modeling with unknown objects",
        year = "2004",
        uri = "http://www.cs.berkeley.edu/~russell/papers/srl04-blog.pdf"
}

@inproceedings{3,
        author = "B. Milch and B. Marthi and D. Sontag and S. Russell and D. L. Ong and A. Kolobov",
        title = "Approximate inference for infinite contingent Bayesian networks",
        year = "2005",
        uri = "http://www.cs.berkeley.edu/~russell/papers/aistats05-inference.pdf"
}

@inproceedings{185,
        author = "D.P. Miranker and W. Xu and R. Mao",
        title = "MoBIoS: A metric-space DBMS to support biological discovery",
        pages = "241--244",
        year = "2004"
}

@article{82,
        author = "B. Mishler",
        title = "The evolution and ecology of desiccation tolerance in mosses",
        journal = "Integrative and Comparative Biology",
        pages = "608-608",
        volume = "44",
        number = "6",
        year = "2004",
        month = "Dec",
        issn = "1540-7063",
        annote = "ISI Document Delivery No.: 893LU",
        howpublished = "Meeting Abstract",
        uri = "<Go to ISI>://000226721400391"
}

@inbook{2,
        author = "B. D. Mishler",
        editor = "V. A. Albert",
        title = "The logic of the data matrix in phylogenetic analysis",
        booktitle = "Parsimony, Phylogeny, and Genomics",
        pages = "57 - 70",
        year = "2005",
        publisher = "Oxford University Press"
}

@inbook{186,
        author = "B.R. Moore and K.M.A. Chan and M. J. Donoghue",
        editor = "O.R.P. Bininda-Edmonds",
        title = "Detecting diversification rate variation in supertrees.",
        booktitle = "Phylogenetic Supertrees: Combining information to reveal the Tree of Life",
        pages = "487--533",
        year = "2004",
        publisher = "Kluwer Aca¬demic Publishers"
}

@article{187,
        author = "B.R. Moore and R.S. Smith and M. J. Donoghue",
        title = "Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping.",
        journal = "Syst. Biol.",
        pages = "662-676",
        volume = "55",
        number = "4",
        year = "2006",
        uri = "http://lib.bioinfo.pl/pmid:16969942"
}

@article{188,
        author = "B.R. Moore and S. A. Smith and H. R. Ree and M. J. Donoghue",
        title = "Incorporating fossil data in biogeographic inference: a likelihood approach",
        journal = "Evolution",
        volume = "In press",
        year = "2007"
}

@inbook{189,
        author = "S. Moran and S. Rao and S. Snir",
        title = "Using semi-definite programming to enhance supertree resolvability",
        booktitle = "5th Workshop Algorithms in Bioinformatics (WABI'05)",
        series = "Lecture Notes in Computer Science",
        pages = "89--103",
        volume = "3692",
        year = "2005"
}

@inproceedings{190,
        author = "S. Moran and S. Snir",
        title = "Convex recolorings of strings and trees: Definitions, hardness results and algorithms",
        pages = "218 - 232",
        year = "2005"
}

@inproceedings{19,
        author = "B. M. E. Moret",
        title = "Computational challenges from the Tree of Life",
        year = "2005",
        publisher = "SIAM Press",
        uri = "http://www.siam.org/meetings/alenex05/"
}

@inbook{98,
        author = "B. M. E. Moret and D. A. Bader and T. Warnow",
        title = "High-performance algorithm engineering for computational phylogenetics",
        booktitle = "Computational Science -- ICCS 2001, Proceedings Pt 2",
        series = "Lecture Notes in Computer Science",
        pages = "1012-1021",
        volume = "2074",
        year = "2001",
        issn = "0302-9743",
        abstract = "Phylogeny reconstruction from molecular data poses complex optimization problems: almost all optimization models are NP-hard and thus computationally intractable. Yet approximations must be of very high quality in order to avoid outright biological nonsense. Thus many biologists have been willing to run farms of processors for many months in order to analyze just one dataset. High-performance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing phylogenetic algorithms. We present an overview of algorithm engineering techniques, illustrating them with an application to the "breakpoint analysis" method of Sankoff et al., which resulted in the GRAPPA software suite. GRAPPA demonstrated a million-fold speedup in running time (on a variety of real and simulated datasets) over the original implementation. We show how algorithmic engineering techniques are directly applicable to a large variety of challenging combinatorial problems in computational biology.",
        annote = "ISI Document Delivery No.: BBQ28 Article",
        uri = "<Go to ISI>://000227039400107"
}

@article{65,
        author = "B.M.E. Moret and L. Nakhleh and T. Warnow and C.R. Linder and A. Tholse and A. Padolina and J. Sun and R. Timme",
        title = "Phylogenetic networks: modeling, reconstructibility, and accuracy",
        journal = "IEEE/ACM Trans. on Computational Biology and Biocomputing",
        pages = "13-23",
        volume = "1",
        number = "1",
        year = "2004",
        uri = "http://www.cs.unm.edu/~moret/tcbb04.pdf",
        uri = "http://www.cs.unm.edu/~moret/tcbb04.pdf"
}

@inbook{18,
        author = "B. M. E. Moret and J Tang and T. Warnow",
        editor = "{O. Gascuel}",
        title = "Reconstructing phylogenies from gene-content and gene-order data",
        booktitle = "Mathematics of Evolution and Phylogeny",
        pages = "321-352",
        volume = "2005",
        year = "2005",
        publisher = "Oxford Univ. Press",
        uri = "http://www.lirmm.fr/w3ifa/MAAS/IHP-BOOK/Math-Phylo-Book.html",
        uri = "http://www.cs.unm.edu/~moret/poincare_survey.pdf"
}

@inbook{85,
        author = "B. M. E. Moret and T. Warnow",
        title = "Advances in phylogeny reconstruction from gene order and content data",
        booktitle = "Molecular Evolution: Producing the Biochemical Data, Part B",
        series = "Methods in Enzymology",
        pages = "673 - 700",
        volume = "395",
        year = "2005",
        issn = "0076-6879",
        abstract = "Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systernatists for inferring deep evolutionary histories. This chapter surveys recent developments in the reconstruction of phylogenies from gene order and content, focusing on their performance under various stochastic models of evolution. Because such methods are quite restricted in the type of data they can analyze, we also present research aimed at handling the full range of whole-genome data.",
        annote = "ISI Document Delivery No.: BCM61 Review",
        uri = "<Go to ISI>://000230001100035"
}

@article{191,
        author = "M. M. Morin and B. M. E. Moret",
        title = "NetGen: Generating phylogenetic networks with diploid hybrids",
        journal = "Bioinformatics",
        pages = "1921-1923",
        volume = "22",
        year = "2006"
}

@article{192,
        author = "E. Mossel",
        title = "Phase transitions in phylogeny",
        journal = "Trans. Amer. Math. Soc.",
        pages = "2379--2404",
        volume = "356",
        number = "6",
        year = "2004"
}

@inbook{193,
        author = "E. Mossel",
        editor = "J. Nestril and P. Winkler",
        title = "Survey: Information flow on trees.",
        booktitle = "Graphs, Morphisms and Statistical Physics. DIMACS series in discrete mathematics and theoretical computer science,",
        series = "DIMACS Ser. Discrete Math. Theoret. Comput. Sci.",
        pages = "155-170",
        volume = "63",
        year = "2004",
        publisher = "AMS Press"
}

@article{194,
        author = "E. Mossel",
        title = "Distorted metrics on trees and phylogenetic forests",
        journal = "IEEE/ACM Trans. on Computational Biology and Bioinfor¬matics",
        pages = "108-116",
        volume = "4",
        number = "1",
        year = "2006"
}

@article{197,
        author = "E. Mossel and Steel. M.",
        title = "A phase transition for a random cluster model on phylogenetic trees",
        journal = "Math. Biosci.",
        pages = "189--203",
        volume = "187",
        number = "2",
        year = "2004"
}

@inproceedings{195,
        author = "E. Mossel and S. Roch",
        title = "Learning Nonsingular Phylogenies and Hidden Markov Models",
        pages = "366--376",
        year = "2005",
        publisher = "ACM Press"
}

@article{196,
        author = "E. Mossel and S. Roch",
        title = "Learning nonsingular phylogenies and Hidden Markov Models",
        journal = "Annals of Applied Probability",
        pages = "583-614",
        volume = "16",
        number = "2",
        year = "2006"
}

@inbook{198,
        author = "E. Mossel and M. Steel",
        editor = "O. Gascuel",
        title = "How much can evolved characters tell us about the tree that generated them?",
        booktitle = "Mathematics Of Evolution And Phylogeny",
        pages = "384--412",
        year = "2005",
        publisher = "Oxford University Press"
}

@article{199,
        author = "E. Mossel and E. Vigoda",
        title = "Limitations of Markov Chain Monte Carlo Algorithms for Bayesian Inference of Phylogeny Science.",
        journal = "Science",
        pages = "2207--2209",
        volume = "309",
        number = "5744",
        year = "2005"
}

@article{200,
        author = "E. Mossel and E. Vigoda",
        title = "Limitations of Markov Chain Monte Carlo algorithms for Bayesian inference of phylogeny.",
        journal = "Annals of Applied Probability",
        pages = "2215-2234",
        volume = "16",
        number = "4",
        year = "2006"
}

@misc{15,
        author = "L. Nakhleh and A. Clement and T. Warnow and C.R. Linder and B.M.E. Moret",
        title = "Quality measures for phylogenetic networks",
        booktitle = "Technical Report",
        volume = "TR-CS-2004-06",
        year = "2004",
        publisher = "U. New Mexico",
        uri = "http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-06"
}

@inproceedings{201,
        author = "L. Nakhleh and G. Jin and Zhao. F. and J. Mellor-Crummey",
        title = "Reconstructing phylogenetic networks using maximum parsimony",
        pages = "93--102",
        year = "2005",
        publisher = "IEEE Press"
}

@article{77,
        author = "L. Nakhleh and D. Ringe and T. Warnow",
        title = "Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages.",
        journal = "Language (Journal of the Linguistic Society of America)",
        year = "2005",
        uri = "http://www.cs.rice.edu/~nakhleh/PAPERS/NWRlanguage.pdf",
        uri = "http://www.cs.rice.edu/~nakhleh/PAPERS/NWRlanguage.pdf"
}

@inbook{202,
        author = "L. Nakhleh and D. Ruths and H. Innan",
        editor = "R. Guerra and D. Allison",
        title = "Gene trees, species trees, and species networks",
        booktitle = "Meta-analysis and Combining Information in Genetics",
        pages = "1-27",
        year = "2006",
        publisher = "Chapman & Hall, CRC Press"
}

@inbook{203,
        author = "L. Nakhleh and D. Ruths and L.-S. Wang",
        title = "RIATA-HGT: A fast and accurate heuristic for reconstructing horizontal gene transfer",
        booktitle = "11th Conf. Computing and Combinatorics (COCOON'05)",
        series = "Lecture Notes in Computer Science",
        pages = "84--93",
        volume = "3595",
        year = "2005",
        publisher = "Springer-Verlag"
}

@inbook{204,
        author = "L. Nakhleh and L.-S. Wang",
        editor = "C. Priami and A. Zelikovsky",
        title = "Phylogenetic networks: Properties and relationship to trees and clusters.",
        booktitle = "Transactions on Computational Systems Biology II",
        series = "Lecture Notes in Computer Science",
        pages = "82-99",
        volume = "3680",
        year = "2005",
        publisher = "Springer-Verlag"
}

@inbook{109,
        author = "L. Nakhleh and L. S. Wang",
        title = "Phylogenetic networks, trees, and clusters",
        booktitle = "Computational Science - ICCS 2005, Pt 2",
        series = "Lecture Notes in Computer Science",
        pages = "919-926",
        volume = "3515",
        year = "2005",
        issn = "0302-9743",
        abstract = "Phylogenetic networks model evolutionary histories in the presence of non-treelike events such as hybrid speciation and horizontal gene transfer. In spite of their widely acknowledged importance, very little is known about phylogenetic networks, which have so far been studied mostly for specific datasets. Even when the evolutionary history of a set of species is non-treelike, individual genes in these species usually evolve in a treelike fashion. An important question, then, is whether a gene tree is "contained" inside a species network. This information is used to detect the presence of events such as horizontal gene transfer and hybrid speciation. Another question of interest for biologists is whether a group of taxa forms a clade based on a given phylogeny. This can be efficiently answered when the phylogeny is a tree simply by inspecting the edges of the tree, whereas no efficient solution currently exists for the problem when the phylogeny is a network. In this paper, we give polynomial-time algorithms for answering the above two questions.",
        annote = "ISI Document Delivery No.: BCM76 Article",
        uri = "<Go to ISI>://000230023800117"
}

@article{107,
        author = "L. Nakhleh and T. Warnow and C. R. Linder and K. {St John}",
        title = "Reconstructing reticulate evolution in species - Theory and practice",
        journal = "Journal of Computational Biology",
        pages = "796-811",
        volume = "12",
        number = "6",
        year = "2005",
        month = "Jul",
        issn = "1066-5277",
        abstract = "We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison's approach in his seminal 1997 paper. Our first method is a polynomial time algorithm for constructing phylogenetic networks from two gene trees contained inside the network. We allow the network to have an arbitrary number of reticulations, but we limit the reticulation in the network so that the cycles in the network are node-disjoint ("galled"). Our second method is a polynomial time algorithm for constructing networks with one reticulation, where we allow for errors in the estimated gene trees. Using simulations, we demonstrate improved performance of this method over both NeighborNet and Maddison's method.",
        annote = "ISI Document Delivery No.: 957MP",
        howpublished = "Article",
        uri = "<Go to ISI>://000231374200015"
}

@article{79,
        author = "L. Nakhleh and T. Warnow and D. Ringe and S. N. Evans",
        title = "A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset",
        journal = "The Transactions of the Philological Society",
        pages = "in press",
        year = "2005",
        uri = "http://www.cs.rice.edu/~nakhleh/PAPERS/NWREpaper.pdf",
        uri = "http://www.cs.rice.edu/~nakhleh/PAPERS/NWREpaper.pdf"
}

@article{205,
        author = "L. Pachter and D. E. Speyer",
        title = "Reconstructing trees from subtree weights",
        journal = "Appl. Math. Lett.",
        pages = "615--621",
        volume = "17",
        number = "6",
        year = "2004"
}

@article{206,
        author = "N. D. Pattengale and E. J. Gottleib and B. M. E. Moret",
        title = "Efficiently computing the Robinson-Foulds metric",
        journal = "J. Comput. Biol.",
        pages = "724-735",
        volume = "14",
        number = "6",
        year = "2007"
}

@inbook{207,
        author = "N. D. Pattengale and B. M. E. Moret",
        title = "A sublinear-time randomized approximation scheme for the Robinson-Foulds metric",
        booktitle = "Proc. 10th Ann. Int'l Conf. Comput. Mol. Biol. (RECOMB'06)",
        series = "Lecture Notes in Computer Science",
        pages = "221--230",
        volume = "3909",
        year = "2006"
}

@article{208,
        author = "H. R. Ree and B.R. Moore and C. O. Webb and M. J. Donoghue",
        title = "A likelihood framework for inferring the evolution of geographic range on phylogenetic trees",
        journal = "Evolution",
        pages = "2299--2311",
        volume = "59",
        year = "2005"
}

@article{209,
        author = "S. Roch",
        title = "A short proof that phylogenetic tree reconstruction by maximum likelihood is hard",
        journal = "IEEE Trans. Comput. Biol. and Bioinformatics",
        pages = "92",
        volume = "3",
        number = "1",
        year = "2006"
}

@inproceedings{210,
        author = "U. Roshan and D. R. Livesay and D. La",
        title = "Improving phylogenetic motif prediction using parsimony",
        pages = "19-26",
        year = "2005"
}

@inbook{27,
        author = "U. Roshan and B. M. E. Moret and T. Warnow and T. L. Williams",
        editor = "O. R. P. Bininda-Edmonds",
        title = "Performance of supertree methods on various dataset decompositions",
        booktitle = "Phylogenetic Supertrees: Combining information to reveal the Tree of Life",
        pages = "301-328",
        year = "2004",
        publisher = "Kluwer Academic Publishers",
        uri = "http://www.cs.utexas.edu/users/usman/research/phylogenetics/book_chapter.pdf",
        uri = "http://www.cs.utexas.edu/users/usman/research/phylogenetics/book_chapter.pdf"
}

@inproceedings{211,
        author = "U. Roshan and B. M. E. Moret and T. L. Williams and T. Warnow",
        title = "Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees",
        pages = "98--109",
        year = "2004",
        publisher = "IEEE Press"
}

@inproceedings{31,
        author = "U. Roshan and B. M. E. Moret and T. L. Williams and T. Warnow",
        title = "Rec-I-DCM3: A fast algorithmic technique for reconstructing phylogenetic trees",
        volume = "98-109",
        year = "2004",
        publisher = "IEEE Press",
        uri = "http://www.cs.rice.edu/~nakhleh/pdf.gif",
        uri = "http://www.cs.rice.edu/~nakhleh/pdf.gif"
}

@article{212,
        author = "D. Ruths and L. Nakhleh",
        title = "Recombination and phylogeny: effects and detection",
        journal = "International Journal on Bioinformatics Research and Applications",
        pages = "202--212",
        volume = "1",
        number = "2",
        year = "2005"
}

@inproceedings{213,
        author = "D. Ruths and L. Nakhleh",
        title = "RECOMP: A parsimony-based method for detecting recombination.",
        pages = "59-68",
        year = "2006"
}

@inproceedings{214,
        author = "D. Ruths and L. Nakhleh",
        title = "Techniques for assessing phylogenetic branch support: A performance study",
        pages = "187-196",
        year = "2006"
}

@article{215,
        author = "L. M. Schultheis and M. J. Donoghue",
        title = "Molecular phylogeny and biogeography of Ribes (Grossulariaceae), with an emphasis on gooseberries (subg. Grossularia).",
        journal = "Syst. Bot.,",
        pages = "77--96",
        volume = "29",
        number = "1",
        year = "2004"
}

@article{216,
        author = "A.S. Schwartz and L. Pachter",
        title = "Multiple alignment by sequence annealing.",
        journal = "Bioinformatics",
        pages = "e24-e29",
        volume = "23",
        number = "2",
        year = "2007"
}

@article{217,
        author = "R. Sharan and E. Myers",
        title = "A motif-base framework for recognizing sequence families.",
        journal = "Bioinformatics",
        pages = "i387-i393",
        volume = "21, Suppl 1",
        year = "2005"
}

@article{67,
        author = "M. Snir and D. A. Bader",
        title = "A framework for measuring supercomputer productivity",
        journal = "Int'l J. of High-Performance Comput. Applic",
        pages = "417-432",
        volume = "18",
        number = "4",
        year = "2004",
        uri = "http://www-faculty.cs.uiuc.edu/~snir/PDF/productivity%20final.pdf",
        uri = "http://www-faculty.cs.uiuc.edu/~snir/PDF/productivity%20final.pdf"
}

@inbook{218,
        author = "S. Snir and L. Pachter",
        title = "Phylogenetic profiling of insertions and deletions in vertebrate genomes",
        booktitle = "Proc. 10th Ann. Int'l Conf. Comput. Mol. Biol. (RECOMB'06)",
        series = "Lecture Notes in Computer Science",
        pages = "265-280",
        volume = "3909",
        year = "2006",
        publisher = "Springer-Verlag"
}

@inproceedings{219,
        author = "M. Sottile and V. Chandu and D.A. Bader",
        title = "Performance analysis of parallel programs via message-passing graph traversal",
        year = "2006"
}

@article{34,
        author = "K. {St. John} and T. Warnow and B. M. E. Moret and L. Vawter",
        title = "Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining",
        journal = "J. Algorithms",
        shorttitle = "Special issue on best papers from SODA'01",
        pages = "173 - 193",
        volume = "48",
        number = "1",
        year = "2003",
        uri = "http://www.cs.unm.edu/~moret/jalgs.pdf",
        uri = "http://www.cs.unm.edu/~moret/jalgs.pdf"
}

@inbook{220,
        author = "D.R.B Stockwell and J.T.L. Wang",
        title = "Biomonitoring, phylogenetics and anomaly aggregation systems",
        booktitle = "Proc. 3rd IEEE Conf. on Intelligence and Security Informatics (ISI'05)",
        series = "Lecture Notes in Computer Science",
        pages = "523--529",
        volume = "3495",
        year = "2005",
        publisher = "Springer-Verlag"
}

@article{221,
        author = "E. Strain and S. V. Muse",
        title = "Positively selected sites in the arabidopsis receptor-like kinase gene family",
        journal = "J. Mol. Evol",
        pages = "1--9",
        volume = "60",
        year = "2005"
}

@article{90,
        author = "J. Sullivan and Z. Abdo and P. Joyce and D. L. Swofford",
        title = "Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation",
        journal = "Molecular Biology and Evolution",
        pages = "1386-1392",
        volume = "22",
        number = "6",
        year = "2005",
        month = "Jun",
        issn = "0737-4038",
        abstract = "Almost all studies that estimate phylogenies from DNA sequence data under the maximum-likelihood (ML) criterion employ an approximate approach. Most commonly, model parameters are estimated on some initial phylogenetic estimate derived using a rapid method (neighbor-joining or parsimony). Parameters are then held constant during a tree search, and ideally, the procedure is repeated until convergence is achieved. However, the effectiveness of this approximation has not been formally assessed, in part because doing so requires computationally intensive, full-optimization analyses. Here, we report both indirect and direct evaluations of the effectiveness of successive approximations. We obtained an indirect evaluation by comparing the results of replicate runs on real data that use random trees to provide initial parameter estimates. For six real data sets taken from the literature, all replicate iterative searches converged to the same joint estimates of topology and model parameters, suggesting that the approximation is not starting-point dependent, as long as the heuristic searches of tree space are rigorous. We conducted a more direct assessment using simulations in which we compared the accuracy of phylogenies estimated using full optimization of all model parameters on each tree evaluated to the accuracy of trees estimated via successive approximations. There is no significant difference between the accuracy of the approximation searches relative to full-optimization searches. Our results demonstrate that successive approximation is reliable and provide reassurance that this much faster approach is safe to use for ML estimation of topology.",
        annote = "ISI Document Delivery No.: 928NS",
        howpublished = "Article",
        uri = "<Go to ISI>://000229279100003"
}

@inproceedings{61,
        author = "K.M., Marron, M., Earnest-DeYoung, J.V., and Moret, B.M.E., Swenson",
        title = "Approximating the true evolutionary distance between two genomes",
        year = "2005",
        publisher = "SIAM Press.",
        uri = "http://www.siam.org/meetings/alenex05/"
}

@article{222,
        author = "K.M. Swenson and M. Marron and J. V. Earnest-DeYoung and B. M. E. Moret",
        title = "Approximating the true evolutionary distance between two genomes",
        journal = "ACM J. of Experimental Algorithmics",
        volume = "In Press",
        year = "2007"
}

@inbook{223,
        author = "K.M. Swenson and N. D. Pattengale and B. M. E. Moret",
        title = "A framework for orthology assignment from gene rearrangement data",
        booktitle = "Proc. 3rd RECOMB Workshop on Comparative Genomics",
        series = "Lecture Notes in Computer Science",
        pages = "153--166",
        year = "2005",
        publisher = "Springer-Verlag"
}

@article{13,
        author = "J Tang and B. M. E. Moret",
        title = "Distance correction for large pairwise genomic distances,",
        journal = "Technical Report",
        volume = "TR-CS-2004-26",
        year = "2004",
        publisher = "U. New Mexico",
        uri = "http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-26"
}

@inproceedings{29,
        author = "J Tang and B. M. E. Moret and L. Cui and C. W. dePamphilis",
        title = "Phylogenetic reconstruction from arbitrary gene-order data",
        pages = "592-599",
        year = "2004",
        publisher = "IEEE Press",
        uri = "www.cs.unm.edu/~moret/bibe04.pdf",
        uri = "www.cs.unm.edu/~moret/bibe04.pdf"
}

@inproceedings{224,
        author = "J. Tang and L.-S. Wang",
        title = "Improving genome rearrangement phylogeny using sequence-style parsimony",
        pages = "137--144",
        year = "2005"
}

@inbook{84,
        author = "J. J. Tang and B. M. E. Moret",
        title = "Linear programming for phylogenetic reconstruction based on gene rearrangements",
        booktitle = "Combinatorial Pattern Matching, Proceedings",
        series = "Lecture Notes in Computer Science",
        pages = "406-416",
        volume = "3537",
        year = "2005",
        issn = "0302-9743",
        abstract = "Phylogenetic reconstruction from gene rearrangements has attracted increasing attention from biologists and computer scientists over the last few years. Methods used in reconstruction include distance-based methods, parsimony methods using sequence-based encodings, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach, but has been limited to small genomes because the running time of its scoring algorithm grows exponentially with the number of genes in the genome. We report here on a new method to compute a tight lower bound on the score of a given tree, using a set of linear constraints generated through selective applications of the triangle inequality (in the spirit of GESTALT). Our method generates an integer linear program with a carefully limited number of constraints, rapidly solves its relaxed version, and uses the result to provide a tight lower bound. Since this bound is very close to the optimal tree score, it can be used directly as a selection criterion, thereby enabling us to bypass entirely the expensive scoring procedure. We have implemented this method within our GRAPPA software and run several series of experiments on both biological and simulated datasets to assess its accuracy. Our results show that using the bound as a selection criterion yields excellent trees, with error rates below 5% up to very large evolutionary distances, consistently beating the baseline Neighbor-Joining. Our new method enables us to extend the range of applicability of the direct optimization method to chromosomes of size comparable to those of bacteria, as well as to datasets with complex combinations of evolutionary events.",
        annote = "ISI Document Delivery No.: BCO99 Article",
        uri = "<Go to ISI>://000230459400035"
}

@article{225,
        author = "D. J. Taylor and W. H. Piel",
        title = "An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data",
        journal = "Mol. Biol. Evol.",
        pages = "1534--1537",
        volume = "21",
        number = "8",
        year = "2004"
}

@article{226,
        author = "S. G. Tringe and C. {von Mering} and A. Kobayashi and A. A. Salamov and K. Chen and H. W. Chang and M. Podar and J. M. Short and E. J. Mathur and J. C. Detter and P. Bork and P. Hugenholtz and E. M. Rubin",
        title = "Comparative metagenomics of microbial communities",
        journal = "Science",
        pages = "554--557",
        volume = "308",
        number = "5721",
        year = "2005"
}

@inbook{37,
        author = "L.-S. Wang and T. Warnow",
        editor = "O. Gascuel",
        title = "Distance-based genome rearrangement phylogeny",
        booktitle = "In Mathematics of Evolution and Phylogeny",
        pages = "in press",
        year = "2005",
        publisher = "Oxford University Press",
        uri = "http://kim.bio.upenn.edu/~lisan/ihp.pdf",
        uri = "http://kim.bio.upenn.edu/~lisan/ihp.pdf"
}

@article{227,
        author = "L.-S. Wang and T. Warnow",
        title = "Reconstructing chromosomal evolution",
        journal = "SIAM Journal on Computing",
        pages = "99 - 131",
        volume = "36",
        number = "1",
        year = "2006"
}

@article{228,
        author = "L.-S. Wang and T. Warnow and B. M. E. Moret and R. K. Jansen and L. A. Raubeson",
        title = "Distance-based genome rearrangement phylogeny",
        journal = "J. Mol. Evol.",
        pages = "473 - 483",
        volume = "63",
        number = "4",
        year = "2006"
}

@inbook{229,
        author = "T. Warnow",
        editor = "S. Aluru",
        title = "Large-scale phylogenetic analyses",
        booktitle = "Handbook of Computational Molecular Biology",
        pages = "21-1 21-21",
        year = "2006",
        publisher = "Chapman & Hall"
}

@article{42,
        author = "T. Warnow and S. N. Evans and D. Ringe and L. Nakhleh",
        title = "A stochastic model of language evolution that incorporates homoplasy and borrowing",
        journal = "a special volume on Phylogenetic Methods and the Prehistory of Languages.",
        year = "2005",
        publisher = "Cambridge University Press",
        uri = "http://www.cs.rice.edu/~nakhleh/PAPERS/WarnowRevComplete.pdf",
        uri = "http://www.cs.rice.edu/~nakhleh/PAPERS/WarnowRevComplete.pdf"
}

@article{96,
        author = "C. O. Webb and M. J. Donoghue",
        title = "Phylomatic: tree assembly for applied phylogenetics",
        journal = "Molecular Ecology Notes",
        pages = "181-183",
        volume = "5",
        number = "1",
        year = "2005",
        month = "Mar",
        issn = "1471-8278",
        abstract = "Phylomatic (http://www.phylodiversity.net/phylomatic) is an online phylogenetic query tool where users submit a list of taxa (e.g. from an ecological community), with modern family and genus names, and which returns a phylogenetic hypothesis for the relationships among taxa. Any set of stored phylogenies, or a user-supplied one, can be chosen as the basis for the returned phylogeny, and several output formats for the tree can be selected. Currently, the source databases cover seed plants.",
        annote = "ISI Document Delivery No.: 905VJ",
        howpublished = "Article",
        uri = "<Go to ISI>://000227598500058"
}

@article{230,
        author = "C. O. Webb and G. S. Gilbert and M. J. Donoghue",
        title = "Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forest.",
        journal = "Ecology",
        pages = "123--131",
        volume = "87",
        number = "7",
        year = "2006"
}

@article{231,
        author = "W. C. Wheeler",
        title = "Dynamic homology and the likelihood criterion.",
        journal = "Cladistics",
        pages = "157--170",
        volume = "22",
        year = "2006"
}

@article{104,
        author = "J. J. Wiens and M. J. Donoghue",
        title = "Historical biogeography, ecology and species richness",
        journal = "Trends in Ecology & Evolution",
        pages = "639-644",
        volume = "19",
        number = "12",
        year = "2004",
        month = "Dec",
        issn = "0169-5347",
        abstract = "Ecology and historical (phylogeny-based) biogeography have much to offer one another, but exchanges between these fields have been limited. Historical biogeography has become narrowly focused on using phylogenies to discover the history of geological connections among regions. Conversely, ecologists often ignore historical biogeography, even when its input can be crucial. Both historical biogeographers and ecologists have more-or-less abandoned attempts to understand the processes that determine the large-scale distribution of clades. Here we describe the chasm that has developed between ecology and historical biogeography, some of the important questions that have fallen into it and how it might be bridged. To illustrate the benefits of an integrated approach, we expand on a model that can help explain the latitudinal gradient of species richness.",
        annote = "ISI Document Delivery No.: 880GX",
        howpublished = "Review",
        uri = "<Go to ISI>://000225778100010"
}

@article{93,
        author = "K. W. Will and J. K. Liebherr and D. R. Maddison and K. W. W. Galian",
        title = "Absence asymmetry: The evolution of monorchid beetles (Insecta : Coleoptera : Carabidae)",
        journal = "Journal of Morphology",
        pages = "75-93",
        volume = "264",
        number = "1",
        year = "2005",
        month = "Apr",
        issn = "0362-2525",
        abstract = "Asymmetrical monorchy, or the complete absence of one testis coupled with the presence of its bilateral counterpart, is reported for 174 species of the carabid beetle tribes Abacetini, Harpalini, and Platynini (Insecta: Coleoptera: Carabidae) based on a survey of over 820 species from throughout the family. This condition was not found in examined individuals of any other carabid beetle tribes, or of other adephagan beetle families. One monorchid taxon within Platynini exhibits symmetrical vasa deferentia at the beginning of the pupal stadium, suggesting that developmental arrest of the underdeveloped vas deferens takes place in pupation. The point at which development of the testis is interrupted is unknown. Complete absence of one organ of a bilateral pair-absence asymmetry-is rarely found in any animal clade and among insects is otherwise only known for testes in the minute-sized beetles of the family Ptiliidae, ovaries in Scarabaeinae dung beetles, and ovaries of some aphids. Based on current phylogenetic hypotheses for Carabidae, testis loss has occurred independently at least three times, and up to five origins are possible, given the variation within Abacetini. Clear phylogenetic evidence for multiple independent origins suggests an adaptive or functional cause for this asymmetry. A previously posited taxon-specific hypothesis wherein herbivory in the tribe Harpalini led to testis loss is rejected. Optimal visceral packing of the beetle abdomen is suggested as a general explanation. Specifically, based on the function of various organ systems, we hypothesize that interaction of internal organs and pressure to optimize organ size and space usage in each system led to the multiple origins and maintenance of the monorchid condition. Testes are the only redundant and symmetrically paired structures not thought to be developmentally linked to other symmetrical structures in the abdomen. Among all possible organs, they are the most likely-although the observed frequency is very small-to bypass constraints that maintain bilateral symmetry, resulting in absence asymmetry. However, based solely on our observations of gross morphology of internal organs, no function conclusively explains the ontogenetic loss of one testis in these taxa. Unlike the analogous absence asymmetry of organs in other animal groups, no dramatic body-form constraint- e.g., snakes and lung loss, ptiliid beetles' small body-size and relatively giant sperm-or adaptive scenario of improved locomotory performance- e.g., birds and ovary loss due to flight constraints-applies to these carabid beetles. We tentatively suggest that testis loss is driven wholly by an interaction among the internal organs of these beetles, possibly due to selective pressure to maximize the comparatively large accessory glands found in these taxa. However, as the ordering of these evolutionary events of testis loss and accessory gland size increase is not known, large accessory glands might have secondarily evolved to compensate for a decreased testicular output. (c) 2005 Wiley-Liss, Inc.",
        annote = "ISI Document Delivery No.: 914WR",
        howpublished = "Review",
        uri = "<Go to ISI>://000228259300005"
}

@inbook{232,
        author = "T. L. Williams and D.A. Bader and M. Yan and B. M. E. Moret",
        editor = "A. Zomaya",
        title = "High-performance phylogeny reconstruction under maximum parsi¬mony",
        booktitle = "Parallel Computing for Bioinformatics and Computational Biology",
        year = "2006",
        publisher = "John Wiley & Sons"
}

@misc{16,
        author = "T. L. Williams and T.Y. Berger-Wolf and B. M. E. Moret and U. Roshan and T. Warnow",
        title = "The relationship between maximum parsimony scores and phylogenetic tree topologies",
        booktitle = "Technical Report",
        volume = "TR-CS-2004-04",
        year = "2004",
        publisher = "U. New Mexico",
        uri = "http://www.cs.unm.edu/colloq-bin/tech_reports.cgi?ID=TR-CS-2004-04"
}

@inproceedings{233,
        author = "T. L. Williams and M. L. Smith",
        title = "Cooperative-Rec-I-DCM3: A population-based approach for reconstructing phylogenies",
        pages = "127--134",
        year = "2005",
        publisher = "IEEE Press"
}

@inproceedings{234,
        author = "T. L. Williams and M. L. Smith",
        title = "Phylospaces: Evolutionary trees and tuple space",
        year = "2006",
        month = "25-29 April",
        publisher = "IEEE Press"
}

@inproceedings{235,
        author = "T. L. Williams and M. L. Smith",
        title = "The role of diverse populations in phylogenetic analysis",
        pages = "287 - 294",
        year = "2006"
}

@article{94,
        author = "R. C. Winkworth and M. J. Donoghue",
        title = "Viburnum phylogeny based on combined molecular data: Implications for taxonomy and biogeography",
        journal = "American Journal of Botany",
        pages = "653-666",
        volume = "92",
        number = "4",
        year = "2005",
        month = "Apr",
        issn = "0002-9122",
        abstract = "We investigated Viburnum phylogeny using separate and combined analyses of DNA sequence data from two chloroplast and three nuclear loci. Separate analyses of nuclear and chloroplast data sets resulted in gene trees that were generally congruent with one another and with trees from two previous analyses. Our gene trees do differ in the position of section Pseudotinus, as well as in species relationships within sections Pseudotinus and Lentago. However, tests for incongruence indicate that differences between the nuclear and chloroplast data are not significant. Furthermore, gene trees from combined analyses were highly similar to those found in separate analyses, suggesting that these localized differences do not affect other parts of the tree. Our analyses provide convincing support for numerous relationships, although there is still uncertainty at the base of the tree. To facilitate future study, we propose informal names for 12 well-supported species groups, as well as for several higher-level clades. We also discuss the biogeographic implications of our phylogeny, focusing on repeated, although apparently temporally incongruent, patterns of disjunction between the Old and New Worlds.",
        annote = "ISI Document Delivery No.: 913CB",
        howpublished = "Article",
        uri = "<Go to ISI>://000228126800009"
}

@inproceedings{236,
        author = "W. Xu and W. Briggs and J. Padolina and W. Liu and C. R. Linder and D.P. Miranker",
        title = "Using MoBIos scalable genome join to find conserved primer pair candidates between two genomes",
        pages = "i355--i362",
        volume = "20",
        year = "2004"
}

@inproceedings{242,
        author = "F. Yue and J. Tang",
        title = "A divide-and-conquer implementation of three sequence alignment and ancestor inference.",
        pages = "143--150",
        year = "2007"
}

@article{241,
        author = "F. Yue and J. Tang",
        title = "A space-effecient algorithm for three sequence alignment and ancestor inference (accepted).",
        journal = "International Journal of Data Mining and Bioinformatics",
        volume = "In press",
        year = "2008"
}

@inproceedings{237,
        author = "S. Zhang and K.G. Herbert and J. Wang and W. H. Piel and D.R.B Stockwell",
        title = "PhyloMiner: A Tool for Evolutionary Data Analysis",
        pages = "129 - 132",
        year = "2006"
}

@inproceedings{238,
        author = "Y. Zheng and S. Fisher and S. Cohen and S. Guo and J. Kim and S. B. Davidson",
        title = "Crimson: A data management system to support evaluating phylogenetic tree reconstruction algorithms",
        pages = "1231-1234",
        year = "2006"
}

@article{102,
        author = "D. J. Zwickl and M. T. Holder",
        title = "Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics",
        journal = "Systematic Biology",
        pages = "877-888",
        volume = "53",
        number = "6",
        year = "2004",
        month = "Dec",
        issn = "1063-5157",
        abstract = "Bayesian phylogenetic methods require the selection of prior probability distributions for all parameters of the model of evolution. These distributions allow one to incorporate prior information into a Bayesian analysis, but even in the absence of meaningful prior information, a prior distribution must be chosen. In such situations, researchers typically seek to choose a prior that will have little effect on the posterior estimates produced by an analysis, allowing the data to dominate. Sometimes a prior that is uniform (assigning equal prior probability density to all points within some range) is chosen for this purpose. In reality, the appropriate prior depends on the parameterization chosen for the model of evolution, a choice that is largely arbitrary There is an extensive Bayesian literature on appropriate prior choice, and it has long been appreciated that there are parameterizations for which uniform priors can have a strong influence on posterior estimates. We here discuss the relationship between model parameterization and prior specification, using the general time-reversible model of nucleotide evolution as an example. We present Bayesian analyses of 10 simulated data sets obtained using a variety of prior distributions and parameterizations of the general time-reversible model. Uniform priors can produce biased parameter estimates under realistic conditions, and a variety of alternative priors avoid this bias.",
        annote = "ISI Document Delivery No.: 887LC",
        howpublished = "Article",
        uri = "<Go to ISI>://000226306600003"
}