Publications

(2018). Rerooting Trees Increases Opportunities for Concurrent Computation and Results in Markedly Improved Performance for Phylogenetic Inference. 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) (pp. 247–256). IEEE.

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(2017). Heterogeneous hardware support in BEAGLE, a high-performance computing library for statistical phylogenetics. 2017 46th International Conference on Parallel Processing Workshops (ICPPW) (pp. 23–32). IEEE.

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(2017). Configuring concurrent computation of phylogenetic partial likelihoods: accelerating analyses using the BEAGLE library. In S Ibrahim, KK Choo, Z Yan, and W Pedrycz (Eds.), Algorithms and Architectures for Parallel Processing. ICA3PP 2017. Lecture Notes in Computer Science (pp. 533–547). Springer, Cham.

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(2017). Phylogeny and Evolution of Lepidoptera. Annu Rev Entomol, 62, 265–283.

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(2014). AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite, MIGRATE-N, Modeltest, Mr- Bayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, Structure, Structurama, Tracer, TreeStat, TreeView X. Concise Encyclopaedia of Bioinformatics and Computational Biology (pp. 33–34, 40, 45–46, 54, 135, 145, 156, 184–185, 219, 238, 271–272, 325, 330–331, 352–353, 372–373, 395, 407, 409, 428, 440, 460–461, 510–511, 516–517, 524–525, 607, 611, 672–663, 684, 701–702, 727, 741, 757). Wiley-Liss, 2nd edition.

(2011). Computing the Tree of Life: leveraging the Power of Desktop and Service Grids. 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW) (pp. 1896–1902). IEEE.

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(2010). Evolutionary framework for Lepidoptera model systems. In M Goldsmith and F Marec (Eds.), Genetics and Molecular Biology of Lepidoptera (pp. 1–24). CRC Press, Boca Raton.

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(2008). The Lattice Project: a Grid research and production environment combining multiple Grid computing models. Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities.

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(2007). Expanding the reach of Grid computing: combining Globus-and BOINC-based systems. In E-G Talbi and AY Zomaya (Eds.), Grid Computing for Bioinformatics and Computational Biology (chapter 4). Wiley-Interscience, Hoboken.

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(2005). Grid computing. EDUCAUSE review, 40, 116–117.

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(2005). Data sharing in ecology and evolution. Trends Ecol Evol, 20, 362-363.

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(2004). BAMBE, DnaSP, ENCprime/SeqCount, LAMARC, MacClade, MEGA, Modeltest, MrBayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, TreeView. In JM Hancock and MJ Zvelebil (Eds.), Dictionary of Bioinformatics and Computational Biology (pp. 39–40, 123–124, 146, 288–289, 305, 318, 337, 352, 388, 392, 398–399, 455, 457, 502, 522, 568). Wiley-Liss, Hoboken.

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(2004). A book like its cover. Heredity, 93, 234–235.

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(2004). Applying permutation tests to tree-based statistical models: extending the R package rpart. Technical Report CS-TR-4581, UMIACS-TR-2004-24, University of Maryland.

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(1997). The evolution of plant nuclear genes. Proc Natl Acad Sci USA, 94, 7791–7798.

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(1996). Inferring phylogenies from DNA sequence data: the effects of sampling. In. PH Harvey, AJ Leigh Brown, JM Smith and S Nee (Eds.), New Uses for New Phylogenies (pp. 103–115). Oxford University Press.

(1992). Patterns and processes of sequence evolution: Plant organelle genomes and copia-like retrotransposons. PhD thesis, Harvard University, Cambridge, Massachusetts USA.

(1992). Copia-like retrotransposons in plants: a brief introduction. Plant Genetics Newsletter, 8, 38–41.