Software

Cadence - A Mac OSX program for Bayesian relative rates tests

Program detailed in:

Wilcox, T. P., García de Leon, F. J., D. A. Hendrickson, and D. M. Hillis. 2004. Convergence among cave catfishes: Long-branch attraction and a Bayesian relative rates test. Molecular Phylogenetics and Evolution 31:1101-1113.

DOGMA - Dual Organellar GenoMe Annotator

Program detailed in: Wyman, S. K., J. L. Boore, and R. K. Jansen. 2004, Automatic annotation of organellar genomes with DOGMA. Bioinformatics, in press.

GARLI - Genetic Algorithm for Rapid Likelihood Inference (GARLI) - Derrick Zwickl

Open Proteomics Database - public database of mass spectrometry based proteomics data link:

       Program detailed in:

       http://bioinformatics.icmb.utexas.edu/OPD/ detailed in: Prince, J. T., Carlson, M. W, Wang,        R., Lu, P., Marcotte, E. M. The need for a public proteomics repository. Nature Biotechnol.        22, 471-2 (2004).

SequenceJuxtaposer - Compare DNA/RNA Sequences

TreeJuxtaposer - Compare phylogenetic evolutionary trees interactively and automatically

Tree Set Viz - Tree Set Visualization

Program detailed in:

Amenta, N., and J. Klingner. 2002. Case study: Visualizing sets of evolutionary trees. 8th IEEE Symposium on Information Visualization 2002:71-74.

Hillis, D. M., T. Heath, and K. St. John. In press. Analysis and visualization of tree space. Systematic Biology.

Wolfram Research Mathematica Code - Orly Alter 2006: Wolfram Research Mathematica Code for SVD and Hermite transform reconstruction of DNA microarray data; distributed freely online at http://www.bme.utexas.edu/research/orly/network_decomposition

Wolfram Research Mathematica Code - Orly Alter 2005: Wolfram Research Mathematica code for integrative higher-order eigenvalue decomposition of DNA microarray data; distributed freely online at http://www.bme.utexas.edu/research/orly/pseudoinverse

Wolfram Research Mathematica Code - Orly Alter 2004: Wolfram Research Mathematica code for integrative pseudoinverse projection of DNA microarray data; distributed freely
online at http://www.bme.utexas.edu/research/orly/pseudoinverse

Publications:

Adami, C., and C. O. Wilke.  2004.  Experiments in Evolution. Artificial Life 10:117-122.

Alter, O. and G. H. Golub.  2006.  Singular Value Decomposition of Genome-Scale mRNA
Lengths Distribution Reveals Asymmetry in RNA Gel Electrophoresis Band
Broadening," Proc. Natl. Acad. Sci. USA 103, 11828, dx.doi.org/10.1073/pnas.0604756103

Alter, O. and G. H. Golub.  2005.  Reconstructing the Pathways of a Cellular System from Genome-Scale Signals Using Matrix and Tensor Computations, "http://dx.doi.org/10.1073/pnas.0509033102". Proceedings of the National Academy of Sciences 102 (49), pp. 17559 – 17564.  Supplemental material at "http://www.bme.utexas.edu/research/orly/network_decomposition/".

Alter, O. and G. H. Golub.  2004.  Integrative Analysis of Genome-Scale Data Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNATranscription. "http://dx.doi.org/10.1073/pnas.0406767101" Proceedings of the National Academy of Sciences 101 (47), pp. 16577 – 16582.  Supplemental material at "http://www.bme.utexas.edu/research/orly/pseudoinverse/".

Alter, O.  2006. Discovery of Principles of Nature From Mathematical Modeling of DNA Microarray Data.   Proc. Natl. Acad. Sci. USA 103, 16063. dx.doi.org/10.1073/pnas.0607650103

Alverson, A.J., J.J. Cannone, R.R. Gutell, and E.C. Theriot.  2006.  The evolution of elongate cell shape in diatoms. Journal of Phycology

Alverson, A.J. and L. Kolnick.  2007.  Intragenomic nucleotide polymorphism among SSU rDNA paralogs in the diatom genus Skeletonema. Journal of Phycology 41: 1248--1257

Amenta, N., and J. Klingner.  2002.  Case study: Visualizing sets of evolutionary trees. 8th IEEE Symposium on Information Visualization 2002:71-74.

Andrus, N., J. Trusty, A. Santos-Guerra, R. K. Jansen and J. Francisco-Ortega.  2004. Using molecular phylogenies to test phytogeographical links between East/South Africa – Southern Arabia and the Macaronesian islands – A review and the case of Pulicaria section Vieraeopsis and Vierea (Asteraceae).  Taxon 53: 333 - 346.

Arnqvist, G., and M. Kirkpatrick.  2005.  The evolution of infidelity in socially monogamous passerines:  the strength of direct and indirect selection on extra-pair copulation behavior in females.  American Naturalist 165: S26-S37.

Bader, D., Usman Roshan, and Alexandros Stamatakis. 2005.  Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions.

Bailey, J.R., A. R. Sedaghat, T. Kieffer, T. Brennan, P. K. Lee, M. Wind-Rotolo, C. M. Haggerty, A. R. Kamireddi, Y. Liu, J. Lee, D. Persaud, J. E. Gallant, J. Cofrancesco, Jr., T. C. Quinn, C. O. Wilke, S. C. Ray, J. D. Siliciano, R. E. Nettles, and R. F. Siliciano.  2006. Residual human immunodeciency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4 + T cells. J. Virol. 80:6441–6457.

Bain, J.F. and R.K. Jansen.  2006.  A chloroplast DNA hairpin structure provides useful phylogenetic data with subtribe Senecioneae (Asteraceae).  Canadian Journal of Botany 84:862-868.

Baird,* A. B., J. K. Krejca, J. R. Reddell, C. E. Peden*, M. J. Mahoney, and D. M. Hillis.  2006.  Phylogeographic structure and color pattern variation among populations of Plethodon albagula on the Edwards Plateau of central Texas. Copeia 2006:760-768.

Baird,* A. B., D. M. Hillis, J. C. Patton, and J. W. Bickham.  2008.  Evolutionary history of the genus Rhogeessa (Chiroptera: Vespertilionidae) as revealed by mitochondrial DNA sequences. J. Mammalogy.

Barber, J. C., J. Francisco-Ortega, A. Santos-Guerra, K. G. Turner, and R. K. Jansen.  2002.  Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets.  Mol. Phyl. Evol. 23: 293-306.

Baird*, A. B., D. M. Hillis, J. C. Patton, and J. W. Bickham. 2008. Evolutionary history of the genus Rhogeessa (Chiroptera: Vespertilionidae) as revealed by mitochondrial DNA sequences. J. Mammalogy.

Barbancon, F., T. Warnow, D. Ringe, S. Evans, and L. Nakhleh, 2007. “An experimental study comparing linguistic phylogenetic reconstruction methods.” Proceedings of the conference Languages and Genes, held at UC Santa Barbara (Cambridge University Press). To appear.

Barber, J.C., C.C. Finch, J. Francisco-Ortega, A. Santos-Guerra, and R.K. Jansen.  2006.  Evolution of Macaronesian Sideritis (Lamiaceae) revisited: A re-evaluation based upon incongruence of multiple independent nuclear and chloroplast datasets.  Taxon.

Bausher, M. G., , N. D. Singh Mozoruk, J., S.-B. Lee, R. K. Jansen, and H. Daniell.   2006. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var. 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms. BMC Plant Biology 6:21.

Bednar, J. A., and Miikkulainen, R.  2006.  Joint maps for orientation, eye, and direction preference in a self-organizing model of V1. Neurocomputing 69:1272--1276.

Bednar, J. A., De Paula, J., and Miikkulainen, R.  2005.  Self-Organization of color opponent receptive fields and laterally connected orientation maps. Neurocomputing 65-66:69--76.

Bednar, J. A., Kelkar, A., and Miikkulainen, R.  2004.  Scaling Self-Organizing Maps to Model Large Cortical Networks. Neuroinformatics 2:275--302.

Bednar, J. A. and Miikkulainen, R.  2004.  Prenatal and Postnatal Development of Laterally Connected Orientation Maps. Neurocomputing 58--60:985--992.

Bednar, J. A., Choe, Y., De Paula, J. B., Miikkulainen, R., Provost, J., Tversky, T.  2004. Modeling Cortical Maps with Topographica. Neurocomputing 58-60:1129--1135.

Bednar, J. A. and Miikkulainen, R.  2003.  Self-Organization of Spatiotemporal Receptive Fields and Laterally Connected Direction and Orientation Maps. Neurocomputing, 52--54:473--480.

Bednar, J. A., and Miikkulainen, R.  2003.  Learning Innate Face Preferences. Neural Computation, 15:1525--1557.

Bednar, J. A., Kelkar, A., and Miikkulainen, R.  2002.  Modeling Large Cortical Networks with Growing Self-Organizing Maps. Neurocomputing 44--46:315--321.

Bhattacharya D., Simon D., Huang J.,  Cannone J.J., and Gutell R.R.  2003.  The Exon Context and Distribution of Euascomycetes  rRNA Spliceosomal  Introns.   BioMed Central (BMC) Evolutionary Biology 3:7.

Bhattacharya D., Cannone J.J., and Gutell R.R.  2001.  Group I Intron Lateral Transfer Between Red and Brown Algal Ribosomal RNA.  Current  Genetics,  40:82-90.

Bloom, J.D., F. H. Arnold, and C. O. Wilke.  2007.  Breaking proteins with mutations: threads and thresholds in evolution. Mol. Syst. Biol. 3:76.

Bloom, J.D., A. Raval, and C. O. Wilke.  2007.  Thermodynamics of neutral protein evolution. Genetics 175:255-266.

Bloom, J.D., D. A. Drummond, F. H. Arnold, and C. O. Wilke.  2006.  Structural determinants of the rate of protein evolution in yeast. Mol. Biol. Evol. 23:1751–1761.

Bloom, J.D., J. J. Silberg, C. O. Wilke, D. A. Drummond, C. Adami, and F. H. Arnold. 2005. Thermodynamic prediction of protein neutrality. Proc. Natl. Acad. Sci. USA 102:606-611.

Bloom, J.D., C. O. Wilke, F. H. Arnold, and C. Adami.  2004.  Stability and the evolvability of function in a model protein. Biophys. J. 86:2758–2764.

Bossuyt, F., R. M. Brown, D. M. Hillis, D. C. Cannatella, and M. C.  Milinkovitch. 2006. Phylogeny and biogeography of a cosmopolitan frog radiation: Late Cretaceous diversification resulted in continent-scale endemism in the family Ranidae. Systematic Biology 55:579-594.

Boul, K. E., W. C. Funk, C. R. Darst, D. C. Cannatella, and M. J. Ryan. (2007). Sexual selection drives speciation in an Amazonian frog. Proceedings of the Royal Society B: Biological Sciences 274(1608):399-406.

Boyer, Robert S., Warren A. Hunt Jr., and Serita M. Nelesen*.  2005.  A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance. Algorithms in Bioinformatics: 5th International Workshop, WABI 2005. Lecture Notes in Computer Science 3692:353-364, Springer-Verlag.

Brauer, M. J., M. T. Holder, L. A. Dries, D. J. Zwickl*, P. O. Lewis, and D. M. Hillis.  2002. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Molecular Biology and Evolution 19:1717-1726.

Brown, J.M., and A.R. Lemmon*.  2007.  The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Systematic Biology. In Press.

Brown, J.M. and G.B. Pauly*.  2005.  Increased rates of molecular evolution in an equatorial plant clade: an effect of environment or phylogenetic nonindependence? Evolution 59:238-242.

Bull, J.J., R. Sanju, and C. O. Wilke.  2007.  Theory of lethal mutagenesis for viruses. J. Virol. 81:2930-2939.

Cai, Z., C. Penaflor, J.V. Kuehl, J. Leebens-Mack, J. Carlson, C.W. dePamphilis, and R.K. Jansen. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids. BMC Evolutionary Biology 6:77.

Cannatella, D. C., and D. M. Hillis.  2004.  Amphibians: Living a life of slime. In Assembling the Tree of Life (J. Cracraft and M. J. Donoghue, editors). Oxford University Press, New York.

Cannatella, D. C., and D. M. Hillis.  2004.  Amphibians. Pp. 430-450 in Assembling the Tree of Life (J. Cracraft and M. J. Donoghue, editors). Oxford University Press, New York.

Cannone J.J. and Gutell R.R.  2004.  Entries in the Dictionary of Bioinformatics and Computational Biology, eds. Hancock J.M. and Zvelebil M.J.  John Wiley & Sons, Inc.

Cannone J.J., Subramanian S., Schnare M.N., Collett* J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Muller K.M., Pande N., Shang Z., Yu N., and Gutell R.R.  2002.  The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and other RNAs.BioMed Central(BMC) Bioinformatics 3:2.

Caujapé-Castells, J., R. K. Jansen, N. Membrives, J. Pedrola-Monfort, J. M. Montserrat, and A. Ardanuy.  2001.  Historical biogeography of Androcymbium Willd. (Colchicaceae) in Africa: evidence from cpDNA RFLPs.  Bot. J. Linn. Soc., 136: 379 - 392.

Caujapé-Castells, J.,  R. K. Jansen, N. Membrives, J. Pedrola-Monfort.  2002.  Space-time diversification of Androcymbium Willd. (Colchicaceae) in western South Africa.  Plt. Syst. Evol. 232: 73-88.

Caujape-Castells, J. and R. K. Jansen.  2003.  The influence of the Miocene Mediterranean desiccation on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.) McBride (Colchicaceae).  Mol. Ecol. 12: 1515-1525.

Chen X., Gutell R.R., Lambowitz A.M.  2000.  Function of Tyrosyl-tRNA synthetase in splicing group I introns. An induced fit model for binding to the P4-P6 domain based on analysis of mutations at the junction of the P4-P6 stacked helices.  Journal of Molecular Biology, 301:265-283.

Chen, M., Ha, M., Lackey, E., Wang, J., and Chen, Z. J. (2008) RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics (in press).

Chen, Z. J. and Tian, L. (2007). Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim. Biophy. Acta 1769:295-307.

Choe, Y. and Miikkulainen, R.  2004.  Contour Integration and Segmentation with Self-Organized Lateral Connections. Biological Cybernetics, 90:75--88.

Choe, Y. and Miikkulainen, R.  2003.  The Role of Postsynaptic Potential Decay Rate in Neural Synchrony. Neurocomputing, 52--54:707--712.

Chow, S.S., C. O. Wilke, C. Ofria, R. E. Lenski, and C. Adami.  2004.  Adaptive radiation from resource competition in digital organisms. Science 305:84-86. ∗Joint first authorship.

Chumley, T.W., J.D. Palmer, J.P. Mower, J.L. Boore, H.M. Fourcade, P.J. Caile, and R.K. Jansen. 2006.  The completed chloroplast genome sequence of Pelargonium x hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molecular Biology and Evolution 23: 1-16.

Collett*, JR., Cho, EJ., Ellington, AD.  2005.  Production and processing of aptamer microarrays. Methods.  Sep; 37(1):4-15.

Coarfa, C., Yuri Dotsenko, John Mellor-Crummey, Luay Nakhleh, and Usman Roshan. 2005.  PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction.

Cosner, M.E., L.A. Raubeson, and R.K. Jansen. 2004. Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evolutionary Biology 4: 27.

Cui, L., N. Veeraraghavan, K. Wall, R.K. Jansen, J. Leebens-Mack, I. Makalowska, C. W. dePamphilis.  2006. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research 34:D692-D696.

Currie, C.R., B. Wong, A.E. Stuart, T.R. Schultz, S.A. Rehner, U.G. Mueller, G.-H. Sung, J.W. Spatafora, N.A.Straus.  2003.  Ancient tripartite coevolution in the attine ant microbe symbiosis. Science 299: 386-388.

Daniell, H., S.-B. Lee,* J. Grevich, C. Saski, C. Guda, J. Tompkins, and R. K. Jansen.  2006.  Complete chloroplast genome sequences of Solanum tuberosum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theoretical and Applied Genetics 112: 1503-1518.

Darst, C. R., and D. C. Cannatella.  2003.  Novel relationships among hyloid frogs inferred from 12S and 16S mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 31(3):462-475.

Dearborn, D.C., A.D. Anders, E.A. Schreiber, R.M.M. Adams, U.G. Mueller.  2003.  Inter-island movements and population differentiation in a pelagic seabird. Molecular Ecology 12: 2835-2843.

de Cara, M.A.R., N.H. Barton, and M. Kirkpatrick.  2008.  The evolution of assortative mating.  American Naturalist.

Dopman, E. B., G. A. Sword, and D. M. Hillis.  2002.  On the importance of the ontogenetic niche in resource-associated divergence: evidence from a polyphagous grasshopper. Evolution 56:731-740.

Doshi,* Kishore J , Jamie J Cannone, Christian W Cobaugh and Robin R Gutell.  2004.  Evaluation of the suitablity of free-energy minimzation using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics, 5:105

Drummond, D.A., A. Raval, and C. O. Wilke.  2006.  A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23:327-337.

Drummond, D.A., J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold.  2005.  Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA 102:14338-14343.

Drummond, D.A., J. J. Silberg, M. M. Meyer, C. O. Wilke, and F. H. Arnold.  2005.  On the conservative nature of intragenic recombination. Proc. Natl. Acad. Sci. USA 102:53805385.

Du, Z., A. Stamatakis, F. Lin, U. Roshan, L. Nakhleh.  2005.  Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood.

Du, Z., Feng Lin, and Usman Roshan.  2005.  Reconstruction of Large Phylogenetic Trees: A Parallel Approach.

Ebert, D., C. Haag, M. Kirkpatrick, M. Riek, J.W. Hottinger, and V.I. Pajunen.  2005. Outbreeding confers a selective advantage to immigrant genes in a metapopulation.  Science 295: 485-488.

Eddie, W. M. M, T. Shulkina, J. Gaskin, R. C. Haberle, and R. K. Jansen.  2003.  Phylogeny of the Campanulaceae s. str. inferred from ITS sequences of nuclear ribosomal DNA.  Ann. Missouri Bot. Gard. 90: 554-575.

Elena, S.F., C. O. Wilke, C. Ofria, and R. E. Lenski. 2003.  Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61:666-674, 2007.

Elgavish T., Cannone J.J., Lee J.C., Harvey S., and Gutell R.R.  2001.  AA.AG@helix.ends: A:A and A:G base-pairs at the end of 16S and 23S rRNA helices.  Journal of Molecular Biology, 310:735-753.

Ellington, AD, Cox JC, Lee JF*, Collett JR*.  2005.  Automated in vitro selection and microarray applications for functional RNA sequences, in The RNA World, 3rd Ed., Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York. p. 683-719.

Evans, B. J., D. B. Kelley, D. J. Melnick, and D. C. Cannatella. 2005. Evolution of RAG-1 in polyploid clawed frogs. Mol. Biol. Evol. 22(5):1193-1207.

Evans, B. J., D. B. Kelley, R. Tinsley, D. J. Melnick, and D. C. Cannatella.  2004.  A mitochondrial DNA phylogeny of clawed frogs: phylogeography on sub-saharan Africa and implications for polyploid evolution. Molecular Phylogenetics and Evolution 33(1):197-213.

Evans, S.N., and Tandy Warnow.  2004. Unidentifiable Divergence Times in Rates-Across-Sites Models.

Evans, S.N., Don Ringe, and Tandy Warnow.  2004.  Inference of Divergence Times as a Statistical Inverse Problem.

Ferguson, C. J. and R. K. Jansen.   2002.  A chloroplast DNA phylogeny or eastern Phlox (Polemoniaceae): implications of congruence and incongruence with the ITS phylogeny.  Amer. J. Bot. 89: 1324-1335.

Forster, R., and C. O. Wilke. Frequency-dependent selection in a periodic environment. Physica A, in press.

Forster, R., C. Adami, and C. O. Wilke.  2006.  Selection for mutational robustness in finite populations. J. Theor. Biol. 243:181–190.

Forster, R. and C. O. Wilke.  2005.  Tradeoff between short-term and long-term adaptation in a changing environment. Phys. Rev. E 72:041922.

Francisco-J., J. C. Barber, A. Santos-Guerra, R. Febbles-Hernandez, and R. K. Jansen.  2001.  Origin and evolution of the endemic genera of Gonosperminae (Asteraceae: Anthemideae) from the Canary Islands: Evidence from nucleotide sequences of the internal transcribed spacers of the nuclear ribosomal repeat.  Amer. J. Bot. 88: 161-169.

Francisco-J., J., S.-J. Park, A. Santos-Guerra, A. Benabid, and R. K. Jansen.  2001.  Origin and evolution of the endemic Macaronesian Inuleae (Asteraceae): Evidence from the internal transcribed spacers of nuclear ribosomal DNA. Biol. J. Linn. Soc. 72: 77-97.

Francisco-Ortega, J., J. Furetes-Aguilar, Kim, S.C., A. Santos-Guerra, D. J. Crawford, and R. K. Jansen.  2002.  Phylogeny of the Macaronesian endemic Crambe section Dendrocrambe (Brassicaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA.  Amer. J. Bot., 89 (12): 1984-1990.

Froissart, R., C. O. Wilke, R. Montville, S. K. Remold, L. Chao, and P. E. Turner.  2004. Coinfection weakens selection against epistatic mutations in RNA viruses. Genetics 168:919.

Fuertes-Aguilar, J., M. C. Ray, J. Francisco-Ortega, A. Santos-Guerra, and R. K. Jansen.  2002.  Molecular evidence from chloroplast and nuclear markers for multiple colonizations of Lavatera (Malvaceae) in the Canary Islands.  Syst. Bot.27:74-83.

Fuertes-Aguilar, J., P. A. Fryxell, and R. K. Jansen.  2003.  Phylogenetic relationships and classification of the Sida  generic alliance (Malvaceae) based on nrDNA ITS evidence.  Syst. Bot. 28: 352-364.

Funk, V. A., R. J. Bayer, S. Keeley, R. Chan, L. Watson, B. Gemeinholzer, E. Schilling, J. L. Panero, B. G. Baldwin, N. Garcia-Jacas, A. Susanna and R. K. Jansen. 2005.  Everywhere but Antarctica: Using a supertree to understand the diversity and distribution of the Compositae. Biol. Skr. 55: 343-374.

Funk, W. C., J. P. Caldwell, C. E. Peden*, J. M. Padial, I. de la Riva, D. C. Cannatella. (2007). Tests of biogeographic hypotheses for diversification in the Amazonian forest frog, Physalaemus petersi. Molecular Phylogenetics and Evolution 44:825-837.

Ganapathy, G., V. Ramachandran, and T. Warnow, 2003. Better Hill-Climbing Seaches for
Parsimony. In Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI), pp. 245–258, 2003.

Ganapathy, G., V. Ramachandran, and T. Warnow. 2004. On Contract-and-Refine-Transformations Between Phylogenetic Trees. In Proceedings of the Fifteenth ACM-SIAM Symposium on Discrete Algorithms (SODA 2004), pp. 893-902.

Ganapathy, G., B. Goodson*, R. Jansen, V. Ramachandran, and T. Warnow, 2005. Pattern identification in biogeography: metrics and algorithms for comparing area cladograms. Proceedings of the Fifth International Workshop on Algorithms for Bioinformatics (WABI), October 2005.

Ganapathy, G., B. Goodson*, R. K. Jansen, H.-S. Le, V. Ramachandran, and T. Warnow.  2006.  Pattern identification in biogeography. IEEE/ACM Transactions on Computational Biology and Bioinformatics (invited paper) 3 (4): 334-346.

Ganapathy, G., B. Goodson*, R. Jansen, V. Ramachandran, and T. Warnow.  2005.  Pattern matching in biogeography. In R. Casadio and G. Myers [eds.], Algorithms in Bioinformatics: Proceedings of the 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Springer-Verlag, Berlin, pp. 112-127.

Garda, A. A., and D. C. Cannatella. (2007). Phylogeny and biogeography of paradoxical frogs (Anura, Hylidae, Pseudae) inferred from 12S and 16S mitochondrial DNA. Molecular Phylogenetics and Evolution 44:104-114.

Garrick, R. C., C. J. Sands, D. M. Rowell, D. M. Hillis, and P. Sunnucks.  2007.  Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands – a multi-gene approach. Molecular Ecology 16: 1865-1882.

Garrick, R. C., D. M. Rowell, C. S. Simmons, D. M. Hillis, and P. Sunnucks. In press. Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saproxylic springtails. Evolution.

Gerardo, N.M., C.R. Currie,S.L. Price, U.G. Mueller.  2004.  Exploitation of amutualism: specialization of fungal parasites on cultivars in the attine ant symbiosis. Proceedings of the Royal Society of London B in press.

Gillespie J., Johnston J.S., Cannone J.J.,  and Gutell R.R. 2006. Characteristics of the nuclear (18S, 5.8S, 28S, and 5S) and mitochondrial (12S and 16S) rDNA genes of Apis Mellifera (Insecta:Hymenoptera): Structure, organization, and retrotransposition. Insect Molecular Biology, 15:657-686.

Gillespie J., McKenna C., Yoder M.J., Gutell R., Johnston J., Kathirithamby J., and Cognato A. 2005. Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta:Strepsiptera).  Insect Molecular Biology. 14:625-643.

Gillespie J., Cannone J., Gutell R.R., Cognato A. 2004. A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae;Galerucinae).   Insect Molecular Biology.  13:495-518.

Goertzen, L. G., J. Francisco-Ortega, A. Santos-Guerra, J. Mower, C. R. Linder, and R. K. Jansen.  2002. Molecular systematics of the Asteriscus alliance (Asteraceae: Inuleae) II: Combined nuclear and chloroplast data.  Syst. Bot. 27:815-823.

Goertzen L.R., Cannone J.J., Gutell R.R., and Jansen R.K. 2003.  ITS Secondary Structure derived from Comparative Analysis: Implications for Sequence Alignment and Phylogeny of the Asteraceae.   Molecular Phylogenetics and Evolution 29:216-234.

Goldman, D. H., J. V. Freudenstein, P. J. Kores, M. Molvray, D. D. Jarrell, M. W. Whitten, K. M. Cameron, R. K. Jansen, and M. W. Chase.  2001.  Phylogenetics of Arethuseae (Orchidaceae) based on plastid matK and rbcL sequences.  Syst. Bot. 26: 670-695.

Goldman, D.H., C. van den Berg, R.K. Jansen, I.J. Leitch, M.F. Fay, and M.W. Chase.  2004.  Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and potential hybrid speciation.  Amer. J. Bot. 91:707-723.

Goodson*, B. E., A. Santos-Guerra, and R. K. Jansen. 2006. Molecular systematics of Descurainia (Brassicaceae) in the Canary Islands: biogeographic and taxonomic implications. Taxon 55: 671-682.

Green, A., R.M. Adams, U.G. Mueller. 2002. Extensive exchange of fungal cultivars between two sympatric species of fungus-growing ants. Molecular Ecology 11: 191-195.

Grunewald, S., Steel, M. and Swenson*, M.Shel. (2007). Closure operations in phylogenetics. Mathematical Biosciences 208, 521—537.

Guisinger-Bellian*, M., C. R. Linder,R. K. Jansen, P.R. Steele. 2008. Molecular Phylogenetics and Evolution. Phylogenetic utility of 144 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids.

Gutell R.R., Lee J., and Cannone J.J.  2002.  The Accuracy of Ribosomal RNA Comparative Structure models.  Current Opinion in Structural Biology 12:301-310.

Gutell R.R., Cannone J.J., Konings D. and Gautheret D.   2000.  Predicting U-turns in Ribosomal RNA with Comparative Sequence Analysis.  Journal of Molecular Biology, 300:791-803.

Gutell R.R.,  Cannone J.J., Shang Z., Du Y., and Serra M. 2000. A Story: Unpaired Adenosine Bases in Ribosomal RNAs.  Journal of Molecular Biology,  304:335-354.

Ha, M., Pang, M., Agarwal, V. Chen, Z. J. (2008) Interspecies regulation of microRNAs and their targets. Biochim. Biophy. Acta (in press).

Hall, D.W., and M. Kirkpatrick.  2006.  Reinforcement and sex linkage.  Evolution.

Hansen, A. K., L. E. Gilbert, B. B. Simpson, S. R. Downie, A. C. Cervi, and R. K. Jansen. 2006. Phylogenetic relationships and chromosome number evolution in Passiflora.  Systematic Botany 31: 138-150.

Hansen, A. K., L. E. Escobar, L. E. Gilbert, and R. K. Jansen.  2006. Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): Implications for phylogenetic studies.  American Journal of Botany, in press.

Heath*, T. A., D. J. Zwickl*, J Kim, and D. M. Hillis. 2008. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology.

Heath*, T. A., S. M. Hedtke*, and D. M. Hillis. In press. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution.

Hedtke*, S.M., T. Townsend, and D. M. Hillis. 2006.  Resolution of phylogenetic conflict in large data sets by increased taxon sampling.  Systematic Biology 55:522-529.

Hedtke*, S. M., K. Stanger-Hall, R. J. Baker, and D. M. Hillis. 2008. All-male asexuality: Origin and maintenance of androgenesis in the Asian clam Corbicula. Evolution.

Hewitt E.A., Müller K.M., Cannone J.J., Hogan D.J., Gutell R.R., and  Prescott D.M. 2003. Phylogenetic Relationships Among 28 Spirotrichous Ciliates Documented by rDNA.  Molecular Phylogenetics and Evolution. 29:258-267.

Hillis, D. M. 2007. Constraints in naming parts of the Tree of Life. Molecular Phylogenetics and Evolution 42:331-338.

Hillis, D. M. 2007. Asexual evolution: Can species exist without sex? Current Biology 17:R543-R544.

Hillis, D. M. 2007. Making evolution relevant and exciting to biology students. Evolution 61:1261-1264.

Hillis, D. M. 2007. Constraints in naming parts of the Tree of Life.  Molecular Phylogenetics and Evolution 42:331-338.

Hillis, D. M., T. Heath*, and K. St. John. 2005. Analysis and visualization of tree space. Systematic Biology 54:471-482 (cover article).

Hillis, D. M. 2004. The Tree of Life and the Grand Synthesis of biology. In Assembling the Tree of Life (J. Cracraft and M. J. Donoghue, editors). Oxford University Press, New York.

Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl*. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Systematic Biology 52:124-126.

Hillis, D. M., D. A. Chamberlain, T. P. Wilcox, and P. T. Chippindale. 2001. A new species of subterranean blind salamander (Plethodontidae: Hemidactyliini: Eurycea: Typhlomolge) from Austin, Texas, and a systematic revision of central Texas paedomorphic salamanders. Herpetologica 57:266-280.

Hillis, D. M. 2001. The emergence of Systematic Biology. Syst. Biol. 50:301-303.

Hillis, D. M. 2002. Molecular systematics. Pp. 756-760 in Encyclopedia of Evolution (M. Pagel, ed.). Oxford Univ. Press, New York.

Hillis, D. M., and T. P. Wilcox. 2005. Phylogeny of the New World true frogs (Rana). Molecular Phylogenetics and Evolution 34:299-314.

Hillis, D. M. 2005. Health applications of the Tree of Life. Pages 139-144 in Evolutionary Science and Society: Educating a New Generation (J. Cracraft and R. Bybee, eds.). Biological Sciences Curriculum Study, Colorado Springs.

Hillis, D. M. In press. Asexual evolution: Can species exist without sex? Current Biology.

Holloway*, A. K., D. C. Cannatella, H. C. Gerhardt, and D. M. Hillis.  2006.  Polyploids with different origins and ancestors form a single sexual polyploid species. American Naturalist 167: E88-E101.  [Highlighted in Current Biology 16:R245-R247]

Jackson S.A., Cannone J.J., Lee J.C., Gutell R.R. , and Woodson S.A.  2002.  Distribution of rRNA introns in the Three-Dimensional Structure of the Ribosome.   Journal of Molecular Biology.   323:35-52.

Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian* M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL. 2007. Proc. Natl. Acad. Sci. USA. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Epub 2007 Nov 28. Dec 4;104(49):19369-74.

Jansen, R.K., L. A. Raubeson, J.L. Boore, C.W. dePamphilis, T.W. Chumley, R.C. Haberle, S.K. Wyman*, A.J. Alverson, R.Peery, S.J. Herman, H.M. Fourcade, J.V. Kuehl, J.R. McNeal, J. Leebens-Mack, and L. Cui.  2005.  Methods for obtaining and analyzing chloroplast genome sequences.  Methods in Enzymology 395: 348-384.

Jansen, R.K., C. Kaittanis, C. Saski, S-B. Lee, J. Tompkins, A. J. Alverson, and, H. Daniell.  2006. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: Effects of taxon sampling and phylogenetic methods on resolving relationships among Rosids. BMC Evolutionary Biology 6: 32.

Jansen, R.K  2001.  Treatments of Acmella and tribe Lactuceae for the Flora of Nicaragua, Missouri Botanical Garden.

Jansen, R.K., L. A. Raubeson, J. L. Boore, C. W. dePamphilis, T. W. Chumley, R. C. Haberle, S. K. Wyman*, A. J. Alverson, R. Peery, S. J. Herman, H. M. Fourcade, J. V. Kuehl, J. R. McNeal, J. Leebens-Mack, and L. Cui.  2005.  Methods for obtaining and analyzing chloroplast genome sequences.  Methods in Enzymology 395: 348 - 384.

Jegelka, S., Bednar, J. A., and Miikkulainen, R.  2006.  Prenatal Development of Ocular Dominance and Orientation Maps in a Self-Organizing Model of V1. Neurocomputing 69:1291--1296

Jin, Guohua, Luay Nakhleh, Sagi Snir, Tamir Tuller. 2007.  Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. Bioinformatics.  23(2) 123-128.

Jin, Guohua, Luay Nakhleh, Sagi Snir, and Tamir Tuller. 2007.  Maximum Likelyhood of Phylogenetic Networks.  Bioinformatics.  23: 1046-1047.

Joseph, S., and M. Kirkpatrick.  2004.  Haploid selection in animals.  Trends in Ecology and Evolution 19: 592-597.

Joseph, S.B., and M. Kirkpatrick.  2007.  The [PSI+] prion may enhance rates of adaptation in yeast.  Evolution (submitted).

Jost, M. C., D. M. Hillis, Y. Lu, J. W. Kyle, H. A. Fozzard, and H. H. Zakon. In press. Toxin-resistant sodium channels: Parallel adaptive evolution across a complete gene family. Molecular Biology and Evolution.

Kanj, Iyad A., Luay Nakhleh, and Ge Xia. 2006.  Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms.  Vol. 4112/2006, p. 299-308.

Kim, H.-G.,  D. J. Loockerman, and R. K. Jansen.  2002.  Systematic implications of ndhF sequence variation in the Mutisieae (Asteraceae).  Syst. Bot. 27: 598-609.

Kim, K.-J., K.-S. Choi, and R. K. Jansen.  2005.  Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Molecular Biology and Evolution 22: 1783-1792.

Kim, Y.-D., S.-H. Kim, and R. K. Jansen.  2004.  Phylogeny of the Berberidaceae based on sequences of the chloroplast gene ndhF.  Biochem. Syst. Ecol., 32: 291-302.

Kirkpatrick, M., and S.L. Nuismer. 2004.  Sexual selection can constrain sympatric speciation. Proceedings of the Royal Society of London B 271: 687-693.

Kirkpatrick, M., and V. Ravign. 2002.  Speciation by natural and sexual selection: Models and experiments. American Naturalist 159: S22-S35.

Kirkpatrick, M., and D.W. Hall.  2004.  Sexual selection and sex linkage. Evolution 58: 683-691.

Kirkpatrick, M.  2001.  Reinforcement during ecological speciation.  Proceedings of the Royal Society of London B 268: 1259-1263.

Kirkpatrick, M., T. Johnson, and N. Barton.  2002.  General models of multilocus evolution.  Genetics 161: 1727-1750.

Kirkpatrick, M.  2006.  Artificial selection on age-dependent traits.  Proceedings of the 7th World Congress of Genetics Applied to Livestock Production.  (Published in CD)

Kirkpatrick, M., and D.W. Hall. 2004.  Male-biased mutation, sex linkage, and the rate of adaptive evolution.  Evolution 58: 437-440.

Kirkpatrick, M, and K. Meyer.  2004.  Direct estimation of genetic principal components:  Simplified analysis of complex phenotypes.  Genetics 168: 2295-2306.

Kirkpatrick, M., and F. Rousset.  Wright meets AD:  Not all landscapes are adaptive.  Journal of Evolutionary Biology 18: 1166-1169.

Kirkpatrick, M., and N. Barton.  2006.  Chromosome inversions, local adaptation, and speciation.  Genetics.

Kirkpatrick, M., A.S. Rand, and M. Ryan.  2006.  Mate choice rules in animals.  Animal Behavior. Volume 71, Issue 5,  Pages 1215-1225.

Krumpelman, C., and J. Ghosh,  2007.  Matching and Visualization of Multiple Overlapping Clustering of Microarray Data, in Proc. 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 121-126.

Larkin, L. L., J. L. Neff, and B. B. Simpson.  2006.  Phylogeny of the Callandrena subgenus of Andrena (Hymenoptera: Andrenidae):  Discrediting monophyly with mitochondrial and nuclear DNA data.  Molecular Phylogenetics and Evolution 38: 330-343.

Lee, J., Woodward, A. W., and Chen, Z. J. (2007) Gene expression changes and early events in cotton fiber development. Annals of Botany 100:1391-1401.

Lee, H-L., R.K. Jansen, T.W. Chumley, and K-J. Kim. 2006. Apparent gene translocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Molecular Biology and Evolution.

Lee*, J.F., Hesselberth, J.R., Meyers, L.A., Ellington, A.D.  2004.  Aptamer Database. Nucleic Acids Research, 32:D95-D100. Database Issue.

Lee, J.C., Gutell R.R., and Russell R. 2006. The UAA/GAN Internal Loop Motif: A New RNA Structural Element That Forms a Cross-strand AAA stack and Long-range Tertiary Interactions. Journal of Molecular Biology. 360:978-988.

Lee, J.C. and Gutell R.R. 2004.  Diversity of Base Pair Conformations and Their Occurrence in rRNA Structure and RNA Structural Motifs. Journal of Molecular Biology   344:1225-1249.

Lee, J.,  Cannone J.J., and Gutell R.R. 2003. The LonePair Triloop: a new motif in RNA Structure. Journal of Molecular Biology.  325:65-83. 

Lee, S-B., Kaittanis, C.,J., Hostetler, C. Town, R.K. Jansen, and H. Daniell.  2006. The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms.  BMC Genomics 7: 61.

Leebens-Mack, J., L.A. Raubeson, L. Cui, J. Kuehl, M. Fourcade, T. Chumley, J.L. Boore, R.K. Jansen, and C.W. dePamphilis.  2005.  Identifying the basal angiosperms in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone.  Molecular Biology and Evolution 22: 1948-1963.

Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, Depamphilis C, Desalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. 2006. Taking the First Steps Towards a Standard for Reporting on Phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA). OMICS: A Journal of Integrative Biology10: 231-237.

Lehtinen, R M., Nussbaum, R A., Richards, C. R., Cannatella, D. C., and Miguel Vences. (2007). Mitochondrial genes reveal cryptic diversity in plant-breeding frogs from Madagascar (Anura, Mantellidae, Guibemantis). Molecular Phylogenetics and Evolution 44:1121-1229.

Lemmon*, E. M., A. R. Lemmon*, J. T. Collins, and D. C. Cannatella. (2008). A new North American chorus frog species (Amphibia: Hylidae: Pseudacris) from the south-central United States. Zootaxa 1675:1–30.

Lemmon*, E. M., A. R. Lemmon*, and D. C. Cannatella. (2007). Geological and climatic forces driving speciation in the continentally distributed trilling frogs (Pseudacris). Evolution 61(9):2086-2103.

Lemmon*, E. M., A. R. Lemmon*, J. T. Collins, J. A. Lee-Yaw, and D. C. Cannatella. (2007). Phylogeny-based delimitation of species boundaries and and contact zones in the trilling chorus frogs. Molecular Phylogenetics and Evolution 44:1068-1082.

Lemmon,* A.R., J.M. Brown, E.C. Moriarty Lemmon*, and K. Stanger-Hall.  2007.  Missing data and gaps can positively mislead Bayesian and maximum likelihood phylogenetic inference. In Prep.

Lemmon,* A., C. Smadja, and M. Kirkpatrick. 2003.  Reproductive character displacement is not the only possible outcome of reinforcement. J. Evol. Biol. 17: 177-183.

Li, Y., and C. O. Wilke.  2004.  Digital Evolution in Time-Dependent Fitness Landscapes. Artificial Life 10:123-134.

Linder, C. Randal, and Tandy Warnow.  2005.  An Overview of Phylogeny Reconstruction.  Bergey’s Manual of Systematic Bacteriology.  Springer, pp. 49-66.

Loockerman, D. L., B. L. Turner, and R. K. Jansen.  2003.  Phylogenetic relationships within the Tageteae (Asteraceae) based on nuclear ribosomal ITS and chloroplast ndhF gene sequences.  Syst. Bot. 28: 191-207.

Lopreato, G. F., Y. Lu, A. Southwell, N. Atkinson, D. M. Hillis, T. P. Wilcox, and H. H. Zakon. 2001. Evolution and divergence of sodium channel genes in vertebrates. Proc. National Academy Sciences USA 98:7588-7592.

Lydeard C., Holznagel W.E., Schnare M.N., and  Gutell R.R. 2000.    Phylogenetic Analysis of Molluscan Mitochondrial LSU rDNA Sequences and Secondary Structures.   Molecular Phylogenetics and Evolution 15:83-102.

Macke T., Ecker D., Gutell R.R., Gautheret D., Case D., Sampath R. 2001. RNAMotif - A new RNA secondary structure definition and discovery algorithm.  Nucleic Acids Research.  29:4724-4735.

Mank, J.E., D.W. Hall, M. Kirkpatrick, and J.C. Avise.  2006.  Sex chromosomes and male ornaments:  a comparative evaluation in ray-finned fishes.  Proceedings of the Royal Society of London B 273: 233-236.

Mark-Welch, D. B., M. P. Cummings, D. M. Hillis, and M. Meselson. 2004. Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families. Proc. National Academy of Sciences 101:1622-1625.

Mayberry, M. R. III and Miikkulainen, R. 2005. Broad-Coverage Parsing with Neural Networks. Neural Processing Letters 21:121-132.

Mears J.A., Sharma M.R., Gutell R.R., McCook A.S., Richardson P.E., Caulfield T.R., Agrawal R.K., and Harvey S.C. 2006. A Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome. Journal of Molecular Biology, 358:193-212.

Mears J.A., Cannone J.J., Stagg S.M., Gutell R.R., Agrawal R.K., and Harvey S.C. 2002.  Modeling a Minimal Ribosome Based on Comparative Sequence Analysis. Journal of Molecular Biology 321:215-234.

Metzker, M. L., D. P. Mindell, X.-M. Liu, R. G. Ptak, R. A. Gibbs, and D. M. Hillis. 2002. Molecular evidence of HIV-1 transmission in a criminal case. Proc. National Academy Sciences USA 99: 99:14292-14297.

Meudt, H. M. and B. B. Simpson. 2006. The biogeography of the austral, subalpine genus Ourisia (Plantaginaceae) based on molecular phylogenetic evidence: South American origin and dispersal to New Zealand and Tasmania. Biological Journal of the Linnaean Society. 87: 479-513.

Meudt, Heidi M. and Beryl Simpson. In press. Phylogeny and systematics of the genus Ourisia (Plantaginaceae): insights from morphology, and nuclear and chloroplast sequences. Ann. Missouri Bot. Gard.

Meyer, K., and M. Kirkpatrick.  2005.  Restricted maximum likelihood estimation of genetic principal components and smoothed covariance matrices.  Genetics, Selection, and Evolution 37: 1-30.

Meyer, K., and M. Kirkpatrick.  2005.  Up hill, down dale:  the quantitative genetics of curvaceous traits.  Phil. Trans. R. Soc. B 360: 1443-1455.

Meyers, L.A., Lee,* J.F., Cowperthwaite*, M., Ellington, A.D.  2003.  The robustness of naturally-and artificially-selected nucleic acid secondary structures. Journal of Molecular Evolution,

Miikkulainen, R. 2006.  Creating Intelligent Agents in Games. The Bridge, 36(4):5--13.

Moore, M. J., J. Francisco-Ortega, A. Santos-Guerra, and R. K. Jansen. 2002.  Chloroplast DNA evidence for the roles of island colonization and extinction in Tolpis (Asteraceae: Lactuceae).  Amer. J. Bot. 89: 518-526.

Moore, M. J., A. Tye, and R. K. Jansen.  2006.  Patterns of long-distance dispersal in Tiquilia subg. Tiquilia (Boraginaceae): Implications for the origins of amphitropical disjuncts and Galapogos island endemics. American Journal of Botany 93: 1163-1177.

Moore, M.J. and R. K. Jansen. 2006. The origins and biogeography of obligate gypsophily in the Chihuahuan desert plant group Tiquilia subg. Eddya (Boraginaceae). Systematic Botany.

Moore, M. L. and R. K. Jansen.  2006.  Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae).  Molecular Phylogenetics and Evolution 39: 668-687.

Moret, B., Usman Roshan, and Tandy Warnow.  2002.  Sequence-length requirements for phylogenetic methods.  Lecture notes in Computer Sciences, Springer Berlin, Volume 2452/2002m pp. 343-356.

Moret, B., Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, and Ruth Timme*. 2004. Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE Transactions on Computational Biology and Bioinformatics, Vol. 1, No. 1.

Moriarty*, E. C., and D. C. Cannatella 2004.  Phylogenetic relationships of North American chorus frogs (genus Pseudacris), from 12S and 16S mtDNA. Molecular Phylogenetics and Evolution 30(2):409-420.

Müller K.M., Ellenor D.W., Sherwood A.R., Sheath R.G., Cannone J.J., and Gutell R.R. 2005.  Evidence for Lateral Transfer of a IE Intron Between Fungal and Red Algal Small Subunit Ribosomal RNA Genes. Journal of Phycology,  41:380-390.

Müller K.M., Sherwood A.R., Pueschel C.M., Gutell R.R. and  Sheath R.G. 2002.  A proposal for a new red algal order, the Thoreales.   Journal of Phycology  38:807-820.

Mueller, U.G., N. Gerardo. 2003. Fungus-farming insects: Multiple origins and diverse evolutionary histories. Proceedings of the National Academy of Sciences 99: 15247-15249.

Mueller, M. Ryan. 2003. Fine scale genetic pattern and evidence for male-biased dispersal in the tngara frog, Physalaemus pustulosus. Molecular Ecology 12: 3325-3334.

Müller K.M., Cannone J.J., Gutell R.R., and Sheath R.G. 2001.  A Structural and Phylogenetic Analysis of the Group IC1 Introns in the Order Bangiales (Rhodophyta).  Molecular Biology and Evolution, 18:1654-1667.

Munkacsi, A., P. Villesen, U.G. Mueller, D. McLaughlin. 2004. Domestication of coral mushrooms by attine ants. Proceedings of the Royal Society of London B in press.

Nakhleh, L., and Li-San Wang.  2005. Phylogenetic Networks, Trees, and Clusters.  Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA 05). Lecture Notes in Computer Science, LNCS #3515, pp. 919-926.

Nakhleh, L., Usman Roshan, Katherine St. John, Jerry Sun, and Tandy Warnow. 2001.  Designing Fast Converging Phylogenetic Methods.  Bioinformatics, 17(90001), pp S190-S198. Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 01), Copenhagen, Denmark.

Nakhleh, L., Tandy Warnow, and C. Randal Linder.   2004.  Reconstructing Reticulate Evolution in Species -- Theory and Practice." Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), 337-346.

Nakhleh, L., Bernard M.E. Moret, Usman Rosha, Katherine St. John, Jerry Sun, and Tandy Warnow.  2002.  The Accuracy of Phylogenetic Methods for Large Datasets." Proceedings of the Seventh Pacific Symposium on Biocomputing (PSB 02), 7:211-222.

Nakhleh, L., Usman Roshan, Katherine St. John, Jerry Sun, and Tandy Warnow.  2001.  The Performance of Phylogenetic Methods on Trees of Bounded Diameter. Proceedings of the First International Workshop on Algorithms in Bioinformatics (WABI 01), Aarhus, Denmark, Lecture Notes in Computer Science (  LNCS #2149). Pages 214-226.

Nakhleh, L., Don Ringe, and Tandy Warnow.  2005.  Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages. LANGUAGE, Journal of the Linguistic Society of America. 81(2):382-420.

Nakhleh, L., Tandy Warnow, Don Ringe, and Steven N. Evans.   2005.  A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset. Transactions of the Philological Society, 3(2): 171-192.

Nakhleh, L., Tandy Warnow, C. Randal Linder, and Katherine St. John.  2005.  Reconstructing Reticulate Evolution in Species -- Theory and Practice." Journal of Computational Biology, 12(6-7), 796-811.

Nelesen*, S., K. Liu, D. Zhao, R. Linder, and T. Warnow, 2007. “The effect of the guide tree on multiple sequence alignment and subsequent phylogenetic analyses”, Proceedings of the 2008 Pacific Symposium on Biocomputing.

Nosil, P., B.J. Crespi, C.P. Sandoval, and M. Kirkpatrick.  2006.  Migration and the genetic covariance between habitat choice and performance.  American Naturalist, Vol. 167, pp. E66-E78.

Novella, I.S., D. D. Reissig, and C. O. Wilke. 2004.  Density-dependent selection in vesicular stomatitis virus. J. Virol. 78:5799–5804.

Nuismer, S.L., and M. Kirkpatrick.   2003.  Host gene flow and the coevolution of parasite range.  Evolution 57: 1746-1754.

Ofria, C., and C. O. Wilke. 2005.  Avida: Evolution experiments with self-replicating computer programs. In: A. Adamatzky and M. Komosinski, eds. Artificial Life Models in Software, Springer.

Omberg, L., G. H. Golub and O. Alter, (2007). A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies,” accepted for publication in Proc. Natl. Acad. Sci. USA.

Park, S.-J., E. Korompai., J. Francisco-Ortega, A. Santos-Guerra, and R. K. Jansen.  2001.  Phylogenetic relationships of Tolpis (Asteraceae: Lactuceae) based on ndhF sequence data.  Plt. Syst. Evol. 226: 23-33.

Pauly,* G. B., D. M. Hillis, and D. C. Cannatella. 2004. The history of a Nearctic colonization: molecular phylogenetics and biogeography of the Nearctic Toads (Bufo). Evolution 58(11):2517--2535.

Pauly,* G. B., X. E. Bernal, A. S. Rand, and M. J. Ryan. (In press) The vocal sac increases call rate in the túngara frog, Physalaemus pustulosus. Physiological and Biochemical Zoology 79 (4).

Pollock, D. D., D. J. Zwickl*, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology 51:664-671.

Prince, J. T., Carlson,* M. W, Wang, R., Lu, P., Marcotte, E. M. The need for a public proteomics repository. Nature Biotechnology 22, 471-2 (2004).

Provost, J., Kuipers, B. J. and Miikkulainen, R. 2006. Developing navigation behavior through self-organizing distinctive state abstraction. Connection Science 18:159--172.

Qui Y-L., Dombrovska O., Lee J., Li L., Whitlock B.A., Bernasconi-Quadroni F., Rest J.S.,  Davis C.C., Borsch T., Hilu K.W., Renner S.S., Soltis D.E., Soltis P.S., Zanis M.J., Cannone J.J., Gutell R.R., Powell M. Savolainen V., Chatrou L.W., and Chase M.W. 2005. Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes. International Journal of Plant Sciences, 166:815-842.

Ragan M.A., MacCallum G.S., Murphy C.A., Cannone J.J., Gutell R.R., and McGladdery S.E. 2000. Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota. Diseases of Aquatic Organisms,  42:185-190.

Rand T.G., White K., Cannone J.J., Gutell R.R., Murphy C.A., and Ragan M.A. 2000. Ichthyophonus irregularis sp. nov. from the yellowtail flounder Limanda ferruginea Storeer from the Nova Scotia shelf. Diseases of Aquatic Organisms,  41:31-36.

Raubeson. L.A. and R.K. Jansen.  2005.  Chloroplast genomes of plants.  In, Diversity and Evolution of Plants - Genotypic and Phenotypic Variation in Higher Plants (ed., R. Henry).  CABI Publishing, UK. Pp. 45-68.

Redford, M. and Miikkulainen, R. (in press).  Effects of Acquisition Rate on Emergent Structure in Phonological Development. Language.

Redford, M. A., Davis,, B. L., and Miikkulainen, R. 2004. Phonetic Variability and Prosodic Structure in Motherese: Does One Mask the Other? Infant Behavior and Development 27:477--532.

Redford, M., Chen, C-C., and Miikkulainen, R. 2001. Constrained Emergence of Universals and Variation in Syllable Systems. Language and Speech, 44:27--56.

Ron, S. R., J. C. Santos, and D. C. Cannatella. In Press. Phylogeny of the Angara frog genus Engystomops (Physalaemus pustulosus species group; Anura: Leptodactylidae). Molecular Phylogenetics and Evolution.

Ronce, O., and M. Kirkpatrick.  2001.  When sources become sinks:  migrational meltdown in heterogeneous habitats.  Evolution 55: 1520-1531.

Roshan, Usman.  2004.  Algorithmic Techniques for Improving the Speed and Accuracy of Phylogenetic Methods. Dissertation.

Roshan, U., B.M.E. Moret, T.L. Williams, and T. Warnow. 2004. Performance of supertree
methods on various dataset decompositions. In O. R. P. Bininda-Emonds, editor, Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Volume 3 of Computational Biology, pp. 301-328, Kluwer Academics, 2004 (Andreas Dress, series editor).

Roshan, U., B.M.E. Moret, T.L. Williams, and T. Warnow, 2004. Rec-I-DCM3: A fast algo-
rithmic technique for reconstructing large phylogenetic trees, Proc. IEEE Computer Society
Bioinformatics Conference (CSB) 2004, Stanford University, pp. 98-109 (2004).

Ruhlman, T., S-B. Lee, R. K. Jansen, J. B. Hostetler, L. J. Tallon, C. D. Town, and H. Daniell. 2006.  Complete chloroplast genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7: 222.

Ruths, D., L. Nakhleh.  2005.  Recombination and Phylogeny: effects and detection. Int. J. Bioinformatics Research and Applications, Vol. 1, No. 2.

Ruths, D., and Luay Nakhleh.2005.   Recomp: A Parsimony-Based Method for Detecting Recombination. Proceedings of The Fourth Asia-Pacific Bioinformatics, 15:52.

Santos, J. C., L. A. Coloma, and D. C. Cannatella.  2003.  Multiple, recurring origins of aposematism and diet specialization in poison frogs. Proceedings of the National Academy of Sciences 100 (22):12792-12797.

Saski, C., S. Lee, H. Daniell, T. Wood, J. Tomkins, H.-G. Kim, and R.K. Jansen.  2005.  Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes.  Plant Molecular Biology 59:309-322.

Schönhuth, S., I. Doadrio, O. Dominguez-Dominguez, D. M. Hillis, and R. L. Mayden. 2008. Molecular evolution of southern North American Cyprinidae (Actinopterygii), with the description of the new genus Tampichthys from central Mexico. Molecular Phylogenetics and Evolution.

Silberman, Y., Bentin, S., and Miikkulainen, R.  2007.  Semantic Boost on Episodic Associations: An Empirically Based Computational Model. Cognitive Science, Vol. 31:4, pp. 645-671.

Silberman, Y., Miikkulainen, R., and Bentin, S. (005. Associating Unseen Events: Semantically Mediated Formation of Episodic Associations. Psychological Science 16:161--166.

Simpson, B.B., L. Larkin, A. Weeks, and J. MiDill. 2006. Phylogeny and biogeography of Pomaria (Caesalpinioideae: Leguminosae). Syst. Bot. 31: 792-804.

Simpson, B. B., J. A. Tate, and A. Weeks. 2005. The biogeography of Hoffmannseggia (Leguminosae, Caesalpinioideae, Caesalpinieae): a tale of many travels.  Journal of Biogeography 32: 15-27.

Simpson, B. B., D. M. Helfgott, A. Weeks, and L. L. Larkin. 2004. Species relationships in Krameria (Krameriaceae) based on ITS sequences and morphology: Implications for character utility and biogeography. Systematic Botany 29: 97-108.

Simpson, B. B., J. A. Tate, and A. Weeks. 2004. Phylogeny and character evolution of Hoffmannseggia (Caesalpinieae: Caesalpinioideae: Leguminosae).  Systematic Botany 29: 933-946.

Simpson, B. B. L. L. Larkin, and A. Weeks. 2003. Progress towards resolving the relationships of the Caesalpinia group (Caesalpinieae: Caesalpinioideae: Fabaceae). Pp. 123-148 in B. Klitgaard  and A. Bruneau (editors).  Advances in Legume Systematics X. Higher level Systematics and Biogeography.  Royal Botanic Gardens, Kew, Richmond.

Sit, Y. F., and Miikkulainen, R. 2007.  A Computational Model of the Signals in Optical Imaging with Voltage-Sensitive Dyes. Neurocomputing 70(10--12).

Sit, Y. F., and Miikkulainen, R. 2006.  Self-Organization of Hierarchical Visual Maps with Feedback Connections. Neurocomputing 69:1309--1312.

Snir, S., T. Warnow and S. Rao, Short Quartet Puzzling: A New Quartet-based Phylogeny Reconstruction Algorithm. Journal of Computational Biology, Vol. 15, No. 1, January 2008, pp. 91-103.

Stanger-Hall, K. F., J. E. Lloyd, and D. M. Hillis. 2007. Phylogeny of North American fireflies (Coleoptera: Lampyridae): Implications for the evolution of light signals. Molecular Phylogenetics and Evolution 45:33-49.

Stanley, K., Bryant, B., and Miikkulainen, R. 2005. The NERO Real-time Video Game. IEEE Transactions on Evolutionary Computation, 9:653--668.

Stanley, K. and Miikkulainen, R. 2004. Competitive Coevolution through Evolutionary Complexification.  Journal of Artificial Intelligence Research 21:63--100.

Stanley, K. and Miikkulainen R. 2003. A Taxonomy for Artificial Embryogeny.  Artificial Life, 9:93--130.

Stanley, K. and Miikkulainen, R. 2002. Evolution of Neural Networks through Augmenting Topologies. Evolutionary Computation, 10:99--127.

Symula, R., J. S. Keogh, and D. C. Cannatella. (2008). Ancient phylogeographic divergence in southeastern Australia among populations of the widespread common froglet, Crinia signifera. In press, Molecular Phylogenetics and Evolution.

Tate, J. A., J. Fuertes A., S.J. Wagstaff, J. C. La Duke, T. A. Boda Slotta, and B. B. Simpson.  2005. Phylogenetic relationships within the Malveae (Malvaceae, subfamily Malvoideae) as inferred from ITS sequences.  American Journal of Botany. 92: 584-602.

Tate, J. A. and B. B. Simpson. 2004. Breeding system evolution in Tarasa (Malvaceae) and selection for reduced pollen grain size in the polyploid species. American Journal of Botany 91: 207-213.

Tate, J. A. and B. B. Simpson. 2003. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Syst. Bot. 28: 723-737.

Thamatrakoln, K., A.J. Alverson, and M. Hildebrand. 2006.  Comparative sequence analysis of diatom silicon transporters: towards a mechanistic model of silicon transport. Journal of Phycology, Vol. 42:4, pp. 822-834.

Timme,* Ruth E. Beryl B. Simpson, C. Randal Linder. In press. High resolution phylogeny for Helianthus (Asteraceae) using the 18S-26S ribosomal DNA external transcribed spacer. American Journal of Botany.

Timme,* R. E., J. V. Kuehl, J. L. Boore, R. K. Jansen.  2006. A comparison of the first two sequenced chloroplast genomes in Asteraceae: Lettuce and Sunflower. American Journal of Botany.

Tsitrone, A., M. Kirkpatrick, and D.A. Levin.  2003.  A model for chloroplast capture. Evolution 57: 1776-1782.

Tversky, T. and Miikkulainen, R. 2002. Modeling Directional Selectivity Using Self-Organizing Delay-Adaptation Maps. Neurocomputing 44--46:679--684.

Valsalam, V., Bednar, J. A., and Miikkulainen, R. (in press). Developing Complex Systems using Evolved Pattern Generators. IEEE Transactions on Evolutionary Computation.

Vernon D., Gutell R.R., Cannone J.J., Rumpf R.W., and Birky C.W. Jr.  2001. Accelerated Evolution of Functional Plastid rRNA and Elongation Factor Genes Due to Reduced Protein Synthetic Load After the Loss of Photosynthesis in the Chlorophyte Alga Polytoma. Molecular Biology and Evolution, 18:1810-1822.

Villesen P., U.G. Mueller, T. Schultz, A. Bouk. 2004. Evolution of ant-cultivar specialization and cultivar switching in Apterostigma fungus-growing ants. Evolution in press.

van Doorn, S., and M. Kirkpatrick.  Turnover of sex chromosomes induced by sexual conflict.  Nature (submitted).

Wang, L.-S., T. Warnow, B.M.E. Moret, and R.K. Jansen.  2006.  Distance-based genome rearrangement phylogeny.  2006.  Journal of Molecular Evolution 63 (4): 473-483.

Wang, L.-S., R, K. Jansen, B. M. E. Moret, L. A. Raubeson, and T. Warnow.  2002.  Fast phylogenetic methods for analysis of genome rearrangement data: An empirical study.   In Proc., 7th Pacific Symp. Biocomputing PSB 2002.

Wang, L.-S. and T. Warnow. “Distance-based genome rearrangement phylogeny,” 2005. In
Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford Univ. Press, pp. 353-380.

Wang, L.-S., T. Warnow, B.M.E. Moret, R.K. Jansen, and L.A. Raubeson, 2006. Distance-
based Genome Rearrangement Phylogeny. Journal of Molecular Evolution. 63(4):473-83, October 2006.

Wang, L.-S. and T. Warnow, 2006. Reconstructing Chromosomal Evolution. SIAM J. Com-
puting, Vol. 36, Issue 2, 99-131, 2006.

Warnow, T., B.M.E. Moret, and K. St. John, 2001. Absolute convergence: true trees from
short sequences, Proc. 12th Ann. Symp. Discrete Algs. (SODA 01), Washington DC, SIAM
Press, pp. 186-195.

Warnow, T. 2005. Large-scale phylogenetic reconstruction. Book chapter, in S. Aluru (edi-
tor), Handbook of Computational Biology, Chapman & Hall, CRC Computer and Information Science Series.

Warnow, T., S. N. Evans, D. Ringe, and L. Nakhleh.  2006.  A Stochastic Model of Language Evolution that Incorporates Homoplasy and Borrowing.” Book chapter in Phylogenetic methods and the prehistory of languages, pp.75-87. Edited by Peter Forster and Colin Renfrew. Edited for the Institute by Chris Scarre (Series Editor) and Dora A. Kemp (Production Editor). Publisher: McDonald Institute for Archaeological Research/University of Cambridge.

Weeks, A. and B.B. Simpson. 2006. Molecular phylogenetic analysis of Commiphora (Burseraceae) yields insight on the evolution and historical biogeography of an "impossible" genus. Molecular Phylogenetics and Evolution 42: 62-79.

Weeks, A., D. C. Daly, and B. B. Simpson. 2005. The phylogenetic history and biogeography of the frankincense and myrrh family (Burseraceae) based on nuclear and chloroplast sequence data. Molecular Phylogenetics and Evolution. 35: 85-101.

Weeks, A. and B. B. Simpson. 2004. Molecular genetic evidence for interspecific hybridization among Hispaniolan Bursera (Burseraceae).  Amer. J. Bot. 91: 976-983.

The Honey Bee Genome Sequencing Consortium: Weinstock et al. (81 authors), Gillespie J.J., Cannone J.J., Gutell R.R. , et al. (100 authors). 2006. Insights into social insects from the genome of the honey bee Apis mellifera. Nature 443:931-949.

Welch, D. B., M. P. Cummings, D. M. Hillis, and M. Meselson. 2004. Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families. Proc. National Academy of Sciences 101:1622-1625.

Whiteson, S., Kohl, N., Miikkulainen, R., and Stone, P.  2005. Evolving Keepaway Soccer Players through Task Decomposition. Machine Learning 59:5--30.

Wiens, J. J., P. T. Chippindale, and D. M. Hillis. 2003. When are phylogenetic analyses misled by convergence?  A case study in Texas cave salamanders. Systematic Biology 52:501-514.

Wilcox, T. P., García de Leon, F. J., D. A. Hendrickson, and D. M. Hillis. 2004. Convergence among cave catfishes: Long-branch attraction and a Bayesian relative rates test. Molecular Phylogenetics and Evolution 31:1101-1113.

Wilcox, T. P., D. J. Zwickl,* T. Heath,* and D. M. Hillis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution 25:361-371.

Wilke. C.O. 2006.  Biology through the robustness lens (book review). BioScience 56:695–696.

Wilke, C.O., and D. Allan Drummond. 2006.  Population genetics of translational robustness. Genetics 173:473–481.

Wilke, C.O., R. Forster, and I. S. Novella. 2006.  Quasispecies in time-dependent environments. Curr. Topics Microbiol. Immun. 299:33-50.

Wilke, C.O., J. D. Bloom, D. A. Drummond, and A. Raval. 2005.  Predicting the tolerance of proteins to random amino acid substitution. Biophys. J. 89:3714-3720.

Wilke. C.O., 2005.  Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5:44.

Wilke. C.O., 2005. The heavy, the cold and the slow. Heredity 95:115.

Wilke, C.O., and S. S. Chow.  2005.  Exploring the evolution of ecosystems with digital organisms. In: M. Pascual and J. Dunne, eds. Food Webs as Complex Adaptive Networks: Linking Structure to Dynamics, Oxford University Press.

Wilke. C.O.,  2004.  Molecular clock in neutral protein evolution. BMC Genetics 5:25.

Wilke. C.O., 2004. Supplementary materials need the right format. Nature 430:291.

Wilke. C.O., 2004.  The speed of adaptation in large asexual populations. Genetics 167:2045– 2053.

Wilke, C.O., D. D. Reissig, and I. S. Novella. 2004.  Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations. Evolution 58:900–905.

Wilsker D, Probst L, Wain HM, Maltais L, Tucker PW, Moran E.  2005.  Nomenclature of the ARID family of DNA-binding proteins.  Genomics. 86:242-51.

Wyman,* S. K., J. L. Boore, and R. K. Jansen. 2004, Automatic annotation of organellar genomes with DOGMA. Bioinformatics.

Zakon, H. H., Y. Lu, D. J. Zwickl,* and D. M. Hillis. 2006. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: Convergent molecular evolution. Proceedings of the National Academy of Sciences USA 103:3675-3680.

Zhao, Z, J. J. Skvarla, and R. K. Jansen.  2006. Mutisieae (Asteraceae) pollen ultrastructure atlas.  Lundellia 9: 51-76.

Zwickl,* D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51:588-598.

Conference Presentations:

Alter, O. (2007). Genomic Signal Processing, or Discovery of Principles of Nature From Matrix and Tensor Modeling of DNA Microarray Data, scheduled for the Summer School on Statistical Physics of Gene Regulation – From Networks to Expression Data and Back (Bremen, Germany, July 16–28, 2007), invited tutorials and computational laboratory sessions.

Alter, O. July 16-28, 2007. Integrative and Comparative Analyses of DNA Microarray Data from Different Studies of the Cell Division Cycle, Heraeus International Summer School on Statistical Physics of Gene Regulation – From Networks to Expression Data and Back (Bremen, Germany), invited tutorials and computational laboratory sessions.

Alter, O. July 16-20, 2007. Tensor Computations For Genomic Signal Processing, 6th International Congress on Industrial and Applied Mathematics (Zürich, Switzerland), invited talk.

Alter, O. April 26-28, 2007. Discovery of Principles of Nature From Matrix and Tensor Modeling of DNA Microarray Data, 2007 SIAM Conference on Data Mining (Minneapolis, Minnesota), invited talk.

Alter, O. February 22, 2007. Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data, Argonne National Laboratory and University of Chicago Symposium on Mathematics for Systems Biology (Chicago, Illinois), plenary talk.

Alter, O. (2006). Genomic Signal Processing: From Matrix and Tensor Computations to Genetic Networks, Institute for Operations Research and the Management Science Conference on Optimization and Health Care (San Antonio, Texas, February 3–5 2006), invited talk.

Brown, J. June 2007. Ambiguous sites can positively bias Bayesian phylogeny inference. Joint meetings of the American Society of Naturalists, Society for the Study of Evolution, and Society of Systematic Biologists, Christchurch, New Zealand.

Cannatella, D. June 2007. Phylogeny of Andean eleutherodactyline frogs (Eleutherodactylus and Phrynopus), and how convergent loss of characters can mislead phylogeny. (with Edgar Lehr). ASIH-SSAR-HL meetings, St. Louis, Missouri.

Cannatella, D. June 2007. The phylogenetic utility of POMC in assessing frog evolution. (with Kristin Hook) Society of Systematic Biologists, Christchurch, New Zealand.

Cannatella, D. June 2007. Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris). (with Emily C. Moriarty Lemmon) Society of Systematic Biologists, Christchurch, New Zealand.

Cannatella, D. June 2007. Climbing the tree of frogs. Society of Systematic Biologists, Christchurch, New Zealand. Filogenia das anfíbios: Avanços, questionamentos, e futuro (in Portuguese). Roundtable discussion. III Congreso Brasileira de Herpetologia. Belem, Brazil.

Cannatella, D. July 2007. Taxonomia e nomenclatura dos anfíbios (in Portuguese). Plenary lecture. III Congreso Brasileira de Herpetologia. Belem, Brazil.

Cannatella, David, Hillis, David, Wake, David. (2003). AmphibiaTree: A community based phylogeny of amphibians. Society for the Study of Evolution, Society of Systematic Biologists, Chico, California.

Heath*, T.A. and D.M. Hillis. 2007. Factors contributing to systematic biases in phylogenetic tree shape. Evolution 2007, Christchurch, New Zealand. (Oral Presentation)

Hillis, D. 2007. Workshops on Improving Biology Education Held in Denver, Colorado; Chicago, Illinois; Berkeley, California; Columbus, Ohio, and New York, New York. Making Evolution Exciting and Relevant for Biology Students.

Hillis, D. 2007. Chinese Academy of Sciences, Beijing, China Evolutionary Biology in the 21st Century-Tracing Patterns of Evolution through the Tree of Life: Keynote talk. The Importance of Dense Taxon Sampling for Improving Analyses on the Tree of Life.

Hillis, D., 2007. Symposium on Herpetology in the Age of Genomics; Society for the Study of Reptiles and Amphibians (St. Louis, MO). Biodiversity Discovery in the Age of Genomics”

Hillis, D. 2007. University of Texas Outreach Lecture Series, Sept. 14. DNA in Hollywood: Fact, Fiction, and Future.

Hillis, D. 2007. Field Museum, Chicago. Plenary Talk for Darwin Day Celebration. Applications of Evolutionary Biology.

Hillis, D. 2008. Workshops on Improving Biology Education. Held in Charleston, S.C.; St. Louis, Mo.; Montreal, Canada

Hillis, D., D. J. Zwickl* and J. Balhoff . 2006. CIPRES Annual Meeting, Austin, TXGARLI: Genetic Algorithm for Rapid Likelihood Inference.

Hillis, D., with Tracy Heath*, D.J. Zwickl*, and J. Kim . 2006. NSF IGERT Project Meeting, Arlington, VA. Large-scale macroevolution simulation of phylogenetic tree topology.

Hillis, D., with Tracy Heath*, S. Gao, D. J. Zwickl*, and J. Kim . 2006. CIPRES Symposium on Evolutionary Simulation, Philadelphia, PA. Million-taxon macroevolution simulation for phylogenetic algorithm benchmarks.

Hillis, D. 2006. National Evolutionary Synthesis Center SELECTION Working Group (Synergistic Evolutionary Learning Consortium: Evolution in Action). Effective Strategies for Teaching Evolutionary Biology.

Hillis, D. 2006. NSF Assembling the Tree of Life Project Meeting, Durham, NC.Breakout Discussion Leader: “Training: Integrating Computational Biology and Phylogenetics”

Hillis, D. 2006. Nature Conservancy Annual Meeting, Keynote Speaker, Austin, TX. The Discovery of Life on Earth.

Hillis,, D. 2006. International Society for Phylogenetic Nomenclature, New Haven, CT. Keynote Speaker. Why is taxonomy lagging behind the rest of biology in the phylogenetic revolution?

Hillis, D. 2006. American Association for the Advancement of Science, St. Louis. Addressing Computational Challenges for the Tree of Life Project.

Hillis, D. 2006. Workshops on Improving Biology Education Held in Austin, Texas and in Orlando, Florida. Making Evolution Exciting and Relevant for Biology Students.

Hillis, D. 2006: National Research Council, Workshop on Concepts in Biology Washington, D.C. Concepts in Phylogenetics and Evolutionary Theory.

Hillis, D. (2005). The Discovery of Life of Earth. Workshop on Model-Based Methods in Phylogenetics, Organizer Stellenbosch University South Africa Society for Systematic Biology, Plenary Talk.

Hillis, D. (2005). The Importance of Phylogenetics for Biology Education. Biology Leadership Conference, San Diego, California.

Hillis, D. (2005). Automated Molecular Approaches for Studying Biodiversity . Radcliffe Seminar: Solving Darwin's Mystery: The Genomics of Speciation and Modern Approaches to Biodiversity, Harvard University, Cambridge, MA.

Hillis, D. (2005). Priorities and the Future of Systematics Research. Diversitas: International Open Scientific Conference on Biodiversity, Oaxaca, Mexico. Plenary Talk.

Jost, M.C., Hillis, D., Zakon, H. (2004). From paralogs to pufferfish: Phylogeny and evolution of voltage-gated sodium channels. Society for the Study of Evolution, Society of Systematic Biologists, Ft. Collins, Colorado. 7th International Congress for Neuroethology, Denmark. Zakon,

H., Lu, Y., Zwickl, D., Hillis, D. Gene duplication, convergence, divergence, and the evolution of communication signals in electric fish.

 

Jost, M.C., Hillis, D., and Zakon, H. (2003). Phylogeny and function of sodium channel genes in teleost fishes. Society for the Study of Evolution, Society of Systematic Biologists, Chico, California.

Hillis, D., (2003). Phylogenetics and the Tree of Life . American Physical Society, DNA and Bioinfomatics,

Hillis, D., (2003). The Tree of Life and the Discovery of Life on Earth. DNA and Taxonomy, Banbury Conference, Cold Spring Harbor.

Hillis, D., (2003). Building a Biocorder of Life. TEDMED3, Phildelphia, PA.

Hillis, D. (2003). The Discovery of Life on Earth . Vanguard Conference: Where Life Meets Technology, Madrid, Spain.

Hillis, D. (2003). The Tree of Life and All-Species Initiatives. Presidential Address, Society for the Study of Evolution, Chico, California.

Hillis, D., (2002). Analysis and Visualization of Phylogenetic Tree Space . Society of Systematic Biologists and Society for the Study of Evolution, Champaign, Illinois.

Hillis, D. (2002). DNA and the History of Life. Alumni Spring Lecture, University of Kansas.

Hillis, D. (2002). Assembling the Tree of Life, American Museum of Natural History, Roundtable Discussion.

Hillis, D. (2002). The Tree of Life and Its Importance for the Discovery of Life on Earth. All Species Foundation, San Francisco, CA.

Hillis, D. (2002). Molecular Approaches to Studying Amphibian and Reptile Evolution: A Two-Decade Retrospective. Joint meeting: American Society of Ichthyologists and Herpetologists, Herpetologists' League, Society for the Study of Amphibians and Reptiles, Kansas City, MO, Symposium in Honor of Robert Jaeger.

Hillis, D. (2001). Computational Problems in Phylogenetics. Institute for Theoretical Physics, Santa Barbara.

Hillis, D. (2001). Molecular Approaches for Studying Biodiversity. All Species Foundation Symposium, Harvard University.

Hillis, D. (2001). Biology Recapitulates Phylogeny . Colloquium on Research in the Biosphere and Geosphere, Dedication of the Yale Environmental Science Center.

Dr. Risto Miikkulainen:

Reisinger, J. and Miikkulainen, R. (2007). Acquiring Evolvability through Adaptive Representations. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2007, London, UK).

Lockett, A. J., Chen, C. L., and Miikkulainen, R. (2007). Evolving Explicit Opponent Models in Game Playing. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2007, London, UK).

Bryant, B. D. and Miikkulainen, R. (2007). Acquiring Visibly Intelligent Behavior with Example-Guided Neuroevolution. In Proceedings of the Twenty-Second Conference on Advancement of Artificial Intelligence (AAAI-07, Vancouver, Canada).

Grasemann, U., Miikkulainen, R., and Hoffman R. (2007). A Subsymbolic Model of Language Pathology in Schizophrenia. In Proceedings of the 29th Annual Conference of the Cognitive Science Society (COGSCI-07, Nashville, TN). Hillsdale, NJ: Erlbaum.

Saggar, M., Markman, A. B., Maddox, W. T., and Miikkulainen, R. (2007). A Computational Model of the Motivation-Learning Interface. In Proceedings of the 29th Annual Conference of the Cognitive Science Society (COGSCI-07, Nashville, TN). Hillsdale, NJ: Erlbaum.

Andoni, S., Saggar, M., Mericli, T., and Miikkulainen, R. (2007). System Identification for the Hodgkin-Huxley Model using Artificial Neural Networks. In Proceedings of the International Joint Conference on Neural Networks (IJCNN-07, Orlando, FL).

Reisinger, J., Bahceci, E., Karpov, I., and Miikkulainen, R. (2007). Coevolving Strategies for General Game Playing. In Proceedings of the IEEE Symposium on Computational Intelligence and Games (CIG-07). Piscataway, NJ: IEEE.

Gomez, F. Schmidhuber, J., and Miikkulainen, R. (2006). Efficient Non-Linear Control through Neuroevolution. In Proceedings of the 17th European Conference on Machine Learning (ECML-06, Berlin), 654--662. Berlin: Springer.

Stanley, K. O., Bryant, B. D., Karpov, I., and Miikkulainen R. (2006). Real-Time Evolution of Neural Networks in the NERO Video Game. In Proceedings of the Twenty-First National Conference on Artificial Intelligence (AAAI-06, Boston, MA), 1671-1674.

Valsalam, V., Bednar, J. A., and Miikkulainen, R. (2006). Giving Learners a Good Bias via Development. In Proceedings of the Fifth International Conference on Development and Learning (ICDL5, Bloomington, IN).

Reisinger, J. and Miikkulainen, R. (2006). Selecting for Evolvabl Representations. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2006, Seattle, WA).

Kohl, N., Stanley, K. O., Miikkulainen, R., Samples, M., and Sherony, R. (2006). Evolving a Real-World Vehicle Warning System. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2006, Seattle, WA).

Monroy, G. A., Stanley, K. O., and Miikkulainen, R. (2006). Coevolution of Neural Networks Using a Layered Pareto Archive. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2006, Seattle, WA).

Fidelman, M., Coffman, T., Miikkulainen, R. (2006). Detecting Motion in the Environment with a Moving Quadruped Robot. In Proceedings of the RoboCup Symposium 2006.

Williams, P. and Miikkulainen, R. (2006). Grounding Language in Descriptions of Scenes. In Proceedings of the 28th Annual Conference of the Cognitive Science Society (COGSCI-06, Vancouver, Canada). Hillsdale, NJ: Erlbaum.

Kaczmarczyk, L. C., Last, M. Z., and Miikkulainen, R. (2006). The Effect of Delivery Method on Conceptual and Strategy Development. In Proceedings of the 28th Annual Conference of the Cognitive Science Society (COGSCI-06, Vancouver, Canada). Hillsdale, NJ: Erlbaum.

Bryant, B. D. and Miikkulainen R. (2006). Evolving Stochastic Bobby D. Bryant and Risto Miikkulainen (2006). Evolving Stochastic Controller Networks for Intelligent Game Agents. In Proceedings of the 2006 IEEE World Congress on Computational Intelligence (Vancouver, Canada: WCCI-2006), 3752--3759. Piscataway, NJ: IEEE.

Yong, C. H., Stanley, K. O., Miikkulainen, R., and Karpov, I. (2006). Incorporating Advice into Evolution of Neural Networks. In Proceedings of the Second Artificial Intelligence and Interactive Digital Entertainment Conference (AIIDE-2006, Marina del Rey, CA), 96--104. Menlo Park, CA: AAAI Press.

Bryant, B. D. and Miikkulainen, R. (2006). Exploiting Sensor Symmetries in Example-based Training for Intelligent Agents. In Proceedings of the IEEE Symposium on Computational Intelligence and Games (CIG-06). Piscataway, NJ: IEEE. Best Student Paper Award.

Karpov, I., D'Silva, T., Varrichio, C., Stanley, K. O., and Miikkulainen, R. (2006). Integration and Evaluation of Exploration-Based Learning in Games. In Proceedings of the IEEE Symposium on Computational Intelligence and Games (CIG-06). Piscataway, NJ: IEEE.

Fidelman, M., Hoffman, R., and Miikkulainen, R. (2005). A Subsymbolic Model of Complex Story Processing. In Proceedings of the 27th Annual Conference of the Cognitive Science Society (COGSCI-05, Stresa, Italy). Hillsdale, NJ: Erlbaum.

Valsalam, V., Bednar, J. A., and Miikkulainen, R. (2005). Constructing Good Learners using Evolved Pattern Generators. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2005, Washington, DC).

Pardoe, D., Ryoo, M., and Miikkulainen, R. (2005). Evolving Neural Network Ensembles for Control Problems. In Proceeedings of the Genetic and Evolutionary Computation Conference (GECCO-2005, Washington, DC).

Agogino, A., Tumer, K., and Miikkulainen, R. (2005). Efficient Credit Assignment through Evaluation Function Decomposition. In Proceeedings of the Genetic and Evolutionary Computation Conference (GECCO-2005, Washington, DC).

Grasemann, U. and Miikkulainen, R. (2005). Effective Image Compression using Evolved Wavelets. In Proceeedings of the Genetic and Evolutionary Computation Conference (GECCO-2005, Washington, DC).

Stanley, K., Kohl, N., Sherony, R., and Miikkulainen, R. (2005). Neuroevolution of an Automobile Crash Warning System. In Proceeedings of the Genetic and Evolutionary Computation Conference (GECCO-2005, Washington, DC). Whiteson, S., Stone, P., Stanley, K., Miikkulainen, R., Kohl, N. (2005). Automatic Feature Selection in Neuroevolution. In Proceeedings of the Genetic and

Greg Pauly*:

Pauly,* G.B., X. E. Bernal, M. J. Ryan, and A. S. Rand. (2005). The vocal sac increases call rate in the túngara frog. 2005 Texas Herpetological Society Symposium, Austin, Texas.

Pauly,* G.B., X. E. Bernal, M. J. Ryan, and A. S. Rand. (2005). The vocal sac increases call rate in the túngara frog, Physalaemus pustulosus. 2005 Annual Joint Ichthyology and Herpetology Meetings. Tampa, Florida.

Pauly,* G.B. (2002). Evolution in the genus Bufo revisited: Phylogenetic relationships of North American bufonids. Section of Integrative Biology, University of Texas, Austin, September, 2002.

Pauly,* G.B. and D. C. Cannatella. (2002). Phylogenetic relationships of North American bufonids. 2002 Annual Joint Ichthyology and Herpetology Meetings. Kansas City, Missouri.

Wagner*, J. R. 2007. Morphological variation and phylogenetic relationships in the Caiman crocodilus complex (Reptilia: Alligatoridae). pp. 134-135. In Program of the 110th Annual Meeting of the Texas Academy of Science, Waco.

Books:

Miikkulainen, R., Bednar, J. A., Choe, Y., and Sirosh, J. (2005). Computational Maps in the Visual Cortex. New York: Springer.

Book Chapters:

Alter, O. "Genomic Signal Processing: From Matrix Algebra to Genetic
Networks," in Microarray Data Analysis: Methods and Applications, edited
by M. J. Korenberg (Humana Press, Totowa, 2007) pp. 17--59.

Cannatella, D. C., and D. M. Hillis. 2004. Amphibians. Pp. 430-450 in Assembling the Tree of Life (J. Cracraft and M. J. Donoghue, editors). Oxford University Press, New York.

Hillis, D. M. 2002. Molecular systematics. Pp. 756-760 in Encyclopedia of Evolution (M. Pagel, ed.). Oxford Univ. Press, New York.

Hillis, D. M. 2005. Health applications of the Tree of Life. Pages 139-144 in Evolutionary Science and Society: Educating a New Generation (J. Cracraft and R. Bybee, eds.). Biological Sciences Curriculum Study, Colorado Springs.

Bednar, J. A., and Miikkulainen, R. (2007). Constructing Visual Function Through Prenatal and Postnatal Learning. In D. Mareschal, M. Johnson, S. Sirois, M. Spratling, M. S. C. Thomas and G.  Westermann (editors) Neuroconstructivism: How the Brain Constructs Cognition.  Oxford University Press.

Miikkulainen, R., Bryant, B. D., Cornelius, R., Karpov, I. V., Stanley, K. O., and Yong, C. H. (2006). Computational Intelligence in Games. In Yen, G. Y. and Fogel, D. B. (editors), Computational Intelligence: Principles and Practice, 155-191. IEEE Computational Intelligence Society.

Cornelius, R., Stanley, K., and Miikkulainen, R. (2006). Constructing Adaptive AI using Knowledge-Based Neuroevolution.  In Rabin, S. (editor), AI Game Programming Wisdom 3, 693--708. Revere, MA: Charles River Media.

Moriarty, D., and Miikkulainen, R. (2001). Learning Sequential Decision Tasks through Symbiotic Evolution of Neural Networks. In M. Patel, V. Honavar, and K. Balakrishnan (editors), Advances in the Evolutionary Synthesis of Intelligent Agents, 367--382 Cambridge, MA: MIT Press.

Mayberry, M. R. III, and Miikkulainen, R. (2000). Combining Maps and Distributed Representations for Shift-Reduce Parsing. In Stefan Wermter and Ron Sun (editors) Hybrid Neural Systems,144--157. Heidelberg: Springer.

Miikkulainen, R. (2000). Text and Discourse Understanding: The DISCERN System. In R. Dale, H. Moisl, and H. Somers (editors), A Handbook of Natural Language Processing: Techniques and Applications for the Processing of Language as Text, 905--919. New York: Marcel Dekker.

Awards:

Alter, Orly: Linear Algebra and its Application Lecture of the International Linear Algebra Society 6/2005.