Publications

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2011

  • Yuannian Jiao, N. J. Wickett, S. Ayyampalayam, A. S. Chanderbali, L. Landherr, P. E. Ralph, L. P. Tomsho, Y. Hu, H. Liang, P. S. Soltis, D. E. Soltis, S. W. Clifton, S. E. Schlarbaum, S. C. Schuster, H. Ma, J. Leebens-Mack, C. W. dePamphilis. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature [epub ahead of print]
  • Zuccolo, A. J.E. Bowers, J.C. Estill, Z. Xiong, M. Luo,, A. Sebastian, J.L. Goicoechea, K.Collura, Y. Yu, Y. Jiao, J. Duarte, H. Tang,, S. Ayyampalayam, S. Rounsley, D. Kudrna, A.H. Paterson,, J. C. Pires, D.E. Soltis, S. Chamala, B. Barbazuk, P.S. Soltis, V.A. Albert, H. Ma, D. Mandoli, J. Banks, J.E. Carlson, J. Tomkins, C.W. dePamphilis, R.A. Wing. J. Leebens-Mack. 2011. A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure. Provisionally Accepted: Genome Biology.

2010

  • Chanderbali AS, Yoo MJ, Zahn LM, Brockington SF, Wall PK, Gitzendanner MA, Albert VA, Leebens-Mack J, Altman NS, Ma H, dePamphilis CW, Soltis DE, Soltis PS. 2010. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22570-5.
  • Duarte, J.M., P. K. Wall, P. P. Edger, L. L. Landherr, H. Ma, J. C. Pires, J. Leebens-Mack and C. W. dePamphilis. 2010. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 10:61.
  • Yoo, M.-J., P. S. Soltis, and D. E. Soltis. 2010. Expression of floral MADS box genes in two divergent “water lilies”: Nymphaeales and Nelumbo. International J. of Plant Sciences 171: 121-146.
  • Yoo M-J, Chanderbali AS, Altman NS, Soltis PS, and Soltis DE. 2010. Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae). Plant J. 64:687-98
  • Zahn LM, Ma X, Altman NS, Zhang Q, Wall PK, Tian D, Gibas CJ, Gharaibeh R, Leebens-Mack JH, dePamphilis CW, Ma H. 2010. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biol. 2010 Oct 15;11(10):R101.
  • Zhou X, Lin Z, Ma H. 2010. Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants. Genome Biol., 11: R38.1-R38.13.

2009

  • Bliss, B.J., L. Landherr, C.W. dePamphilis, H. Ma, Y. Hu and S.N. Maximova (2009) Regeneration and plantlet development from somatic tissues of Aristolochia fimbriata. Plant Cell, Tissue and Organ Culture, 98:105-114.
  • Chanderbali A. S., V. A. Albert, J. Leebens-Mack, N. S. Altman, D. E. Soltis, and P. S. Soltis. (2009) Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae). Proceedings of the National Academy of Sciences, USA, 106: 8929-34.
  • Sankoff, D., Zheng, C., Wall, P.K., dePamphilis, C.W., Leebens-Mack, J., Albert, V.A. (2009) Towards improved reconstruction of ancestral gene order in angiosperm phylogeny. Journal of Computational Biology, 16(10):1353-1367.
  • Shan, H., Zahn, L., Guindon, S., Wall, P.K., Kong, H., Ma, H., dePamphilis, C.W., and Leebens-Mack, J. (2009) Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Molecular Biology and Evolution 10:2229-2244.
  • Altman, N. (2009) Batches and blocks, sample pools and subsamples in the design and analysis of gene expression studies. In Batch Effects and Noise in Microarray Experiments: Sources and Solutions A. Scherer, ed. John Wiley & Sons Ltd., UK.
  • Soltis, P.S., S.F. Brockington, M.-J. Yoo, A. Piedrahita, M. Latvis, M.J. Moore, A.S. Chanderbali and D.E. Soltis. (2009) Floral variation and floral genetics in basal angiosperms. American Journal of Botany, 96:110-128.
  • Soltis, D.E., V.A. Albert, J. Leebens-Mack, C.D. Bell, A. Paterson, C. Zheng, D. Sankoff, C.W. dePamphilis, P. Kerr Wall and P.S. Soltis. (2009) Polyploidy and angiosperm diversification. American Journal of Botany, 96:336-348.
  • Wall, P.K., Leebens-Mack, J.H., Chanderbali, A., Barakat, A., Wolcott, E., Liang, H., Landherr, L., Tomsho, L.P., Hu, Y., Carlson, J.E., Ma, H., Schuster, S.C., Soltis, D.E., Soltis, P.S., Altman, N., and dePamphilis, C.W. (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics, 10:347.
  • Wang, L.-S., Leebens-Mack, J., Wall, P.K., Beckmann, K., dePamphilis, C.W., and Warnow, T. (2009) The impact of multiple protein sequence alignment on phylogenetic estimation. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 01 Sept. 2009. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.68>.
  • Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. (2009) Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19(2):243-54.
  • Warner, K.A., P. J. Rudall and M. W. Frohlich. (2009) Environmental control of sepalness and petalness in perianth organs of waterlilies: a new Mosaic Theory for the evolutionary origin of a differentiated perianth. Journal of Experimental Botany, 60(12):3559-3574.
  • Zheng, C., Wall, P.K., Leebens-Mack, J., dePamphilis, C.W., Albert, V.A., and Sankoff, D. (2009) Gene loss under neighbourhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. Journal of Bioinformatics and Computational Biology, 3:499-520.

2008

  • Chanderbali, A.S., V. Albert, V.E.T.M. Ashworth, M.T. Clegg, R.E. Litz, D.E. Soltis and P.S. Soltis. (2008) Persea americana (avocado): bringing ancient flowers to fruit in the genomics era. Bioessays, 4:386-396.
  • Duarte, J.M., Wall, P.K., Zahn, L.M., Soltis, P.S., Soltis, D.E., Leebens-Mack, J.H., Carlson, J.E., Ma, H., and dePamphilis, C.W. (2008) Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis. Taxon, 57(4): 1110-1122.
  • Field, Dawn, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude dePamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank Oliver Glöckner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E Lewis, Kelvin Li, Allyson L Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson and Anil Wipat. (2008) The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26(5):541-547. Published online: 8 May 2008.
  • Hu, W., C.W. dePamphilis and H. Ma. (2008) Phylogenetic analysis of the plant-specific Zinc Finger-Homeobox and Mini Zinc Finger gene families. Journal of Integrative Plant Biology, 50 (8):1031-1045.
  • Liang, H., J.E. Carlson, J.H. Leebens-Mack, P. K. Wall, L. A. Mueller, M. Buzgo, L. L. Landherr, Y. Hu, D. S. DiLoreto, D. C. Ilut, D. Field, S. Tanksley, H. Ma, and C.W. dePamphilis. (2008) An EST Database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics and Genomes, 4:419-433.
  • Soltis, D. E., V. A. Albert, J. Leebens-Mack, J. Palmer, R. Wing, C. W. dePamphilis, H. Ma, J. E. Carlson, N. Altman, S. Kim, K. Wall, A. Zuccolo, P. Soltis. (2008) The Amborella Genome: An evolutionary reference for plant biology. Genome Biology, 9:402.
  • Wall, P.K., J. Leebens-Mack, K. Muller, D. Field, N. Altman and C.W. dePamphilis. (2008) PlantTribes: A gene and gene family resource for comparative genomics in plants. Nucleic Acids Research, 36:D970-976.
  • Warner, K.A., P.J. Rudall and M.W. Frohlich. (2008) Differentiation of perianth organs in Nymphaeales. Taxon, 57(4): 1096-1109.
  • Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CM, D'Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ Jr, Sasaki T, Souza MT Jr, Miller RN, Glaszmann JC, Town CD. (2008) Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics. 9:58.
  • Ming, R., S. Hou, Y. Feng, Q. Yu, A. Dionne-Laporte, J.H. Saw, P. Senin, W. Wang, B.V. Ly, K.L. Lewis, S.L. Salzberg, L. Feng, M.R. Jones, R.L. Skelton, J.E. Murray, C. Chen, W. Qian, J. Shen, P. Du, M. Eustice, E. Tong, H. Tang, E. Lyons, R.E. Paull, T.P. Michael, K. Wall, D.W. Rice, H. Albert, M.L. Wang, Y.J. Zhu, M. Schatz, N. Nagarajan, R.A. Acob, P. Guan, A. Blas, C.M. Wai, C.M. Ackerman, Y. Ren, C. Liu, J. Wang, J. Wang, J.K. Na, E.V. Shakirov, B. Haas, J. Thimmapuram, D. Nelson, X. Wang, J.E. Bowers, A.R. Gschwend, A.L. Delcher, R. Singh, J.Y. Suzuki, S. Tripathi, K. Neupane, H. Wei, B. Irikura, M. Paidi, N. Jiang, W. Zhang, G. Presting, A. Windsor, R. Navajas-Perez, M.J. Torres, F.A. Feltus, B. Porter, Y. Li, A.M. Burroughs, M.C. Luo, L. Liu, D.A. Christopher, S.M. Mount, P.H. Moore, T. Sugimura, J. Jiang, M.A. Schuler, V. Friedman, T. Mitchell-Olds, D.E. Shippen, C.W. dePamphilis, J.D. Palmer, M. Freeling, A.H. Paterson, D. Gonsalves, L. Wang, and M. Alam. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991- 996. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed& [space limitations did not permit most sources of support to be indicated]
  • Sankoff D., C. Zheng, P.K. Wall, C. dePamphilis, J. Leebens-Mack, and V.A. Albert (2008) Internal validation of ancestral gene order reconstruction in angiosperm phylogeny. Lecture Notes in Computer Science. 5267:252-264.
  • Chapman MA, Leebens-Mack JH, Burke JM. (2008) Positive selection and expression divergence following gene duplication in the sunflower CYCLOIDEA gene family. Mol Biol Evol. 25(7):1260-73.
     

2007

  • Barakat, A., P.K. Wall, S. DiLoretto, C.W. dePamphilis and J.E. Carlson. (2007) Conservation and divergence of microRNAs in Populus. BMC Genomics, 8:481.
  • Barakat, A., P.K. Wall, J.H. Leebens-Mack, Y.J. Wang, and C.W. dePamphilis. (2007) Large scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. The Plant Journal 51:991-1003.
  • Buzgo, M., A. S. Chanderbali, S. Kim, Z. Zheng, D. Oppenheimer, P. S. Soltis, and D. E. Soltis. (2007) Floral developmental morphology of Persea americana (avocado, Lauraceae): the oddities of male organ identity. International Journal of Plant Sciences, 168(3): 261-284.
  • Gilbert M.T., J. Binladen, W. Miller, C. Wiuf, E. Willerslev, H. Poinar, J.E. Carlson, J.H. Leebens-Mack, and S.C. Schuster. (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research, 35(1):1-10.
  • Jansen, R.K., Z. Cai, L. A. Raubeson, H. Daniell, C. W. dePamphilis, J. H. Leebens-Mack, K. F. Müller, M. Guisinger-Bellian, R. C. Haberle, A. K. Hansen, T. W. Chumley, S.-B. Lee, R. Peery, J. McNeal, J. V. Kuehl, and J. L. Boore. (2007) Analysis of 81 genes from 64 chloroplast genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences, 104(49): 19369-19374.
  • Kong, H., L. Landherr, M. Frohlich, J.H. Leebens-Mack, H. Ma, and C.W. dePamphilis. (2007) Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. The Plant Journal, 50:873-885.
  • Morris, A. B., C. D. Bell, W. S. Judd, D. E. Soltis, and P. S. Soltis. (2007) Phylogeny and divergence time estimation in Illicium with implications for New World biogeography. Systematic Botany, 32:236–249.
  • Soltis, D.E., A. Chanderbali, S. Kim, M. Buzgo, and P.S. Soltis. (2007) The ABC model and its applicability to basal angiosperms. Annals of Botany, 100: 155–163.
  • Soltis, D. E., M. A. Gitzendanner, and P. S. Soltis. (2007) 567-taxon data set for angiosperms: the challenges posed by Bayesian analyses of large data sets. International Journal of Plant Sciences, 168(2):137–157.
  • Soltis D.E., H. Ma, M.W. Frohlich, P.S. Soltis, V.A. Albert, D.G. Oppenheimer, N.S. Altman, C.W. dePamphilis and J.H. Leebens-Mack. (2007) The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends in Plant Science, 12(8):358-367. 
  • Wijeratne A.J., W. Zhang, Y. Sun, W. Liu, R. Albert, Z. Zheng, D.G. Oppenheimer, D. Zhao, and H. Ma. (2007) Differential gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networks. The Plant Journal, 52(1):14–29.
  • Soltis DE, Chanderbali AS, Kim S, Buzgo M, Soltis PS. 2007. The ABC model and its applicability to basal angiosperms. Ann Bot. 100:155-63. 

 2006

  • Altman, N. and J. Hua. (2006) Extending the loop design for two-channel microarray experiments. Genetical Research,3:153-163.
  • Altman, N., Leebens-Mack, J.H., Zahn, L., Chanderbali, A., Tian, D., Werner, L., Ma, H. and dePamphilis, C.W. (2006) Behind the scenes: planning a multispecies microarray experiment. Chance 19(3):28-39.
  • Buzgo, M., Soltis, D.E., Soltis, P.S., Ma, H., Hauser, B.A., Leebens-Mack, J.H. and Johansen, B. (2006) Perianth development in the basal monocot Triglochin maritima (Juncaginaceae). In: Monocots: comparative biology and evolution, 2 vols., Rancho Santa Ana Botanic Gardens, CA.
  • Cai, Z., C. Penaflor, J.V. Kuehl, J.H. Leebens-Mack, J.E. Carlson, C.W. dePamphilis, J.L. Boore and R.K. Jansen. (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogenetic relationships of magnoliids. BMC Evol. Biol. 6:77.
  • Carlson, J.E., Leebens-Mack, J.H., Wall, K., Zahn, L.M., Mueller, L.A., Landherr, L.L., Hu, Y., Ilut, D.C., Arrington, J.M., Choirean, S., Becker, A., Field, D., Tanksley, S.D., Ma, H. and dePamphilis, C.W. (2006) EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot. Plant Molecular Biology, 62:351-369.
  • Chanderbali, A., S. Kim, M. Buzgo, P. Zheng, D. G. Oppenheimer, D. E. Soltis, and P. S. Soltis. (2006) Genetic footprints of stamen ancestors guide perianth evolution in Persea (Lauraceae). International Journal of Plant Sciences, 167(6):1075–1089.
  • Churchman, M. L., M. L. Brown, N. K. Kirik, M. Hülskamp, D. Inzé, L. De Veylder, J. D. Walker, Z. Zheng, D. G. Oppenheimer, T. Gwin, J. Churchman, and J. C. Larkin. (2006) SIAMESE, a novel plant-specific cell cycle regulator controls endoreplication onset in Arabidopsis thaliana. Plant Cell 18(11):3145-3157.
  • Cui, L., Leebens-Mack, J.H., Wang, L-S., J. Tang, Rymarquis, L., Stern, D., and dePamphilis, C.W. (2006) Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evol. Biol. 6:13.
  • Cui, L., Veeraraghavan, N., Richter, A., Wall, K., Jansen, R. K., Leebens-Mack, J.H., Makalowska, I., and dePamphilis, C.W. (2006) ChloroplastDB: the chloroplast genome database. Nucleic Acids Research. 34: D692-D696.
  • Cui, L., Wall K., Leebens-Mack, J.H., Lindsay, B.G., D.E., Soltis, Doyle, J.J., Soltis, P.S., Carlson, J. E. Arumuganathan , K., Barakat, A., Albert, V.A., Ma, H., and dePamphilis, C.W. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Research. 16:738-749.
  • Duarte, J. M., Cui, L., Wall, K., Zhang, Q., Zhang, X., Leebens-Mack, J.H., Ma, H., Altman, N., and dePamphilis, C.W. (2006) Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol. 23:469-478.
  • Frohlich M. (2006) Recommendations and goals for evo-devo research: scenarios, genetic constraint, and developmental homeostasis. In: Monocots: comparative biology and evolution, 2 vols., Rancho Santa Ana Botanic Gardens, CA.
  • Frohlich, M. (2006) Recent developments regarding the evolutionary origin of flowers. In Developmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series Elsevier Limited, London, vol. 44, pp. 63-127.
  • Hu, W. and Ma, H. (2006) Characterization of a novel putative zinc-finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development. The Plant Journal, 45: 399-422.
  • Kim, S., Soltis, P.S., Wall, K., and Soltis, D. E. (2006) Phylogeny and domain evolution in the APETALA2-like gene family. Mol. Biol. Evol. 23:107-120.
  • Leebens-Mack, J.H., Vision, T., Brenner, E., Bowers, J.E., Cannon, S., Clement, M.J., Cunningham, C.W., dePamphilis, C.W., deSalle, R., Doyle, J.J., Eisen, J.A., Gu, X., Harshman, J., Jansen, R. K., Kellogg, E. A., Koonin, E.V., Mishler, B.D., Philippe, H., Pires, J.C., Qiu, Y-L., Rhee, S.Y., Sjölander, K., Soltis, D.E., Soltis, P.S., Stevenson, D.W., Wall, K., Warnow, T., and Zmasek, C. (2006) Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analysis (MIAPA). Omics 10(2): 231-237.
  • Leebens-Mack, J.H., Wall, K., Duarte, J., Zheng, Z., Oppenheimer, D. and dePamphilis, C.W. (2006) A genomics approach to the study of ancient polyploidy and floral developmental genetics. In Developmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series, Elsevier Limited, London, vol. 44, pp. 528-549.
  • Lindqvist, C., Scheen, A.-C., Yoo, M.-J., Grey, P., Oppenheimer, D.G., Leebens-Mack, J.H., Soltis, D.E., Soltis, P.S. and Albert, V.A. (2006) An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers. BMC Plant Biology, 6:16.
  • Ma, H. (2006) A molecular portrait of Arabidopsis meiosis. In The Arabidopsis Book. Eds. C.R. Somerville, E.M. Meyerowitz, J. Dangl, and M. Stitt, American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0095, http://www.aspb.org/publications/arabidopsis/
  • McNeal J.R., J.H. Leebens-Mack, K. Arumuganathan, J.V. Kuehl, J.L. Boore, and C.W. dePamphilis. (2006) Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques 41(1):69-73.
  • Soltis, D.E., Leebens-Mack, J.H. and Soltis, P. S. (eds.). (2006) Developmental Genetics of the Flower. Advances in Botanical Research series Elsevier Limited, London, vol. 44, 594 pp.
  • Soltis, P.S., D.E. Soltis, S. Kim, A. Chanderbali, and M. Buzgo. (2006) Expression of floral regulators in basal angiosperms and the origin and evolution of ABC-function. In Developmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series Elsevier Limited, London, vol. 44, pp. 484-506.
  • Teeri, T. H., M. Kotilainen, A. Uimari, S. Ruokolainen, Y. P. Ng, U. Malm, E. Pöllänen, S. Broholm, R. Laitinen, P. Elomaa and V. A. Albert. (2006) Floral developmental genetics of Gerbera (Asteraceae). In Developmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series Elsevier Limited, London, vol. 44, pp. 324-351.
  • Tuskan, G.A., S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R.R. Bhalerao, R.P. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G.-L. Chen, D. Cooper, P.M. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Déjardin, C. dePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jorgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J.-C. Leplé, P. Locascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D. R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C.-J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. Van de Peer, D. Rokhsar. (2006) The genome of black cottonwood, Populus trichcarpa (Torr. & Gray ex Brayshaw). Science, 313:1596-1604. Article highlighted in News of the Week by Eric Stokstad, “Poplar tree sequence yields genome double take,” Science 313:1596-1604. (JIF: 30.927)
  • Yoo M.J., Albert V.A., Soltis P.S., and Soltis D.E. (2006) Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants. BMC Plant Biol. 6:3-12
  • Zahn, L. M., Feng, B., and Ma, H. (2006) Beyond the ABC model: regulation of floral homeotic genes. In Developmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series Elsevier Limited, London, vol. 44, pp. 164-207.
  • Zahn, L.M., Leebens-Mack, J.H., Arrington, J.M., Hu, Y., Landherr, L., dePamphilis C.W., Becker, A., Theissen, G., and Ma, H. (2006) Conservation and divergence in the AGAMOUS Subfamily of MADS-Box Genes: evidence of independent sub- and neofunctionalization events. Evol. Dev. 8:30-45.

 2005

  • Albert, V. A., ed. (2005) Parsimony, Phylogeny, and Genomics. Oxford Univ. Press. Revised paperback edition published in 2006.
  • Albert, V. A. (2005) Parsimony and phylogenetics in the genomic age. Pp. 1-11 in Parsimony, Phylogeny, and Genomics, ed. V. A. Albert, Oxford Univ. Press.
  • Albert, V.A., Soltis, D.E., Carlson, J.E., Farmerie, W.G., Wall, P.K., Ilut, D.C., Solow, T.M., Mueller, L.A., Landherr, L.L., Hu,Y., Buzgo, M., Kim, S., Yoo, M.-J., Frohlich, M.W., Perl-Treves, R., Schlarbaum, S.E., Bliss, B.J., Zhang, X., Tanksley, S.D., Oppenheimer, D.G., Soltis, P.S., Ma, H., dePamphilis, C.W., and Leebens-Mack, J.H. (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol. 5(1):5.
  • Buzgo, M., Soltis, P.S., Kim, S., and Soltis, D.E. (2005) The making of a flower. Biologist. 52(3):149-154.
  • Kim, S., J. Koh, H. Ma, Y. Hu, P. Endress, B. Hauser, M. Buzgo, P.S. Soltis, and D.E. Soltis. (2005). Sequence and expression studies of A-, B-, and E-class MADS-box genes in Eupomatia (Eupomatiaceae): Support for the bracteate origin of the calyptra. International Journal of Plant Sciences, 166(2):185–198.
  • Kim, S., J. Koh , M-J.Yoo, H. Kong, Y. Hu, H. Ma, P.S. Soltis and D.E. Soltis. (2005) Expression of floral MADS-box genes in basal angiosperms: Implications for the evolution of floral regulators. The Plant Journal, 43(5):724-744.
  • Kirik, V., Lee, M.M., Wester, K., Herrmann, U., Zheng, Z., Oppenheimer, D., Schiefelbein, J. and Hülskamp, M. (2005) Functional diversification of MYB23 and GL1 genes in trichome morphogenesis and initiation. Development, 132(7):1477-1485
  • Kuhl, J.C., Havey, M.J., Martin, W.J., Cheung, F., Yuan, Q., Landherr, L., Hu, Y., Leebens-Mack, J.H., Town, C.D., and Sink, K.C. (2005) Comparative genomic analyses of in Asparagus. Genome 48(6):1052-1060.
  • Leebens-Mack, J.H., Raubeson, L.A., Cui, L., Kuehl, J.V., Fourcade, M.H., Chumley, T.W., Boore, J.L., Jansen, R.K., and dePamphilis, C.W. (2005) Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one’s way out of the Felsenstein zone. Mol. Biol. Evol. 22(10):1948-1963.
  • Leebens-Mack, J.H., Soltis, D.E., and Soltis, P.S. (2005) Plant reproductive genomics at the Plant and Animal Genome Conference. Comp. Funct. Genomics 6: 159–169.
  • Ma, H. (2005) Molecular genetic analysis of microsporogenesis and microgametogenesis. 2005. Annu. Rev. Plant Biol. 56: 393-434.
  • Park, S.O., Zheng, Z., Oppenheimer, D.G., and Hauser, B.A. (2005) The PRETTY FEW SEEDS 2 gene encodes an Arabidopsis homeodomain protein that regulates ovule development. Development 132(4):841-849.
  • Soltis, D. E., Albert, V. A., Kim, S., Yoo, M.-J. Soltis, P. S., Frohlich, M. W., Leebens-Mack, J.H., Kong, H., Wall, K., dePamphilis, C.W. and Ma, H. (2005) Evolution of the Flower. In R. Henry (ed.) Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants, CABI Publishers, pp.165-199.
  • Soltis, D. E., Soltis, P. S., Endress, P.K. and Chase, M. W. (2005) Phylogeny and Evolution of Angiosperms. Sinauer Associates, Sunderland, MA.
  • Wang, J., B.G. Lindsay, L. Cui, P.K. Wall, J. Marion, J. Zhang, and dePamphilis, C. W. (2005) Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. BMC Bioinf. 6:300.
  • Yoo, M., Bell, C. D., Soltis, P. S., and Soltis, D. E. (2005) Divergence times and historical biogeography in Nymphaeales. Sys. Bot. 30: 693-704.
  • Zahn, L.M., Kong, H., Leebens-Mack, J.H., Kim, S., Soltis, P.S., Landherr, L.L., Soltis, D.E., dePamphilis, C. W., and Ma, H. (2005) The evolution of the SEPALLATA subfamily of MADS-box genes: A pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics 169(4):2209-2223.
  • Zahn, L. M., Leebens-Mack, J.H., dePamphilis, C. W., Ma, H., and Theissen, G. (2005) To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. J. Hered. 96(3):225-240.
  • Zhang, X., Feng, B., Zhang, Q., Zhang, D., Altman, N., and Ma, H. (2005) Genome-wide expression profiling and identification of gene activities during early flower development in Arabidopsis. Plant Mol. Biol. 58: 401-419. 

2004

  • Buzgo, M., Soltis, D. E., Soltis, P. S., and Ma, H. (2004) Towards a comprehensive integration of morphological and genetic studies of floral development. Trends Plant Sci. 9: 164-173.
  • Buzgo, M., Soltis, P. S., and Soltis, D. E. (2004) Floral developmental morphology of Amborella trichopoda (Amborellaceae). Intl. J. Plant Sci., 165: 925-947.
  • Jobson R.W., Nielsen R., Laakkonen L., Wikstrom M., and Albert V.A. (2004) Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation. Proc. Natl. Acad. Sci. U.S.A., 101(52):18064-18068.
  • Kim, S, Yoo, M-J., Albert, V. A., Farris, J. S., Soltis, P. S., and Soltis, D. E. (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Am. J. Bot. 91:2102-2118.
  • Kong, H.-Z., Leebens-Mack, J.H. Ni, W., dePamphilis, C. W., and Ma, H. (2004) Highly heterogeneous rates of evolution in the SKP1 gene family in animals and plants: functional and evolutionary implications. Mol. Biol. Evol. 21:117-128.
  • Soltis, D. E. and Soltis, P. S. (2004) Amborella not a basal angiosperm? Not so fast. Am. J. Bot. 91: 997-1001.
  • Soltis, P. S. and Soltis, D. E. (2004) Origin and diversification of angiosperms. Am. J. Bot. 91: 1614-1626.
  • Soltis, P. S., Soltis, D. E., Chase, M. W., Endress, P. K., and Crane, P. R. (2004) The diversification of flowering plants. In Assembling the Tree of Life (J. Cracraft and M. Donoghue, eds.). pp. 154-167. Oxford University Press, New York.
  • Uimari, A., Kotilainen, M., Elomaa, P., Yu, D., Albert, V.A., and Teeri, T.H. (2004) Integration of reproductive meristem fates by a SEPALLATA-like MADS-box gene. Proc. Natl. Acad. Sci. U.S.A., 101(44):15817-22.
  • Wang, G., Kong, H., Sun, Y., Zhang, X., Zhang, W., Altman, N., dePamphilis, C. W., and Ma, H. (2004) Genome-wide analysis of cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiology, 135:1084–1099.
  • Wang, J-P.Z. Lindsay, B.G., Leebens-Mack, J, Cui, L., Wall, K, Miller, W.C. and dePamphilis, C.W. (2004) EST clustering error evaluation and correction. Bioinfomatics 20:2973-84.

2003

  • Albert, V. A. (2003) Genetics of flower morphology. In Yearbook of Science and Technology McGraw-Hill. Pp. 151-153.
  • Elomaa, P., Uimari, A., Mehto, M., Albert, V. A., Laitinen, R. A. E., and Teeri, T. H. (2003) Activation of anthocyanin biosynthesis in Gerbera hybrida (Asteraceae) suggests conserved protein-protein and protein-promoter interactions between the anciently diverged monocots and eudicots. Plant Physiol. 133: 1831-1842.
  • Frohlich, M.W. (2003) An evolutionary scenario for the origin of flowers. Nat. Rev. Genet. 4:559-556.
  • Hu, W., Wang, Y., Bowers, C., and Ma, H. (2003) Isolation, sequence analysis, and expression studies of florally expressed genes in Arabidopsis. Plant Mol. Biol. 53: 545-563.
  • Ronse de Craene, L., Soltis, D. E., and Soltis P.S. (2003) Evolution of floral structures in basal angiosperms. Intl. J. Plant Sci. 164: S329-363.
  • Soltis, D.E., Fishbein, M., and Kuzoff R. K. (2003) Reevaluating the evolution of epigyny: data from phylogenetics and floral ontogeny. Intl. J. Plant Sci. 164: S251-S264.
  • Soltis, D. E. and Soltis, P. S. (2003) The role of phylogenetics in comparative genetics. Plant Physiol. 132: 1790-1800.
  • Soltis, P. S. and Soltis, D.E. (2003) Applying the bootstrap in phylogeny reconstruction. Statist. Sci. 18: 1-12. 

2002

  • Albert, V.A., Oppenheimer, D.G. and Lindqvist, C. (2002) Pleiotropy, redundancy, and the evolution of flowers. Trends Plant Sci. 7: 297-300.
  • Jobson, R. W., and Albert, V.A. (2002) Molecular rates parallel diversification contrasts between carnivorous plant sister lineages. Cladistics 18: 127-136.
  • Soltis, D. E., Soltis, P. S., Albert, V. A., Oppenheimer, D. G., dePamphilis, C.W., Ma, H., Frohlich, M. W. and Theissen, G. (2002) Missing links: the genetic architecture of flower and floral diversification. Trends Plant Sci. 7:22-31.