Papers
(You can also search PubMed or Google Scholar for C.W. dePamphilis papers.)
2022
Bellis, E.S., C.S. von Munchow, A. Kronberer, C.O. Odero, E.A. Kelly, T. Xia, X. Huang, S. Wicke, S.M. Runo, C.W. dePamphilis, J.R. Lasky. Genomic signatures of host-specific selection in a parasitic plant. bioRxiv June 23, 2022. doi: https://doi.org/10.1101/2022.02.01.478712. Link to Article 
Garrett, P., H. Becher, G. Gussarova, C.W. dePamphilis, R.W. Ness, S. Gopalakrishnan, and A.D. Twyford. Pervasive phylogenomic incongruence underlies evolutionary relationships in Eyebrights (Euphrasia, Orobanchaceae). Frontiers in Plant Science May 2022; 13, doi: 10.3389/fpls.2022.869583 Link to Article
2021
Bellis, E.S., C. McLaughlin, C.W. dePamphilis, and J.R. Lasky. The geography of parasite local adaptation to host communities. Ecography August 2021, 44(8). [First appeared at Authorea 11 Sept. 2020, DOI: 10.22541/au.159985357.77273677/v2] Link to Article
Honaas, L., H. Hargarten, J. Hadish, S.P. Ficklin, S. Serra, S. Musacchi, E. Wafula, J. Mattheis, C.W. dePamphilis, and D. Rudell. Transcriptomics of differential ripening in ‘d’Anjou’ pear (Pyrus communis L.). Frontiers in Plant Science June 2021, DOI: https://doi.org/10.3389/fpls.2021.609684. Link to Article
Hamala, T., E.K. Wafula, M.J. Guiltinan, P.E. Ralph, C.W. dePamphilis, and P. Tiffin. Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree. Proceedings of the National Academy of Sciences August 31, 2021; 118 (35) e2102914118; doi: https://doi.org/10.1073/pnas.2102914118. Link to Article
Qin, L.Y., Y.H. Hu, J.P. Wang, X.L. Wang, R. Zhao, H.Y. Shan, K.P. Li, P. Xu, H.Y. Wu, X.Q. Yan, L. Liu, X. Yi, S. Wanke, J.E. Bowers, J.H. Leebens-Mack, C.W. dePamphilis, P.S. Soltis, D.E. Soltis, H. Kong, and Y. Jiao. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. Nature Plants September 2021; 7(9):1239-1253. doi: 10.1038/s41477-021-00990-2. 
Zhang, H., E.K. WAfula, J. Eilers, A.E. Harkess, P.E. Ralph, P.R. Timilsena, C.W. dePamphilis, J.M. Waite, and L.A. Honaas. Towards a catalog of pome tree architecture genes: the draft ‘d’Anjou’ genome (Pyrus communis L.). bioRxiv 19 November 2021, doi: https://doi.org/10.1101/2021.11.17.467977 Link to Article
2020
Bellis, E.S., E.A. Kelly, C.M. Lorts, H. Gao, V.L. DeLeo, G. Rouhan, A. Budden, G.B. Bhaskara, Z. Hu, R. Muscarella, M.P. Timko, B. Nebie, S.M. Runo, N.D. Chilcoat, T.E. Juenger, G.P. Morris, C.W. dePamphilis, and J.R. Lasky. Genomics of sorghum local adaptation to a parasitic plant. Proceedings of the National Academy of Sciences 2020 Feb 25;117(8):4243-4251. https://doi.org/10.1073/pnas.1908707117.
Ali, R., Y. Jiao, P.K. Wall, S.G. Patching, I. Ahmad, G. Lutfulla, and C.W. dePamphilis. In silico identification and structure function analysis of a putative coclaurine N-methyltransferase from Aristolochia fimbriata. Computational Biology and Chemistry 85 (2020) 107201. https://doi.org/10.1016/j.compbiolchem.2020.107201. Link to Article
Fister, A.S., M.E. Leandro-Muñoz, D. Zhang, J.H. Marden, P. Tiffin, C.W. dePamphilis, S. Maximova, and M.J. Guiltinan. Widely distributed variation in tolerance to Phytophthora palmivora in four genetic groups of cacao. Tree Genetics & Genomes 2020, 16:1, doi.org/10.1007/s11295-019-1396-8. Link to Article
Jin, J-J., W.B. Yu, J.B. Yang, Y. Song, C.W. dePamphilis, T-S. Yi and D-Z. Li GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 2020 (21):241. https://doi.org/10.1186/s13059-020-02154-5. [first appeared online at bioRxiv Oct. 2019] Link to Article
Kafer, J., A. Bewick, A. Andres-Robin, G. Lapetoule, A. Harkess, J. Caius, B. Fogliani, G. Gateble, P. Ralph, C.W. dePamphilis, F. Picard, C.P. Scutt, J. Leebens-Mack, G.A.B. Marais. A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants. bioRxiv posted 22 Dec 2020 (not peer reviewed), doi.org/10.1101/2020.12.21.423833. Link to Article
2019
Clermont, K., Y. Wang, S. Liu, Z. Yang, C.W. dePamphilis, J.I. Yoder, E. Collakova, and J.H. Westwood. Comparative metabolomics of early development of the parasitic plants Phelipanche aegyptiaca and Triphysaria versicolor. Metabolites 2019 Jun 13;9(6).
Hamala, T., M.J. Guiltinan, J.H. Marden, J.H., S.N. Maximova, C.W. dePamphilis and P. Tiffin. Gene expression modularity reveals footprints of polygenic adaptation in Theobroma cacao. Molecular Biology and Evolution 2019 Sep 10. pii: msz206. doi: 10.1093/molbev/msz206. [Epub ahead of print].
Honaas, L.A., H.L. Hargerten, S.P. Ficklin, J.A. Hadish, E. Wafula, C.W. dePamphilis, J.P. Mattheis, and D.R. Rudell. Co-expression networks provide insights into molecular mechanisms of postharvest temperature modulation of apple fruit to reduce superficial scald. Postharvest Biology and Technology 2019 (149):27-41.
Honass, L.A., S. Jones, N. Farrell, W. Kamerow, H. Zhang, K. Vescio, N.S. Altman, J.I. Yoder, and C.W. dePamphilis. Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor. BMC Plant Biology 2019, 19:334. Link to Article
Johnson, N.R., C.W. dePamphilis, and M.J. Axtell. Compensatory sequence variation between trans-specific small RNAs and their target sites. Posted online at bioRxiv June 19, 2019. doi: https://doi.org/10.1101/675900 (Not peer reviewed.)
Lopez, L., E. Bellis, E. Wafula, S.J. Hearne, L. Honaas, P.E. Ralph, M.P. Timko, N. Unachukwu, C.W. dePamphilis, and J.R. Lasky. Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica). Weed Science Accepted 13 April 2019. doi: 10.1017/wsc.2019.20.
Misra, V., E.K. Wafula, Y. Wang, C.W. dePamphilis, and M.P. Timko. Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism. BMC Plant Biology 2019, 19:196. Link to Article
One Thousand Plant Transcriptomes Initiative (C.W. dePamphilis, co-author and lead of Penn State effort). One thousand plant transcriptomes and the phylogenomics of green plants. Nature Published online 23 Oct. 2019. doi: 10.1038/s41586-019-1693-2.
Su, H-J., T.J. Barkman, H. Weilong, S.S. Jones, J. Naumann, E. Skippington, E.K. Wafula, J-M. Hu, J.D. Palmer, and C.W. dePamphilis. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proceedings of the National Academy of Sciences 2019 Jan 15;116(3):934-943. doi: 10.1073/pnas.1816822116.
Su, C., H. Liu, E.K. Wafula, E.K., L. Honaas, C.W. dePamphilis and M.P. Timko. SHR4z, a novel decoy effector from the haustorium of the parasitic weed Striga gesneriodies, suppresses host plant immunity. New Phytologist 2019 Dec 1. doi: 10.1111/nph.16351. [Epub ahead of print].
Yang, Z., E.K. Wafula, G. Kim, S. Shahid, J.R. McNeal, P.E. Ralph, P.R. Timilsena, W-B. Yu, E.A. Kelly, H. Zhang, T.N. Person, N.S. Altman, M.J. Axtell, J.H. Westwood, and C.W. dePamphilis. Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants. Nature Plants Epub ahead of print 22 July, 2019. doi: 10.1038/s41477-019-0458-0.
Yoshida,S., S. Kim, E.K. Wafula, J. Tanskanen, Y.-M. Kim, L. Honaas, Z. Yang, T. Spallek, C.E. Conn, Y. Ichihashi, K. Cheong, S. Cui, J.P. Der, H. Gundlach, Y. Jiao, C. Hori, J.K. Ishida, H. Kasahara, T. Kiba, M.-S. Kim, N. Koo, A. Laohavisit, Y.-H. Lee, S. Lumba, P. McCourt, J.C. Mortimer, J.M. Mutuku, T. Nomura, Y. Sasaki-Sekimoto, Y. Seto, Y. Wang, T. Wakatake, H. Sakakibara, T. Demura, S. Yamaguchi, K. Yoneyama, R. Manabe, D.C. Nelson, A.H. Schulman, M.P. Timko, C.W. dePamphilis, D. Choi, and Ken Shirasu. Genome sequence of Striga asiatica provides insight into the evolution of plant parasitism. Current Biology 29, 1-12, Sept. 23 2019. Link to Article
2018
Givinish, T.J., A. Zuluaga, D. Spalink, M.S. Gomez, V.K.Y. Lam, J.M. Saarela, C. Sass, W.J.D. Iles, D.J.L. de Sousa, J. Leebens-Mack, J.C. Piers, W.B. Zomlefer, M.A. Gandolfo, J.I. Davis, D.W. Stevenson, C.W. dePamphilis, C.D. Specht, S.W. Graham, C.F. Barrett, and C. Ane. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. American Journal of Botany 2018, 105(11):1888-1910.
Lane, A., M.M. Augustin, S. Ayyampalayam, A. Plant, S. Gleissberg, V.S. Di Stilio, C.W. dePamphilis, G.K-S. Wong, T.M. Kutchan, and J.H. Leebens-Mack. Phylogenomic analysis of Ranunculales resolves branching events across the order. Botanical Journal of the Linnean Society 2018, XX, 1-10.
Li, F.W., P. Brouwer, L. Carretero-Paulet, S. Cheng, J. de Vries, P.M. Delaux, A. Eily, N. Koppers, L.Y. Kuo, Z. Li, M. Simenc, I. Small, E. Wafula, S. Angarita, M.S. Barker, A. Brautigam, C. dePamphilis, S. Gould, P.S. Hosmani, Y.M. Huang, B. Huettel, Y. Kato, X. Liu, S. Maere, R. McDowell, L.A. Mueller, K.G.J. Nierop, S.A. Rensing, T. Robison, C.J. Rothfels, E.M. Sigel, Y. Song, P.R. Timilsena, Y. Van de Peer, H. Wang, P.K.I. Wilhelmsson, P.G. Wolf, X. Xu, J.P. Der, H. Schluepmann, G.K. Wong, and K.M. Pryer. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants 2018, Jul;4(7):460-472.
Shahid, S., G. Kim, N.R. Johnson, E. Wafula, F. Wang, C. Coruh, V. Bernal, C.W. dePamphilis, J.H. Westwood, and M.J. Axtell. MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature 2018 Jan 3;553(7686):82-85.
Yu, W-B., C.P. Randle, L. Lu, H. Wang, J-B. Yang, C.W. dePamphilis, R.T. Cortlett, and D-Z. Li. The hemiparasitic plant Phtheirospermum (Orobanchaceae) is polyphyletic and contains cryptic species in the Hengduan Mountains of southwest China. Frontiers in Plant Science 2018 Feb 9;9:142.
2017
Caraballo-Ortiz, M.A., A. Gonzalez-Castro, S. Yang, C.W. dePamphilis, and T.A. Carlo. Dissecting the contributions of dispersal and host properties to the local abundance of a tropical mistletoe. Journal of Ecology 2017, 105, 1657-1667.
Clawson, G.A., G.L. Matters, P. Xin, C. McGovern, E. Wafula, C.W. DEPAMPHILIS, M. Meckley, J. Wong, L. Stewart, C. D'Jamoos, N. Altman, Y. Imamura Kawasawa, Z. Du, L. Honaas, and T. Abraham. "Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma. PLoSOne 2017, Sep 28;12(9). Link to Article
Lin, C.S., J.J.W. Chen, C.C. Chui, H.C.W. Hsiao, C.J. Yang, X.H. Jin, J. Leebens-Mack, C.W. dePamphilis, Y.T. Huang, L.H. Yang, W.J. Chang, L. Kui, G.K. Wong, J.M. Hu, W. Wang, and M.C. Shih. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. Plant Journal 2017, Jun;90(5):994-1006.
Marden, J.H., S.A. Mangan, M.P. Peterson, E. Wafula, H.W. Fescemyer, J.P. Der, C.W. dePamphilis, and L.S Comita. Ecological genomics of tropical trees: how local population size and allelic diversity of resistance genes relate to immune responses, cosusceptibility to pathogens, and negative density dependence. Molecular Ecology 2017, May;26(9):2498-2513.
2016
Honaas, L.A., E.K. Wafula, N.J. Wickett, J.P. Der, Y. Zhang, P.P. Edger, N.S. Altman, J.C. Pires, J.H. Leebens-Mack, and C.W. dePamphilis. Selecting superior de novo transcriptome assemblies: Lessons learned by leveraging the best plant genome. PLoS One 2016, Jan 5;11(1):e0146062. Link to Article
Ishida J.K., T. Wakatake, S. Yoshida, Y. Takebayashi, H. Kasahara, E. Wafula, C.W. dePamphilis, S. Namba, and K. Shirasu. Local auxin biosynthesis mediated by a YUCCA flavin monooxygenase regulates haustorium development in the parasitic plant Phtheirospermum japonicum. The Plant Cell 2016, Aug; 28(8):1795-1814.
McKain, M.R., H. Tang, J.R. McNeal, S. Ayyampalayam, J.I. Davis, C.W. dePampilis, T.J. Givnish, J.C. Pires, D.W. Stevenson, and J.H. Leebens-Mack. A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales. Genome Biology and Evolution 2016, Apr 21;8(4):1150-64. Link to Article
Naumann, J., J.P. Der, E.K. Wafula, S.S. Jones, S.T. Wagner, L.A. Honaas, P.E. Ralph, J.F. Bolin, E. Maass, C. Neinhuis, C. Neinhuis, S. Wanke, and C.W. dePamphilis. Detecting and characterizing the highly divergent plastid genome of the nonphotosynthetic parasitic plant Hydnora visseri (Hydnoraceae). Genome Biology and Evolution 2016, 8(2):345-363. Link to Article
Wicke, S., K.F. Mueller, C.W. dePamphilis, D. Quandt, S. Bellot, and G.M. Schneeweiss. Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants. Proceedings of the National Academy of Sciences, U.S.A. 2016, Aug. 9;113(32):9045-9050.
Yang, Z., Y. Zhang, E.K. Wafula, L.A. Honaas, P.E. Ralph, S. Jones, C.R. Clarke, S. Liu, C. Su, H. Zhang, N.S. Altman, S.C. Schuster, M.P. Timko, J.I. Yoder, J.H. Westwood, and C.W. dePamphilis. Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation Proceedings of the National Academy of Sciences 2016, 13(45):E7010-E7019.
2015
Das, M., M. Fernandez-Aparicio, Z. Yang, K. Huang, N.J. Wickett, S. Alford, E.K. Wafula, C.W. dePamphilis,
H. Bouwmeester, M.P. Timko, J.I. Yoder, and J.H. Westwood. Parasitic plants Striga and Phelipanche dependent upon exogenous strigolactones for germination have retained genes for strigolactone biosynthesis.American Journal of Plant Sciences 2015, 6, 1151-1166.
Edger, P.P., H.M. Heidel-Fischer, M. Bekaert, J. Rota, G. Glöckner, A.E. Platts, D.G. Henkel, J.P. Der, E.K. Wafula, M. Tang, J.A. Hofberger, A. Smithson, J.C. Hall, M. Blanchette, T.E. Bureau, S.I. Wright, C.W. dePampilis, M.E. Schranz, M.S. Barker, G.C. Conant, N. Wahlberg, H. Vogel, J.C. Pires, and C.W. Wheat. The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences 2015, 112(27):8362-6.
Honaas, L.A., M. Caraballo-Ortiz, J.R. McNeal and C.W. dePamphilis. Cultivation of parasitic flower plants for research and teaching.AERGC Newsletter Spring 2015, vol. 27, no. 1.
Rothfels, C.J., F.W. Li, E.M. Sigel, L. Huiet, A. Larsson, D.O. Burge, M. Ruhsam, M. Deyholos, D.E. Soltis, C.N. Stewart, Jr., S.W. Shaw, L. Pokorny, T. Chen, C. dePampilis, L. DeGironimo, L. Chen, X. Wei, X. Sun, P. Korall, D.W. Stevenson, S.W. Graham, G.K. Wong, and K.M. Pryer. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. American Journal of Botany 2015, Jul;102(7):1089-107.
Yang, Z., E.K. Wafula, L.A. Honaas, H. Zhang, M. Das, M. Fernandez-Aparicio, K. Huang, P.C. Bandaranayake, B. Wu, J.P. Der, C.R. Clarke, P.E. Ralph, L. Landherr, N.S. Altman, M.P. Timko, J.I. Yoder, J.H. Westwood, and C.W. dePamphilis. Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. Molecular Biology & Evolution 2015 Mar 32(3):767-90 [2014, Dec. 21 Epub ahead of print].
2014
Kim, G., M.L. LeBlanc, E.K. Wafula, C.W. dePamphilis, and J.H. Westwood. Genomic-scale exchange of mRNA between a parasitic plant and its host. Science 2014 Aug 15;345(6198):808-811.
Matasci, N., H.L-H. Hung, Z. Yan, E.J. Carpenter, N.J. Wickett, S. Mirarab, N. Nguyen, T. Warnow, S. Ayyampalayam, M. Barker, J.G. Burleigh, M.A. Gitzendanner, E. Wafula, J.P. Der, C.W. DEPAMPHILIS, B. Roure, H. Philippe, B.R. Ruhfel, N.W. Miles, S.W. Graham, S. Mathews, B. Burek, M. Melkonian, D.E. Soltis, P.S. Soltis, C. Rothfels, L. Pokorny, J.A. Shaw, L. DeGironimo, D.W. Stevenson, J.C. Villarreal, T. Chen, T.M. Kutchan, M. Rolf, R.S. Baucom, M.K. Deyholos, R. Samudrala, Z. Tian, X. Wu, X. Sun, Y. Zhang, J. Wang, J. Leebens-Mack, and G.K-S. Wong. Data access for the 1,000 Plants (1KP) project. GigaScience 2014, 3:17.
McCarthy, T.W., J.P. Der, L.A. Honaas, C.W. dePamphilis, and C.T. Anderson. Phylogenetic analysis of pectin-related gene families in Physcomitrella patens and nine other plant species yields evolutionary insights into cell walls. BMC Plant Biology 2014, Mar 26;14;79. Link to Article
Wicke, S., B. Schaferhoff, C.W. dePamphilis, and K.F. Muller. Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae. Molecular Biology & Evolution 2014, Mar 31(3):529-45.
Wickett, N.J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, M.S. Barker, J.G. Burleigh, M.A. Gitzendanner, B.R. Ruhfel, E. Wafula, J.P. Der, S.W. Graham, S. Mathews, M. Melkonian, D.E. Soltis, P.S. Soltis, N.W. Miles, C.J. Rothfels, L. Pokorny, A.J. Shaw, L. DeGironimo, D.W. Stevenson, B. Surek, J.C. Villarreal, B. Roure, H. Philippe, C.W. dePamphilis, T. Chen, M.K. Deyholos, R.S. Baucom, T.M. Kutchan, M.M. Augustin, J. Wang, Y. Zhang, Z. Tian, Z. Yan, X. Wu, X. Sun, G.K. Wong, J. Leebens-Mack. Phylotranscriptomic analysis of the origin and early diversification of land plants. PNAS 2014, Nov 11;111(45):E4859-68.
Williams, J.S., J.P. Der, C.W. dePamphilis, and T. H. Kao. Transcriptome analysis reveals the same 17 S-locus F-Box genes in two haplotypes of the self-incompatibility locus of Petunia inflata. Plant Cell 2014 vol. 26 (7):2873-88.
2013
The Amborella Genome Project. The Amborella genome and the evolution of flowering plants. Science 2013, 342:1467.
Bliss, B.J., S. Wanke, A. Barakat, S. Ayyampalayam, N. Wickett, P.K. Wall, Y. Jiao, L. Landherr, P.E. Ralph, Y. Hu, C. Neinhuis, J. Leebens-Mack, K. Arumuganathan, S.W. Clifton, S.N. Maximova, H. Ma, and C.W. dePamphilis. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies. BMC Plant Biology 2013, 13:13. Link to Article
Chamala, S., A.S. Chanderbali, J.P. Der, T. Lan, B. Walts, V.A. Albert, C.W. dePamphilis, J. Leebens-Mack, S. Roundsley, S.C. Schuster, R.A. Wing, N. Xiao, R. Moore, P.S. Soltis, D.E. Soltis, W.B. Barbazuk. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science 2013, 342:1516.
Fernandez-Aparicio, M.K. Huang, E.K. Wafula, L.A. Honaas, N.J. Wickett, M.P. Timko, C.W. dePamphilis, J.I. Yoder, and J.H. Westwood. Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values during Striga hermonthica development. Molecular Biology Reports 2013, 40(4):3395-3407.
Honaas, L.A., E.K. Wafula, Z. Yang, J.P. Der, N.J. Wickett, N.S. Altman, C.G. Taylor, J.I. Yoder, M.P. Timko, J.H. Westwood, C.W. dePamphilis. Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression BMC Plant Biology 2013, 13:9. Link to Article
Ming, Ray, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C. Schatz, Michael Campbell, Jingping Li, John E. Bowers, Haibao Tang, Eric Lyons, Ann A. Ferguson, Giuseppe Narzisi, David R. Nelson, Crysten E. Blaby-Haas, Andrea R. Gschwend, Yuannian Jiao, Joshua P. Der, Fanchang Zeng, Jennifer Ha, Xiangjia Min, Karen A. Hudson, Ratnesh Singh, Aleel K.Grennan, Steven J. Karpowicz, Jennifer R. Watling, Kikukatsu Ito, Sharon A. Robinson, Matthew E. Hudson, Qingyi Yu, Todd C. Mockler, Andrew Carroll, Yun Zheng, Ramanjulu Sunkar, Ruizong Jia, Nancy Chen, Jie Arro, Ching Man Wai, Eric Wafula, Ashley Spence, Yanni Han, Liming Xu, Jisen Zhang, Rhiannon Peery, Miranda J. Haus, Wenwei Xiong, James A. Walsh, Jun Wu, Ming-Li Wang, Yun J. Zhu, Robert E. Paull, Anne B. Britt, Chunguang Du, Stephen R. Downie, Mary A. Schuler, Todd P. Michael, Steve P. Long, Donald R. Ort, J. William Schopf, David R. Gang, Ning Jiang, Mark Yandell, Claude W. dePamphilis, Sabeeha S. Merchant, Andrew H. Paterson, Bob B. Buchanan, Shaohua Li, Jane Shen-Miller. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology 2013 May 10, 14(5):R41.
Naumann, J., K. Salomo, J.P. Der, E.K. Wafula, J.F. Bolin, E. Maass, L. Frenzke, M.S. Samain, C. Neinhuis, C.W. dePamphilis, and S. Wanke. Single-copy nuclear genes place haustorial Hydnoraceae within Piperales and reveal a Cretaceous origin of multiple parasitic angiosperm lineages. PLoS One 2013, 8(11):e79204. Link to Article
Rice, D.W., A.J. Alverson, A.O. Richardson, G.J. Young, M.V. Sanchez-Puerta, J. Munzinger, K. Barry, J.L. Boore, Y. Zhang, C.W. dePamphilis, E.B. Knox, and J.D. Palmer. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 2013, 342:1468.
Wicke, S., K.F. Muller, C.W. dePamphilis, D. Quandt, N.J. Wickett, Y. Zhang, S.S. Renner, G.M. Schneeweiss. Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family. Plant Cell 2013, 10:3711-3725.
Zhang, Y., M. Fernandez-Aparicio, E. Wafula, M. Das, Y. Jiao, N.J. Wickett, L.A. Honaas, P.E. Ralph, M.F. Wojciechowski, M.P. Timko, J.I. Yoder, J.H. Westwood, and C. dePamphilis. Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species. BMC Evolutionary Biology 2013, 13:48. Link to Article
2012
Adams, J.P., A. Adeli, C.Y. Hsu, R.L. Harkess, G.P. Page, C.W. dePamphilis, E.B. Schultz, and C. Yuceer. Plant-based FRET biosensor discriminates environmental zinc levels. Plant Biotechnology Journal 2012, 10(2):207-216.
Bandaranayake, P.C.G., A. Tomilov, N.B. Tomilova, Q. Ngo, K. Mahan, N. Wickett, C.W. dePamphilis, and J. Yoder. The TvPirin gene is necessary for haustorium development in the parasitic plant T. versicolor. Plant Physiology 2012, 158(2):1046-1053.
Johnson, M.T., E.J. Carpenter, Z. Tian , R. Bruskiewich, J.N. Burris, C.T. Carrigan, M.W. Chase, N.D. Clarke, S. Covshoff , C.W. dePamphilis, P.P. Edger, F. Goh, S. Graham, S. Greiner, J.M Hibberd, I. Jordon-Thaden, T.M. Kutchan, J. Leebens-Mack, M. Melkonian, N. Miles, H. Myburg, J. Patterson, J.C. Pires, P. Ralph, M. Rolf, R.F. Sage, D. Soltis, P. Soltis, D. Stevenson, C.N. Stewart, Jr., B. Surek, C.J. Thomsen, J.C. Villarreal, X. Wu, Y. Zhang, M.K. Deyholos, and G.K. Wong Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 2012;7(11):e50226. Link to Article
Jiao Y, J. Leebens-Mack, S. Ayyampalayam, J.E. Bowers, M.R. McKain, J. McNeal, M. Rolf, D.R. Ruzicka, E. Wafula, N.J. Wickett, X. Wu, Y. Zhang, J. Wang, Y. Zhang, E.J. Carpenter, M.K. Deyholos, T.M. Kutchan, A.S. Chanderbali, P.S. Soltis, D.W. Stevenson, R. McCombie, C.J. Pires, G.K. Wong, D.E. Soltis, and C.W. dePamphilis. A genome triplication associated with early diversification of the core eudicots. Genome Biology 2012, 13(1):R3.
McKain, M.R., N. Wickett, Y. Zhang, S. Ayyampalayam, W.R. McCombie, M. Chase, J.C. Pires, C.W. dePamphilis, J.H. Leebens-Mack. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany 2012, 99:397-406.
Westwood, J.H., C.W. dePamphilis, M. Das, M. Fernandez-Aparicio, L.A. Honaas, M.P. Timko, N.J. Wickett, and J.I. Yoder. The Parasitic Plant Genome Project: New Tools for Understanding the Biology of Orobanche and Striga. Weed Science 2012, 60: 295-306.
2011
Adams, J.P., A. Adeli, C.Y. Hsu, R.L. Harkess, G.P. Page, C.W. dePamphilis, E.B. Schultz, and C. Yuceer. Poplar maintains zinc homeostasis with heavy metal genes HMA4 and PCS1. Journal of Experimental Botany 2011, 62(11) 3737-3752.
Banks, J.A., T. Nishiyama, M. Hasebe, J.L. Bowman, M. Griskov, C. W. dePamphilis, V.A. Albert, N. Aono, T. Aoyama, B.A. Ambrose, N.W. Ashton, M.J. axtell, E. Barker, M.S. Barker, J.L. Bennetzen, N.D. Bonawitz, C. Chapple, C. Cheng, L.G. Correa, M. Dacre, J. DeBarry, I. Dreyer, M. Elias, E.M. Engstrom, M. Estelle, L. Feng, C. Finet, S.K. Floyd, W.B. Frommer, T. Fujita, L. Gramzow, M. Gutensohn, J. Harholt, M. Hattori, A. Heyl., T. Hirai, Y. Hiwatashi, M. Ishikawa, M. Iwata, K.G. Karol, B. Koehler, U. Kolukisaoglu, M. Kubo, T. Kurata, S. Lalonde, K. Li, Y. Li, A. Litt, E. Lyons, G. Manning, T. Maruyama, T.P. Michael, K. Mikami, S. Miyazaki, S. Morinaga, T. Murata, B. Mueller-Roeber, D.R. Nelson, M. Obara, Y. Oguri, R.G. Olmstead, N. Onodera, B.L. Peterson, B. Pils, M. Prigge, S.A. Rensing, D.M. Riano-Pachon, A.W. Roberts, Y. Sato, H.V. Scheller, B. Schulz, C. Schulz, E.V. Shakirov, N. Shibagaki, N. Shinohara, D.E. Shippen, I. Sorensen, R. Sotooka, N. Sugimoto, M. Sugita, N. Sumikawa, M. Tanurdzic, G. Theissen, P. Ulvskov, S. Wakazuki, J.K. Weng, W.W. Willats, D. Wipf, P.G. Wolf, L. Yang, A.D. Zimmer, Q. Zhu, T. Mitros, U. Hellsten, D. Logue, R. Otillar, A. Salamov, J. Schmutz, H. Shapiro, E. Lindquist, S. Lucas, D. Rokhsar, and I.V. Grigoriev. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 2011, May 20; 332(6032):960-963. Epub 2011 May 5.
Der, J.P., M.S. Barker, N.J. Wickett, C.W. dePamphilis, and P.G. Wolf. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 2011, Feb 8;12:99. Link to Article
Hsu, C-Y, J.P. Adams, H. Kim, K. No, C. Ma, S.H. Strauss, J. Drnevich, L. Vandervelde, J.D. Ellis, B.M. Rice, N. Wickett, L.E. Gunter, G.A. Tuskan, A.M. Brunner, G.P. Page, A. Barakat, J.E. Carlson, C.W. dePamphilis, D.S. Luthe, and C. Yuceer. FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar. Proceedings of the National Academy of Sciences, USA 2011, 108(26);10756-10761.
Jiao, Y., 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, and C.W. dePamphilis Ancestral polyploidy in seed plants and angiosperms. Nature 2011, May 5;473(7345):97-100.
Liang, H., S. Ayyampalayam, N. Wickett, A. Barakat, Y. Xu, L. Landherr, P. Ralph, Y. Jiao, T. Xu, S.E. Schlarbaum, H. Ma, J.H. Leebens-Mac, and C.W. dePamphilis. Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. Tree Genetics and Genomes 2011, 7(5):941-954.
Naumann, J., L. Symmank, S. Marie-Stephanie, K.F. Mueller, C. Neinhuis, C.W. dePamphilis, and S. Wanke. Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level. BMC Evolutionary Biology 2011, 11(1):357. Link to Article
Wang, L.S., J. Leebens-Mack, P.K. Wall, K. Beckmann, C.W. dePamphilis, and T. Warnow. The impact of multiple protein sequence alignment on phylogenetic estimation. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011, Jul-Aug;8(4):1108-19.
Wicke, S., G.M. Schneeweiss, C.W. dePamphilis, K.F. Muller, and D. Quandt. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Molecular Biology 2011, Jul;76(3-5):273-97.
Wicket, N.J., L.A. Honaas, E.K. Wafula, M. Das, K. Huang, B. Wu, L. Landherr, M.P. Timko, J. Yoder, J.H. Westwood, C.W. dePamphilis. Transcriptomes of the parasitic plant family Orobanchaceae reveal surprising conservation of chlorophyll synthesis. Current Biology 2011, Dec. 20;21(24): 2098-2104.
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. Kudma, A.H. Paterson, J.C. Pires, A. Chanderbali, 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. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology 2011, May 27;12(5):R48.
2010
Duarte, J.M., P.K. Wall, P.P. Edger, L.L. Landherr, H. Ma, J.C. Pires, J. Leebens-Mack, and C.W. dePamphilis. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 2010, 10:61. Link to Article
Chanderbali, A.S., M.J. Yoo, L.M. Zahn, S.F. Brockington, P.K. Wall, M.A. Gitzendanner, V.A. Albert, J. Leebens-Mack, N.S. Altman, H. Ma, C.W. dePamphilis, D.E. Soltis, and P.S. Soltis. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proceedings of the National Academy of Science U S A 2010, Dec 28;107(52):22570-22575.
Givnish, T.J., M. Ames, J.R. McNeal, M.R. McKain, P.R. Steele, C.W. dePamphilis, S.W. Graham, J.C. Pires, D.W. Stevenson, W.B. Zomlefer, B.G. Briggs, M.R. Duvall, M.J. Moore, J. M. Heaney, D.E. Soltis, P.S. Soltis, K. Thiele, and J.H. Leebens-Mack. Assembling the tree of the Monocotyledons: Plastome sequence phylogeny and evolution of Poales. Annals of the Missouri Botanical Gardens 2010, 97:587-616.
Singh, R., A.L. Levitt, E.G. Rajotte, E.C. Holmes, N. Ostiguy, D. Vanengelsdorp, W.I. Lipkin, C.W. dePamphilis, A.L. Toth, and D.L. Cox-Foster. RNA viruses in hymenopteran pollinators: Evidence of inter-taxa virus transmission via pollen and potential impact on non-Apis hymenotpteran species. PLoS One 2010, Dec. 22;5(12):e14357. Link to Article
Westwood, J.H., J.I. Yoder, M.P. Timko, and C.W. dePamphilis. The evolution of parasitism in plants. Trends in Plant Science 2010, (4):227-235.
Zahn, L.M., X. Ma, N.X. Altman, Q. Zhang, P.K. Wall, D. Tian, C.J. Gibas, R. Gharaibeh, J.H. Leebens-Mack, C.W. dePamphilis, and H. Ma. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biology 2010, 11(10):R101.
2009
Bliss, B.J., L. Landherr, C.W. dePamphilis, H. Ma, Y. Hu, and S.N. Maximova. Regeneration and Plantlet development from somatic tissues of Aristolochia fimbriata. Plant Cell Tissue and Organ Culture, 2009, 98:105-114.
Sankoff, D., C. Zheng, P.K. Wall, C.W. dePamphilis, J. Leebens-Mack, and V.A. Albert. Towards improved reconstruction of ancestral gene order in angiosperm phylogeny. Journal of Computational Biology 2009 Oct;16(10):1353-1367.
McNeal, J.R., J.V. Kuehl, J.L. Boore, J. Leebens-Mack, and C.W. dePamphilis. Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta. PLoS ONE 2009, 4(6): e5982. Link to Article
Soltis, D.E., Albert, V.A., Leebens-Mack, J., Bell, C.D., Paterson, A., Zheng, C., Sankoff, D, dePamphilis, C.W., Wall, P.K., and Soltis, P.S. Polyploidy and angiosperm diversification. American Journal of Botany 2009, 96:336-348.
Shan, H., Zahn, L., Guindon, S., Wall, P.K., Kong, H., Ma, H., dePamphilis, C.W., and Leebens-Mack, J. 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 2009, 10:2229-2244.
Wall, P.K., Leebens-Mack, J.H., Barakat, A., Chanderbali, A., Landherr, L., Altman, N., Carlson, J.E., Ma, H., Miller, W., Schuster, S., Soltis, D.E., Soltis, P.S., and dePamphilis, C.W. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 2009, 10:347. Link to Article
Zheng, C., Wall, P.K., Leebens-Mack, J., dePamphilis, C.W., Albert, V.A., and Sankoff, D. Gene loss under neighbourhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. Journal of Bioinformatics and Computational Biology 2009, 3:499-520.
2008
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. Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis. Taxon 2008, 57(4): 1110-1122.
Field D., Garrity G., Gray T., Morrison N., Selengut J., Sterk P., Tatusova T., Thomson N., Allen M.J., Angiuoli S.V., Ashburner M., Axelrod N., Baldauf S., Ballard S., Boore J., Cochrane G., Cole J., Dawyndt P., De Vos P., DePamphilis C., Edwards R., Faruque N., Feldman R., Gilbert J., Gilnda P., Glockner F.O., Goldstein P., Guralnick R., Haft D., Hancock D., Hermjakob H., Hertz-Fowler C., Hugenholtz P., Joint I., Kagan L, Kane M., Kennedy J., Kowalchuk G., Kottmann R., Kolker E., Kravitz S., Kyrpides N., Leebens-mack J., Lewis S.E., Li K., Lister A.L., Lord P., Maltsex N., Markowitz V., Martiny J., Methe B., Mizrachi I., Moxon R., Nelson K., Parkhill J., Proctor L., White O., Sansone S.A., Spiers A., Stevens R., Swift P., Taylor C., Tateno Y., Tett A., Turner S., Ussery D., Vaughan B., Ward N., Whetzel T., San Gil I., Wilson G., and Wipat A. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology 2008, 26(5):541-547.
Hu, W., dePamphilis, C.W., and Ma, H. Phylogenetic analysis of the plant-specific Zinc Finger-Homeobox and Mini Zinc Finger gene families. Journal of Integrative Plant Biology 2008, 50(8):1031-1045.
Liang, L., Carlson, J.E., Leebens-Mack, J., Wall, P.K., Mueller, L., Buzgo, M., Landherr, L., Hu, Y., DiLoreto, D.S., Ilut, D. S., Field, D., Tanksley, S.D., Ma, H., and dePamphilis, C.W. An EST Database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics and Genomes 2008, 4:419-433.
Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J.H., Senin P., Wang W., Ly B.V., Lewis K.L., Salzberg S.L., Feng L., Jones M.R., Skelton R.L., Murray J.E., Chen C., Qian W., Shen J., Du P., Eustice M., Tong E., Tang H., Lyons E., Paull R.E., Michael T.P., Wall K., Rice D.W., Albert H., Wang M.L., Zhu Y.J., Schatz M., Nagarajan N., Acob R.A., Guan P., Blas A., wai C.M., Ackerman C.M., Ren Y., Liu C., wang J., Wang J., Na J.K., Shakirov E.V., Haas B., Thimmapuram J., Nelson D., Wang X., Bowers J.E., Gschwend A.R., Delcher A.L., Singh R., Suzuki J.Y., Thripathi S., Neupane K., Wei H., Irikura B., Paidi M., Jiang N., Zhang W., Presting G., Windsor A., Navajas-Perez R., Torres M.J., Feltus F.A., Porter B., Li Y., Burroughs A.M., Luo M.C., liu L., Christopher D.A., Mount S.M., Moore P.H., Sugimura T., Jiang J., Schuler M.A., Friedman V., Mitchell-Olds T., Shippen D.E., dePamphilis C.W., Palmer J.D., Freeling M., Paterson A.H., Gonsalvez D., Wang L., and Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 2008 Apr 24; 452(7190):991-6.
Sankoff, D., Zheng, C., Wall, P.K., dePamphilis, C.W., Leebens-Mack, J., and Albert, V.A. Internal validation of ancestral gene order reconstruction in angiosperm phylogeny. In Comparative Genomics, In book series, Lecture Notes in Computer Science, vol. 5267, pp. 252-264. Springer Berlin, Heidelberg, 2008.
Soltis, D.E., Albert, V.A., Leebens_Mack, J., Palmer, J.D., Wing, R.A., dePamphilis, C.W., Ma,, H., Carlson, J.E., Altman, N., Kim, S., Wall, P.K., Zuccolo, A., and Soltis, P.S. The Amborella genome: an evolutionary reference for plant biology. Genome Biology 2008; 9(3):402.
Wall, P.K., Leebens-Mack, J., Muller, K.F., Field, D., Altman, N.S., and dePamphilis, C.W. PlantTribes: a gene and gene family resource for comparative genomics in plants. Nucleic Acids Research 2008, vol.36, Database issue: D970-6.
Wickett, N.J., Zhang, Y., Hansen, S.K., Roper, J.M., Kuehl, J.V., Plock, S.A., Wolf, P.G., dePamphilis, C.W., Boore, J.L., and Goffinet, B. Functional gene losses occur with minimal size reduction on the plastid genome of the parasitic liverwort Aneura mirabilis. Molecular Biology and Evolution 2008, Feb 25(2):393-401.
Yue, F., Cui, L., dePamphilis, C.W., Moret, B.M., and Tang, J. Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat. BMC Genomics 2008, 9 Suppl 1:S25. Link to Article
Zheng, C., Wall, P.K., Leebens-Mack, J., Albert, V.A., dePamphilis, C.W., and Sankoff, D. The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral Populus diploid. In Computational Systems Bioinformatics: Proceedings of the CSB 2008 Conference (eds. P. Markstein and Y. Xu). World Scientific Publishing Co.
2007
Barakat, A., P.K. Wall, S. DiLoretto, C.W. dePamphilis and J.E. Carlson. Conservation and divergence of microRNAs in Populus. BMC Genomics 2007, 8:481. Link to Article
Barakat, A., K. Wall, J. Leebens-Mack, Y.J. Wang, J.E. Carlson and C.W. dePamphilis. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia califonica) and conservation in flowering plants. The Plant Journal 2007, 51:991-1003.
Barkman, T.J., J.R. McNeal, S.H. Lim, G. Coat, H.B. Croom, N. Young, and C.W. dePamphilis. Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evolutionary Biology 2007, 7:248. Link to Article
Jansen, R.K., Z. Cai, L.A. Raubeson, H. Daniell, C.W. dePamphilis, J. Leebens-Mack, K.F. Muller, M. Guisinger-Bellian, R.C. Haberle, A.K. Hansen, T.W. Chumley, S.B. Lee, R. Peery, J.R. McNeal, J.V. Kuehl, J.L. Boore. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Nat. Acad. Sci. USA 2007, 104(49):19369-19374.
Kong, H., L. Landherr, M. Frohlich, J. Leebens-Mack, H. Ma and C.W. dePamphilis. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. The Plant Journal 2007, 50:873-885.
Liang, H., E.G. Fang, J.P. Tomkins, M. Luo, D. Kudrna, K. Arumuganathan, S. Zhao, S.E. Schlarbaum, J.A. Banks, C.W. dePamphilis, D.F. Mandoli, R.A. Wing, and J.E. Carlson. Development of a BAC library resource for yellow poplar (Liriodendron tulipifera) and the identification of genomic regions associated with flower development and lignin biosynthesis. Tree Genetics and Genomes 2007, 3(3):215-225.
McNeal, J.R., J.V. Kuehl, J.L. Boore and C.W. dePamphilis. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biology 2007, 7:57. Link to Article
McNeal, J.R., K. Arumugunathan, J.V. Kuehl, J.L. Boore and C.W. dePamphilis. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). BMC Biology 2007, 5:55. Link to Article
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. Leebens-Mack. The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends in Plant Science 2007, 12(8):358-367.
2006
Altman, N., Leebens-Mack, J., Zahn, L., Chanderbali, A., Tian, D., Werner, L., Ma, H. and dePamphilis, C.. Behind the scenes: Planning a multispecies microarray experiment. Chance 2006, 19(3):28-39.
Cai, Z., C. Penaflor, J.V. Kuehl, J.H. Leebens-Mack, J.E. Carlson, C.W. dePamphilis , J.L. Boore and R.K. Jansen. Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids. BMC Evolutionary Biology 2006, 6(1):77. Link to Article
Carlson, J.E., J.H. Leebens-Mack, P.K. Wall, L.M. Zahn, L.A. Mueller, L.L. Landherr, Y. Hu, D.C. Ilut, J.M. Arrington S. Choirean, A. Becker, D. Field, S.D. Tanksley, H. Ma, C.W. dePamphilis.. EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot. Plant Molecular Biology 2006, 62:351-369.
Cui, L., P.K. Wall, J.H. Leebens-Mack, B.G. Lindsay, D.E. Soltis, J.J. Doyle, P.S. Soltis, J.E. Carlson, K. Arumuganathan, A. Barakat, V.A. Albert, H. Ma and C.W. dePamphilis. Widespread genome duplications throughout the history of flowering plants. Genome Research 2006, 16:738:739.
Cui, L., J.H. Leebens-Mack, L-S.Wang, J. Tang, L. Rymarquis, D.B. Stern, and C.W. dePamphilis. Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evolutionary Biology 2006, 6:13. Link to Article
Cui, L, N. Veeraraghavan, A. Richter, K. Wall, R.K. Jansen, J. Leebens-Mack, I. Makalowska, and C. W. dePamphilis. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research 2006, vol. 34, Database issue, D692-D696.
Duarte, J.M., L. Cui, K. Wall, Q. Zhang, X. Zhang, J.H. Leebens-Mack, H. Ma, N. Altman, and C.W. dePamphilis.Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Molecular Biology and Evolution 2006, 23(2): 469-478.
Leebens-Mack, J.H., Wall, K., Duarte, J., Zheng, Z., Oppenheimer, D. and dePamphilis, C.W.A Genomics Approach to the Study of Ancient Polyploidy and Floral Developmental Genetics. In Developmental Genetics of the Flower, D.E. Solits, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series, Elsevier Limited, London 2006, vol 44, pp. 527-549.
Leebens-Mack, J.H., T. Vision, E. Brenner, J.E. Bowers, S. Cannon, M.J. Clement, C.W. Cunningham, C.W. dePamphilis, R. deSalle, J.J. Doyle, J.A. Eisen, X. Gu, J. Harshman, R.K. Jansen, E.A. Kellogg, E.V. Koonin, B.D. Mishler, H. Philippe, J.C. Pires, Y.L. Qiu, S.Y. Rhee, K. Sjolander, D.E. Soltis, P.S. Soltis, D.W. Stevenson, K. Wall, T. Warnow, C. Zmasek.Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analysis(MIAPA). Omics 2006, 10(2):231-237.
McNeal, J.R., J.H. Leebens-Mack, K. Arumuganathan, J. Kuehl, J.L. Boore and C.W. dePamphilis. Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques 2006, 41:69-73.
Modliszewski, J.L., D.T. Thomas, C. Fan, C.J. Crawford, C.W. dePamphilis, and Q-Y. (Jenny) Xiang. Ancestral chlorplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus (Sapindaceae). American Journal of Botany 2006, 93(3):377-388.
Tuskan, G.A. and 103 others. The genome of black cottonwood, Populus trichcarpa (Torr. and Gray ex Brayshaw). Science 2006, 313:1596-1604.
Zahn, L.M., J. Leebens-Mack, J.M. Arrington, Y. Hu, L. Landherr, C.W. dePamphilis, A. Becker, G. Theissen, and H. Ma. Conservation and divergence in the AGAMOUS Subfamily of MADS-Box Genes: evidence of independent sub- and neofunctionalization events. Evolution and Development 2006, 8(1):30-45.
2005
Albert, V.A., D.E. Soltis, J. Carlson, W.G. Farmerie, K. Wall, D.C. Ilut, T. M. Solow, L.A. Mueller, L.L. Landherr, Y. Hu, M. Buzgo, S. Kim, M-J. Yoo, M.W. Frohlich, R. Perl-Treves, S. Schlarbaum, B. Bliss, X. Zhang, S. Tanksley, D.G. Oppenheimer, P.S. Soltis, H. Ma, C.W. dePamphilis, and J.H. Leebens-Mack. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biology 2005, 5:5. Link to Article
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.H. Leebens-Mack, and L. Cui. Methods for obtaining and analyzing chloroplast genome sequences. In Methods in Enzymology Vol. 395, pp. 348-384. E.A. Zimmer, ed., Elsevier 2005.
Leebens-Mack, J.H., L.A. Raubeson, L. Cui, J.V. Kuehl, M.H. Fourcade, T.W. Chumley, J.L. Boore, R.K. Jansen, and C.W. dePamphilis. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution 2005, 22(10):1948-1963.
Parkinson, C.L., J.P. Mower, Y-L. Qiu, A.J. Shirk, K. Song, N.D. Young, C.W. dePamphilis and J.D. Palmer. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evolutionary Biology 2005, 5:73. Link to Article
Sampedro, J., Y. Lee, R.E. Carey, C. dePamphilis and D.J. Cosgrove. Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family. The Plant Journal 2005, 44(3): 409-419.
Soltis, D.E., V.A. Albert, S. Kim, M.-J. Yoo, P.S. Soltis, M.W. Frohlich, J.H. Leebens-Mack, H.-Z. Kong, K. Wall, H. Ma, and C.W. dePamphilis. Evolutions of the Flower. In Plant Diversity and Evolution: Genotype and Phenotypic Variation in Higher Plants, Ed. R.J. Henry. CABI Publishers. 2005.
Wang, J.Z., B.G. Lindsay, L. Cui, P.K. Wall, J. Marion, J. Zhang, and C.W. dePamphilis.Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. BMC Bioinformatics 2005, 6:300. Link to Article
Wang, W., M. Tanurdzic, M. Luo, N. Sisneros, H.R. Kim, J-K. Weng, D. Kudrna, C. Mueller, K. Arumuganathan, J. Carlson, C. Chapple, C.W. dePamphilis, D. Mandoli, J. Tomkins, R.A. Wing, and J.A. Banks. Construction of a bacterial artificial chromosome library from spikemoss Selaginella moellendorffii: A new resource for plant comparative genomics. BMC Plant Biology 2005, 5:10. Link to Article
Young, N.D. and C.W. dePamphilis. Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function. BMC Evolutionary Biology 2005, 5:16. Link to Article
Zahn, L.M., J.H. Leebens-Mack, C.W. dePamphilis, H. Ma, and G. Theissen.To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of angiosperms. Journal of Hereditry 2005, 96(3):225-240.
Selected Publications prior to 2005:
Barkman, T.J., G. Chenery, J.R. McNeal, J. Lyons-Weiler, W.J. Elisens, G. Moore, A.D. Wolfe, and C.W. dePamphilis. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proceedings of the National Academy of Sciences 2000, 97: 13166-13171.
Bowe, L.M., G. Coat, and Claude W. dePamphilis. Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales'closest relatives are conifers. Proceedings of the National Academy of Sciences 2000, 97.
Bowe, L.M. and C.W. dePamphilis. Effects of RNA editing and gene processing on phylogenetic reconstruction. Molecular Biology and Evolution 1996, 13: 1159-1166.
Burke, J.M., R. Wyatt, C.W. dePamphilis and M.L. Arnold. Nectar characteristics of interspecific hybrids and their parents in Aesculus (Hippocastanaceae) and Iris (Iridaceae). Journal of the Torrey Botanical Club 2002, 127: 200-206.
dePamphilis, C.W. Genes and genomes (of parasitic plants). pp. 177-205. In Parasitic Plants. Edited by Malcolm C. Press and Jonathan D. Graves. Chapman and Hall, London. 1995. ISBN 0 412 37120 0.
dePamphilis, C.W. and H.S. Neufeld. Phenology and ecophysiology of Aesculus sylvatica, a vernal understory tree. Canadian Journal of Botany 1988, 67:2161-2167.
dePamphilis, C.W. and Palmer, J.D. Loss of photosynthetic and chlororespiratory genes from the plastid genome of a nonphotosynthetic plant. Nature 1990, 348:337-339.
dePamphilis, C.W. and R. Wyatt. Electrophoretic confirmation of interspecific hybridization in Aesculus and the genetic structure of a broad hybrid zone. Evolution 1990, 44: 1295-1317.
dePamphilis, C.W. and R. Wyatt. Hybridization and introgression in buckeyes (Aesculus: Hippocastanaceae): A review of the evidence and a hypothesis to explain long-distance gene flow. Systematic Botany 1989, 14: 593-611.
dePamphilis, C.W., N.D. Young and A.D. Wolfe. Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: Many losses of photosynthesis and complex patterns of rate variation. Proceedings of the National Academy of Sciences 1997, 94:7367-7372.
Ems, S.C., C.W. Morden, C.K. Dixon, K.H. Wolfe, C.W. dePamphilis and J.D. Palmer. Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Molecular Biology 1995, 29:721-733.
Kong, H.-Z., J. Leebens-Mack, W. Ni, C.W. depamphilis and H. Ma. Highly heterogeneous rates of evolution in the SKP1 gene family in animals and plants: functional and evolutionary implications. Molecular Biology and Evolution 2004, 21:117-128.
Leebens-Mack, J.H. and C.W. dePamphilis. Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages. Molecular Biology and Evolution 2002, 19:1292-1302.
Ma, H. and Claude dePamphilis. The ABCs of flower evolution. Cell 2000, 101: 5-8.
Maul, J.E., J.W. Lilly, L. Cui., C.W. dePamphilis, W. Miller, E.H. Harris and D.B. Stern. The Chlamydomonas reinhardtii plastid chromosome: Islands of genes in a sea of repeats. The Plant Cell 2002, 14: 2659-2679.
Nam, J., C.W. dePamphilis, H. Ma, and M. Nei. Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Molecular Biology Evolution 2003, 20:1435-47.
Nickrent , D.L., R.J. Duff, A.E. Colwell, A.D. Wolfe, N.D. Young, K.E. Steiner and C.W. dePamphilis. Molecular phylogenetic and evolutionary studies of parasitic plants. In Chapter 14 of Molecular Systematics of Plants, II, D. Soltis, P. Soltis, and J. Doyle, eds. pp. 211-241. 1998.
Nickrent, D., Y. Ouyang, J. Duff, and C.W. dePamphilis. Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Molecular Biology 1997, 34: 717-729.
Olmstead, R.G., C.W. dePamphilis, A.D. Wolfe, N.D. Young, W. Elisens, P. Reeves. Disintegration of the Scrophulariaceae. American Journal of Botany 2001, 88(2): 348-361.
Smith, D., T. J., Barkman and C.W. dePamphilis. Hemiparasitism. In Encyclopedia of Biodiversity. S.A. Levin, ed. V. 3, pp. 317-328. Academic Press. 2001.
Soltis, D.E., P.S. Soltis, V.A. Albert, D.G. Oppenheimer, C.W. dePamphilis, H. Ma, M.W. Frohlich and G. Theissen Missing Links: The genetic architecture of the flower and floral diversification. Trends In Plant Science 2002, 7: 22-31.
Wang, J-P. Z., B.G. Lindsay, J. Leebens-Mack, L. Cui, K. Wall, W.C. Miller, and C.W. dePamphilis. EST Clustering Error Evaluation and Correction. Bioinformatics 2004, 20:2973-84.
Wang, G., H. Kong, Y. Sun, X. Zhang, W. Zhang, N. Altman, C.W. dePamphilis, and H. Ma. Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiology 2004, Jun;135(2):1084-99.
Wolfe, A.D. and C.W. dePamphilis. The effect of relaxed functional constraints on rbcL in photosynthetic and nonphotosynthetic plants. Molecular Biology and Evolution 1998, 15: 1243-1258.
Wolfe, A.D. and C.W. dePamphilis. Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche. Plant Molecular Biology 1997, 33: 965-977.
Xiang, Q-Y., D.J. Crawford, A.D. Wolfe, Y-C Tang and C.W. dePamphilis. Origin and biogeography of Aesculus L. (Hippocastanaceae) in a molecular phylogenetic perspective. Evolution 1998, 52:988-997.
Young, N.D., K.E. Steiner, and C.W. dePamphilis. Evolution of parasitism in the Scrophulariaceae/Orobanchaceae: Plastid gene sequences refute an evolutionary transition series. Annals of the Missouri Botanical Garden 1999, 86:876-893.
Young, N.D. and Claude W. dePamphilis. Purifying selection detected in the plastid matK and flanking ribozyme regions within a group II intron of non-photosynthetic plants. Molecular Biology and Evolution 2000, 17: 1933-1941.
You can also search PubMed for dePamphilis papers.