GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Jin, Jian-Jun, Yu, Wen-Bin, Yang, Jun-Bo, Song, Yu, dePamphilis, Claude W, Yi, Ting-Shuang, Li, De-Zhu
Published in Genome Biology (10.09.2020)
Published in Genome Biology (10.09.2020)
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Journal Article
MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs
Shahid, Saima, Kim, Gunjune, Johnson, Nathan R., Wafula, Eric, Wang, Feng, Coruh, Ceyda, Bernal-Galeano, Vivian, Phifer, Tamia, dePamphilis, Claude W., Westwood, James H., Axtell, Michael J.
Published in Nature (London) (04.01.2018)
Published in Nature (London) (04.01.2018)
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Journal Article
Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants
Wicke, Susann, Müller, Kai F., dePamphilis, Claude W., Quandt, Dietmar, Bellot, Sidonie, Schneeweiss, Gerald M.
Published in Proceedings of the National Academy of Sciences - PNAS (09.08.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (09.08.2016)
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Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum
Ishida, Juliane K., Wakatake, Takanori, Yoshida, Satoko, Takebayashi, Yumiko, Kasahara, Hiroyuki, Wafula, Eric, de Pamphilis, Claude W., Namba, Shigetou, Shirasu, Ken
Published in The Plant cell (01.08.2016)
Published in The Plant cell (01.08.2016)
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Journal Article
Genomics of sorghum local adaptation to a parasitic plant
Bellis, Emily S., Kelly, Elizabeth A., Lorts, Claire M., Gao, Huirong, DeLeo, Victoria L., Rouhan, Germinal, Budden, Andrew, Bhaskara, Govinal B., Hu, Zhenbin, Muscarella, Robert, Timko, Michael P., Nebie, Baloua, Runo, Steven M., Chilcoat, N. Doane, Juenger, Thomas E., Morris, Geoffrey P., dePamphilis, Claude W., Lasky, Jesse R.
Published in Proceedings of the National Academy of Sciences - PNAS (25.02.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (25.02.2020)
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Journal Article
RNA viruses in hymenopteran pollinators: evidence of inter-Taxa virus transmission via pollen and potential impact on non-Apis hymenopteran species
Singh, Rajwinder, Levitt, Abby L, Rajotte, Edwin G, Holmes, Edward C, Ostiguy, Nancy, Vanengelsdorp, Dennis, Lipkin, W Ian, Depamphilis, Claude W, Toth, Amy L, Cox-Foster, Diana L
Published in PloS one (22.12.2010)
Published in PloS one (22.12.2010)
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Journal Article
Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages
Naumann, Julia, Salomo, Karsten, Der, Joshua P, Wafula, Eric K, Bolin, Jay F, Maass, Erika, Frenzke, Lena, Samain, Marie-Stéphanie, Neinhuis, Christoph, dePamphilis, Claude W, Wanke, Stefan
Published in PloS one (12.11.2013)
Published in PloS one (12.11.2013)
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Journal Article
FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar
Hsu, Chuan-Yu, Adams, Joshua P, Kim, Hyejin, No, Kyoungok, Ma, Caiping, Strauss, Steven H, Drnevich, Jenny, Vandervelde, Lindsay, Ellis, Jeffrey D, Rice, Brandon M, Wickett, Norman, Gunter, Lee E, Tuskan, Gerald A, Brunner, Amy M, Page, Grier P, Barakat, Abdelali, Carlson, John E, dePamphilis, Claude W, Luthe, Dawn S, Yuceer, Cetin
Published in Proceedings of the National Academy of Sciences - PNAS (28.06.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (28.06.2011)
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Journal Article
Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism
Misra, Vikram A, Wafula, Eric K, Wang, Yu, dePamphilis, Claude W, Timko, Michael P
Published in BMC plant biology (14.05.2019)
Published in BMC plant biology (14.05.2019)
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Journal Article
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome
Honaas, Loren A, Wafula, Eric K, Wickett, Norman J, Der, Joshua P, Zhang, Yeting, Edger, Patrick P, Altman, Naomi S, Pires, J Chris, Leebens-Mack, James H, dePamphilis, Claude W
Published in PloS one (05.01.2016)
Published in PloS one (05.01.2016)
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Journal Article
Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth
Kong, Hongzhi, Landherr, Lena L., Frohlich, Michael W., Leebens‐Mack, Jim, Ma, Hong, DePamphilis, Claude W.
Published in The Plant journal : for cell and molecular biology (01.06.2007)
Published in The Plant journal : for cell and molecular biology (01.06.2007)
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Journal Article
Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis
Wickett, Norman J., Honaas, Loren A., Wafula, Eric K., Das, Malay, Huang, Kan, Wu, Biao, Landherr, Lena, Timko, Michael P., Yoder, John, Westwood, James H., dePamphilis, Claude W.
Published in Current biology (20.12.2011)
Published in Current biology (20.12.2011)
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Journal Article
Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes
Johnson, Marc T J, Carpenter, Eric J, Tian, Zhijian, Bruskiewich, Richard, Burris, Jason N, Carrigan, Charlotte T, Chase, Mark W, Clarke, Neil D, Covshoff, Sarah, Depamphilis, Claude W, Edger, Patrick P, Goh, Falicia, Graham, Sean, Greiner, Stephan, Hibberd, Julian M, Jordon-Thaden, Ingrid, Kutchan, Toni M, Leebens-Mack, James, Melkonian, Michael, Miles, Nicholas, Myburg, Henrietta, Patterson, Jordan, Pires, J Chris, Ralph, Paula, Rolf, Megan, Sage, Rowan F, Soltis, Douglas, Soltis, Pamela, Stevenson, Dennis, Stewart, Jr, C Neal, Surek, Barbara, Thomsen, Christina J M, Villarreal, Juan Carlos, Wu, Xiaolei, Zhang, Yong, Deyholos, Michael K, Wong, Gane Ka-Shu
Published in PloS one (21.11.2012)
Published in PloS one (21.11.2012)
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Journal Article
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
Jansen, Robert K, Cai, Zhengqiu, Raubeson, Linda A, Daniell, Henry, dePamphilis, Claude W, Leebens-Mack, James, Müller, Kai F, Guisinger-Bellian, Mary, Haberle, Rosemarie C, Hansen, Anne K, Chumley, Timothy W, Lee, Seung-Bum, Peery, Rhiannon, McNeal, Joel R, Kuehl, Jennifer V, Boore, Jeffrey L
Published in Proceedings of the National Academy of Sciences - PNAS (04.12.2007)
Published in Proceedings of the National Academy of Sciences - PNAS (04.12.2007)
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Journal Article
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels
Duarte, Jill M, Wall, P Kerr, Edger, Patrick P, Landherr, Lena L, Ma, Hong, Pires, J Chris, Leebens-Mack, Jim, dePamphilis, Claude W
Published in BMC evolutionary biology (24.02.2010)
Published in BMC evolutionary biology (24.02.2010)
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Journal Article
De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum
Der, Joshua P, Barker, Michael S, Wickett, Norman J, dePamphilis, Claude W, Wolf, Paul G
Published in BMC genomics (08.02.2011)
Published in BMC genomics (08.02.2011)
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