Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree
Hämälä, Tuomas, Wafula, Eric K., Guiltinan, Mark J., Ralph, Paula E., dePamphilis, Claude W., Tiffin, Peter
Published in Proceedings of the National Academy of Sciences - PNAS (31.08.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (31.08.2021)
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Ancestral polyploidy in seed plants and angiosperms
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Published in Nature (London) (05.05.2011)
Published in Nature (London) (05.05.2011)
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Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation
Yang, Zhenzhen, Zhang, Yeting, Wafula, Eric K., Honaas, Loren A., Ralph, Paula E., Jones, Sam, Clarke, Christopher R., Liu, Siming, Su, Chun, Zhang, Huiting, Altman, Naomi S., Schuster, Stephan C., Timko, Michael P., Yoder, John I., Westwood, James H., dePamphilis, Claude W.
Published in Proceedings of the National Academy of Sciences - PNAS (08.11.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (08.11.2016)
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Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty
Yang, Zhenzhen, Wafula, Eric K, Honaas, Loren A, Zhang, Huiting, Das, Malay, Fernandez-Aparicio, Monica, Huang, Kan, Bandaranayake, Pradeepa C G, Wu, Biao, Der, Joshua P, Clarke, Christopher R, Ralph, Paula E, Landherr, Lena, Altman, Naomi S, Timko, Michael P, Yoder, John I, Westwood, James H, dePamphilis, Claude W
Published in Molecular biology and evolution (01.03.2015)
Published in Molecular biology and evolution (01.03.2015)
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Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes
Zhang, Huiting, Wafula, Eric K, Eilers, Jon, Harkess, Alex E, Ralph, Paula E, Timilsena, Prakash Raj, dePamphilis, Claude W, Waite, Jessica M, Honaas, Loren A
Published in Frontiers in plant science (14.11.2022)
Published in Frontiers in plant science (14.11.2022)
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A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora
Winters, Noah P, Wafula, Eric K, Knollenberg, Benjamin J, Hämälä, Tuomas, Timilsena, Prakash R, Perryman, Melanie, Zhang, Dapeng, Sheaffer, Lena L, Praul, Craig A, Ralph, Paula E, Prewitt, Sarah, Leandro-Muñoz, Mariela E, Delgadillo-Duran, Diego A, Altman, Naomi S, Tiffin, Peter, Maximova, Siela N, dePamphilis, Claude W, Marden, James H, Guiltinan, Mark J
Published in BMC biology (16.02.2024)
Published in BMC biology (16.02.2024)
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Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants
Yang, Zhenzhen, Wafula, Eric K., Kim, Gunjune, Shahid, Saima, McNeal, Joel R., Ralph, Paula E., Timilsena, Prakash R., Yu, Wen-bin, Kelly, Elizabeth A., Zhang, Huiting, Person, Thomas Nate, Altman, Naomi S., Axtell, Michael J., Westwood, James H., dePamphilis, Claude W.
Published in Nature plants (01.09.2019)
Published in Nature plants (01.09.2019)
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Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae)
Naumann, Julia, Der, Joshua P, Wafula, Eric K, Jones, Samuel S, Wagner, Sarah T, Honaas, Loren A, Ralph, Paula E, Bolin, Jay F, Maass, Erika, Neinhuis, Christoph, Wanke, Stefan, dePamphilis, Claude W
Published in Genome biology and evolution (01.02.2016)
Published in Genome biology and evolution (01.02.2016)
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Transcriptomics of Host-Specific Interactions in Natural Populations of the Parasitic Plant Purple Witchweed (Striga hermonthica)
Lopez, Lua, Bellis, Emily S., Wafula, Eric, Hearne, Sarah J., Honaas, Loren, Ralph, Paula E., Timko, Michael P., Unachukwu, Nnanna, dePamphilis, Claude W., Lasky, Jesse R.
Published in Weed science (01.07.2019)
Published in Weed science (01.07.2019)
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Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species
Zhang, Yeting, Fernandez-Aparicio, Monica, Wafula, Eric K, Das, Malay, Jiao, Yuannian, Wickett, Norman J, Honaas, Loren A, Ralph, Paula E, Wojciechowski, Martin F, Timko, Michael P, Yoder, John I, Westwood, James H, Depamphilis, Claude W
Published in BMC evolutionary biology (20.02.2013)
Published in BMC evolutionary biology (20.02.2013)
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Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies
Bliss, Barbara J, Wanke, Stefan, Barakat, Abdelali, Ayyampalayam, Saravanaraj, Wickett, Norman, Wall, P Kerr, Jiao, Yuannian, Landherr, Lena, Ralph, Paula E, Hu, Yi, Neinhuis, Christoph, Leebens-Mack, Jim, Arumuganathan, Kathiravetpilla, Clifton, Sandra W, Maximova, Siela N, Ma, Hong, dePamphilis, Claude W
Published in BMC plant biology (24.01.2013)
Published in BMC plant biology (24.01.2013)
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Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L
Liang, Haiying, Ayyampalayam, Saravanaraj, Wickett, Norman, Barakat, Abdelali, Xu, Yi, Landherr, Lena, Ralph, Paula E, Jiao, Yuannian, Xu, Tao, Schlarbaum, Scott E, Ma, Hong, Leebens-Mack, James H, dePamphilis, Claude W
Published in Tree genetics & genomes (01.10.2011)
Published in Tree genetics & genomes (01.10.2011)
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The Amborella Genome and the Evolution of Flowering Plants
Albert, Victor A, Barbazuk, WBradley, dePamphilis, Claude W, Der, Joshua P, Leebens-Mack, James, Ma, Hong, Palmer, Jeffrey D, Rounsley, Steve, Sankoff, David, Schuster, Stephan C, Soltis, Douglas E, Soltis, Pamela S, Wessler, Susan R, Wing, Rod A, Ammiraju, Jetty SS, Chamala, Srikar, Chanderbali, Andre S, Determann, Ronald, Ralph, Paula, Talag, Jason, Tomsho, Lynn, Walts, Brandon, Wanke, Stefan, Chang, Tien-Hao, Lan, Tianying, Arikit, Siwaret, Axtell, Michael J, Ayyampalayam, Saravanaraj, Burnette, James M, De Paoli, Emanuele, et. al
Published in Science (American Association for the Advancement of Science) (20.12.2013)
Published in Science (American Association for the Advancement of Science) (20.12.2013)
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A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants
Käfer, Jos, Bewick, Adam, Andres‐Robin, Amélie, Lapetoule, Garance, Harkess, Alex, Caïus, José, Fogliani, Bruno, Gâteblé, Gildas, Ralph, Paula, dePamphilis, Claude W., Picard, Franck, Scutt, Charlie, Marais, Gabriel A. B., Leebens‐Mack, James
Published in The New phytologist (01.02.2022)
Published in The New phytologist (01.02.2022)
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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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Towards a catalog of pome tree architecture genes: the draft 'd'Anjou' genome (Pyrus communis L.)
Zhang, Huiting, Wafula, Eric K, Eilers, Jon, Harkess, Alex, Ralph, Paula E, Prakash Raj Timilsena, Depamphilis, Claude, Waite, Jessica, Honaas, Loren A
Published in bioRxiv (19.11.2021)
Published in bioRxiv (19.11.2021)
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A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants
Käfer, Jos, Bewick, Adam, Andres-Robin, Amélie, Lapetoule, Garance, Harkess, Alex, Caïus, José, Fogliani, Bruno, Gâteblé, Gildas, Ralph, Paula, Depamphilis, Claude W, Picard, Franck, Scutt, Charlie P, Leebens-Mack, James, Gabriel Ab Marais
Published in bioRxiv (22.12.2020)
Published in bioRxiv (22.12.2020)
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