Claude dePamphilis - Publications

Affiliations: 
Pennsylvania State University, State College, PA, United States 
Area:
General Biology, Botany Biology, Genetics, Evolution and Development Biology

124 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Cantos CF, dePamphilis CW, Assmann SM. Extra-large G proteins have extra-large effects on agronomic traits and stress tolerance in maize and rice. Trends in Plant Science. PMID 37156701 DOI: 10.1016/j.tplants.2023.04.005  0.318
2023 Yu R, Chen X, Long L, Jost M, Zhao R, Liu L, Mower JP, dePamphilis CW, Wanke S, Jiao Y. De novo assembly and comparative analyses of mitochondrial genomes in Piperales. Genome Biology and Evolution. PMID 36896589 DOI: 10.1093/gbe/evad041  0.601
2023 Wafula EK, Zhang H, Von Kuster G, Leebens-Mack JH, Honaas LA, dePamphilis CW. PlantTribes2: Tools for comparative gene family analysis in plant genomics. Frontiers in Plant Science. 13: 1011199. PMID 36798801 DOI: 10.3389/fpls.2022.1011199  0.51
2022 Timilsena PR, Barrett CF, Nelson AP, Wafula EK, Ayyampalayam S, McNeal JR, Yukawa T, Givnish TJ, Graham SW, Pires JC, Davis JI, Ané C, Stevenson DW, Leebens-Mack J, Martínez-Salas E, ... ... dePamphilis CW, et al. Phylotranscriptomic analyses of mycoheterotrophic monocots show a continuum of convergent evolutionary changes in expressed nuclear genes from three independent nonphotosynthetic lineages. Genome Biology and Evolution. PMID 36582124 DOI: 10.1093/gbe/evac183  0.754
2022 Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, ... ... dePamphilis CW, et al. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. Frontiers in Plant Science. 13: 876779. PMID 36483967 DOI: 10.3389/fpls.2022.876779  0.738
2022 Zhang H, Wafula EK, Eilers J, Harkess AE, Ralph PE, Timilsena PR, dePamphilis CW, Waite JM, Honaas LA. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in architecture genes. Frontiers in Plant Science. 13: 975942. PMID 36452099 DOI: 10.3389/fpls.2022.975942  0.534
2022 Garrett P, Becher H, Gussarova G, dePamphilis CW, Ness RW, Gopalakrishnan S, Twyford AD. Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (, Orobanchaceae). Frontiers in Plant Science. 13: 869583. PMID 35720561 DOI: 10.3389/fpls.2022.869583  0.487
2021 Qin L, Hu Y, Wang J, Wang X, Zhao R, Shan H, Li K, Xu P, Wu H, Yan X, Liu L, Yi X, Wanke S, Bowers JE, Leebens-Mack JH, ... dePamphilis CW, et al. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. Nature Plants. PMID 34475528 DOI: 10.1038/s41477-021-00990-2  0.689
2021 Hämälä T, Wafula EK, Guiltinan MJ, Ralph PE, dePamphilis CW, Tiffin P. Genomic structural variants constrain and facilitate adaptation in natural populations of , the chocolate tree. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34408075 DOI: 10.1073/pnas.2102914118  0.435
2021 Käfer J, Bewick A, Andres-Robin A, Lapetoule G, Harkess A, Caïus J, Fogliani B, Gâteblé G, Ralph P, dePamphilis CW, Picard F, Scutt C, Marais GAB, Leebens-Mack J. A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants. The New Phytologist. PMID 34342006 DOI: 10.1111/nph.17662  0.412
2020 Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology. 21: 241. PMID 32912315 DOI: 10.1186/S13059-020-02154-5  0.666
2020 Bellis ES, Kelly EA, Lorts CM, Gao H, DeLeo VL, Rouhan G, Budden A, Bhaskara GB, Hu Z, Muscarella R, Timko MP, Nebie B, Runo SM, Chilcoat ND, Juenger TE, ... ... dePamphilis CW, et al. Genomics of sorghum local adaptation to a parasitic plant. Proceedings of the National Academy of Sciences of the United States of America. PMID 32047036 DOI: 10.1073/Pnas.1908707117  0.35
2020 Ali R, Jiao Y, Kerr Wall P, Patching SG, Ahmad I, Lutfulla G, dePamphilis CW. In silico identification and structure function analysis of a putative coclaurine N-methyltransferase from Aristolochia fimbriata. Computational Biology and Chemistry. 85: 107201. PMID 31986303 DOI: 10.1016/J.Compbiolchem.2020.107201  0.493
2019 Yoshida S, Kim S, Wafula EK, Tanskanen J, Kim YM, Honaas L, Yang Z, Spallek T, Conn CE, Ichihashi Y, Cheong K, Cui S, Der JP, Gundlach H, Jiao Y, ... ... dePamphilis CW, et al. Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism. Current Biology : Cb. PMID 31522940 DOI: 10.1016/J.Cub.2019.07.086  0.685
2019 Hämälä T, Guiltinan MJ, Marden JH, Maximova S, dePamphilis C, Tiffin P. Gene expression modularity reveals footprints of polygenic adaptation in Theobroma cacao. Molecular Biology and Evolution. PMID 31501906 DOI: 10.1093/Molbev/Msz206  0.328
2019 Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu WB, Kelly EA, Zhang H, Person TN, Altman NS, Axtell MJ, Westwood JH, dePamphilis CW. Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants. Nature Plants. PMID 31332314 DOI: 10.1038/S41477-019-0458-0  0.773
2019 Lopez L, Bellis ES, Wafula E, Hearne SJ, Honaas L, Ralph PE, Timko MP, Unachukwu N, dePamphilis CW, Lasky JR. Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica) Weed Science. 67: 397-411. DOI: 10.1017/Wsc.2019.20  0.304
2019 Fister AS, Leandro-Muñoz ME, Zhang D, Marden JH, Tiffin P, dePamphilis C, Maximova S, Guiltinan MJ. Widely distributed variation in tolerance to Phytophthora palmivora in four genetic groups of cacao Tree Genetics & Genomes. 16. DOI: 10.1007/S11295-019-1396-8  0.34
2018 Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant . Proceedings of the National Academy of Sciences of the United States of America. PMID 30598433 DOI: 10.1073/Pnas.1816822116  0.533
2018 Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, ... ... dePamphilis C, et al. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants. PMID 29967517 DOI: 10.1038/S41477-018-0188-8  0.607
2018 Yu WB, Randle CP, Lu L, Wang H, Yang JB, dePamphilis CW, Corlett RT, Li DZ. The Hemiparasitic Plant(Orobanchaceae) Is Polyphyletic and Contains Cryptic Species in the Hengduan Mountains of Southwest China. Frontiers in Plant Science. 9: 142. PMID 29479366 DOI: 10.3389/fpls.2018.00142  0.628
2018 Shahid S, Kim G, Johnson NR, Wafula E, Wang F, Coruh C, Bernal-Galeano V, Phifer T, dePamphilis CW, Westwood JH, Axtell MJ. MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature. 553: 82-85. PMID 29300014 DOI: 10.1038/Nature25027  0.687
2017 Lin CS, Chen JJ, Chiu CC, Hsiao HC, Yang CJ, Jin XH, Leebens-Mack J, dePamphilis CW, Huang YT, Yang LH, Chang WJ, Kui L, Wong GK, Hu JM, Wang W, et al. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant Journal : For Cell and Molecular Biology. PMID 28258650 DOI: 10.1111/tpj.13525  0.522
2016 Yang Z, Zhang Y, Wafula EK, Honaas LA, Ralph PE, Jones S, Clarke CR, Liu S, Su C, Zhang H, Altman NS, Schuster SC, Timko MP, Yoder JI, Westwood JH, ... dePamphilis CW, et al. Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791104 DOI: 10.1073/Pnas.1608765113  0.482
2016 Wicke S, Müller KF, dePamphilis CW, Quandt D, Bellot S, Schneeweiss GM. Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants. Proceedings of the National Academy of Sciences of the United States of America. PMID 27450087 DOI: 10.1073/pnas.1607576113  0.34
2016 Ishida JK, Wakatake T, Yoshida S, Takebayashi Y, Kasahara H, Wafula E, dePamphilis CW, Namba S, Shirasu K. Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum. The Plant Cell. PMID 27385817 DOI: 10.1105/Tpc.16.00310  0.308
2016 McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, dePamphilis CW, Givnish TJ, Pires JC, Stevenson DW, Leebens-Mack JH. A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales. Genome Biology and Evolution. PMID 26988252 DOI: 10.1093/Gbe/Evw060  0.784
2016 Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, Honaas LA, Ralph PE, Bolin JF, Maass E, Neinhuis C, Wanke S, dePamphilis CW. Detecting and characterizing the highly divergent plastid genome of the nonphotosynthetic parasitic plant Hydnora visseri (Hydnoraceae). Genome Biology and Evolution. PMID 26739167 DOI: 10.1093/Gbe/Evv256  0.556
2015 Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, et al. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. American Journal of Botany. 102: 1089-107. PMID 26199366 DOI: 10.3732/Ajb.1500089  0.343
2015 Edger PP, Heidel-Fischer HM, Bekaert M, Rota J, Glöckner G, Platts AE, Heckel DG, Der JP, Wafula EK, Tang M, Hofberger JA, Smithson A, Hall JC, Blanchette M, Bureau TE, ... ... dePamphilis CW, et al. The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences of the United States of America. PMID 26100883 DOI: 10.1073/Pnas.1503926112  0.473
2015 Yang Z, Wafula EK, Honaas LA, Zhang H, Das M, Fernandez-Aparicio M, Huang K, Bandaranayake PC, Wu B, Der JP, Clarke CR, Ralph PE, Landherr L, Altman NS, Timko MP, ... ... dePamphilis CW, et al. Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. Molecular Biology and Evolution. 32: 767-90. PMID 25534030 DOI: 10.1093/Molbev/Msu343  0.406
2015 Das M, Fernández-Aparicio M, Yang Z, Huang K, Wickett NJ, Alford S, Wafula EK, dePamphilis C, Bouwmeester H, Timko MP, Yoder JI, Westwood JH. Parasitic Plants <i>Striga</i> and <i>Phelipanche</i> Dependent upon Exogenous Strigolactones for Germination Have Retained Genes for Strigolactone Biosynthesis American Journal of Plant Sciences. 6: 1151-1166. DOI: 10.4236/Ajps.2015.68120  0.381
2014 Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, ... ... dePamphilis CW, et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America. 111: E4859-68. PMID 25355905 DOI: 10.1073/Pnas.1323926111  0.422
2014 Kim G, LeBlanc ML, Wafula EK, dePamphilis CW, Westwood JH. Plant science. Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science (New York, N.Y.). 345: 808-11. PMID 25124438 DOI: 10.1126/science.1253122  0.364
2014 McCarthy TW, Der JP, Honaas LA, dePamphilis CW, Anderson CT. Phylogenetic analysis of pectin-related gene families in Physcomitrella patens and nine other plant species yields evolutionary insights into cell walls. Bmc Plant Biology. 14: 79. PMID 24666997 DOI: 10.1186/1471-2229-14-79  0.421
2014 Wicke S, Schäferhoff B, dePamphilis CW, Müller KF. Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae. Molecular Biology and Evolution. 31: 529-45. PMID 24344209 DOI: 10.1093/molbev/mst261  0.399
2013 Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, et al. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science (New York, N.Y.). 342: 1516-7. PMID 24357320 DOI: 10.1126/Science.1241130  0.459
2013 Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW, Knox EB, Palmer JD. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science (New York, N.Y.). 342: 1468-73. PMID 24357311 DOI: 10.1126/Science.1246275  0.37
2013 Naumann J, Salomo K, Der JP, Wafula EK, Bolin JF, Maass E, Frenzke L, Samain MS, Neinhuis C, dePamphilis CW, Wanke S. Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages. Plos One. 8: e79204. PMID 24265760 DOI: 10.1371/Journal.Pone.0079204  0.455
2013 Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, ... ... dePamphilis CW, et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology. 14: R41. PMID 23663246 DOI: 10.1186/Gb-2013-14-5-R41  0.504
2013 Zhang Y, Fernandez-Aparicio M, Wafula EK, Das M, Jiao Y, Wickett NJ, Honaas LA, Ralph PE, Wojciechowski MF, Timko MP, Yoder JI, Westwood JH, Depamphilis CW. Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species. Bmc Evolutionary Biology. 13: 48. PMID 23425243 DOI: 10.1186/1471-2148-13-48  0.595
2013 Bliss BJ, Wanke S, Barakat A, Ayyampalayam S, Wickett N, Wall PK, Jiao Y, Landherr L, Ralph PE, Hu Y, Neinhuis C, Leebens-Mack J, Arumuganathan K, Clifton SW, Maximova SN, ... ... dePamphilis CW, et al. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies. Bmc Plant Biology. 13: 13. PMID 23347749 DOI: 10.1186/1471-2229-13-13  0.548
2013 Honaas LA, Wafula EK, Yang Z, Der JP, Wickett NJ, Altman NS, Taylor CG, Yoder JI, Timko MP, Westwood JH, dePamphilis CW. Functional genomics of a generalist parasitic plant: laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. Bmc Plant Biology. 13: 9. PMID 23302495 DOI: 10.1186/1471-2229-13-9  0.313
2013 Fernández-Aparicio M, Huang K, Wafula EK, Honaas LA, Wickett NJ, Timko MP, Depamphilis CW, Yoder JI, Westwood JH. 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. 40: 3395-3407. PMID 23271128 DOI: 10.1007/S11033-012-2417-Y  0.355
2013 DePamphilis CW, Palmer JD, Rounsley S, Sankoff D, Schuster SC, Ammiraju JSS, Barbazuk WB, Chamala S, Chanderbali AS, Determann R, Hong M, Ralph P, Talag J, Tomsho L, Walts B, et al. The Amborella genome and the evolution of flowering plants Science. 342. DOI: 10.1126/science.1241089  0.437
2012 Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, ... ... Depamphilis CW, et al. A genome triplication associated with early diversification of the core eudicots. Genome Biology. 13: R3. PMID 22280555 DOI: 10.1186/Gb-2012-13-1-R3  0.737
2012 Bandaranayake PC, Tomilov A, Tomilova NB, Ngo QA, Wickett N, dePamphilis CW, Yoder JI. The TvPirin gene is necessary for haustorium development in the parasitic plant Triphysaria versicolor. Plant Physiology. 158: 1046-53. PMID 22128136 DOI: 10.1104/Pp.111.186858  0.326
2012 Westwood JH, Depamphilis CW, Das M, Fernndez-Aparicio M, Honaas LA, Timko MP, Wafula EK, Wickett NJ, Yoder JI. The parasitic plant genome project: New tools for understanding the biology of Orobanche and Striga Weed Science. 60: 295-306. DOI: 10.1614/Ws-D-11-00113.1  0.437
2011 Wickett NJ, Honaas LA, Wafula EK, Das M, Huang K, Wu B, Landherr L, Timko MP, Yoder J, Westwood JH, dePamphilis CW. Transcriptomes of the parasitic plant family Orobanchaceae reveal surprising conservation of chlorophyll synthesis. Current Biology : Cb. 21: 2098-104. PMID 22169535 DOI: 10.1016/J.Cub.2011.11.011  0.477
2011 Naumann J, Symmank L, Samain MS, Müller KF, Neinhuis C, dePamphilis CW, Wanke S. Chasing the hare - evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae). Bmc Evolutionary Biology. 11: 357. PMID 22151585 DOI: 10.1186/1471-2148-11-357  0.488
2011 Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, ... ... dePamphilis CW, et al. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology. 12: R48. PMID 21619600 DOI: 10.1186/Gb-2011-12-5-R48  0.763
2011 Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science (New York, N.Y.). 332: 960-3. PMID 21551031 DOI: 10.1126/Science.1203810  0.456
2011 Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, ... ... dePamphilis CW, et al. Ancestral polyploidy in seed plants and angiosperms. Nature. 473: 97-100. PMID 21478875 DOI: 10.1038/Nature09916  0.706
2011 Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Molecular Biology. 76: 273-97. PMID 21424877 DOI: 10.1007/s11103-011-9762-4  0.411
2011 Der JP, Barker MS, Wickett NJ, dePamphilis CW, Wolf PG. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. Bmc Genomics. 12: 99. PMID 21303537 DOI: 10.1186/1471-2164-12-99  0.536
2011 Liang H, Ayyampalayam S, Wickett N, Barakat A, Xu Y, Landherr L, Ralph PE, Jiao Y, Xu T, Schlarbaum SE, Ma H, Leebens-Mack JH, dePamphilis CW. Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L Tree Genetics and Genomes. 7: 941-954. DOI: 10.1007/S11295-011-0386-2  0.679
2010 Zahn LM, Ma X, Altman NS, Zhang Q, Wall PK, Tian D, Gibas CJ, Gharaibeh R, Leebens-Mack JH, Depamphilis CW, Ma H. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biology. 11: R101. PMID 20950453 DOI: 10.1186/Gb-2010-11-10-R101  0.388
2010 Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, dePamphilis CW. 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. PMID 20181251 DOI: 10.1186/1471-2148-10-61  0.72
2010 Westwood JH, Yoder JI, Timko MP, dePamphilis CW. The evolution of parasitism in plants. Trends in Plant Science. 15: 227-35. PMID 20153240 DOI: 10.1016/j.tplants.2010.01.004  0.338
2010 Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, Depamphilis CW, Graham SW, Pires JC, Stevenson DW, Zomlefer WB, Briggs BG, Duvall MR, Moore MJ, Heaney JM, Soltis DE, et al. Assembling the tree of the monocotyledons: Plastome sequence phylogeny and evolution of Poales Annals of the Missouri Botanical Garden. 97: 584-616. DOI: 10.3417/2010023  0.723
2009 Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Depamphilis CW, Wall PK, Soltis PS. Polyploidy and angiosperm diversification. American Journal of Botany. 96: 336-48. PMID 21628192 DOI: 10.3732/Ajb.0800079  0.487
2009 Sankoff D, Zheng C, Wall PK, dePamphilis C, Leebens-Mack J, Albert VA. Towards improved reconstruction of ancestral gene order in angiosperm phylogeny. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1353-67. PMID 19803735 DOI: 10.1089/Cmb.2009.0103  0.547
2009 Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, ... dePamphilis CW, et al. Comparison of next generation sequencing technologies for transcriptome characterization. Bmc Genomics. 10: 347. PMID 19646272 DOI: 10.1186/1471-2164-10-347  0.319
2009 Shan H, Zahn L, Guindon S, Wall PK, Kong H, Ma H, DePamphilis CW, 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. 26: 2229-44. PMID 19578156 DOI: 10.1093/Molbev/Msp129  0.387
2009 McNeal JR, Kuehl JV, Boore JL, Leebens-Mack J, dePamphilis CW. Parallel loss of plastid introns and their maturase in the genus Cuscuta. Plos One. 4: e5982. PMID 19543388 DOI: 10.1371/Journal.Pone.0005982  0.775
2008 Zheng C, Wall PK, Leebens-Mack J, Albert VA, dePamphilis C, Sankoff D. The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral populus diploid. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7: 261-71. PMID 19642286  0.382
2008 Hu W, dePamphilis CW, Ma H. Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families. Journal of Integrative Plant Biology. 50: 1031-45. PMID 18713354 DOI: 10.1111/J.1744-7909.2008.00681.X  0.421
2008 Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, ... ... DePamphilis C, et al. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology. 26: 541-7. PMID 18464787 DOI: 10.1038/Nbt1360  0.493
2008 Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, ... ... dePamphilis CW, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 452: 991-6. PMID 18432245 DOI: 10.1038/Nature06856  0.513
2008 Yue F, Cui L, dePamphilis CW, Moret BM, Tang J. Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat. Bmc Genomics. 9: S25. PMID 18366615 DOI: 10.1186/1471-2164-9-S1-S25  0.488
2008 Soltis DE, Albert VA, Leebens-Mack J, Palmer JD, Wing RA, dePamphilis CW, Ma H, Carlson JE, Altman N, Kim S, Wall PK, Zuccolo A, Soltis PS. The Amborella genome: an evolutionary reference for plant biology. Genome Biology. 9: 402. PMID 18341710 DOI: 10.1186/Gb-2008-9-3-402  0.503
2008 Wall PK, Leebens-Mack J, Müller KF, Field D, Altman NS, dePamphilis CW. PlantTribes: a gene and gene family resource for comparative genomics in plants. Nucleic Acids Research. 36: D970-6. PMID 18073194 DOI: 10.1093/Nar/Gkm972  0.42
2008 Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV, Plock SA, Wolf PG, DePamphilis CW, Boore JL, Goffinet B. Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. Molecular Biology and Evolution. 25: 393-401. PMID 18056074 DOI: 10.1093/Molbev/Msm267  0.553
2008 Thomas DT, Ahedor AR, Williams CF, DePamphilis C, Crawford DJ, Xiang QY. Genetic analysis of a broad hybrid zone in Aesculus (Sapindaceae): Is there evidence of long-distance pollen dispersal? International Journal of Plant Sciences. 169: 647-657. DOI: 10.1086/533605  0.341
2008 Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, Buzgo M, Landherr LL, Hu Y, DiLoreto DS, Ilut DC, Field D, Tanksley SD, Ma H, DePamphilis CW. 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. DOI: 10.1007/S11295-007-0120-2  0.511
2008 Duarte JM, Wall PK, Zahn LM, Soltis PS, Soltis DE, Leebens-Mack J, Carlson JE, Ma H, DePamphilis CW. Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis Taxon. 57: 1110-1122. DOI: 10.1002/Tax.574007  0.704
2007 Barkman TJ, McNeal JR, Lim SH, Coat G, Croom HB, Young ND, Depamphilis CW. Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. Bmc Evolutionary Biology. 7: 248. PMID 18154671 DOI: 10.1186/1471-2148-7-248  0.73
2007 McNeal JR, Arumugunathan K, Kuehl JV, Boore JL, Depamphilis CW. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). Bmc Biology. 5: 55. PMID 18078516 DOI: 10.1186/1741-7007-5-55  0.779
2007 Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences of the United States of America. 104: 19369-74. PMID 18048330 DOI: 10.1073/Pnas.0709121104  0.798
2007 Soltis DE, Ma H, Frohlich MW, Soltis PS, Albert VA, Oppenheimer DG, Altman NS, dePamphilis C, Leebens-Mack J. The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression Trends in Plant Science. 12: 358-367. PMID 17658290 DOI: 10.1016/J.Tplants.2007.06.012  0.506
2007 Kong H, Landherr LL, Frohlich MW, Leebens-Mack J, Ma H, dePamphilis CW. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. The Plant Journal : For Cell and Molecular Biology. 50: 873-85. PMID 17470057 DOI: 10.1111/J.1365-313X.2007.03097.X  0.387
2007 Liang H, Fang EG, Tomkins JP, Luo M, Kudrna D, Kim HR, Arumuganathan K, Zhao S, Leebens-Mack J, Schlarbaum SE, Banks JA, Depamphilis CW, Mandoli DF, Wing RA, Carlson JE. Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis Tree Genetics and Genomes. 3: 215-225. DOI: 10.1007/S11295-006-0057-X  0.467
2006 Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. Bmc Evolutionary Biology. 6: 77. PMID 17020608 DOI: 10.1186/1471-2148-6-77  0.525
2006 Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, ... ... Depamphilis C, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science (New York, N.Y.). 313: 1596-604. PMID 16973872 DOI: 10.1126/Science.1128691  0.497
2006 Carlson JE, Leebens-Mack JH, Wall PK, Zahn LM, Mueller LA, Landherr LL, Hu Y, Ilut DC, Arrington JM, Choirean S, Becker A, Field D, Tanksley SD, Ma H, dePamphilis CW. EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot. Plant Molecular Biology. 62: 351-69. PMID 16915518 DOI: 10.1007/S11103-006-9025-Y  0.468
2006 Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, et al. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). Omics : a Journal of Integrative Biology. 10: 231-7. PMID 16901231 DOI: 10.1089/Omi.2006.10.231  0.533
2006 McNeal JR, Leebens-Mack JH, Arumuganathan K, Kuehl JV, Boore JL, DePamphilis CW. Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques. 41: 69-73. PMID 16869516 DOI: 10.2144/000112202  0.75
2006 Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, DePamphilis CW. Widespread genome duplications throughout the history of flowering plants Genome Research. 16: 738-749. PMID 16702410 DOI: 10.1101/Gr.4825606  0.517
2006 Cui L, Leebens-Mack J, Wang LS, Tang J, Rymarquis L, Stern DB, dePamphilis CW. Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. Bmc Evolutionary Biology. 6: 13. PMID 16469102 DOI: 10.1186/1471-2148-6-13  0.454
2006 Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, dePamphilis CW. ChloroplastDB: the Chloroplast Genome Database. Nucleic Acids Research. 34: D692-6. PMID 16381961 DOI: 10.1093/Nar/Gkj055  0.504
2006 Duarte JM, Cui L, Wall PK, Zhang Q, Zhang X, Leebens-Mack J, Ma H, Altman N, dePamphilis CW. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Molecular Biology and Evolution. 23: 469-78. PMID 16280546 DOI: 10.1093/Molbev/Msj051  0.625
2006 Leebens-Mack JH, Wall K, Duarte J, Zheng Z, Oppenheimer D, Depamphilis C. A Genomics Approach to the Study of Ancient Polyploidy and Floral Developmental Genetics Advances in Botanical Research. 44: 527-549. DOI: 10.1016/S0065-2296(06)44014-3  0.759
2005 Wang JP, Lindsay BG, Cui L, Wall PK, Marion J, Zhang J, dePamphilis CW. Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. Bmc Bioinformatics. 6: 300. PMID 16351717 DOI: 10.1186/1471-2105-6-300  0.334
2005 Sampedro J, Lee Y, Carey RE, dePamphilis C, Cosgrove DJ. Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family. The Plant Journal : For Cell and Molecular Biology. 44: 409-19. PMID 16236151 DOI: 10.1111/J.1365-313X.2005.02540.X  0.57
2005 Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution. 22: 1948-63. PMID 15944438 DOI: 10.1093/Molbev/Msi191  0.453
2005 Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology. 395: 348-84. PMID 15865976 DOI: 10.1016/S0076-6879(05)95020-9  0.762
2005 Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Solow TM, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo MJ, Frohlich MW, Perl-Treves R, ... ... DePamphilis CW, et al. Floral gene resources from basal angiosperms for comparative genomics research. Bmc Plant Biology. 5: 5. PMID 15799777 DOI: 10.1186/1471-2229-5-5  0.571
2005 Zahn LM, Leebens-Mack J, DePamphilis CW, Ma H, Theissen G. To B or Not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. The Journal of Heredity. 96: 225-40. PMID 15695551 DOI: 10.1093/jhered/esi033  0.33
2005 Zahn LM, Kong H, Leebens-Mack JH, Kim S, Soltis PS, Landherr LL, Soltis DE, Depamphilis CW, Ma H. The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history. Genetics. 169: 2209-23. PMID 15687268 DOI: 10.1534/Genetics.104.037770  0.483
2004 Wang G, Kong H, Sun Y, Zhang X, Zhang W, Altman N, DePamphilis CW, Ma H. Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiology. 135: 1084-99. PMID 15208425 DOI: 10.1104/Pp.104.040436  0.403
2004 Kong H, Leebens-Mack J, Ni W, dePamphilis CW, Ma H. Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications. Molecular Biology and Evolution. 21: 117-28. PMID 14595103 DOI: 10.1093/Molbev/Msh001  0.304
2004 Tang J, Moret BME, Cui L, DePamphilis CW. Phylogenetic reconstruction from arbitrary gene-order data Proceedings - Fourth Ieee Symposium On Bioinformatics and Bioengineering, Bibe 2004. 592-599.  0.42
2003 Nam J, dePamphilis CW, Ma H, Nei M. Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Molecular Biology and Evolution. 20: 1435-47. PMID 12777513 DOI: 10.1093/Molbev/Msg152  0.385
2002 Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, Harris EH, Stern DB. The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. The Plant Cell. 14: 2659-79. PMID 12417694 DOI: 10.1105/Tpc.006155  0.498
2002 Leebens-Mack J, DePamphilis C. Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages. Molecular Biology and Evolution. 19: 1292-302. PMID 12140241 DOI: 10.1093/Oxfordjournals.Molbev.A004190  0.4
2002 Soltis DE, Soltis PS, Albert VA, Oppenheimer DG, DePamphilis CW, Ma H, Frohlich MW, Theißen G. Missing links: The genetic architecture of flower and floral diversification Trends in Plant Science. 7: 22-31. PMID 11804823 DOI: 10.1016/S1360-1385(01)02098-2  0.377
2000 Young ND, DePamphilis CW. Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants Molecular Biology and Evolution. 17: 1933-1941. PMID 11110910  0.377
2000 Barkman TJ, Chenery G, McNeal JR, Lyons-Weiler J, Ellisens WJ, Moore G, Wolfe AD, dePamphilis CW. 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 of the United States of America. 97: 13166-71. PMID 11069280 DOI: 10.1073/Pnas.220427497  0.76
2000 Ma H, DePamphilis C. The ABCs of floral evolution Cell. 101: 5-8. PMID 10778850 DOI: 10.1016/S0092-8674(00)80618-2  0.341
2000 Bowe LM, Coat G, DePamphilis CW. 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 of the United States of America. 97: 4092-4097. PMID 10760278 DOI: 10.1073/pnas.97.8.4092  0.432
2000 Burke JM, Wyatt R, DePamphilis CW, Arnold ML. Nectar characteristics of interspecific hybrids and their parents in Aesculus (Hippocastanaceae) and Iris (Iridaceae) Journal of the Torrey Botanical Society. 127: 200-206. DOI: 10.2307/3088757  0.374
1999 Young ND, Steiner KE, DePamphilis CW. The evolution of parasitism in scrophulariaceae/orobanchaceae: Plastid gene sequences refute an evolutionary transition series Annals of the Missouri Botanical Garden. 86: 876-893.  0.345
1998 Xiang QY, Crawford DJ, Wolfe AD, Tang YC, DePamphilis CW. ORIGIN AND BIOGEOGRAPHY OF AESCULUS L. (HIPPOCASTANACEAE): A MOLECULAR PHYLOGENETIC PERSPECTIVE. Evolution; International Journal of Organic Evolution. 52: 988-997. PMID 28565208 DOI: 10.1111/J.1558-5646.1998.Tb01828.X  0.34
1998 Wolfe AD, dePamphilis CW. The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants. Molecular Biology and Evolution. 15: 1243-58. PMID 9787431  0.387
1997 Nickrent DL, Ouyang Y, Duff RJ, DePamphilis CW. Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Molecular Biology. 34: 717-729. PMID 9278163 DOI: 10.1023/A:1005860632601  0.529
1997 dePamphilis CW, Young ND, Wolfe AD. 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 of the United States of America. 94: 7367-72. PMID 9207097 DOI: 10.1073/pnas.94.14.7367  0.488
1997 Wolfe AD, dePamphilis CW. Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche. Plant Molecular Biology. 33: 965-77. PMID 9154979 DOI: 10.1023/A:1005739223993  0.344
1996 Bowe LM, DePamphilis CW. Effects of RNA editing and gene processing on phylogenetic reconstruction Molecular Biology and Evolution. 13: 1159-1166. PMID 8896368  0.408
1994 Chapell JD, Goral MI, Rodgers SE, dePamphilis CW, Dermody TS. Sequence diversity within the reovirus S2 gene: reovirus genes reassort in nature, and their termini are predicted to form a panhandle motif. Journal of Virology. 68: 750-6. PMID 8289378 DOI: 10.1128/Jvi.68.2.750-756.1994  0.319
1991 Morden CW, Wolfe KH, dePamphilis CW, Palmer JD. Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes. The Embo Journal. 10: 3281-8. PMID 1915295 DOI: 10.1002/J.1460-2075.1991.Tb04892.X  0.453
1991 Taylor GW, Wolfe KH, Morden CW, dePamphilis CW, Palmer JD. Lack of a functional plastid tRNA(Cys) gene is associated with loss of photosynthesis in a lineage of parasitic plants. Current Genetics. 20: 515-8. PMID 1723664 DOI: 10.1007/Bf00334780  0.45
1990 dePamphilis CW, Wyatt R. ELECTROPHORETIC CONFIRMATION OF INTERSPECIFIC HYBRIDIZATION IN AESCULUS (HIPPOCASTANACEAE) AND THE GENETIC STRUCTURE OF A BROAD HYBRID ZONE. Evolution; International Journal of Organic Evolution. 44: 1295-1317. PMID 28563891 DOI: 10.1111/j.1558-5646.1990.tb05233.x  0.449
1990 DePamphilis CW, Palmer JD. Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant Nature. 348: 337-339. PMID 2250706 DOI: 10.1038/348337A0  0.497
1989 dePamphilis CW, Wyatt R. Hybridization and Introgression in Buckeyes (Aesculus: Hippocastanaceae): A Review of the Evidence and a Hypothesis to Explain Long-Distance Gene Flow Systematic Botany. 14: 593. DOI: 10.2307/2419005  0.502
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