Claude dePamphilis - Publications

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

130 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
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  0.4
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  0.32
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  0.4
2019 Honaas LA, Jones S, Farrell N, Kamerow W, Zhang H, Vescio K, Altman NS, Yoder JI, dePamphilis CW. Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor. Bmc Plant Biology. 19: 334. PMID 31370799 DOI: 10.1186/S12870-019-1856-1  0.32
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  0.6
2019 Clermont K, Wang Y, Liu S, Yang Z, dePamphilis CW, Yoder JI, Collakova E, Westwood JH. Comparative Metabolomics of Early Development of the Parasitic Plants and . Metabolites. 9. PMID 31200467 DOI: 10.3390/metabo9060114  0.4
2019 Misra VA, Wafula EK, Wang Y, dePamphilis CW, Timko MP. 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. 19: 196. PMID 31088371 DOI: 10.1186/S12870-019-1786-Y  0.4
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  0.4
2018 Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, ... dePamphilis C, et al. 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. PMID 30368769 DOI: 10.1002/Ajb2.1178  0.4
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  0.32
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  0.4
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  0.4
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  0.6
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  0.6
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  0.6
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  0.4
2016 Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. Plos One. 11: e0146062. PMID 26731733 DOI: 10.1371/Journal.Pone.0146062  0.6
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  0.6
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  0.6
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  0.6
2014 Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, et al. Data access for the 1,000 Plants (1KP) project. Gigascience. 3: 17. PMID 25625010 DOI: 10.1186/2047-217X-3-17  0.6
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  0.6
2014 Williams JS, Der JP, dePamphilis CW, Kao TH. Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata. The Plant Cell. 26: 2873-88. PMID 25070642 DOI: 10.1105/Tpc.114.126920  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.32
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2012 Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, et al. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. Plos One. 7: e50226. PMID 23185583 DOI: 10.1371/Journal.Pone.0050226  0.6
2012 McKain MR, Wickett N, Zhang Y, Ayyampalayam S, McCombie WR, Chase MW, Pires JC, dePamphilis CW, Leebens-Mack J. 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. 99: 397-406. PMID 22301890 DOI: 10.3732/Ajb.1100537  0.6
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  0.4
2012 Adams JP, Adeli A, Hsu CY, Harkess RL, Page GP, Depamphilis CW, Schultz EB, Yuceer C. Plant-based FRET biosensor discriminates environmental zinc levels. Plant Biotechnology Journal. 10: 207-16. PMID 21910820 DOI: 10.1111/J.1467-7652.2011.00656.X  0.6
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  0.6
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  0.6
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  0.6
2011 Hsu CY, Adams JP, Kim H, No K, Ma C, Strauss SH, Drnevich J, Vandervelde L, Ellis JD, Rice BM, Wickett N, Gunter LE, Tuskan GA, Brunner AM, Page GP, ... ... DePamphilis CW, et al. FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar. Proceedings of the National Academy of Sciences of the United States of America. 108: 10756-61. PMID 21653885 DOI: 10.1073/Pnas.1104713108  0.6
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  0.4
2011 Wang LS, Leebens-Mack J, Wall PK, Beckmann K, Depamphilis CW, Warnow T. The impact of multiple protein sequence alignment on phylogenetic estimation Ieee/Acm Transactions On Computational Biology and Bioinformatics. 8: 1108-1119. PMID 21566256 DOI: 10.1109/Tcbb.2009.68  0.6
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  0.6
2011 Adams JP, Adeli A, Hsu CY, Harkess RL, Page GP, dePamphilis CW, Schultz EB, Yuceer C. Poplar maintains zinc homeostasis with heavy metal genes HMA4 and PCS1. Journal of Experimental Botany. 62: 3737-52. PMID 21504875 DOI: 10.1093/Jxb/Err025  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2010 Singh R, Levitt AL, Rajotte EG, Holmes EC, Ostiguy N, Vanengelsdorp D, Lipkin WI, Depamphilis CW, Toth AL, Cox-Foster DL. RNA viruses in hymenopteran pollinators: evidence of inter-Taxa virus transmission via pollen and potential impact on non-Apis hymenopteran species. Plos One. 5: e14357. PMID 21203504 DOI: 10.1371/Journal.Pone.0014357  0.6
2010 Chanderbali AS, Yoo MJ, Zahn LM, Brockington SF, Wall PK, Gitzendanner MA, Albert VA, Leebens-Mack J, Altman NS, Ma H, dePamphilis CW, Soltis DE, Soltis PS. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proceedings of the National Academy of Sciences of the United States of America. 107: 22570-5. PMID 21149731 DOI: 10.1073/Pnas.1013395108  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2009 Zheng C, Kerr Wall P, Leebens-Mack J, DE Pamphilis C, Albert VA, Sankoff D. Gene loss under neighborhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. Journal of Bioinformatics and Computational Biology. 7: 499-520. PMID 19507287 DOI: 10.1142/S0219720009004199  0.6
2009 Bliss BJ, Landherr L, DePamphilis CW, Ma H, Hu Y, Maximova SN. Regeneration and plantlet devel'pment from somatic tissues of Aristolochia fimbriata Plant Cell, Tissue and Organ Culture. 98: 105-114. DOI: 10.1007/S11240-009-9543-9  0.6
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  0.6
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  0.6
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  0.6
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  0.32
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2008 Sankoff D, Zheng C, Wall PK, DePamphilis C, Leebens-Mack J, Albert VA. Internal validation of ancestral gene order reconstruction in angiosperm phylogeny Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5267: 252-264. DOI: 10.1007/978-3-540-87989-3_19  0.6
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  0.6
2007 Barakat A, Wall PK, Diloreto S, Depamphilis CW, Carlson JE. Conservation and divergence of microRNAs in Populus. Bmc Genomics. 8: 481. PMID 18166134 DOI: 10.1186/1471-2164-8-481  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2007 Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, Depamphilis CW. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. The Plant Journal : For Cell and Molecular Biology. 51: 991-1003. PMID 17635767 DOI: 10.1111/J.1365-313X.2007.03197.X  0.6
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  0.6
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  0.6
2006 Modliszewski JL, Thomas DT, Fan C, Crawford DJ, Depamphilis CW, Xiang QY. Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus (Sapindaceae). American Journal of Botany. 93: 377-88. PMID 21646198 DOI: 10.3732/Ajb.93.3.377  0.6
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  0.6
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  0.6
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  0.6
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  0.4
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  0.6
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  0.6
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  0.6
2006 Zahn LM, Leebens-Mack JH, Arrington JM, Hu Y, Landherr LL, dePamphilis CW, Becker A, Theissen G, Ma H. Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events. Evolution & Development. 8: 30-45. PMID 16409381 DOI: 10.1111/J.1525-142X.2006.05073.X  0.6
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  0.6
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  0.6
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  0.6
2005 Parkinson CL, Mower JP, Qiu YL, Shirk AJ, Song K, Young ND, DePamphilis CW, Palmer JD. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. Bmc Evolutionary Biology. 5: 73. PMID 16368004 DOI: 10.1186/1471-2148-5-73  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2005 Young ND, dePamphilis CW. Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function. Bmc Evolutionary Biology. 5: 16. PMID 15713237 DOI: 10.1186/1471-2148-5-16  0.6
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  0.6
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  0.6
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  0.6
2004 Wang JP, Lindsay BG, Leebens-Mack J, Cui L, Wall K, Miller WC, dePamphilis CW. EST clustering error evaluation and correction. Bioinformatics (Oxford, England). 20: 2973-84. PMID 15189818 DOI: 10.1093/Bioinformatics/Bth342  0.6
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  0.6
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.  0.6
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  0.6
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  0.6
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  0.6
2001 Olmstead RG, Depamphilis CW, Wolfe AD, Young ND, Elisons WJ, Reeves PA. Disintegration of the scrophulariaceae. American Journal of Botany. 88: 348-61. PMID 11222255  0.6
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  0.6
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  0.6
2000 Ma H, DePamphilis C. The ABCs of floral evolution Cell. 101: 5-8. PMID 10778850 DOI: 10.1016/S0092-8674(00)80618-2  0.6
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  0.6
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  0.6
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.  0.6
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  0.36
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  0.6
1998 Xiang QY, Crawford DJ, Wolfe AD, Tang YC, DePamphilis CW. Origin and biogeography of Aesculus L. (Hippocastanaceae): A molecular phylogenetic perspective Evolution. 52: 988-997.  0.6
1997 Wolfe A, Elisens W, Watson L, Depamphilis C. Using restriction-site variation of PCR-amplified cpDNA genes for phylogenetic analysis of tribe Cheloneae (Scrophulariaceae). American Journal of Botany. 84: 555. PMID 21708607  0.6
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  0.6
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  0.6
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  0.6
1996 Bowe LM, DePamphilis CW. Effects of RNA editing and gene processing on phylogenetic reconstruction Molecular Biology and Evolution. 13: 1159-1166. PMID 8896368  0.6
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  0.6
1994 Garrison SJ, Depamphilis C. Polymerase Chain Reaction for Educational Settings American Biology Teacher. 56: 476-481. DOI: 10.2307/4449892  0.6
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  0.6
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  0.6
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  0.6
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