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Items: 23

1.

Ecological genomics of tropical trees: how local population size and allelic diversity of resistance genes relate to immune responses, cosusceptibility to pathogens, and negative density dependence.

Marden JH, Mangan SA, Peterson MP, Wafula E, Fescemyer HW, Der JP, dePamphilis CW, Comita LS.

Mol Ecol. 2017 May;26(9):2498-2513. doi: 10.1111/mec.13999. Epub 2017 Feb 1.

PMID:
28042895
2.

Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae).

Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, Honaas LA, Ralph PE, Bolin JF, Maass E, Neinhuis C, Wanke S, dePamphilis CW.

Genome Biol Evol. 2016 Jan 6;8(2):345-63. doi: 10.1093/gbe/evv256.

3.

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW.

PLoS One. 2016 Jan 5;11(1):e0146062. doi: 10.1371/journal.pone.0146062. eCollection 2016.

4.

Origin and diversification of wings: Insights from a neopteran insect.

Medved V, Marden JH, Fescemyer HW, Der JP, Liu J, Mahfooz N, Popadić A.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15946-51. doi: 10.1073/pnas.1509517112. Epub 2015 Dec 14.

5.

Origins and diversity of a cosmopolitan fern genus on an island archipelago.

Wolf PG, Rowe CA, Der JP, Schilling MP, Visger CJ, Thomson JA.

AoB Plants. 2015 Oct 20;7. pii: plv118. doi: 10.1093/aobpla/plv118.

6.

An Exploration into Fern Genome Space.

Wolf PG, Sessa EB, Marchant DB, Li FW, Rothfels CJ, Sigel EM, Gitzendanner MA, Visger CJ, Banks JA, Soltis DE, Soltis PS, Pryer KM, Der JP.

Genome Biol Evol. 2015 Aug 26;7(9):2533-44. doi: 10.1093/gbe/evv163.

7.

The butterfly plant arms-race escalated by gene and genome duplications.

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, Wright SI, dePamphilis CW, Eric Schranz M, Barker MS, Conant GC, Wahlberg N, Vogel H, Pires JC, Wheat CW.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8362-6. doi: 10.1073/pnas.1503926112. Epub 2015 Jun 22.

8.

Data access for the 1,000 Plants (1KP) project.

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, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.

9.

Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty.

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, Yoder JI, Westwood JH, dePamphilis CW.

Mol Biol Evol. 2015 Mar;32(3):767-90. doi: 10.1093/molbev/msu343. Epub 2014 Dec 21.

10.

Phylotranscriptomic analysis of the origin and early diversification of land plants.

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, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK, Leebens-Mack J.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68. doi: 10.1073/pnas.1323926111. Epub 2014 Oct 29.

11.

Between two fern genomes.

Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li FW, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG.

Gigascience. 2014 Sep 25;3:15. doi: 10.1186/2047-217X-3-15. eCollection 2014. Review.

12.

Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata.

Williams JS, Der JP, dePamphilis CW, Kao TH.

Plant Cell. 2014 Jul;26(7):2873-88. doi: 10.1105/tpc.114.126920. Epub 2014 Jul 28.

13.

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.

Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J, Burge DO, Pokorny L, Larsson A, Chen T, Weststrand S, Thomas P, Carpenter E, Zhang Y, Tian Z, Chen L, Yan Z, Zhu Y, Sun X, Wang J, Stevenson DW, Crandall-Stotler BJ, Shaw AJ, Deyholos MK, Soltis DE, Graham SW, Windham MD, Langdale JA, Wong GK, Mathews S, Pryer KM.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6672-7. doi: 10.1073/pnas.1319929111. Epub 2014 Apr 14.

14.

Phylogenetic analysis of pectin-related gene families in Physcomitrella patens and nine other plant species yields evolutionary insights into cell walls.

McCarthy TW, Der JP, Honaas LA, dePamphilis CW, Anderson CT.

BMC Plant Biol. 2014 Mar 26;14:79. doi: 10.1186/1471-2229-14-79.

15.

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.

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, Barbazuk WB.

Science. 2013 Dec 20;342(6165):1516-7. doi: 10.1126/science.1241130.

PMID:
24357320
16.

Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages.

Naumann J, Salomo K, Der JP, Wafula EK, Bolin JF, Maass E, Frenzke L, Samain MS, Neinhuis C, dePamphilis CW, Wanke S.

PLoS One. 2013 Nov 12;8(11):e79204. doi: 10.1371/journal.pone.0079204. eCollection 2013.

17.

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).

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, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J.

Genome Biol. 2013 May 10;14(5):R41. doi: 10.1186/gb-2013-14-5-r41.

18.

Functional genomics of a generalist parasitic plant: laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression.

Honaas LA, Wafula EK, Yang Z, Der JP, Wickett NJ, Altman NS, Taylor CG, Yoder JI, Timko MP, Westwood JH, dePamphilis CW.

BMC Plant Biol. 2013 Jan 9;13:9. doi: 10.1186/1471-2229-13-9.

19.

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum.

Der JP, Barker MS, Wickett NJ, dePamphilis CW, Wolf PG.

BMC Genomics. 2011 Feb 8;12:99. doi: 10.1186/1471-2164-12-99.

20.

The evolution of chloroplast genes and genomes in ferns.

Wolf PG, Der JP, Duffy AM, Davidson JB, Grusz AL, Pryer KM.

Plant Mol Biol. 2011 Jul;76(3-5):251-61. doi: 10.1007/s11103-010-9706-4. Epub 2010 Oct 26.

PMID:
20976559
21.

Global chloroplast phylogeny and biogeography of bracken (Pteridium; Dennstaedtiaceae).

Der JP, Thomson JA, Stratford JK, Wolf PG.

Am J Bot. 2009 May;96(5):1041-9. doi: 10.3732/ajb.0800333.

22.

Diversity of soil mycobacterium isolates from three sites that degrade polycyclic aromatic hydrocarbons.

Miller CD, Child R, Hughes JE, Benscai M, Der JP, Sims RC, Anderson AJ.

J Appl Microbiol. 2007 Jun;102(6):1612-24.

23.

Discovery of the photosynthetic relatives of the "Maltese mushroom" Cynomorium.

Nickrent DL, Der JP, Anderson FE.

BMC Evol Biol. 2005 Jun 21;5:38.

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