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Items: 12

1.

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.

Johnson MG, Gardner EM, Liu Y, Medina R, Goffinet B, Shaw AJ, Zerega NJ, Wickett NJ.

Appl Plant Sci. 2016 Jul 12;4(7). pii: apps.1600016. doi: 10.3732/apps.1600016. eCollection 2016 Jul.

2.

Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery.

Gardner EM, Johnson MG, Ragone D, Wickett NJ, Zerega NJ.

Appl Plant Sci. 2016 Jul 13;4(7). pii: apps.1600017. doi: 10.3732/apps.1600017. eCollection 2016 Jul.

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.

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.

5.

Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology.

Wilson AW, Wickett NJ, Grabowski P, Fant J, Borevitz J, Mueller GM.

Mycologia. 2015 Jan-Feb;107(1):217-26. doi: 10.3852/13-278. Epub 2014 Oct 31.

6.

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.

7.

Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family.

Wicke S, Müller KF, de Pamphilis CW, Quandt D, Wickett NJ, Zhang Y, Renner SS, Schneeweiss GM.

Plant Cell. 2013 Oct;25(10):3711-25. doi: 10.1105/tpc.113.113373. Epub 2013 Oct 18.

8.

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species.

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.

BMC Evol Biol. 2013 Feb 20;13:48. doi: 10.1186/1471-2148-13-48.

9.

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.

10.

A genome triplication associated with early diversification of the core eudicots.

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, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GK, Soltis DE, Depamphilis CW.

Genome Biol. 2012 Jan 26;13(1):R3. doi: 10.1186/gb-2012-13-1-r3.

11.

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.

12.

Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta).

Goffinet B, Wickett NJ, Werner O, Ros RM, Shaw AJ, Cox CJ.

Ann Bot. 2007 Apr;99(4):747-53. Epub 2007 Mar 2.

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