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Items: 9

1.

Monitoring dynamic cytotoxic chemotherapy response in castration-resistant prostate cancer using plasma cell-free DNA (cfDNA).

Patsch K, Matasci N, Soundararajan A, Diaz P, Agus DB, Ruderman D, Gross ME.

BMC Res Notes. 2019 May 15;12(1):275. doi: 10.1186/s13104-019-4312-2.

2.

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.

3.

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.

4.

Data mining with iPlant: a meeting report from the 2013 GARNet workshop, Data mining with iPlant.

Martin L, Cook C, Matasci N, Williams J, Bastow R.

J Exp Bot. 2015 Jan;66(1):1-6. doi: 10.1093/jxb/eru402. Epub 2014 Oct 17.

PMID:
25326627
5.

Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls.

Miller AJ, Matasci N, Schwaninger H, Aradhya MK, Prins B, Zhong GY, Simon C, Buckler ES, Myles S.

PLoS One. 2013 Nov 13;8(11):e78680. doi: 10.1371/journal.pone.0078680. eCollection 2013. Erratum in: PLoS One. 2014;9(1). doi:10.1371/annotation/283e5eba-a65d-42a3-a430-6ca0be86147c.

6.

Phylogenetic analysis with the iPlant discovery environment.

Matasci N, McKay S.

Curr Protoc Bioinformatics. 2013 Jun;Chapter 6:Unit6.13. doi: 10.1002/0471250953.bi0613s42.

PMID:
23749754
7.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G.

BMC Bioinformatics. 2013 May 13;14:158. doi: 10.1186/1471-2105-14-158.

8.

The taxonomic name resolution service: an online tool for automated standardization of plant names.

Boyle B, Hopkins N, Lu Z, Raygoza Garay JA, Mozzherin D, Rees T, Matasci N, Narro ML, Piel WH, McKay SJ, Lowry S, Freeland C, Peet RK, Enquist BJ.

BMC Bioinformatics. 2013 Jan 16;14:16. doi: 10.1186/1471-2105-14-16.

9.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D.

Front Plant Sci. 2011 Jul 25;2:34. doi: 10.3389/fpls.2011.00034. eCollection 2011.

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