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Items: 1 to 50 of 124

1.

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace.

Li M, An H, Angelovici R, Bagaza C, Batushansky A, Clark L, Coneva V, Donoghue MJ, Edwards E, Fajardo D, Fang H, Frank MH, Gallaher T, Gebken S, Hill T, Jansky S, Kaur B, Klahs PC, Klein LL, Kuraparthy V, Londo J, Migicovsky Z, Miller A, Mohn R, Myles S, Otoni WC, Pires JC, Rieffer E, Schmerler S, Spriggs E, Topp CN, Van Deynze A, Zhang K, Zhu L, Zink BM, Chitwood DH.

Front Plant Sci. 2018 Apr 25;9:553. doi: 10.3389/fpls.2018.00553. eCollection 2018.

2.

Editorial overview: Genome studies and molecular genetics: Treasure troves of evolution.

Van de Peer Y, Pires JC.

Curr Opin Plant Biol. 2018 Apr;42:iii-v. doi: 10.1016/j.pbi.2018.04.015. Epub 2018 May 8. No abstract available.

PMID:
29748036
3.

Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses.

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2018 May 2;8(1):7120. doi: 10.1038/s41598-018-25620-4.

4.

Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived.

Hao Y, Washburn JD, Rosenthal J, Nielsen B, Lyons E, Edger PP, Pires JC, Conant GC.

Genome Biol Evol. 2018 Mar 1;10(3):999-1011. doi: 10.1093/gbe/evy061.

5.

Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae).

Unruh SA, McKain MR, Lee YI, Yukawa T, McCormick MK, Shefferson RP, Smithson A, Leebens-Mack JH, Pires JC.

Am J Bot. 2018 Apr;105(4):631-640. doi: 10.1002/ajb2.1047. Epub 2018 Apr 2. Erratum in: Am J Bot. 2018 May;105(5):957.

PMID:
29608785
6.

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.

Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, Schmutz J, Lyons E, Pires JC, Edger PP, Conant GC.

PLoS Genet. 2018 Mar 28;14(3):e1007267. doi: 10.1371/journal.pgen.1007267. eCollection 2018 Mar.

7.

Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses.

Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC.

Am J Bot. 2018 Mar;105(3):463-469. doi: 10.1002/ajb2.1040. Epub 2018 Mar 25.

PMID:
29574686
8.

Transcriptome-wide comparison of selenium hyperaccumulator and nonaccumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome.

Wang J, Cappa JJ, Harris JP, Edger PP, Zhou W, Pires JC, Adair M, Unruh SA, Simmons MP, Schiavon M, Pilon-Smits EAH.

Plant Biotechnol J. 2018 Feb 7. doi: 10.1111/pbi.12897. [Epub ahead of print]

9.

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus.

Hurgobin B, Golicz AA, Bayer PE, Chan CK, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin IAP, Pires JC, Chalhoub B, King GJ, Snowdon R, Batley J, Edwards D.

Plant Biotechnol J. 2018 Jul;16(7):1265-1274. doi: 10.1111/pbi.12867. Epub 2018 Jan 10.

10.

Central Obesity is the Key Component in the Association of Metabolic Syndrome With Left Ventricular Global Longitudinal Strain Impairment.

Cañon-Montañez W, Santos ABS, Nunes LA, Pires JCG, Freire CMV, Ribeiro ALP, Mill JG, Bessel M, Duncan BB, Schmidt MI, Foppa M.

Rev Esp Cardiol (Engl Ed). 2018 Jul;71(7):524-530. doi: 10.1016/j.rec.2017.10.008. Epub 2017 Nov 14. English, Spanish.

PMID:
29146481
11.

The asparagus genome sheds light on the origin and evolution of a young Y chromosome.

Harkess A, Zhou J, Xu C, Bowers JE, Van der Hulst R, Ayyampalayam S, Mercati F, Riccardi P, McKain MR, Kakrana A, Tang H, Ray J, Groenendijk J, Arikit S, Mathioni SM, Nakano M, Shan H, Telgmann-Rauber A, Kanno A, Yue Z, Chen H, Li W, Chen Y, Xu X, Zhang Y, Luo S, Chen H, Gao J, Mao Z, Pires JC, Luo M, Kudrna D, Wing RA, Meyers BC, Yi K, Kong H, Lavrijsen P, Sunseri F, Falavigna A, Ye Y, Leebens-Mack JH, Chen G.

Nat Commun. 2017 Nov 2;8(1):1279. doi: 10.1038/s41467-017-01064-8.

12.

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2017 Oct 19;7(1):13528. doi: 10.1038/s41598-017-13236-z. Erratum in: Sci Rep. 2018 May 2;8(1):7120.

13.

Molecular Resources from Transcriptomes in the Brassicaceae Family.

Lopez L, Wolf EM, Pires JC, Edger PP, Koch MA.

Front Plant Sci. 2017 Aug 29;8:1488. doi: 10.3389/fpls.2017.01488. eCollection 2017.

14.

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower.

Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, Childs KL, Washburn JD, Schmitz RJ, Smith GD, Pires JC, Puzey JR.

Plant Cell. 2017 Sep;29(9):2150-2167. doi: 10.1105/tpc.17.00010. Epub 2017 Aug 16.

15.

Anatolian origins and diversification of Aethionema, the sister lineage of the core Brassicaceae.

Mohammadin S, Peterse K, van de Kerke SJ, Chatrou LW, Dönmez AA, Mummenhoff K, Pires JC, Edger PP, Al-Shehbaz IA, Schranz ME.

Am J Bot. 2017 Jul 25. doi: 10.3732/ajb.1700091. [Epub ahead of print]

PMID:
28743759
16.

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

Johnson KL, Cassin AM, Lonsdale A, Wong GK, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ.

Plant Physiol. 2017 Jun;174(2):904-921. doi: 10.1104/pp.17.00295. Epub 2017 Apr 26.

17.

Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

Bird KA, An H, Gazave E, Gore MA, Pires JC, Robertson LD, Labate JA.

Front Plant Sci. 2017 Mar 13;8:321. doi: 10.3389/fpls.2017.00321. eCollection 2017.

18.

Nitrogen Removal from Landfill Leachate by Microalgae.

Pereira SF, Gonçalves AL, Moreira FC, Silva TF, Vilar VJ, Pires JC.

Int J Mol Sci. 2016 Nov 17;17(11). pii: E1926.

19.

The pangenome of an agronomically important crop plant Brassica oleracea.

Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CK, Severn-Ellis A, McCombie WR, Parkin IA, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D.

Nat Commun. 2016 Nov 11;7:13390. doi: 10.1038/ncomms13390.

20.

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae).

McKain MR, McNeal JR, Kellar PR, Eguiarte LE, Pires JC, Leebens-Mack J.

Am J Bot. 2016 Oct;103(10):1717-1729. Epub 2016 Oct 20.

21.

The Evolution of HD2 Proteins in Green Plants.

Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V.

Trends Plant Sci. 2016 Dec;21(12):1008-1016. doi: 10.1016/j.tplants.2016.10.001. Epub 2016 Oct 24. Review.

PMID:
27789157
22.

Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants.

Hackenberg D, McKain MR, Lee SG, Roy Choudhury S, McCann T, Schreier S, Harkess A, Pires JC, Wong GK, Jez JM, Kellogg EA, Pandey S.

New Phytol. 2017 Oct;216(2):562-575. doi: 10.1111/nph.14180. Epub 2016 Sep 16. Erratum in: New Phytol. 2018 Jan;217(2):960.

PMID:
27634188
23.

Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes.

Pires JC, Conant GC.

Annu Rev Genet. 2016 Nov 23;50:113-131. Epub 2016 Sep 12. Review.

PMID:
27617972
24.

Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study.

Barker MS, Husband BC, Pires JC.

Am J Bot. 2016 Jul;103(7):1139-45. doi: 10.3732/ajb.1600272. Epub 2016 Aug 1. No abstract available.

25.

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

Harkess A, Mercati F, Abbate L, McKain M, Pires JC, Sala T, Sunseri F, Falavigna A, Leebens-Mack J.

G3 (Bethesda). 2016 Sep 8;6(9):2679-85. doi: 10.1534/g3.116.030239.

26.

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae).

Burke SV, Wysocki WP, Zuloaga FO, Craine JM, Pires JC, Edger PP, Mayfield-Jones D, Clark LG, Kelchner SA, Duvall MR.

BMC Plant Biol. 2016 Jun 18;16(1):140. doi: 10.1186/s12870-016-0823-3.

27.

Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.

Lane TS, Rempe CS, Davitt J, Staton ME, Peng Y, Soltis DE, Melkonian M, Deyholos M, Leebens-Mack JH, Chase M, Rothfels CJ, Stevenson D, Graham SW, Yu J, Liu T, Pires JC, Edger PP, Zhang Y, Xie Y, Zhu Y, Carpenter E, Wong GK, Stewart CN Jr.

BMC Biotechnol. 2016 May 31;16(1):47. doi: 10.1186/s12896-016-0277-6.

28.

Editorial overview: Genome studies and molecular genetics: Of plant genes, genomes, and genomics.

Van de Peer Y, Pires JC.

Curr Opin Plant Biol. 2016 Apr;30:iv-vi. doi: 10.1016/j.pbi.2016.03.010. Epub 2016 Apr 1. No abstract available.

PMID:
27052806
29.

Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar.

Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Pires JC, Stajich JE, Thomma BP, Unruh S.

G3 (Bethesda). 2015 Dec;5(12):2523-5. No abstract available.

30.

Atmospheric CO2 capture by algae: Negative carbon dioxide emission path.

Moreira D, Pires JCM.

Bioresour Technol. 2016 Sep;215:371-379. doi: 10.1016/j.biortech.2016.03.060. Epub 2016 Mar 14.

PMID:
27005790
31.

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.

McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, dePamphilis CW, Givnish TJ, Pires JC, Stevenson DW, Leebens-Mack JH.

Genome Biol Evol. 2016 Apr 21;8(4):1150-64. doi: 10.1093/gbe/evw060.

32.

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.

33.

Epicardial fat thickness: distribution and association with diabetes mellitus, hypertension and the metabolic syndrome in the ELSA-Brasil study.

Graeff DB, Foppa M, Pires JC, Vigo A, Schmidt MI, Lotufo PA, Mill JG, Duncan BB.

Int J Cardiovasc Imaging. 2016 Apr;32(4):563-72. doi: 10.1007/s10554-015-0810-z. Epub 2015 Nov 19.

PMID:
26585750
34.

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution.

Huang CH, Sun R, Hu Y, Zeng L, Zhang N, Cai L, Zhang Q, Koch MA, Al-Shehbaz I, Edger PP, Pires JC, Tan DY, Zhong Y, Ma H.

Mol Biol Evol. 2016 Feb;33(2):394-412. doi: 10.1093/molbev/msv226. Epub 2015 Oct 29.

35.

Biotechnological potential of Synechocystis salina co-cultures with selected microalgae and cyanobacteria: Nutrients removal, biomass and lipid production.

Gonçalves AL, Pires JC, Simões M.

Bioresour Technol. 2016 Jan;200:279-86. doi: 10.1016/j.biortech.2015.10.023. Epub 2015 Oct 20.

PMID:
26496217
36.

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.

Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, Schnabel RD, Taylor JF, Kerley MS, Pires JC, Lamberson WR, Conant GC.

Nucleic Acids Res. 2015 Nov 16;43(20):9600-12. doi: 10.1093/nar/gkv973. Epub 2015 Sep 29.

37.

Phylogeny and photosynthesis of the grass tribe Paniceae.

Washburn JD, Schnable JC, Davidse G, Pires JC.

Am J Bot. 2015 Sep;102(9):1493-505. doi: 10.3732/ajb.1500222. Epub 2015 Sep 15.

38.

Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae.

Mohammadin S, Edger PP, Pires JC, Schranz ME.

BMC Plant Biol. 2015 Sep 11;15:217. doi: 10.1186/s12870-015-0603-5.

39.

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.

Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson D, Zomlefer WB, Davis JI.

New Phytol. 2016 Jan;209(2):855-70. doi: 10.1111/nph.13617. Epub 2015 Sep 9.

40.

Biodiversity comparison among phylogenetic diversity metrics and between three North American prairies.

Kellar PR, Ahrendsen DL, Aust SK, Jones AR, Pires JC.

Appl Plant Sci. 2015 Jul 7;3(7). pii: apps.1400108. doi: 10.3732/apps.1400108. eCollection 2015 Jul.

41.

Resolving deep relationships of PACMAD grasses: a phylogenomic approach.

Cotton JL, Wysocki WP, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield-Jones D, Duvall MR.

BMC Plant Biol. 2015 Jul 11;15:178. doi: 10.1186/s12870-015-0563-9.

42.

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.

43.

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism.

Norup MF, Petersen G, Burrows S, Bouchenak-Khelladi Y, Leebens-Mack J, Pires JC, Linder HP, Seberg O.

Mol Phylogenet Evol. 2015 Nov;92:25-44. doi: 10.1016/j.ympev.2015.06.002. Epub 2015 Jun 14.

PMID:
26079131
44.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR.

AoB Plants. 2015 May 4;7. pii: plv046. doi: 10.1093/aobpla/plv046.

45.

Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.

Augustin MM, Ruzicka DR, Shukla AK, Augustin JM, Starks CM, O'Neil-Johnson M, McKain MR, Evans BS, Barrett MD, Smithson A, Wong GK, Deyholos MK, Edger PP, Pires JC, Leebens-Mack JH, Mann DA, Kutchan TM.

Plant J. 2015 Jun;82(6):991-1003. doi: 10.1111/tpj.12871.

46.

Unreduced gametes: meiotic mishap or evolutionary mechanism?

Mason AS, Pires JC.

Trends Genet. 2015 Jan;31(1):5-10. doi: 10.1016/j.tig.2014.09.011. Epub 2014 Oct 16. Review.

PMID:
25445549
47.

Nonadditive gene expression in polyploids.

Yoo MJ, Liu X, Pires JC, Soltis PS, Soltis DE.

Annu Rev Genet. 2014;48:485-517. doi: 10.1146/annurev-genet-120213-092159. Review.

PMID:
25421600
48.

Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor.

Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C Jr, Wong GK, Bowman JL.

Mol Phylogenet Evol. 2014 Dec;81:159-73. doi: 10.1016/j.ympev.2014.06.017. Epub 2014 Sep 27.

49.

Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms.

Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C.

Mol Biol Evol. 2014 Dec;31(12):3095-112. doi: 10.1093/molbev/msu252. Epub 2014 Aug 28.

PMID:
25172958
50.

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.

Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P.

Science. 2014 Aug 22;345(6199):950-3. doi: 10.1126/science.1253435. Epub 2014 Aug 21.

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