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Items: 50

1.

Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes.

Chu P, Wilson GM, Michael TP, Vaiciunas J, Honig J, Lam E.

Plant Mol Biol. 2018 Sep 6. doi: 10.1007/s11103-018-0774-1. [Epub ahead of print]

PMID:
30191440
2.

Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping and Oxford Nanopore technologies.

Hoang PNT, Michael TP, Gilbert S, Chu P, Motley TS, Appenroth KJ, Schubert I, Lam E.

Plant J. 2018 Jul 28. doi: 10.1111/tpj.14049. [Epub ahead of print]

PMID:
30054939
3.

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption.

Minich JJ, Morris MM, Brown M, Doane M, Edwards MS, Michael TP, Dinsdale EA.

PLoS One. 2018 Feb 23;13(2):e0192772. doi: 10.1371/journal.pone.0192772. eCollection 2018.

4.

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.

Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker JR.

Nat Commun. 2018 Feb 7;9(1):541. doi: 10.1038/s41467-018-03016-2.

5.

Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla.

VanBuren R, Wai CM, Ou S, Pardo J, Bryant D, Jiang N, Mockler TC, Edger P, Michael TP.

Nat Commun. 2018 Jan 2;9(1):13. doi: 10.1038/s41467-017-02546-5.

6.

Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes.

Silva SR, Michael TP, Meer EJ, Pinheiro DG, Varani AM, Miranda VFO.

PLoS One. 2018 Jan 2;13(1):e0190321. doi: 10.1371/journal.pone.0190321. eCollection 2018.

7.

Development of microsatellite markers for the carnivorous plant Genlisea aurea (Lentibulariaceae) using genomics data of NGS.

Aranguren-Díaz YC, Varani AM, Michael TP, Miranda VFO.

Mol Biol Rep. 2018 Feb;45(1):57-61. doi: 10.1007/s11033-017-4140-1. Epub 2017 Dec 23.

PMID:
29275442
8.

Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum.

VanBuren R, Wai CM, Zhang Q, Song X, Edger PP, Bryant D, Michael TP, Mockler TC, Bartels D.

Plant Cell Environ. 2017 Oct;40(10):2292-2306. doi: 10.1111/pce.13027.

PMID:
28730594
9.

The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks.

Silva SR, Alvarenga DO, Aranguren Y, Penha HA, Fernandes CC, Pinheiro DG, Oliveira MT, Michael TP, Miranda VFO, Varani AM.

PLoS One. 2017 Jul 19;12(7):e0180484. doi: 10.1371/journal.pone.0180484. eCollection 2017.

10.

The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family.

Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, Michael TP, Varani AM.

PLoS One. 2016 Oct 20;11(10):e0165176. doi: 10.1371/journal.pone.0165176. eCollection 2016.

11.

Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies.

Michael TP, Bryant D, Gutierrez R, Borisjuk N, Chu P, Zhang H, Xia J, Zhou J, Peng H, El Baidouri M, Ten Hallers B, Hastie AR, Liang T, Acosta K, Gilbert S, McEntee C, Jackson SA, Mockler TC, Zhang W, Lam E.

Plant J. 2017 Feb;89(3):617-635. doi: 10.1111/tpj.13400. Epub 2017 Feb 3.

12.

Tcf4 Regulates Synaptic Plasticity, DNA Methylation, and Memory Function.

Kennedy AJ, Rahn EJ, Paulukaitis BS, Savell KE, Kordasiewicz HB, Wang J, Lewis JW, Posey J, Strange SK, Guzman-Karlsson MC, Phillips SE, Decker K, Motley ST, Swayze EE, Ecker DJ, Michael TP, Day JJ, Sweatt JD.

Cell Rep. 2016 Sep 6;16(10):2666-2685. doi: 10.1016/j.celrep.2016.08.004. Epub 2016 Aug 25.

13.

The genome of black raspberry (Rubus occidentalis).

VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA, Dossett M, Finn CE, Bassil NV, Mockler TC.

Plant J. 2016 Sep;87(6):535-47. doi: 10.1111/tpj.13215. Epub 2016 Jul 20.

14.

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.

VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC.

Nature. 2015 Nov 26;527(7579):508-11. doi: 10.1038/nature15714. Epub 2015 Nov 11.

PMID:
26560029
15.

Progress, challenges and the future of crop genomes.

Michael TP, VanBuren R.

Curr Opin Plant Biol. 2015 Apr;24:71-81. doi: 10.1016/j.pbi.2015.02.002. Epub 2015 Feb 19. Review.

PMID:
25703261
16.

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms.

Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G.

Ann Bot. 2014 Dec;114(8):1651-63. doi: 10.1093/aob/mcu189. Epub 2014 Oct 1.

17.

Plant genome size variation: bloating and purging DNA.

Michael TP.

Brief Funct Genomics. 2014 Jul;13(4):308-17. doi: 10.1093/bfgp/elu005. Epub 2014 Mar 20.

PMID:
24651721
18.

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.

Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KF, Messing J.

Nat Commun. 2014;5:3311. doi: 10.1038/ncomms4311.

19.

Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

Priest HD, Fox SE, Rowley ER, Murray JR, Michael TP, Mockler TC.

PLoS One. 2014 Jan 29;9(1):e87499. doi: 10.1371/journal.pone.0087499. eCollection 2014.

20.

Architecture and evolution of a minute plant genome.

Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Pérez SA, de Jesús Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L.

Nature. 2013 Jun 6;498(7452):94-8. doi: 10.1038/nature12132. Epub 2013 May 12.

21.

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.

22.

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.

Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, Lam E.

Plant J. 2013 Jan;73(1):77-90. doi: 10.1111/tpj.12017. Epub 2012 Oct 26.

23.

The tomato genome fleshed out.

Michael TP, Alba R.

Nat Biotechnol. 2012 Aug;30(8):765-7. doi: 10.1038/nbt.2319. No abstract available.

PMID:
22871715
24.

Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.

Filichkin SA, Breton G, Priest HD, Dharmawardhana P, Jaiswal P, Fox SE, Michael TP, Chory J, Kay SA, Mockler TC.

PLoS One. 2011;6(6):e16907. doi: 10.1371/journal.pone.0016907. Epub 2011 Jun 9.

25.

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing.

Lutz KA, Wang W, Zdepski A, Michael TP.

BMC Biotechnol. 2011 May 20;11:54. doi: 10.1186/1472-6750-11-54.

26.

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

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, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV.

Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.

27.

The genome of woodland strawberry (Fragaria vesca).

Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM.

Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26.

28.

Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana.

Hong S, Song HR, Lutz K, Kerstetter RA, Michael TP, McClung CR.

Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):21211-6. doi: 10.1073/pnas.1011987107. Epub 2010 Nov 19.

29.

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

Dayarian A, Michael TP, Sengupta AM.

BMC Bioinformatics. 2010 Jun 24;11:345. doi: 10.1186/1471-2105-11-345.

30.

Filtering error from SOLiD Output.

Sasson A, Michael TP.

Bioinformatics. 2010 Mar 15;26(6):849-50. doi: 10.1093/bioinformatics/btq045.

PMID:
20207696
31.

An SSR-based genetic linkage map of the model grass Brachypodium distachyon.

Garvin DF, McKenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, Wright J, Cheema JJ, Dicks J, Huo N, Hayden DM, Gu Y, Tobias C, Chang JH, Chu A, Trick M, Michael TP, Bevan MW, Snape JW.

Genome. 2010 Jan;53(1):1-13. doi: 10.1139/g09-079.

PMID:
20130744
32.

The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates.

Albert VA, Jobson RW, Michael TP, Taylor DJ.

J Exp Bot. 2010;61(1):5-9. doi: 10.1093/jxb/erp349.

PMID:
20007200
33.

Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana.

Schwartz C, Balasubramanian S, Warthmann N, Michael TP, Lempe J, Sureshkumar S, Kobayashi Y, Maloof JN, Borevitz JO, Chory J, Weigel D.

Genetics. 2009 Oct;183(2):723-32, 1SI-7SI. doi: 10.1534/genetics.109.104984. Epub 2009 Aug 3.

34.

Cytochrome P450 monooxygenases as reporters for circadian-regulated pathways.

Pan Y, Michael TP, Hudson ME, Kay SA, Chory J, Schuler MA.

Plant Physiol. 2009 Jun;150(2):858-78. doi: 10.1104/pp.108.130757. Epub 2009 Apr 22.

35.

Conserved Daily Transcriptional Programs in Carica papaya.

Zdepski A, Wang W, Priest HD, Ali F, Alam M, Mockler TC, Michael TP.

Trop Plant Biol. 2008 Dec;1(3-4):236-245. Epub 2008 Dec 16.

36.

A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana.

Loudet O, Michael TP, Burger BT, Le Metté C, Mockler TC, Weigel D, Chory J.

Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17193-8. doi: 10.1073/pnas.0807264105. Epub 2008 Oct 29.

37.

A morning-specific phytohormone gene expression program underlying rhythmic plant growth.

Michael TP, Breton G, Hazen SP, Priest H, Mockler TC, Kay SA, Chory J.

PLoS Biol. 2008 Sep 16;6(9):e225. doi: 10.1371/journal.pbio.0060225.

38.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

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, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M.

Nature. 2008 Apr 24;452(7190):991-6. doi: 10.1038/nature06856.

39.

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.

Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.

Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

PMID:
18419293
40.

Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.

Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, Hazen SP, Shen R, Priest HD, Sullivan CM, Givan SA, Yanovsky M, Hong F, Kay SA, Chory J.

PLoS Genet. 2008 Feb;4(2):e14. doi: 10.1371/journal.pgen.0040014.

41.

Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock.

Michael TP, Park S, Kim TS, Booth J, Byer A, Sun Q, Chory J, Lee K.

PLoS One. 2007 Aug 29;2(8):e795.

42.

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.

Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE, Kay SA, Chory J, Weigel D, Jones JD, Ecker JR.

Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62. Epub 2007 Jul 12.

43.

The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana.

Balasubramanian S, Sureshkumar S, Agrawal M, Michael TP, Wessinger C, Maloof JN, Clark R, Warthmann N, Chory J, Weigel D.

Nat Genet. 2006 Jun;38(6):711-5. Epub 2006 May 28.

44.

Regulation of flowering time in Arabidopsis by K homology domain proteins.

Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker JR, Chory J, Lin C.

Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12759-64. Epub 2004 Aug 13.

45.

Enhanced fitness conferred by naturally occurring variation in the circadian clock.

Michael TP, Salomé PA, Yu HJ, Spencer TR, Sharp EL, McPeek MA, Alonso JM, Ecker JR, McClung CR.

Science. 2003 Nov 7;302(5647):1049-53.

46.
47.

Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity.

Michael TP, Salome PA, McClung CR.

Proc Natl Acad Sci U S A. 2003 May 27;100(11):6878-83. Epub 2003 May 7.

48.

Phase-specific circadian clock regulatory elements in Arabidopsis.

Michael TP, McClung CR.

Plant Physiol. 2002 Oct;130(2):627-38.

49.

The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis.

Salomé PA, Michael TP, Kearns EV, Fett-Neto AG, Sharrock RA, McClung CR.

Plant Physiol. 2002 Aug;129(4):1674-85.

50.

The Arabidopsis circadian system.

McClung CR, Salomé PA, Michael TP.

Arabidopsis Book. 2002;1:e0044. doi: 10.1199/tab.0044. Epub 2002 Mar 27.

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