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Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album.

Wai CM, Weise SE, Ozersky P, Mockler TC, Michael TP, VanBuren R.

PLoS Genet. 2019 Jun 14;15(6):e1008209. doi: 10.1371/journal.pgen.1008209. eCollection 2019 Jun.


A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.

VanBuren R, Wai CM, Colle M, Wang J, Sullivan S, Bushakra JM, Liachko I, Vining KJ, Dossett M, Finn CE, Jibran R, Chagné D, Childs K, Edger PP, Mockler TC, Bassil NV.

Gigascience. 2018 Aug 1;7(8). doi: 10.1093/gigascience/giy094.


High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L.

Torello Marinoni D, Valentini N, Portis E, Acquadro A, Beltramo C, Mehlenbacher SA, Mockler TC, Rowley ER, Botta R.

PLoS One. 2018 Apr 2;13(4):e0195408. doi: 10.1371/journal.pone.0195408. eCollection 2018.


Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data.

Jibran R, Dzierzon H, Bassil N, Bushakra JM, Edger PP, Sullivan S, Finn CE, Dossett M, Vining KJ, VanBuren R, Mockler TC, Liachko I, Davies KM, Foster TM, Chagné D.

Hortic Res. 2018 Feb 7;5:8. doi: 10.1038/s41438-017-0013-y. eCollection 2018.


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.


Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots.

Huang H, Gehan MA, Huss SE, Alvarez S, Lizarraga C, Gruebbling EL, Gierer J, Naldrett MJ, Bindbeutel RK, Evans BS, Mockler TC, Nusinow DA.

Plant Direct. 2017 Oct 16;1(4):e00018. doi: 10.1002/pld3.18. eCollection 2017 Oct.


Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases.

Begemann MB, Gray BN, January E, Gordon GC, He Y, Liu H, Wu X, Brutnell TP, Mockler TC, Oufattole M.

Sci Rep. 2017 Sep 14;7(1):11606. doi: 10.1038/s41598-017-11760-6.


Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa.

Greenham K, Guadagno CR, Gehan MA, Mockler TC, Weinig C, Ewers BE, McClung CR.

Elife. 2017 Aug 18;6. pii: e29655. doi: 10.7554/eLife.29655.


High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field.

Shakoor N, Lee S, Mockler TC.

Curr Opin Plant Biol. 2017 Aug;38:184-192. doi: 10.1016/j.pbi.2017.05.006. Epub 2017 Jul 21. Review.


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.


Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes.

Boyle G, Richter K, Priest HD, Traver D, Mockler TC, Chang JT, Kay SA, Breton G.

PLoS One. 2017 Jan 11;12(1):e0169923. doi: 10.1371/journal.pone.0169923. eCollection 2017.


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.


Grasses suppress shoot-borne roots to conserve water during drought.

Sebastian J, Yee MC, Goudinho Viana W, Rellán-Álvarez R, Feldman M, Priest HD, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP, Dinneny JR.

Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):8861-6. doi: 10.1073/pnas.1604021113. Epub 2016 Jul 15.


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.


Rapid Synthesis of a Long Double-Stranded Oligonucleotide from a Single-Stranded Nucleotide Using Magnetic Beads and an Oligo Library.

Pengpumkiat S, Koesdjojo M, Rowley ER, Mockler TC, Remcho VT.

PLoS One. 2016 Mar 1;11(3):e0149774. doi: 10.1371/journal.pone.0149774. eCollection 2016.


A glimpse into the future of genome-enabled plant biology from the shores of Cold Spring Harbor.

Rhee SY, Parker JE, Mockler TC.

Genome Biol. 2016 Jan 11;17:3. doi: 10.1186/s13059-016-0870-y.


Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus.

Howe GT, Horvath DP, Dharmawardhana P, Priest HD, Mockler TC, Strauss SH.

Front Plant Sci. 2015 Dec 17;6:989. doi: 10.3389/fpls.2015.00989. eCollection 2015.


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.


Highly sensitive image-derived indices of water-stressed plants using hyperspectral imaging in SWIR and histogram analysis.

Kim DM, Zhang H, Zhou H, Du T, Wu Q, Mockler TC, Berezin MY.

Sci Rep. 2015 Nov 4;5:15919. doi: 10.1038/srep15919.


A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.

Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, Hill ST, McEntee CJ, Warnasooriya SN, Kumar I, Ficor T, Turnipseed S, Gilbert KB, Brutnell TP, Carrington JC, Mockler TC, Baxter I.

Mol Plant. 2015 Oct 5;8(10):1520-35. doi: 10.1016/j.molp.2015.06.005. Epub 2015 Jun 20.


A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica.

Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV.

Theor Appl Genet. 2015 Aug;128(8):1631-46. doi: 10.1007/s00122-015-2541-x. Epub 2015 Jun 3.


Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress.

Filichkin S, Priest HD, Megraw M, Mockler TC.

Curr Opin Plant Biol. 2015 Apr;24:125-35. doi: 10.1016/j.pbi.2015.02.008. Epub 2015 Mar 30. Review.


Editorial overview: genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops.

Lee I, Mockler TC.

Curr Opin Plant Biol. 2015 Apr;24:iv-vi. doi: 10.1016/j.pbi.2015.03.001. Epub 2015 Mar 26. No abstract available.


Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors.

Carbonell A, Fahlgren N, Mitchell S, Cox KL Jr, Reilly KC, Mockler TC, Carrington JC.

Plant J. 2015 Jun;82(6):1061-75. doi: 10.1111/tpj.12835. Epub 2015 May 20.


Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.

Filichkin SA, Cumbie JS, Dharmawardhana P, Jaiswal P, Chang JH, Palusa SG, Reddy AS, Megraw M, Mockler TC.

Mol Plant. 2015 Feb;8(2):207-27. doi: 10.1016/j.molp.2014.10.011. Epub 2015 Jan 8.


Transcriptional networks-crops, clocks, and abiotic stress.

Gehan MA, Greenham K, Mockler TC, McClung CR.

Curr Opin Plant Biol. 2015 Apr;24:39-46. doi: 10.1016/j.pbi.2015.01.004. Epub 2015 Feb 1. Review.


Translatome analyses capture of opposing tissue-specific brassinosteroid signals orchestrating root meristem differentiation.

Vragović K, Sela A, Friedlander-Shani L, Fridman Y, Hacham Y, Holland N, Bartom E, Mockler TC, Savaldi-Goldstein S.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):923-8. doi: 10.1073/pnas.1417947112. Epub 2015 Jan 5.


Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.

Filichkin SA, Cumbie JS, Dharmawadhana JP, Jaiswal P, Chang JH, Palusa SG, Reddy AS, Megraw M, Mockler TC.

Mol Plant. 2014 Nov 3. pii: ssu130. [Epub ahead of print]


Comparative analyses of C₄ and C₃ photosynthesis in developing leaves of maize and rice.

Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W, Xu J, Weissmann S, Studer A, Li P, Zhang C, LaRue T, Shao Y, Ding Z, Sun Q, Patel RV, Turgeon R, Zhu X, Provart NJ, Mockler TC, Fernie AR, Stitt M, Liu P, Brutnell TP.

Nat Biotechnol. 2014 Nov;32(11):1158-65. doi: 10.1038/nbt.3019. Epub 2014 Oct 12.


A new alternative in plant retrograde signaling.

Jung HS, Mockler TC.

Genome Biol. 2014 May 30;15(5):117. doi: 10.1186/gb4178.


Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.

Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP.

Plant J. 2014 Aug;79(3):361-74. doi: 10.1111/tpj.12569. Epub 2014 Jul 15.


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.


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.


Sequencing and characterization of the anadromous steelhead (Oncorhynchus mykiss) transcriptome.

Fox SE, Christie MR, Marine M, Priest HD, Mockler TC, Blouin MS.

Mar Genomics. 2014 Jun;15:13-5. doi: 10.1016/j.margen.2013.12.001. Epub 2014 Jan 17.


Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon.

Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, Green PJ.

Genome Biol. 2013 Dec 24;14(12):R145. doi: 10.1186/gb-2013-14-12-r145.


Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light.

Jung HS, Crisp PA, Estavillo GM, Cole B, Hong F, Mockler TC, Pogson BJ, Chory J.

Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14474-9. doi: 10.1073/pnas.1311632110. Epub 2013 Aug 5.


Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon.

Trabucco GM, Matos DA, Lee SJ, Saathoff AJ, Priest HD, Mockler TC, Sarath G, Hazen SP.

BMC Biotechnol. 2013 Jul 31;13:61. doi: 10.1186/1472-6750-13-61.


Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.

Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH.

BMC Plant Biol. 2013 Jun 25;13:92. doi: 10.1186/1471-2229-13-92.


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.


Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry.

Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A.

PLoS One. 2012;7(12):e48305. doi: 10.1371/journal.pone.0048305. Epub 2012 Dec 20.


Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.

Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QC, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA.

New Phytol. 2012 Nov;196(3):713-25. doi: 10.1111/j.1469-8137.2012.04258.x. Epub 2012 Aug 3.


Host-selective toxins of Pyrenophora tritici-repentis induce common responses associated with host susceptibility.

Pandelova I, Figueroa M, Wilhelm LJ, Manning VA, Mankaney AN, Mockler TC, Ciuffetti LM.

PLoS One. 2012;7(7):e40240. doi: 10.1371/journal.pone.0040240. Epub 2012 Jul 6.


Unproductive alternative splicing and nonsense mRNAs: a widespread phenomenon among plant circadian clock genes.

Filichkin SA, Mockler TC.

Biol Direct. 2012 Jul 2;7:20. doi: 10.1186/1745-6150-7-20.


Detection and quantification of alternative splicing variants using RNA-seq.

Bryant DW Jr, Priest HD, Mockler TC.

Methods Mol Biol. 2012;883:97-110. doi: 10.1007/978-1-61779-839-9_7.


Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses.

Li C, Rudi H, Stockinger EJ, Cheng H, Cao M, Fox SE, Mockler TC, Westereng B, Fjellheim S, Rognli OA, Sandve SR.

BMC Plant Biol. 2012 May 8;12:65. doi: 10.1186/1471-2229-12-65.


Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm.

Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C.

PLoS One. 2012;7(4):e35668. doi: 10.1371/journal.pone.0035668. Epub 2012 Apr 20. Erratum in: PLoS One. 2012;7(6). doi:10.1371/annotation/33f1ba92-c304-4757-91aa-555de64a0768.


Exploring the switchgrass transcriptome using second-generation sequencing technology.

Wang Y, Zeng X, Iyer NJ, Bryant DW, Mockler TC, Mahalingam R.

PLoS One. 2012;7(3):e34225. doi: 10.1371/journal.pone.0034225. Epub 2012 Mar 29.


Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH.

BMC Genomics. 2012 Jan 17;13:27. doi: 10.1186/1471-2164-13-27.


Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis.

Atwood A, DeConde R, Wang SS, Mockler TC, Sabir JS, Ideker T, Kay SA.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18560-5. doi: 10.1073/pnas.1115753108. Epub 2011 Oct 31.


GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH.

PLoS One. 2011;6(10):e25279. doi: 10.1371/journal.pone.0025279. Epub 2011 Oct 6.

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