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Items: 21

1.

Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants.

Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6494-6499. doi: 10.1073/pnas.1721487115. Epub 2018 May 16.

2.

"Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run".

Doidy J, Li Y, Neymotin B, Edwards MB, Varala K, Gresham D, Coruzzi GM.

BMC Genomics. 2016 Feb 3;17:92. doi: 10.1186/s12864-016-2410-2.

3.

"Hit-and-Run" leaves its mark: catalyst transcription factors and chromatin modification.

Varala K, Li Y, Marshall-Colón A, Para A, Coruzzi GM.

Bioessays. 2015 Aug;37(8):851-6. doi: 10.1002/bies.201400205. Epub 2015 Jun 23. Review.

4.

From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks.

Li Y, Varala K, Coruzzi GM.

Trends Genet. 2015 Sep;31(9):509-15. doi: 10.1016/j.tig.2015.05.005. Epub 2015 Jun 10. Review.

5.

Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.

Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané JM.

PLoS Genet. 2014 Jul 17;10(7):e1004487. doi: 10.1371/journal.pgen.1004487. eCollection 2014 Jul.

6.

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.

Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10371-6. doi: 10.1073/pnas.1404657111. Epub 2014 Jun 23.

7.

A survey of the small RNA population during far-red light-induced apical hook opening.

Li Y, Varala K, Hudson ME.

Front Plant Sci. 2014 Apr 29;5:156. doi: 10.3389/fpls.2014.00156. eCollection 2014.

8.

A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants.

Léran S, Varala K, Boyer JC, Chiurazzi M, Crawford N, Daniel-Vedele F, David L, Dickstein R, Fernandez E, Forde B, Gassmann W, Geiger D, Gojon A, Gong JM, Halkier BA, Harris JM, Hedrich R, Limami AM, Rentsch D, Seo M, Tsay YF, Zhang M, Coruzzi G, Lacombe B.

Trends Plant Sci. 2014 Jan;19(1):5-9. doi: 10.1016/j.tplants.2013.08.008. Epub 2013 Sep 18.

PMID:
24055139
9.

The inheritance pattern of 24 nt siRNA clusters in arabidopsis hybrids is influenced by proximity to transposable elements.

Li Y, Varala K, Moose SP, Hudson ME.

PLoS One. 2012;7(10):e47043. doi: 10.1371/journal.pone.0047043. Epub 2012 Oct 31.

10.

Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max.

Zabala G, Campos E, Varala KK, Bloomfield S, Jones SI, Win H, Tuteja JH, Calla B, Clough SJ, Hudson M, Vodkin LO.

BMC Plant Biol. 2012 Oct 2;12:177. doi: 10.1186/1471-2229-12-177.

11.

Repeat associated small RNAs vary among parents and following hybridization in maize.

Barber WT, Zhang W, Win H, Varala KK, Dorweiler JE, Hudson ME, Moose SP.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10444-9. doi: 10.1073/pnas.1202073109. Epub 2012 Jun 11.

12.

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy.

Swaminathan K, Chae WB, Mitros T, Varala K, Xie L, Barling A, Glowacka K, Hall M, Jezowski S, Ming R, Hudson M, Juvik JA, Rokhsar DS, Moose SP.

BMC Genomics. 2012 Apr 24;13:142. doi: 10.1186/1471-2164-13-142.

13.

Rapid genotyping of soybean cultivars using high throughput sequencing.

Varala K, Swaminathan K, Li Y, Hudson ME.

PLoS One. 2011;6(9):e24811. doi: 10.1371/journal.pone.0024811. Epub 2011 Sep 20.

14.

Genes involved in convergent evolution of eusociality in bees.

Woodard SH, Fischman BJ, Venkat A, Hudson ME, Varala K, Cameron SA, Clark AG, Robinson GE.

Proc Natl Acad Sci U S A. 2011 May 3;108(18):7472-7. doi: 10.1073/pnas.1103457108. Epub 2011 Apr 11.

15.

A fluorescence in situ hybridization system for karyotyping soybean.

Findley SD, Cannon S, Varala K, Du J, Ma J, Hudson ME, Birchler JA, Stacey G.

Genetics. 2010 Jul;185(3):727-44. doi: 10.1534/genetics.109.113753. Epub 2010 Apr 26.

16.

Brain transcriptomic analysis in paper wasps identifies genes associated with behaviour across social insect lineages.

Toth AL, Varala K, Henshaw MT, Rodriguez-Zas SL, Hudson ME, Robinson GE.

Proc Biol Sci. 2010 Jul 22;277(1691):2139-48. doi: 10.1098/rspb.2010.0090. Epub 2010 Mar 17.

17.

Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.

Swaminathan K, Alabady MS, Varala K, De Paoli E, Ho I, Rokhsar DS, Arumuganathan AK, Ming R, Green PJ, Meyers BC, Moose SP, Hudson ME.

Genome Biol. 2010;11(2):R12. doi: 10.1186/gb-2010-11-2-r12. Epub 2010 Feb 3.

18.

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella.

Schwarz D, Robertson HM, Feder JL, Varala K, Hudson ME, Ragland GJ, Hahn DA, Berlocher SH.

BMC Genomics. 2009 Dec 27;10:633. doi: 10.1186/1471-2164-10-633.

19.

Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats.

Tuteja JH, Zabala G, Varala K, Hudson M, Vodkin LO.

Plant Cell. 2009 Oct;21(10):3063-77. doi: 10.1105/tpc.109.069856. Epub 2009 Oct 9. Erratum in: Plant Cell. 2010 May;22(5):1647.

20.

Wasp gene expression supports an evolutionary link between maternal behavior and eusociality.

Toth AL, Varala K, Newman TC, Miguez FE, Hutchison SK, Willoughby DA, Simons JF, Egholm M, Hunt JH, Hudson ME, Robinson GE.

Science. 2007 Oct 19;318(5849):441-4. Epub 2007 Sep 27.

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