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Items: 27

1.

Plant Extracellular Vesicles Contain Diverse Small RNA Species and Are Enriched in 10 to 17 Nucleotide "Tiny" RNAs.

Baldrich P, Rutter BD, Zand Karimi H, Podicheti R, Meyers BC, Innes RW.

Plant Cell. 2019 Jan 31. pii: tpc.00872.2018. doi: 10.1105/tpc.18.00872. [Epub ahead of print]

2.

RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis.

McKinlay A, Podicheti R, Wendte JM, Cocklin R, Rusch DB.

RNA Biol. 2018 Feb 1;15(2):269-279. doi: 10.1080/15476286.2017.1409930. Epub 2017 Dec 21.

3.

Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins.

Yang T, Fang L, Sanders S, Jayanthi S, Rajan G, Podicheti R, Thallapuranam SK, Mockaitis K, Medina-Bolivar F.

J Biol Chem. 2018 Jan 5;293(1):28-46. doi: 10.1074/jbc.RA117.000564. Epub 2017 Nov 20.

4.

Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes.

Wang J, Blevins T, Podicheti R, Haag JR, Tan EH, Wang F, Pikaard CS.

Genes Dev. 2017 Aug 1;31(15):1601-1614. doi: 10.1101/gad.301499.117. Epub 2017 Sep 7.

5.

Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.

Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch DB, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, Decaestecker E, De Schamphelaere KAC, De Meester L.

Mol Ecol. 2018 Feb;27(4):886-897. doi: 10.1111/mec.14261. Epub 2017 Aug 19.

6.

Mismatch Repair Proteins Initiate Epigenetic Alterations during Inflammation-Driven Tumorigenesis.

Maiuri AR, Peng M, Podicheti R, Sriramkumar S, Kamplain CM, Rusch DB, DeStefano Shields CE, Sears CL, O'Hagan HM.

Cancer Res. 2017 Jul 1;77(13):3467-3478. doi: 10.1158/0008-5472.CAN-17-0056. Epub 2017 May 18. Erratum in: Cancer Res. 2018 Jan 15;78(2):584.

7.

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, Laforsch C, Petrusek A, Beckerman AP, Little TJ, Chaturvedi A, Pfrender ME, De Meester L, Frilander MJ.

Sci Data. 2017 Jan 31;4:170006. doi: 10.1038/sdata.2017.6. No abstract available.

8.

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, Laforsch C, Petrusek A, Beckerman AP, Little TJ, Chaturvedi A, Pfrender ME, De Meester L, Frilander MJ.

Sci Data. 2016 May 10;3:160030. doi: 10.1038/sdata.2016.30. Erratum in: Sci Data. 2017 Jan 31;4:170006. Rush, Douglas [corrected to Rusch, Douglas B].

9.

Correction: The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis.

Hématy K, Bellec Y, Podicheti R, Bouteiller N, Anne P, Morineau C, Haslam RP, Beaudoin F, Napier JA, Mockaitis K, Gagliardi D, Vaucheret H, Lange H, Faure JD.

PLoS Genet. 2016 Mar 23;12(3):e1005958. doi: 10.1371/journal.pgen.1005958. eCollection 2016 Mar. No abstract available.

10.

The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis.

Hématy K, Bellec Y, Podicheti R, Bouteiller N, Anne P, Morineau C, Haslam RP, Beaudoin F, Napier JA, Mockaitis K, Gagliardi D, Vaucheret H, Lange H, Faure JD.

PLoS Genet. 2016 Feb 1;12(2):e1005817. doi: 10.1371/journal.pgen.1005817. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 Mar;12(3):e1005958.

11.

Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis.

Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, Tang H, Pikaard CS.

Elife. 2015 Oct 2;4:e09591. doi: 10.7554/eLife.09591.

12.

Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp.

Kilaru A, Cao X, Dabbs PB, Sung HJ, Rahman MM, Thrower N, Zynda G, Podicheti R, Ibarra-Laclette E, Herrera-Estrella L, Mockaitis K, Ohlrogge JB.

BMC Plant Biol. 2015 Aug 16;15:203. doi: 10.1186/s12870-015-0586-2.

13.

DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila.

Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR.

Nucleic Acids Res. 2015 Oct 15;43(18):8746-61. doi: 10.1093/nar/gkv766. Epub 2015 Jul 30.

14.

FEATnotator: A tool for integrated annotation of sequence features and variation, facilitating interpretation in genomics experiments.

Podicheti R, Mockaitis K.

Methods. 2015 Jun;79-80:11-7. doi: 10.1016/j.ymeth.2015.04.028. Epub 2015 Apr 29.

PMID:
25934264
15.

Mapping RNA Sequences that Contact Viral Capsid Proteins in Virions.

Kao CC, Chuang E, Ford J, Huang J, Podicheti R, Rusch DB.

Bio Protoc. 2014 Jul 20;7(14). pii: e2398. doi: 10.21769/BioProtoc.2398.

16.

Evolutionary relationship of disease resistance genes in soybean and Arabidopsis specific for the Pseudomonas syringae effectors AvrB and AvrRpm1.

Ashfield T, Redditt T, Russell A, Kessens R, Rodibaugh N, Galloway L, Kang Q, Podicheti R, Innes RW.

Plant Physiol. 2014 Sep;166(1):235-51. doi: 10.1104/pp.114.244715. Epub 2014 Jul 17.

17.

A two-step process for epigenetic inheritance in Arabidopsis.

Blevins T, Pontvianne F, Cocklin R, Podicheti R, Chandrasekhara C, Yerneni S, Braun C, Lee B, Rusch D, Mockaitis K, Tang H, Pikaard CS.

Mol Cell. 2014 Apr 10;54(1):30-42. doi: 10.1016/j.molcel.2014.02.019. Epub 2014 Mar 20.

18.

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.

Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D 3rd, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffler BE, Stack JC, Feltus FA, Mustiga GM, Amores F, Phillips W, Marelli JP, May GD, Shapiro H, Ma J, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN.

Genome Biol. 2013 Jun 3;14(6):r53. doi: 10.1186/gb-2013-14-6-r53.

19.

Camelina seed transcriptome: a tool for meal and oil improvement and translational research.

Nguyen HT, Silva JE, Podicheti R, Macrander J, Yang W, Nazarenus TJ, Nam JW, Jaworski JG, Lu C, Scheffler BE, Mockaitis K, Cahoon EB.

Plant Biotechnol J. 2013 Aug;11(6):759-69. doi: 10.1111/pbi.12068. Epub 2013 Apr 3.

20.

De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system.

Peterson MP, Whittaker DJ, Ambreth S, Sureshchandra S, Buechlein A, Podicheti R, Choi JH, Lai Z, Mockatis K, Colbourne J, Tang H, Ketterson ED.

BMC Genomics. 2012 Jul 9;13:305. doi: 10.1186/1471-2164-13-305.

21.

Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine.

Ashfield T, Egan AN, Pfeil BE, Chen NW, Podicheti R, Ratnaparkhe MB, Ameline-Torregrosa C, Denny R, Cannon S, Doyle JJ, Geffroy V, Roe BA, Saghai Maroof MA, Young ND, Innes RW.

Plant Physiol. 2012 May;159(1):336-54. doi: 10.1104/pp.112.195040. Epub 2012 Mar 28.

22.

Administering GBrowse sites with WebGBrowse.

Podicheti R, Dong Q.

Curr Protoc Bioinformatics. 2011 Mar;Chapter 9:Unit 9.14. doi: 10.1002/0471250953.bi0914s33.

PMID:
21400697
23.

An Ergatis-based prokaryotic genome annotation web server.

Hemmerich C, Buechlein A, Podicheti R, Revanna KV, Dong Q.

Bioinformatics. 2010 Apr 15;26(8):1122-4. doi: 10.1093/bioinformatics/btq090. Epub 2010 Mar 1.

PMID:
20194626
24.

Using WebGBrowse to visualize genome annotation on GBrowse.

Podicheti R, Dong Q.

Cold Spring Harb Protoc. 2010 Mar;2010(3):pdb.prot5392. doi: 10.1101/pdb.prot5392.

PMID:
20194461
25.

WebGBrowse--a web server for GBrowse.

Podicheti R, Gollapudi R, Dong Q.

Bioinformatics. 2009 Jun 15;25(12):1550-1. doi: 10.1093/bioinformatics/btp239. Epub 2009 Apr 8.

PMID:
19357095
26.

Replication of nonautonomous retroelements in soybean appears to be both recent and common.

Wawrzynski A, Ashfield T, Chen NW, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Howell S, Ilut D, Lai H, Del Campo SM, Metcalf M, O'Bleness M, Pfeil BE, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Tucker DM, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND, Innes RW.

Plant Physiol. 2008 Dec;148(4):1760-71. doi: 10.1104/pp.108.127910. Epub 2008 Oct 24.

27.

Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.

Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NW, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND.

Plant Physiol. 2008 Dec;148(4):1740-59. doi: 10.1104/pp.108.127902. Epub 2008 Oct 8.

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