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Items: 30

1.

PlantSimLab - a modeling and simulation web tool for plant biologists.

Ha S, Dimitrova E, Hoops S, Altarawy D, Ansariola M, Deb D, Glazebrook J, Hillmer R, Shahin H, Katagiri F, McDowell J, Megraw M, Setubal J, Tyler BM, Laubenbacher R.

BMC Bioinformatics. 2019 Oct 21;20(1):508. doi: 10.1186/s12859-019-3094-9.

2.

Identification of transcription factors from NF-Y, NAC, and SPL families responding to osmotic stress in multiple tomato varieties.

Filichkin SA, Ansariola M, Fraser VN, Megraw M.

Plant Sci. 2018 Sep;274:441-450. doi: 10.1016/j.plantsci.2018.06.021. Epub 2018 Jun 27.

PMID:
30080633
3.

NanoCAGE-XL: An Approach to High-Confidence Transcription Start Site Sequencing.

Ivanchenko MG, Megraw M.

Methods Mol Biol. 2018;1830:225-237. doi: 10.1007/978-1-4939-8657-6_13.

PMID:
30043373
4.

IndeCut evaluates performance of network motif discovery algorithms.

Ansariola M, Megraw M, Koslicki D.

Bioinformatics. 2018 May 1;34(9):1514-1521. doi: 10.1093/bioinformatics/btx798.

5.

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. No abstract available.

6.

DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing.

Filichkin SA, Megraw M.

Methods Mol Biol. 2017;1629:141-154. doi: 10.1007/978-1-4939-7125-1_10.

PMID:
28623584
7.

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gordân R, Megraw M, Brady SM, Benfey PN.

Dev Cell. 2016 Dec 5;39(5):585-596. doi: 10.1016/j.devcel.2016.09.031. Epub 2016 Oct 27.

8.

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.

Megraw M, Cumbie JS, Ivanchenko MG, Filichkin SA.

Plant Cell. 2016 Feb;28(2):286-303. doi: 10.1105/tpc.15.00852. Epub 2016 Feb 11. Review.

9.

Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana.

Cumbie JS, Filichkin SA, Megraw M.

Plant Methods. 2015 Sep 4;11:42. doi: 10.1186/s13007-015-0087-1. eCollection 2015.

10.

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.

Cumbie JS, Ivanchenko MG, Megraw M.

BMC Genomics. 2015 Aug 13;16:597. doi: 10.1186/s12864-015-1670-6.

11.

TIPR: transcription initiation pattern recognition on a genome scale.

Morton T, Wong WK, Megraw M.

Bioinformatics. 2015 Dec 1;31(23):3725-32. doi: 10.1093/bioinformatics/btv464. Epub 2015 Aug 8.

12.

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.

PMID:
25835141
13.

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.

14.

The cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation.

Ivanchenko MG, Zhu J, Wang B, Medvecká E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky JG, Friml J, Geisler M.

Development. 2015 Feb 15;142(4):712-21. doi: 10.1242/dev.113225. Epub 2015 Jan 23.

15.

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]

PMID:
25366180
16.

A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.

Gouthu S, O'Neil ST, Di Y, Ansarolia M, Megraw M, Deluc LG.

J Exp Bot. 2014 Nov;65(20):5889-902. doi: 10.1093/jxb/eru329. Epub 2014 Aug 18.

17.

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M.

Plant Cell. 2014 Jul;26(7):2746-60. doi: 10.1105/tpc.114.125617. Epub 2014 Jul 17.

18.

Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.

Megraw M, Mukherjee S, Ohler U.

Genome Biol. 2013 Aug 23;14(8):R85. doi: 10.1186/gb-2013-14-8-r85.

19.

The protein expression landscape of the Arabidopsis root.

Petricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA, Grossniklaus U, Benfey PN.

Proc Natl Acad Sci U S A. 2012 May 1;109(18):6811-8. doi: 10.1073/pnas.1202546109. Epub 2012 Mar 23.

20.

A stele-enriched gene regulatory network in the Arabidopsis root.

Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN.

Mol Syst Biol. 2011 Jan 18;7:459. doi: 10.1038/msb.2010.114.

21.

Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency.

Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K.

J Biol Chem. 2010 Oct 22;285(43):33358-70. doi: 10.1074/jbc.M110.138362. Epub 2010 Aug 17.

22.

miRGen 2.0: a database of microRNA genomic information and regulation.

Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG.

Nucleic Acids Res. 2010 Jan;38(Database issue):D137-41. doi: 10.1093/nar/gkp888. Epub 2009 Oct 22.

23.

MicroRNA promoter analysis.

Megraw M, Hatzigeorgiou AG.

Methods Mol Biol. 2010;592:149-61. doi: 10.1007/978-1-60327-005-2_11.

PMID:
19802595
24.

A transcription factor affinity-based code for mammalian transcription initiation.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG.

Genome Res. 2009 Apr;19(4):644-56. doi: 10.1101/gr.085449.108. Epub 2009 Jan 13.

25.

Frequency and fate of microRNA editing in human brain.

Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K.

Nucleic Acids Res. 2008 Sep;36(16):5270-80. doi: 10.1093/nar/gkn479. Epub 2008 Aug 6.

26.

Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer.

Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, Yang N, Liu CG, Giannakakis A, Alexiou P, Hasegawa K, Johnstone CN, Megraw MS, Adams S, Lassus H, Huang J, Kaur S, Liang S, Sethupathy P, Leminen A, Simossis VA, Sandaltzopoulos R, Naomoto Y, Katsaros D, Gimotty PA, DeMichele A, Huang Q, Bützow R, Rustgi AK, Weber BL, Birrer MJ, Hatzigeorgiou AG, Croce CM, Coukos G.

Proc Natl Acad Sci U S A. 2008 May 13;105(19):7004-9. doi: 10.1073/pnas.0801615105. Epub 2008 May 5.

27.

miRGen: a database for the study of animal microRNA genomic organization and function.

Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG.

Nucleic Acids Res. 2007 Jan;35(Database issue):D149-55. Epub 2006 Nov 15.

28.

A guide through present computational approaches for the identification of mammalian microRNA targets.

Sethupathy P, Megraw M, Hatzigeorgiou AG.

Nat Methods. 2006 Nov;3(11):881-6.

PMID:
17060911
29.

MicroRNA promoter element discovery in Arabidopsis.

Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG.

RNA. 2006 Sep;12(9):1612-9. Epub 2006 Aug 3.

30.

microRNAs exhibit high frequency genomic alterations in human cancer.

Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O'brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G.

Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9136-41. Epub 2006 Jun 5.

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