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Items: 1 to 50 of 66

1.

An "eFP-Seq Browser" for Visualizing and Exploring RNA-Seq Data.

Sullivan A, Purohit P, Freese NH, Pasha A, Esteban E, Waese J, Wu A, Chen M, Chin CY, Song R, Watharkar SR, Chan AP, Krishnakumar V, Vaughn MW, Town C, Loraine AE, Provart NJ.

Plant J. 2019 Jul 26. doi: 10.1111/tpj.14468. [Epub ahead of print]

PMID:
31350781
2.

Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways.

Anderson SN, Zynda GJ, Song J, Han Z, Vaughn MW, Li Q, Springer NM.

G3 (Bethesda). 2018 May 31;8(6):1921-1932. doi: 10.1534/g3.118.200284.

3.

Platform for Automated Real-Time High Performance Analytics on Medical Image Data.

Allen WJ, Gabr RE, Tefera GB, Pednekar AS, Vaughn MW, Narayana PA.

IEEE J Biomed Health Inform. 2018 Mar;22(2):318-324. doi: 10.1109/JBHI.2017.2771299.

4.

Genome-Wide Analysis of the Arabidopsis Replication Timing Program.

Concia L, Brooks AM, Wheeler E, Zynda GJ, Wear EE, LeBlanc C, Song J, Lee TJ, Pascuzzi PE, Martienssen RA, Vaughn MW, Thompson WF, Hanley-Bowdoin L.

Plant Physiol. 2018 Mar;176(3):2166-2185. doi: 10.1104/pp.17.01537. Epub 2018 Jan 4.

5.

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips.

Wear EE, Song J, Zynda GJ, LeBlanc C, Lee TJ, Mickelson-Young L, Concia L, Mulvaney P, Szymanski ES, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF.

Plant Cell. 2017 Sep;29(9):2126-2149. doi: 10.1105/tpc.17.00037. Epub 2017 Aug 25.

6.

Repliscan: a tool for classifying replication timing regions.

Zynda GJ, Song J, Concia L, Wear EE, Hanley-Bowdoin L, Thompson WF, Vaughn MW.

BMC Bioinformatics. 2017 Aug 7;18(1):362. doi: 10.1186/s12859-017-1774-x.

7.

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.

Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, Miller JR, Vaughn MW, Micklem G, Town CD, Chan AP.

Plant Cell Physiol. 2017 Jan 1;58(1):e4. doi: 10.1093/pcp/pcw200.

PMID:
28013278
8.

Data supporting beta-amyloid dimer structural transitions and protein-lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures.

Cheng SY, Chou G, Buie C, Vaughn MW, Compton C, Cheng KH.

Data Brief. 2016 Mar 10;7:658-72. doi: 10.1016/j.dib.2016.03.015. eCollection 2016 Jun.

9.

Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface.

Cheng SY, Chou G, Buie C, Vaughn MW, Compton C, Cheng KH.

Chem Phys Lipids. 2016 Mar;196:33-51. doi: 10.1016/j.chemphyslip.2016.01.002. Epub 2016 Jan 28.

10.

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.

Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D, Schmitz RJ, Vaughn MW, Springer NM.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14728-33. doi: 10.1073/pnas.1514680112. Epub 2015 Nov 9.

11.

Lipid insertion domain unfolding regulates protein orientational transition behavior in a lipid bilayer.

Cheng KH, Qiu L, Cheng SY, Vaughn MW.

Biophys Chem. 2015 Nov;206:22-39. doi: 10.1016/j.bpc.2015.06.011. Epub 2015 Jul 4.

12.

Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize.

Li Q, Song J, West PT, Zynda G, Eichten SR, Vaughn MW, Springer NM.

Plant Physiol. 2015 Aug;168(4):1262-74. doi: 10.1104/pp.15.00052. Epub 2015 Apr 13.

13.

Characterization of 3D Voronoi tessellation nearest neighbor lipid shells provides atomistic lipid disruption profile of protein containing lipid membranes.

Cheng SY, Duong HV, Compton C, Vaughn MW, Nguyen H, Cheng KH.

Biophys Chem. 2015 Mar;198:22-35. doi: 10.1016/j.bpc.2015.01.005. Epub 2015 Jan 19.

14.

Genetic perturbation of the maize methylome.

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM.

Plant Cell. 2014 Dec;26(12):4602-16. doi: 10.1105/tpc.114.133140. Epub 2014 Dec 19.

15.

Scaling and alpha-helix regulation of protein relaxation in a lipid bilayer.

Qiu L, Buie C, Cheng KH, Vaughn MW.

J Chem Phys. 2014 Dec 14;141(22):225101. doi: 10.1063/1.4902229.

16.

Genomic distribution of H3K9me2 and DNA methylation in a maize genome.

West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM.

PLoS One. 2014 Aug 14;9(8):e105267. doi: 10.1371/journal.pone.0105267. eCollection 2014.

17.

In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts.

Pascuzzi PE, Flores-Vergara MA, Lee TJ, Sosinski B, Vaughn MW, Hanley-Bowdoin L, Thompson WF, Allen GC.

Plant Cell. 2014 Jan;26(1):102-20. doi: 10.1105/tpc.113.121194. Epub 2014 Jan 31.

18.

Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species.

Waters AJ, Bilinski P, Eichten SR, Vaughn MW, Ross-Ibarra J, Gehring M, Springer NM.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19639-44. doi: 10.1073/pnas.1309182110. Epub 2013 Nov 11.

19.

Epigenetic and genetic influences on DNA methylation variation in maize populations.

Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM.

Plant Cell. 2013 Aug;25(8):2783-97. doi: 10.1105/tpc.113.114793. Epub 2013 Aug 6.

20.

Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27.

Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM.

Plant Cell. 2013 Mar;25(3):780-93. doi: 10.1105/tpc.112.106427. Epub 2013 Mar 5.

21.

Spreading of heterochromatin is limited to specific families of maize retrotransposons.

Eichten SR, Ellis NA, Makarevitch I, Yeh CT, Gent JI, Guo L, McGinnis KM, Zhang X, Schnable PS, Vaughn MW, Dawe RK, Springer NM.

PLoS Genet. 2012;8(12):e1003127. doi: 10.1371/journal.pgen.1003127. Epub 2012 Dec 13.

22.

Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm.

Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM.

Plant Cell. 2011 Dec;23(12):4221-33. doi: 10.1105/tpc.111.092668. Epub 2011 Dec 23.

23.

Heritable epigenetic variation among maize inbreds.

Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM.

PLoS Genet. 2011 Nov;7(11):e1002372. doi: 10.1371/journal.pgen.1002372. Epub 2011 Nov 17.

24.

Molecular dynamics simulations reveal the protective role of cholesterol in β-amyloid protein-induced membrane disruptions in neuronal membrane mimics.

Qiu L, Buie C, Reay A, Vaughn MW, Cheng KH.

J Phys Chem B. 2011 Aug 18;115(32):9795-812. doi: 10.1021/jp2012842. Epub 2011 Jul 26.

25.

CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR.

Zaratiegui M, Vaughn MW, Irvine DV, Goto D, Watt S, Bähler J, Arcangioli B, Martienssen RA.

Nature. 2011 Jan 6;469(7328):112-5. doi: 10.1038/nature09608. Epub 2010 Dec 12.

26.

Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state.

Lee TJ, Pascuzzi PE, Settlage SB, Shultz RW, Tanurdzic M, Rabinowicz PD, Menges M, Zheng P, Main D, Murray JA, Sosinski B, Allen GC, Martienssen RA, Hanley-Bowdoin L, Vaughn MW, Thompson WF.

PLoS Genet. 2010 Jun 10;6(6):e1000982. doi: 10.1371/journal.pgen.1000982.

27.

The B73 maize genome: complexity, diversity, and dynamics.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK.

Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534. Erratum in: Science. 2012 Aug 31;337(6098):1040.

28.

Cholesterol modulates the interaction of beta-amyloid peptide with lipid bilayers.

Qiu L, Lewis A, Como J, Vaughn MW, Huang J, Somerharju P, Virtanen J, Cheng KH.

Biophys J. 2009 May 20;96(10):4299-307. doi: 10.1016/j.bpj.2009.02.036.

29.

Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing.

Irvine DV, Goto DB, Vaughn MW, Nakaseko Y, McCombie WR, Yanagida M, Martienssen R.

Genome Res. 2009 Jun;19(6):1077-83. doi: 10.1101/gr.089318.108. Epub 2009 May 7.

30.

Epigenomic consequences of immortalized plant cell suspension culture.

Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA.

PLoS Biol. 2008 Dec 9;6(12):2880-95. doi: 10.1371/journal.pbio.0060302.

31.

Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin.

Li F, Huarte M, Zaratiegui M, Vaughn MW, Shi Y, Martienssen R, Cande WZ.

Cell. 2008 Oct 17;135(2):272-83. doi: 10.1016/j.cell.2008.08.036.

32.

Morphology and amine accessibility of (3-aminopropyl) triethoxysilane films on glass surfaces.

Wang W, Vaughn MW.

Scanning. 2008 Mar-Apr;30(2):65-77. doi: 10.1002/sca.20097.

PMID:
18320600
33.

Small angle X-ray scattering analysis of the effect of cold compaction of Al/MoO3 thermite composites.

Hammons JA, Wang W, Ilavsky J, Pantoya ML, Weeks BL, Vaughn MW.

Phys Chem Chem Phys. 2008 Jan 7;10(1):193-9. Epub 2007 Nov 21.

PMID:
18075699
34.
35.

Epigenetic natural variation in Arabidopsis thaliana.

Vaughn MW, Tanurdzić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, Colot V, Doerge RW, Martienssen RA.

PLoS Biol. 2007 Jul;5(7):e174. Epub 2007 Jun 19.

36.

The fission yeast Jmj2 reverses histone H3 Lysine 4 trimethylation.

Huarte M, Lan F, Kim T, Vaughn MW, Zaratiegui M, Martienssen RA, Buratowski S, Shi Y.

J Biol Chem. 2007 Jul 27;282(30):21662-70. Epub 2007 Jun 5.

37.

S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription.

Lan F, Zaratiegui M, Villén J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed D, Martienssen RA, Shi Y.

Mol Cell. 2007 Apr 13;26(1):89-101.

38.

Recognition and capture of breast cancer cells using an antibody-based platform in a microelectromechanical systems device.

Du Z, Cheng KH, Vaughn MW, Collie NL, Gollahon LS.

Biomed Microdevices. 2007 Feb;9(1):35-42.

PMID:
17103049
39.

Evidence of meniscus interface transport in dip-pen nanolithography: An annular diffusion model.

Nafday OA, Vaughn MW, Weeks BL.

J Chem Phys. 2006 Oct 14;125(14):144703.

PMID:
17042627
40.

Cell detachment model for an antibody-based microfluidic cancer screening system.

Wankhede SP, Du Z, Berg JM, Vaughn MW, Dallas T, Cheng KH, Gollahon L.

Biotechnol Prog. 2006 Sep-Oct;22(5):1426-33.

PMID:
17022683
41.

Lipid headgroup superlattice modulates the activity of surface-acting cholesterol oxidase in ternary phospholipid/cholesterol bilayers.

Cheng KH, Cannon B, Metze J, Lewis A, Huang J, Vaughn MW, Zhu Q, Somerharju P, Virtanen J.

Biochemistry. 2006 Sep 12;45(36):10855-64.

PMID:
16953571
42.

Argonaute slicing is required for heterochromatic silencing and spreading.

Irvine DV, Zaratiegui M, Tolia NH, Goto DB, Chitwood DH, Vaughn MW, Joshua-Tor L, Martienssen RA.

Science. 2006 Aug 25;313(5790):1134-7.

43.

Surface tension effect on transmembrane channel stability in a model membrane.

Zhu Q, Vaughn MW.

J Phys Chem B. 2005 Oct 20;109(41):19474-83.

PMID:
16853516
44.

Molecular dynamics simulation of nanoparticle self-assembly at a liquid-liquid interface.

Luo M, Mazyar OA, Zhu Q, Vaughn MW, Hase WL, Dai LL.

Langmuir. 2006 Jul 4;22(14):6385-90.

PMID:
16800703
45.
46.

Cholesterol supports headgroup superlattice domain formation in fluid phospholipid/cholesterol bilayers.

Cannon B, Lewis A, Metze J, Thiagarajan V, Vaughn MW, Somerharju P, Virtanen J, Huang J, Cheng KH.

J Phys Chem B. 2006 Mar 30;110(12):6339-50.

PMID:
16553452
47.

Replication, repair, and reactivation.

Vaughn MW, Tanurdzic M, Martienssen R.

Dev Cell. 2005 Dec;9(6):724-5. Review.

48.

Microfluidic-based diagnostics for cervical cancer cells.

Du Z, Colls N, Cheng KH, Vaughn MW, Gollahon L.

Biosens Bioelectron. 2006 Apr 15;21(10):1991-5. Epub 2005 Oct 19.

PMID:
16242927
49.

First-passage approach for permeable traps.

Vaughn MW.

J Chem Phys. 2005 Oct 1;123(13):134905.

PMID:
16223329
50.

Cholesterol modulated antibody binding in supported lipid membranes as determined by total internal reflectance microscopy on a microfabricated high-throughput glass chip.

Cannon B, Weaver N, Pu Q, Thiagarajan V, Liu S, Huang J, Vaughn MW, Cheng KH.

Langmuir. 2005 Oct 11;21(21):9666-74.

PMID:
16207051

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