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27 Article(s) on File
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Reading the Second Code: Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment
Berger F,
Cao XF,
Chandler V,
Dennis L,
Martienssen R,
Meyers B,
Pikaard C,
Peacock J,
Richards E,
Wagner D,
Weigel D,
Colot V,
Deal R,
Dean C,
Ecker J,
Gehring M,
Gong ZZ,
Gregory B,
Rodrigo G,
Gutierrez-Marcos J,
Hasebe M,
Hwang ID,
Jacobsen S,
Kakutani T,
Li JY,
Michaels S,
Noh YS,
Provart N,
Vaughn M,
EPIC Planning Comm

The Plant cell
  24 (6): 2257-2261; Jun 2012  
[Abstract]
[DOI] [Full Text]

Taking the Next Step: Building an Arabidopsis Information Portal
Baerenfaller K,
Bastow R,
Beynon J,
Brady S,
Brendel V,
Donaldson S,
Dooley R,
Forster M,
Friesner J,
Gifford D,
Grotewold E,
Gutierrez R,
Huala E,
Jaiswal P,
Joshi H,
Kersey P,
Liu L,
Loraine A,
Lyons E,
May S,
Mayer K,
MacLean D,
Meyers B,
Mueller L,
Muller R,
Muller HM,
Ouellette F,
Pires JC,
Provart N,
Staiger D,
Stanzione D,
Taylor J,
Taylor C,
Town C,
Toyoda T,
Vaughn M,
Walsh S,
Ware D,
Weckwerth W,
Int Arabidopsis I

Plant Cell
  24 (6): 2248-2256; Jun 2012  
[Abstract]
[DOI] [Full Text]

Comparative functional genomics of the fission yeasts
Rhind N,
Chen Z,
Yassour M,
Thompson DA,
Haas BJ,
Habib N,
Wapinski I,
Roy S,
Lin MF,
Heiman DI,
Young SK,
Furuya K,
Guo Y,
Pidoux A,
Chen HM,
Robbertse B,
Goldberg JM,
Aoki K,
Bayne EH,
Berlin AM,
Desjardins CA,
Dobbs E,
Dukaj L,
Fan L,
FitzGerald MG,
French C,
Gujja S,
Hansen K,
Keifenheim D,
Levin JZ,
Mosher RA,
Muller CA,
Pfiffner J,
Priest M,
Russ C,
Smialowska A,
Swoboda P,
Sykes SM,
Vaughn M,
Vengrova S,
Yoder R,
Zeng Q,
Allshire R,
Baulcombe D,
Birren BW,
Brown W,
Ekwall K,
Kellis M,
Leatherwood J,
Levin H,
Margalit H,
Martienssen R,
Nieduszynski CA,
Spatafora JW,
Friedman N,
Dalgaard JZ,
Baumann P,
Niki H,
Regev A,
Nusbaum C

Science
  332 (6032): 930-6; May 20 2011  
[Abstract]
[DOI] [Full Text]

CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR
Zaratiegui BM,
Vaughn MW,
Irvine DV,
Goto D,
Watt S,
Bahler J,
Arcangioli B,
Martienssen RA

Nature
  469 (7328): 112-5; Jan 6 2011   PMC3057531
[Abstract]
[DOI]

The iPlant Collaborative: Cyberinfrastructure for Plant Biology
Goff SA,
Vaughn M,
McKay ,
Lyons E,
Stapleton AE,
Gessler D,
Matasci N,
Wang L,
Hanlon M,
Lenards A,
Muir A,
Merchant N,
Lowry S,
Mock S,
Helmke M,
Kubach A,
Narro M,
Hopkins N,
Micklos D,
Hilgert U,
Gonzales M,
Jordan C,
Skidmore ,
Dooley R,
Cazes J,
McLay R,
Lu Z,
Pasternak S,
Koesterke L,
Piel WH,
Grene R,
Noutsos C,
Gendler K,
Feng X,
Tang C,
Lent M,
Kim SJ,
Kvilekval K,
Manjunath B,
Tannen V,
Stamatakis ,
Sanderson MJ,
Welch SM,
Cranston K,
Soltis P,
Soltis ,
OMeara B,
Ane C,
Brutnell T,
Kleibenstein DJ,
White JW,
Leebens-Mack J,
Donoghue MJ,
Spalding EP,
Vision TJ,
Myers R,
Lowenthal D,
Enquist BJ,
Boyle B,
Akoglu A,
Andrews G,
Ram S,
Ware D,
Stein L,
Stanzione D

Frontiers in Plant Science
  2 (0): Jan 2011  
[Abstract]
[DOI] [Full Text]

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Kundeti VK,
Rajasekaran S,
Dinh H,
Vaughn MW,
Thapar V

BMC Bioinformatics
  11 (0): Artical number 560; Nov 15 2010   PMCID: PMC2996408
[Abstract]
[DOI] [Full Text] [PDF]

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 genetics
  6 (6): e1000982; Jun 2010  
[Abstract]
[DOI] [Full Text]

The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable PS,
Ware DH,
Fulton RS,
Stein JC,
Wei FS,
Pasternak S,
Liang CZ,
Zhang JW,
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 FY,
Kim K,
Abbott RM,
Cotton M,
Levy A,
Marchetto P,
Ochoa K,
Jackson SM,
Gillam B,
Chen WZ,
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 RF,
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 JK,
Dujmic Z,
Kim W,
Talag J,
Zuccolo A,
Fan C,
Sebastian A,
Kramer MR,
Spiegel L,
Nascimento L,
Zutavern T,
Miller B,
Ambroise C,
Muller S,
Spooner W,
Narechania A,
Ren LY,
Wei S,
Kumari S,
Faga BP,
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 YJ,
Lee H,
Li PH,
Lisch DR,
Liu SZ,
Liu ZJ,
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 LX,
Yu Y,
Zhang LF,
Zhou SG,
Zhu Q,
Bennetzen JL,
Dawe RK,
Jiang JM,
Jiang N,
Presting GG,
Wessler SR,
Aluru S,
Martienssen RA,
Clifton SW,
McCombie WR,
Wing RA,
Wilson RK

Science
  326 (5956): 1112-1115; Nov 20 2009  
[Abstract]
[DOI] [Full Text] [PDF]

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 RA

Genome Res
  19 (6): 1077-1083; Jul 2009   PMCID: PMC2694473
[Abstract]
[DOI] [Full Text] [PDF]

Epigenetic reprogramming and small RNA silencing of transposable elements in pollen
Slotkin RK,
Vaughn M,
Borges F,
Tanurdzic M,
Becker JD,
Feijo JA,
Martienssen RA

Cell
  136 (3): 461-72; Feb 6 2009  
[Abstract]
[DOI] [Full Text]

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 biology
  6 (12): 2880-95; Dec 9 2008  
[Abstract]
[DOI] [Full Text]

Lid2 Is Required for Coordinating H3K4 and H3K9 Methylation of Heterochromatin and Euchromatin
Li F,
Huarte M,
Zaratiegui BM,
Vaughn MW,
Shi Y,
Martienssen RA,
Cande WZ

Cell
  135 (2): 272-283; Oct 17 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Genome-wide transposon tagging reveals location-dependent effects on transcription and chromatin organization in Arabidopsis
Rosin FM,
Watanabe N,
Cacas JL,
Kato N,
Arroyo JM,
Fang Y,
May B,
Vaughn MW,
Simorowski J,
Ramu U,
McCombie RW,
Spector DL,
Martienssen RA,
Lam E

Plant J
  55 (3): 514-525; Aug 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Epigenetic natural variation in Arabidopsis thaliana
Vaughn MW,
Tanurdzic M,
Lippman Z,
Jiang H,
Carrasquillo R,
Rabinowicz PD,
Dedhia N,
McCombie WR,
Agier N,
Bulski A,
Colot V,
Doerge RW,
Martienssen RA

PLoS biology
  5 (7): e174; Jul 2007  
[Abstract]
[DOI] [Full Text]

The fission yeast Jmj2 reverses histone H3 lysine 4 trimethylation
Huarte M,
Lan F,
Kim TH,
Vaughn MW,
Zaratiegui BM,
Martienssen RA,
Buratowski S,
Shi Y

Journal of Biological Chemistry
  282 (30): 21662-21670; Jul 2007  
[Abstract]
[DOI] [Full Text] [PDF]

S-pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription
Lan F,
Zaratiegui M,
Villen J,
Vaughn MW,
Verdel A,
Huarte M,
Shi YJ,
Gygi SP,
Moazed D,
Martienssen RA,
Shi Y

Molecular cell
  26 (1): 89-101; Apr 13 2007  
[Abstract]
[DOI] [Full Text]

S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription
Lan F,
Zaratiegui M,
Villen J,
Vaughn MW,
Verdel A,
Huarte M,
Shi Y,
Gygi SP,
Moazed D,
Martienssen RA

Molecular cell
  26 (1): 89-101; Apr 13 2007  
[Abstract]
[DOI] [Full Text]

Silent running: RNA interference and heterochromatic modification
Martienssen R,
Zaratiegui M,
Irvine D,
Goto D,
Slotkin K,
Tanurdzic M,
Lippman Z,
Vaughn M,
May B,
Cande Z,
Colot V,
Doerge RW

Chromosome Research
  15 (0): 20-21; 2007  
[Full Text]

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
  313 (5790): 1134-7; Aug 25 2006   NLM
[Abstract]
[DOI] [Full Text]

MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis
Ronemus M,
Vaughn MW,
Martienssen RA

The Plant cell
  18 (7): 1559-74; Jul 2006  
[Abstract]
[DOI] [Full Text]

Replication, repair, and reactivation
Vaughn MW,
Tanurdzic M,
Martienssen R

Developmental cell
  9 (6): 724-5; Dec 2005  
[Abstract]
[DOI] [Full Text]

Its a small RNA world, after all
Vaughn MW,
Martienssen R

Science
  309 (5740): 1525-6; Sep 2 2005  
[Abstract]
[DOI] [Full Text]

Finding the right template: RNA Pol IV, a plant-specific RNA polymerase
Vaughn MW,
Martienssen RA

Molecular cell
  17 (6): 754-6; Mar 18 2005  
[Abstract]
[DOI] [Full Text]

The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects
Jeffrey Chen Z,
Wang J,
Tian L,
Lee HS,
Wang JJ,
Chen M,
Lee JJ,
Josefsson C,
Madlung A,
Watson B,
Lippman Z,
Vaughn M,
Chris Pires J,
Colot V,
Doerge RW,
Martienssen RA,
Comai L,
Osborn TC

Biological journal of the Linnean Society. Linnean Society of London
  82 (4): 689-700; Aug 2004  
[Abstract]
[DOI] [Full Text]

Role of transposable elements in heterochromatin and epigenetic control
Lippman Z,
Gendrel AV,
Black M,
Vaughn MW,
Dedhia N,
McCombie WR,
Lavine K,
Mittal V,
May B,
Kasschau KD,
Carrington JC,
Doerge RW,
Colot V,
Martienssen R

Nature
  430 (6998): 471-6; Jul 22 2004  
[Abstract]
[DOI] [Full Text]

Transposons, small interfering RNA and the origin of heterochromatin.
Martienssen R,
Lippman Z,
May B,
Vaughn M,
Gendrel AV,
Ronemus M,
Volpe T,
Kidner C,
Colot V

European Journal of Cell Biology
  83 (0): 61-61; Mar 2004  
[Full Text]

Transposons, tandem repeats, and the silencing of imprinted genes
Martienssen R,
Lippman Z,
May B,
Ronemus M,
Vaughn M

Cold Spring Harbor symposia on quantitative biology
  69 (0): 371-9; 2004  
[DOI] [Full Text]


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