PubMed

Human DNA methylomes at base resolution show widespread epigenomic differences.

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR.

Nature. 2009 Nov 19;462(7271):315-322. Epub 2009 Oct 14.PMID: 19829295 [PubMed - as supplied by publisher]Related articles

A Combinatorial Interplay Among the 1-Aminocyclopropane-1-carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana.

Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker JR, Zhang X, Gao S, Theologis A.

Genetics. 2009 Sep 14. [Epub ahead of print]PMID: 19752216 [PubMed - as supplied by publisher]Related articles

Prepublication data sharing.

Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.

Nature. 2009 Sep 10;461(7261):168-70.PMID: 19741685 [PubMed - indexed for MEDLINE]Related articles

Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein.

Liljegren SJ, Leslie ME, Darnielle L, Lewis MW, Taylor SM, Luo R, Geldner N, Chory J, Randazzo PA, Yanofsky MF, Ecker JR.

Development. 2009 Jun;136(11):1909-18.PMID: 19429787 [PubMed - indexed for MEDLINE]Related articles

A family of bacterial cysteine protease type III effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes.

Dowen RH, Engel JL, Shao F, Ecker JR, Dixon JE.

J Biol Chem. 2009 Jun 5;284(23):15867-79. Epub 2009 Apr 3.PMID: 19346252 [PubMed - indexed for MEDLINE]Related articlesFree article

Finding the fifth base: genome-wide sequencing of cytosine methylation.

Lister R, Ecker JR.

Genome Res. 2009 Jun;19(6):959-66. Epub 2009 Mar 9. Review.PMID: 19273618 [PubMed - indexed for MEDLINE]Related articles

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.

Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA.

Genome Biol. 2009 Feb 11;10(2):R17. [Epub ahead of print]PMID: 19210792 [PubMed - as supplied by publisher]Related articlesFree article

Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis.

Qiao H, Chang KN, Yazaki J, Ecker JR.

Genes Dev. 2009 Feb 15;23(4):512-21. Epub 2009 Feb 4.PMID: 19196655 [PubMed - indexed for MEDLINE]Related articlesFree article

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.

Lister R, Gregory BD, Ecker JR.

Curr Opin Plant Biol. 2009 Apr;12(2):107-18. Epub 2009 Jan 20. Review.PMID: 19157957 [PubMed - indexed for MEDLINE]Related articles

Literature-curated protein interaction datasets.

Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, Roth FP, Vidal M.

Nat Methods. 2009 Jan;6(1):39-46.PMID: 19116613 [PubMed - indexed for MEDLINE]Related articlesFree article

A link between RNA metabolism and silencing affecting Arabidopsis development.

Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR.

Dev Cell. 2008 Jun;14(6):854-66. Epub 2008 May 22.PMID: 18486559 [PubMed - indexed for MEDLINE]Related articles

Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR.

Cell. 2008 May 2;133(3):523-36.PMID: 18423832 [PubMed - indexed for MEDLINE]Related articlesFree article

Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis.

Hu J, Mitchum MG, Barnaby N, Ayele BT, Ogawa M, Nam E, Lai WC, Hanada A, Alonso JM, Ecker JR, Swain SM, Yamaguchi S, Kamiya Y, Sun TP.

Plant Cell. 2008 Feb;20(2):320-36. Epub 2008 Feb 29.PMID: 18310462 [PubMed - indexed for MEDLINE]Related articlesFree article

Utilizing tiling microarrays for whole-genome analysis in plants.

Gregory BD, Yazaki J, Ecker JR.

Plant J. 2008 Feb;53(4):636-44. Review.PMID: 18269573 [PubMed - indexed for MEDLINE]Related articles

The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels.

Leivar P, Monte E, Al-Sady B, Carle C, Storer A, Alonso JM, Ecker JR, Quail PH.

Plant Cell. 2008 Feb;20(2):337-52. Epub 2008 Feb 5.PMID: 18252845 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome.

Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, Belostotsky DA.

Cell. 2007 Dec 28;131(7):1340-53.PMID: 18160042 [PubMed - indexed for MEDLINE]Related articles

An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome.

O'Malley RC, Alonso JM, Kim CJ, Leisse TJ, Ecker JR.

Nat Protoc. 2007;2(11):2910-7.PMID: 18007627 [PubMed - indexed for MEDLINE]Related articles

A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis.

Li H, He Z, Lu G, Lee SC, Alonso J, Ecker JR, Luan S.

Plant Cell. 2007 Aug;19(8):2403-16. Epub 2007 Aug 17.PMID: 17704213 [PubMed - indexed for MEDLINE]Related articlesFree article

Mapping the genome landscape using tiling array technology.

Yazaki J, Gregory BD, Ecker JR.

Curr Opin Plant Biol. 2007 Oct;10(5):534-42. Epub 2007 Aug 20. Review.PMID: 17703988 [PubMed - indexed for MEDLINE]Related articlesFree article

Recombination and linkage disequilibrium in Arabidopsis thaliana.

Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M.

Nat Genet. 2007 Sep;39(9):1151-5. Epub 2007 Aug 5.PMID: 17676040 [PubMed - indexed for MEDLINE]Related articles

The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease.

Gentry MS, Dowen RH 3rd, Worby CA, Mattoo S, Ecker JR, Dixon JE.

J Cell Biol. 2007 Jul 30;178(3):477-88. Epub 2007 Jul 23.PMID: 17646401 [PubMed - indexed for MEDLINE]Related articlesFree article

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.

Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Schölkopf B, Nordborg M, Rätsch G, Ecker JR, Weigel D.

Science. 2007 Jul 20;317(5836):338-42.PMID: 17641193 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.

Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE, Kay SA, Chory J, Weigel D, Jones JD, Ecker JR.

Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62. Epub 2007 Jul 12.PMID: 17626786 [PubMed - indexed for MEDLINE]Related articlesFree article

Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC.

Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C.

Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3633-8. Epub 2007 Feb 20.PMID: 17360694 [PubMed - indexed for MEDLINE]Related articlesFree article

Higher plants possess two different types of ATX1-like copper chaperones.

Puig S, Mira H, Dorcey E, Sancenón V, Andrés-Colás N, Garcia-Molina A, Burkhead JL, Gogolin KA, Abdel-Ghany SE, Thiele DJ, Ecker JR, Pilon M, Peñarrubia L.

Biochem Biophys Res Commun. 2007 Mar 9;354(2):385-90. Epub 2007 Jan 9.PMID: 17223078 [PubMed - indexed for MEDLINE]Related articles

The POLARIS peptide of Arabidopsis regulates auxin transport and root growth via effects on ethylene signaling.

Chilley PM, Casson SA, Tarkowski P, Hawkins N, Wang KL, Hussey PJ, Beale M, Ecker JR, Sandberg GK, Lindsey K.

Plant Cell. 2006 Nov;18(11):3058-72. Epub 2006 Nov 30.PMID: 17138700 [PubMed - indexed for MEDLINE]Related articlesFree article

The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling.

Hutchison CE, Li J, Argueso C, Gonzalez M, Lee E, Lewis MW, Maxwell BB, Perdue TD, Schaller GE, Alonso JM, Ecker JR, Kieber JJ.

Plant Cell. 2006 Nov;18(11):3073-87. Epub 2006 Nov 22.PMID: 17122069 [PubMed - indexed for MEDLINE]Related articlesFree article

Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1.

Kim SA, Punshon T, Lanzirotti A, Li L, Alonso JM, Ecker JR, Kaplan J, Guerinot ML.

Science. 2006 Nov 24;314(5803):1295-8. Epub 2006 Nov 2.PMID: 17082420 [PubMed - indexed for MEDLINE]Related articlesFree article

CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion- and Ca(2+)-permeable channels and stomatal closure.

Mori IC, Murata Y, Yang Y, Munemasa S, Wang YF, Andreoli S, Tiriac H, Alonso JM, Harper JF, Ecker JR, Kwak JM, Schroeder JI.

PLoS Biol. 2006 Oct;4(10):e327.PMID: 17032064 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR.

Cell. 2006 Sep 22;126(6):1189-201. Epub 2006 Aug 31.PMID: 16949657 [PubMed - indexed for MEDLINE]Related articles

ETHYLENE-INSENSITIVE5 encodes a 5'-->3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2.

Olmedo G, Guo H, Gregory BD, Nourizadeh SD, Aguilar-Henonin L, Li H, An F, Guzman P, Ecker JR.

Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13286-93. Epub 2006 Aug 18.PMID: 16920797 [PubMed - indexed for MEDLINE]Related articlesFree article

The ACC synthase TOE sequence is required for interaction with ETO1 family proteins and destabilization of target proteins.

Yoshida H, Wang KL, Chang CM, Mori K, Uchida E, Ecker JR.

Plant Mol Biol. 2006 Oct;62(3):427-37. Epub 2006 Aug 1.PMID: 16897471 [PubMed - indexed for MEDLINE]Related articles

RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis.

Chen JG, Ullah H, Temple B, Liang J, Guo J, Alonso JM, Ecker JR, Jones AM.

J Exp Bot. 2006;57(11):2697-708. Epub 2006 Jul 7.PMID: 16829549 [PubMed - indexed for MEDLINE]Related articlesFree article

Retroviral DNA integration: viral and cellular determinants of target-site selection.

Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD.

PLoS Pathog. 2006 Jun;2(6):e60. Epub 2006 Jun 23.PMID: 16789841 [PubMed - indexed for MEDLINE]Related articlesFree article

PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism.

Lariguet P, Schepens I, Hodgson D, Pedmale UV, Trevisan M, Kami C, de Carbonnel M, Alonso JM, Ecker JR, Liscum E, Fankhauser C.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):10134-9. Epub 2006 Jun 15.PMID: 16777956 [PubMed - indexed for MEDLINE]Related articlesFree article

Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis.

Rudella A, Friso G, Alonso JM, Ecker JR, van Wijk KJ.

Plant Cell. 2006 Jul;18(7):1704-21. Epub 2006 Jun 9.PMID: 16766689 [PubMed - indexed for MEDLINE]Related articlesFree article

Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis.

Alonso JM, Ecker JR.

Nat Rev Genet. 2006 Jul;7(7):524-36. Epub 2006 Jun 6. Review.PMID: 16755288 [PubMed - indexed for MEDLINE]Related articles

HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry.

Barr SD, Ciuffi A, Leipzig J, Shinn P, Ecker JR, Bushman FD.

Mol Ther. 2006 Aug;14(2):218-25. Epub 2006 May 2.PMID: 16647883 [PubMed - indexed for MEDLINE]Related articles

The Arabidopsis heavy metal P-type ATPase HMA5 interacts with metallochaperones and functions in copper detoxification of roots.

Andrés-Colás N, Sancenón V, Rodríguez-Navarro S, Mayo S, Thiele DJ, Ecker JR, Puig S, Peñarrubia L.

Plant J. 2006 Jan;45(2):225-36.PMID: 16367966 [PubMed - indexed for MEDLINE]Related articles

Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts.

Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman FD.

Mol Ther. 2006 Feb;13(2):366-73. Epub 2005 Dec 1.PMID: 16325473 [PubMed - indexed for MEDLINE]Related articles

A role for LEDGF/p75 in targeting HIV DNA integration.

Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman F.

Nat Med. 2005 Dec;11(12):1287-9. Epub 2005 Nov 27.PMID: 16311605 [PubMed - indexed for MEDLINE]Related articles

Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana.

Overvoorde PJ, Okushima Y, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Liu A, Onodera C, Quach H, Smith A, Yu G, Theologis A.

Plant Cell. 2005 Dec;17(12):3282-300. Epub 2005 Nov 11.PMID: 16284307 [PubMed - indexed for MEDLINE]Related articlesFree article

Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis.

Mason MG, Mathews DE, Argyros DA, Maxwell BB, Kieber JJ, Alonso JM, Ecker JR, Schaller GE.

Plant Cell. 2005 Nov;17(11):3007-18. Epub 2005 Oct 14.PMID: 16227453 [PubMed - indexed for MEDLINE]Related articlesFree article

Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome.

Barr SD, Leipzig J, Shinn P, Ecker JR, Bushman FD.

J Virol. 2005 Sep;79(18):12035-44.PMID: 16140779 [PubMed - indexed for MEDLINE]Related articlesFree article

Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation.

Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW.

Development. 2005 Sep;132(18):4107-18. Epub 2005 Aug 17.PMID: 16107481 [PubMed - indexed for MEDLINE]Related articlesFree article

Arabidopsis ETO1 specifically interacts with and negatively regulates type 2 1-aminocyclopropane-1-carboxylate synthases.

Yoshida H, Nagata M, Saito K, Wang KL, Ecker JR.

BMC Plant Biol. 2005 Aug 10;5:14.PMID: 16091151 [PubMed - indexed for MEDLINE]Related articlesFree article

LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms.

Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA.

Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10387-92. Epub 2005 Jul 8.PMID: 16006522 [PubMed - indexed for MEDLINE]Related articlesFree article

NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation.

Wilmoth JC, Wang S, Tiwari SB, Joshi AD, Hagen G, Guilfoyle TJ, Alonso JM, Ecker JR, Reed JW.

Plant J. 2005 Jul;43(1):118-30.PMID: 15960621 [PubMed - indexed for MEDLINE]Related articles

FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions.

Werner JD, Borevitz JO, Uhlenhaut NH, Ecker JR, Chory J, Weigel D.

Genetics. 2005 Jul;170(3):1197-207. Epub 2005 May 23.PMID: 15911588 [PubMed - indexed for MEDLINE]Related articlesFree article

Rapid array mapping of circadian clock and developmental mutations in Arabidopsis.

Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA.

Plant Physiol. 2005 Jun;138(2):990-7. Epub 2005 May 20.PMID: 15908595 [PubMed - indexed for MEDLINE]Related articlesFree article