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Ronan O'Malley - Publications

Affiliations: 
Director of Sequencing Operations, JGI 
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24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Wanamaker SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR. Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nature Methods. PMID 36690743 DOI: 10.1038/s41592-023-01768-4  0.699
2022 Strenkert D, Mingay M, Schmollinger S, Chen C, O'Malley RC, Merchant SS. An optimized ChIP-Seq framework for profiling histone modifications in . Plant Direct. 6: e392. PMID 35382117 DOI: 10.1002/pld3.392  0.375
2022 Potok ME, Zhong Z, Picard CL, Liu Q, Do T, Jacobsen CE, Sakr O, Naranbaatar B, Thilakaratne R, Khnkoyan Z, Purl M, Cheng H, Vervaet H, Feng S, Rayatpisheh S, et al. The role of ATXR6 expression in modulating genome stability and transposable element repression in . Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35027454 DOI: 10.1073/pnas.2115570119  0.539
2021 Cole B, Bergmann D, Blaby-Haas CE, Blaby IK, Bouchard KE, Brady SM, Ciobanu D, Coleman-Derr D, Leiboff S, Mortimer JC, Nobori T, Rhee SY, Schmutz J, Simmons BA, Singh AK, et al. Plant single-cell solutions for energy and the environment. Communications Biology. 4: 962. PMID 34385583 DOI: 10.1038/s42003-021-02477-4  0.664
2017 Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nature Protocols. 12: 1659-1672. PMID 28726847 DOI: 10.1038/Nprot.2017.055  0.807
2017 Trigg SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nature Methods. PMID 28650476 DOI: 10.1038/Nmeth.4343  0.684
2017 Hsia MM, O'Malley R, Cartwright A, Nieu R, Gordon SP, Kelly S, Williams TG, Wood DF, Zhao Y, Bragg J, Jordan M, Pauly M, Ecker JR, Gu Y, Vogel JP. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. The Plant Journal : For Cell and Molecular Biology. PMID 28432803 DOI: 10.1111/Tpj.13582  0.548
2017 Trigg S, Garza R, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang Z, Galli M, Ecker JR. CrY2H-seq interactome screening Protocol Exchange. DOI: 10.1038/Protex.2017.058  0.674
2016 Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods. PMID 27749838 DOI: 10.1038/Nmeth.4035  0.702
2016 O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 166: 1598. PMID 27610578 DOI: 10.1016/J.Cell.2016.08.063  0.736
2016 Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, et al. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 166: 492-505. PMID 27419873 DOI: 10.1016/J.Cell.2016.06.044  0.744
2016 O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 165: 1280-1292. PMID 27203113 DOI: 10.1016/J.Cell.2016.04.038  0.771
2016 Prigge M, Greenham K, Zhang Y, Santner A, Castillejo C, Mutka AM, O'Malley RC, Ecker JR, Kunkel BN, Estelle M. The Arabidopsis Auxin Receptor F-box proteins AFB4 and AFB5 are Required for Response to the Synthetic Auxin Picloram. G3 (Bethesda, Md.). PMID 26976444 DOI: 10.1534/G3.115.025585  0.429
2015 O'Malley RC, Barragan CC, Ecker JR. A user's guide to the Arabidopsis T-DNA insertion mutant collections. Methods in Molecular Biology (Clifton, N.J.). 1284: 323-42. PMID 25757780 DOI: 10.1007/978-1-4939-2444-8_16  0.51
2014 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells Nature. 514: 126. DOI: 10.1038/Nature13843  0.598
2012 O'Malley RC, Ecker JR. Epiallelic variation in Arabidopsis thaliana. Cold Spring Harbor Symposia On Quantitative Biology. 77: 135-45. PMID 23223383 DOI: 10.1101/Sqb.2012.77.014571  0.526
2011 Elling U, Taubenschmid J, Wirnsberger G, O'Malley R, Demers SP, Vanhaelen Q, Shukalyuk AI, Schmauss G, Schramek D, Schnuetgen F, Von Melchner H, Ecker JR, Stanford WL, Zuber J, Stark A, et al. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells Cell Stem Cell. 9: 563-574. PMID 22136931 DOI: 10.1016/J.Stem.2011.10.012  0.469
2011 Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. Transgenerational epigenetic instability is a source of novel methylation variants. Science (New York, N.Y.). 334: 369-73. PMID 21921155 DOI: 10.1126/Science.1212959  0.766
2011 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. PMID 21289626 DOI: 10.1038/Nature09798  0.669
2010 O'Malley RC, Ecker JR. Linking genotype to phenotype using the Arabidopsis unimutant collection. The Plant Journal : For Cell and Molecular Biology. 61: 928-40. PMID 20409268 DOI: 10.1111/J.1365-313X.2010.04119.X  0.566
2008 Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. A link between RNA metabolism and silencing affecting Arabidopsis development. Developmental Cell. 14: 854-66. PMID 18486559 DOI: 10.1016/J.Devcel.2008.04.005  0.702
2008 Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 133: 523-36. PMID 18423832 DOI: 10.1016/J.Cell.2008.03.029  0.777
2008 Ecker JR, Lister R, O'Malley RC, Tonti-Filippini J, Berry CC, Millar AH. Genome meets epigenome: Sequencing and analysis of the DNA methylome Developmental Biology. 319: 462. DOI: 10.1016/J.Ydbio.2008.05.004  0.706
2007 O'Malley RC, Alonso JM, Kim CJ, Leisse TJ, Ecker JR. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. Nature Protocols. 2: 2910-7. PMID 18007627 DOI: 10.1038/Nprot.2007.425  0.652
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