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Employment (4)

University of Wisconsin Madison: Madison, WI, US

Post-doc (Botany)
Employment
Source: Self-asserted source
Ronan C O'Malley

Salk Institute for Biological Studies: La Jolla, CA, US

Staff Scientist (Genomic Analysis Laboratory)
Employment
Source: Self-asserted source
Ronan C O'Malley

DOE Joint Genome Institute: Walnut Creek, CA, US

Group lead Sequencing Technologies (Genomic Technologies)
Employment
Source: Self-asserted source
Ronan C O'Malley

University of Chicago: Chicago, IL, US

2023-10-01 to present | Assistant Professor (Human Genetics)
Employment
Source: Self-asserted source
Ronan C O'Malley

Education and qualifications (2)

University of Chicago: Chicago, IL, US

BS
Education
Source: Self-asserted source
Ronan C O'Malley

University of Chicago: Chicago, IL, US

PhD (Chemistry)
Education
Source: Self-asserted source
Ronan C O'Malley

Works (50)

A Multi-omic Characterization of the Physiological Responses to Salt Stress in Scenedesmus obliquus UTEX393

Research Square
2023 | Other
EID:

2-s2.0-85169713036

Contributors: Calhoun, S.; Kamel, B.; Edmundson, S.; Holguin, O.; Mach, P.; Mckie-Krisberg, Z.; Baumgart, L.; Blaby, I.; Bowen, B.; Chen, C. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination

Plant Direct
2023 | Journal article
EID:

2-s2.0-85177056501

Part of ISSN: 24754455
Contributors: Hyden, B.; Carper, D.L.; Abraham, P.E.; Yuan, G.; Yao, T.; Baumgart, L.; Zhang, Y.; Chen, C.; O'Malley, R.; Chen, J.-G. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

High-throughput identification of novel heat tolerance genes via genome-wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii

Plant Cell and Environment
2023 | Journal article
EID:

2-s2.0-85145091208

Part of ISSN: 13653040 01407791
Contributors: Mattoon, E.M.; McHargue, W.E.; Bailey, C.E.; Zhang, N.; Chen, C.; Eckhardt, J.; Daum, C.G.; Zane, M.; Pennacchio, C.; Schmutz, J. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis

bioRxiv
2023 | Other
EID:

2-s2.0-85173870195

Part of ISSN: 26928205
Contributors: Serrano, K.; Bezrutczyk, M.; Goudeau, D.; Dao, T.; O'Malley, R.; Malmstrom, R.R.; Visel, A.; Scheller, H.; Cole, B.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

Plant Physiology
2023 | Journal article
EID:

2-s2.0-85164209195

Part of ISSN: 15322548 00320889
Contributors: Weng, X.; Song, H.; Sreedasyam, A.; Haque, T.; Zhang, L.; Chen, C.; Yoshinaga, Y.; Williams, M.; O'Malley, R.C.; Grimwood, J. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis

Plant Direct
2022 | Journal article
EID:

2-s2.0-85127247247

Part of ISSN: 24754455
Contributors: Strenkert, D.; Mingay, M.; Schmollinger, S.; Chen, C.; O'Malley, R.C.; Merchant, S.S.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

High-throughput Identification of Novel Heat Tolerance Genes via Genome-wide Pooled Mutant Screens in the Model Green Alga Chlamydomonas reinhardtii

bioRxiv
2022 | Other
EID:

2-s2.0-85136895480

Part of ISSN: 26928205
Contributors: Mattoon, E.M.; McHargue, W.; Bailey, C.E.; Zhang, N.; Chen, C.; Eckhardt, J.; Daum, C.G.; Zane, M.; Pennacchio, C.; Schmutz, J. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle

Plant Journal
2022 | Journal article
EID:

2-s2.0-85138252538

Part of ISSN: 1365313X 09607412
Contributors: Strenkert, D.; Yildirim, A.; Yan, J.; Yoshinaga, Y.; Pellegrini, M.; O'Malley, R.C.; Merchant, S.S.; Umen, J.G.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Proceedings of the National Academy of Sciences of the United States of America
2022 | Journal article
EID:

2-s2.0-85123121274

Part of ISSN: 10916490 00278424
Contributors: Potok, M.E.; Zhong, Z.; Picard, C.L.; Liu, Q.; Do, T.; Jacobsen, C.E.; Sakr, O.; Naranbaatar, B.; Thilakaratne, R.; Khnkoyan, Z. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Transcriptome and DNA methylome dynamics reveal differential characteristics of inflorescence development between two ecotypes in Panicum hallii

bioRxiv
2022 | Other
EID:

2-s2.0-85128995473

Part of ISSN: 26928205
Contributors: Weng, X.; Song, H.; Sreedasyam, A.; Haque, T.; Zhang, L.; Chen, C.; Yoshinaga, Y.; Williams, M.; O'Malley, R.C.; Grimwood, J. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

An optimized ChIP-Seq framework for profiling of histone modifications in Chromochloris zofingiensis

bioRxiv
2021 | Other
EID:

2-s2.0-85121515514

Part of ISSN: 26928205
Contributors: Strenkert, D.; Mingay, M.; Schmollinger, S.; Chen, C.; O'Malley, R.C.; Merchant, S.S.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Aspects of the neurospora crassa sulfur starvation response are revealed by transcriptional profiling and dna affinity purification sequencing

mSphere
2021 | Journal article
EID:

2-s2.0-85118865060

Part of ISSN: 23795042
Contributors: Huberman, L.B.; Wu, V.W.; Lee, J.; Daum, C.; O'Malley, R.C.; Louise Glass, N.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

DOE JGI metagenome workflow

mSystems
2021 | Journal article
EID:

2-s2.0-85107123200

Part of ISSN: 23795077
Contributors: Clum, A.; Huntemann, M.; Bushnell, B.; Foster, B.; Foster, B.; Roux, S.; Hajek, P.P.; Varghese, N.; Mukherjee, S.; Reddy, T.B.K. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Genome wide profiling of histone H3 lysine 4 methylation during the Chlamydomonas cell cycle reveals stable and dynamic properties of lysine 4 trimethylation at gene promoters and near ubiquitous lysine 4 monomethylation

bioRxiv
2021 | Other
EID:

2-s2.0-85117861153

Part of ISSN: 26928205
Contributors: Strenkert, D.; Yildirim, A.; Yan, J.; Yoshinaga, Y.; Pellegrini, M.; O'Malley, R.C.; Merchant, S.S.; Umen, J.G.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Mechanotropic bZIP localization is associated with thigmomorphogenic and secondary cell wall associated gene expression

bioRxiv
2021 | Other
EID:

2-s2.0-85167481157

Part of ISSN: 26928205
Contributors: Coomey, J.H.; MacKinnon, K.J.-M.; McCahill, I.W.; Khahani, B.; Handakumbura, P.P.; Trabucco, G.M.; Mazzola, J.; Leblanc, N.A.; Kheam, R.; Hernandez-Romero, M. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

The genome of stress tolerant crop wild relative Paspalum vaginatum leads to increased biomass productivity in the crop Zea mays

bioRxiv
2021 | Other
EID:

2-s2.0-85115524927

Part of ISSN: 26928205
Contributors: Sun, G.; Wase, N.; Shu, S.; Jenkins, J.; Zhou, B.; Chen, C.; Sandor, L.; Plott, C.; Yoshinga, Y.; Daum, C. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Persistence and plasticity in bacterial gene regulation

Nature Methods
2021-12 | Journal article | Author
Part of ISSN: 1548-7091
Part of ISSN: 1548-7105
Contributors: Leo Baumgart; Ji Eun Lee; Asaf Salamov; David J. Dilworth; Hyunsoo Na; Matthew Mingay; Matthew Blow; Yu Zhang; Yuko Yoshinaga; Chris G. Daum et al.
Source: Self-asserted source
Ronan C O'Malley

Draft genome sequence of Yokenella regensburgei strain WCD67, isolated from the boxelder bug

Microbiology Resource Announcements
2020 | Journal article
EID:

2-s2.0-85083275223

Part of ISSN: 2576098X
Contributors: Meyers, D.J.; Leigh, B.A.; Huntemann, M.; Clum, A.; Ritter, S.; Palaniappan, K.; Chen, I.-M.; Stamatis, D.; Reddy, T.B.K.; O'Malley, R. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication

BMC Evolutionary Biology
2019 | Journal article
EID:

2-s2.0-85062859932

Part of ISSN: 14712148
Contributors: Panchy, N.L.; Azodi, C.B.; Winship, E.F.; O'Malley, R.C.; Shiu, S.-H.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Cell Reports
2019 | Journal article
EID:

2-s2.0-85065032772

Part of ISSN: 22111247
Contributors: Shulse, C.N.; Cole, B.J.; Ciobanu, D.; Lin, J.; Yoshinaga, Y.; Gouran, M.; Turco, G.M.; Zhu, Y.; O'Malley, R.C.; Brady, S.M. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses

Proceedings of the National Academy of Sciences of the United States of America
2019 | Journal article
EID:

2-s2.0-85077248062

Part of ISSN: 10916490 00278424
Contributors: Varoquaux, N.; Cole, B.; Gao, C.; Pierroz, G.; Baker, C.R.; Patel, D.; Madera, M.; Jeffers, T.; Hollingsworth, J.; Sievert, J. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Draft genome sequences of new isolates and the known species of the family microbacteriaceae associated with plants

Microbiology Resource Announcements
2018 | Journal article
EID:

2-s2.0-85056279885

Part of ISSN: 2576098X
Contributors: Vasilenko, O.V.; Starodumova, I.P.; Dorofeeva, L.V.; Tarlachkov, S.V.; Prisyazhnaya, N.V.; Chizhov, V.N.; Subbotin, S.A.; Huntemann, M.; Clum, A.; Duffy, K. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae

Plant Journal
2018 | Journal article
EID:

2-s2.0-85053419748

Part of ISSN: 1365313X 09607412
Contributors: Handakumbura, P.P.; Brow, K.; Whitney, I.P.; Zhao, K.; Sanguinet, K.A.; Lee, S.J.; Olins, J.; Romero-Gamboa, S.P.; Harrington, M.J.; Bascom, C.J. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Asymmetric evolution of the transcription profiles and cis-regulatory sites contributes to the retention of transcription factor duplicates

bioRxiv
2017 | Other
EID:

2-s2.0-85095633913

Part of ISSN: 26928205
Contributors: Panchy, N.L.; Azodi, C.B.; Winship, E.F.; O'Malley, R.C.; Shiu, S.-H.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

CrY2H-seq: A massively multiplexed assay for deep-coverage interactome mapping

Nature Methods
2017 | Journal article
EID:

2-s2.0-85026489130

Part of ISSN: 15487105 15487091
Contributors: Trigg, S.A.; Garza, R.M.; MacWilliams, A.; Nery, J.R.; Bartlett, A.; Castanon, R.; Goubil, A.; Feeney, J.; O'Malley, R.; Huang, S.-S.-C. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Mapping genome-wide transcription-factor binding sites using DAP-seq

Nature Protocols
2017 | Journal article
EID:

2-s2.0-85026402362

Part of ISSN: 17502799 17542189
Contributors: Bartlett, A.; O'Malley, R.C.; Huang, S.-S.C.; Galli, M.; Nery, J.R.; Gallavotti, A.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

Plant Journal
2017 | Journal article
EID:

2-s2.0-85021330075

Contributors: Hsia, M.M.; O'Malley, R.; Cartwright, A.; Nieu, R.; Gordon, S.P.; Kelly, S.; Williams, T.G.; Wood, D.F.; Zhao, Y.; Bragg, J. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

Cell
2016 | Journal article
EID:

2-s2.0-84975134214

Contributors: O'Malley, R.C.; Huang, S.-S.C.; Song, L.; Lewsey, M.G.; Bartlett, A.; Nery, J.R.; Galli, M.; Gallavotti, A.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Cell
2016 | Journal article
EID:

2-s2.0-84978196533

Contributors: Kawakatsu, T.; Huang, S.-S.C.; Jupe, F.; Sasaki, E.; Schmitz, R.J.; Urich, M.A.; Castanon, R.; Nery, J.R.; Barragan, C.; He, Y. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Phased diploid genome assembly with single-molecule real-time sequencing

Nature Methods
2016 | Journal article
EID:

2-s2.0-84991694364

Contributors: Chin, C.-S.; Peluso, P.; Sedlazeck, F.J.; Nattestad, M.; Concepcion, G.T.; Clum, A.; Dunn, C.; O'Malley, R.; Figueroa-Balderas, R.; Morales-Cruz, A. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

The Arabidopsis auxin receptor F-box proteins AFB4 and AFB5 are required for response to the synthetic auxin picloram

G3: Genes, Genomes, Genetics
2016 | Journal article
EID:

2-s2.0-84966297147

Contributors: Prigge, M.J.; Greenham, K.; Zhang, Y.; Santner, A.; Castillejo, C.; Mutka, A.M.; O'Malley, R.C.; Ecker, J.R.; Kunkel, B.N.; Estelle, M.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

A user's guide to the arabidopsis T-DNA insertion mutant collections

Plant Functional Genomics: Methods and Protocols: Second Edition
2015 | Book
EID:

2-s2.0-84954580701

Contributors: O'Malley, R.C.; Barragan, C.C.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Nature
2014 | Journal article
EID:

2-s2.0-84926190864

Contributors: Lister, R.; Pelizzola, M.; Kida, Y.S.; Hawkins, R.D.; Nery, J.R.; Hon, G.; Antosiewicz-Bourget, J.; O'Malley, R.; Castanon, R.; Klugman, S. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Epiallelic variation in Arabidopsis thaliana

Cold Spring Harbor Symposia on Quantitative Biology
2012 | Book
EID:

2-s2.0-84881500721

Contributors: O'Malley, R.C.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Forward and reverse genetics through derivation of haploid mouse embryonic stem cells

Cell Stem Cell
2011 | Journal article
EID:

2-s2.0-82755182211

Contributors: Elling, U.; Taubenschmid, J.; Wirnsberger, G.; O'Malley, R.; Demers, S.-P.; Vanhaelen, Q.; Shukalyuk, A.I.; Schmauss, G.; Schramek, D.; Schnuetgen, F. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Transgenerational epigenetic instability is a source of novel methylation variants

Science
2011 | Journal article
EID:

2-s2.0-80054837794

Contributors: Schmitz, R.J.; Schultz, M.D.; Lewsey, M.G.; O'Malley, R.C.; Urich, M.A.; Libiger, O.; Schork, N.J.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Linking genotype to phenotype using the Arabidopsis unimutant collection

Plant Journal
2010 | Journal article
EID:

2-s2.0-77950452042

Contributors: O'Malley, R.C.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

Developmental Cell
2008 | Journal article
EID:

2-s2.0-44449142226

Contributors: Gregory, B.D.; O'Malley, R.C.; Lister, R.; Urich, M.A.; Tonti-Filippini, J.; Chen, H.; Millar, A.H.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

Cell
2008 | Journal article
EID:

2-s2.0-42749087226

Contributors: Lister, R.; O'Malley, R.C.; Tonti-Filippini, J.; Gregory, B.D.; Berry, C.C.; Millar, A.H.; Ecker, J.R.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Ethylene stimulates nutations that are dependent on the ETR1 receptor

Plant Physiology
2006 | Journal article
EID:

2-s2.0-33845612741

Contributors: Binder, B.M.; O'Malley, R.C.; Wang, W.; Zutz, T.C.; Bleecker, A.B.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Ethylene-binding activity, gene expression levels, and receptor system output for ethylene receptor family members from Arabidopsis and tomato

Plant Journal
2005 | Journal article
EID:

2-s2.0-14844283792

Contributors: O'Malley, R.C.; Rodriguez, F.I.; Esch, J.J.; Binder, B.M.; O'Donnell, P.; Klee, H.J.; Bleecker, A.B.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Genomics of plant cell wall biogenesis

Planta
2005 | Journal article
EID:

2-s2.0-23944486169

Contributors: Yong, W.; Link, B.; O'Malley, R.; Tewari, J.; Hunter, C.T.; Lu, C.-A.; Li, X.; Bleecker, A.B.; Koch, K.E.; McCann, M.C. et al.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Arabidopsis seedling growth response and recovery to ethylene. A kinetic analysis

Plant Physiology
2004 | Journal article
EID:

2-s2.0-14844338402

Contributors: Binder, B.M.; O'Malley, R.C.; Wang, W.; Moore, J.M.; Parks, B.M.; Spalding, E.P.; Bleecker, A.B.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Canonical histidine kinase activity of the transmitter domain of the ETR1 ethylene receptor from Arabidopsis is not required for signal transmission

Proceedings of the National Academy of Sciences of the United States of America
2003 | Journal article
EID:

2-s2.0-0037422588

Contributors: Wang, W.; Hall, A.E.; O'Malley, R.; Bleecker, A.B.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

A fully automated hierarchical software strategy for de novo sequencing of whole Q-Tof electrospray LC-MS/MS datasets

Proceedings 50th ASMS Conference on Mass Spectrometry and Allied Topics
2002 | Conference paper
EID:

2-s2.0-1942439308

Contributors: Langridge, J.I.; Millar, A.; Young, P.; O'Malley, R.; Swainston, N.; Skilling, J.; Hoyes, J.; Richardson, K.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Automated LC-MS/MS data analysis of a novel alcohol dehydrogenase form isolated from pigeon liver

Proceedings 50th ASMS Conference on Mass Spectrometry and Allied Topics
2002 | Conference paper
EID:

2-s2.0-2442647922

Contributors: Jonsson, A.; Hjelmqvist, L.; Jörnvall, H.; O'Malley, R.; Swainston, N.; Young, P.; Millar, A.; Goshawk, J.; Langridge, J.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Ethylene Perception in Arabidopsis by the ETRl Receptor Family. Evaluating a Possible Role for Two-Component Signaling in Plant Ethylene Responses

Histidine Kinases in Signal Transduction
2002 | Book
EID:

2-s2.0-84902389553

Contributors: O'Malley, R.C.; Bleecker, A.B.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Expansin message regulation in parasitic angiosperms: Marking time in development

Plant Cell
2000 | Journal article
EID:

2-s2.0-0033831546

Contributors: O'Malley, R.C.; Lynn, D.G.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Signaling organogenesis in parasitic angiosperms: Xenognosin generation, perception, and response

Journal of Plant Growth Regulation
2000 | Journal article
EID:

2-s2.0-0033758805

Contributors: Keyes, W.J.; O'Malley, R.C.; Kim, D.; Lynn, D.G.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

A mechanism for inducing plant development: The genesis of a specific inhibitor

Proceedings of the National Academy of Sciences of the United States of America
1996 | Journal article
EID:

2-s2.0-0029900973

Contributors: Smith, C.E.; Ruttledge, T.; Zeng, Z.; O'Malley, R.C.; Lynn, D.G.
Source: Self-asserted source
Ronan C O'Malley via Scopus - Elsevier

Peer review (4 reviews for 1 publication/grant)

Review activity for Nature communications (4)