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Ronan O'Malley

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
ORCID ORCID Icon0000-0002-4907-0339 Additional info
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Serrano K, Bezrutczyk M, Goudeau D, Dao T, O'Malley R, Malmstrom RR, Visel A, Scheller HV, Cole B. Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis. Nat Plants. 2024 Apr 08. PMID: 38589485.
    2. McCahill IW, Khahani B, Probert CF, Flockhart EL, Abushal LT, Gregory GA, Zhang Y, Baumgart LA, O'Malley RC, Hazen SP. Shoring up the base: the development and regulation of cortical sclerenchyma in grass nodal roots. bioRxiv. 2024 Jan 29. PMID: 38352548; PMCID: PMC10862697.
    3. Hyden B, Carper DL, Abraham PE, Yuan G, Yao T, Baumgart L, Zhang Y, Chen C, O'Malley R, Chen JG, Yang X, Hettich RL, Tuskan GA, Smart LB. Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination. Plant Direct. 2023 Nov; 7(11):e3546. PMID: 38028649; PMCID: PMC10651977.
    4. Ho H, Chovatia M, Egan R, He G, Yoshinaga Y, Liachko I, O'Malley R, Wang Z. Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning. PeerJ. 2023; 11:e16129. PMID: 37753177; PMCID: PMC10519199.
      Citations:    Fields:    Translation:Cells
    5. Weng X, Song H, Sreedasyam A, Haque T, Zhang L, Chen C, Yoshinaga Y, Williams M, O'Malley RC, Grimwood J, Schmutz J, Juenger TE. Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii. Plant Physiol. 2023 07 03; 192(3):2374-2393. PMID: 37018475; PMCID: PMC10315280.
      Citations: 1     Fields:    Translation:AnimalsCells
    6. 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. Nat Methods. 2023 Mar; 20(3):469. PMID: 36690743.
      Citations:    Fields:    
    7. Mattoon EM, McHargue WE, Bailey CE, Zhang N, Chen C, Eckhardt J, Daum CG, Zane M, Pennacchio C, Schmutz J, O'Malley RC, Cheng J, Zhang R. High-throughput identification of novel heat tolerance genes via genome-wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii. Plant Cell Environ. 2023 03; 46(3):865-888. PMID: 36479703; PMCID: PMC9898210.
      Citations:    Fields:    Translation:AnimalsCells
    8. Sun G, Wase N, Shu S, Jenkins J, Zhou B, Torres-Rodríguez JV, Chen C, Sandor L, Plott C, Yoshinga Y, Daum C, Qi P, Barry K, Lipzen A, Berry L, Pedersen C, Gottilla T, Foltz A, Yu H, O'Malley R, Zhang C, Devos KM, Sigmon B, Yu B, Obata T, Schmutz J, Schnable JC. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nat Commun. 2022 12 13; 13(1):7731. PMID: 36513676; PMCID: PMC9747981.
      Citations: 2     Fields:    Translation:Animals
    9. Strenkert D, Yildirim A, Yan J, Yoshinaga Y, Pellegrini M, O'Malley RC, Merchant SS, Umen JG. The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle. Plant J. 2022 10; 112(2):352-368. PMID: 35986497; PMCID: PMC9588799.
      Citations: 1     Fields:    Translation:AnimalsCells
    10. Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina Del Rio T, DeAngelis KM. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiol Spectr. 2022 06 29; 10(3):e0234621. PMID: 35579457; PMCID: PMC9241852.
      Citations:    Fields:    Translation:AnimalsCells
    11. Strenkert D, Mingay M, Schmollinger S, Chen C, O'Malley RC, Merchant SS. An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis. Plant Direct. 2022 Mar; 6(3):e392. PMID: 35382117; PMCID: PMC8961045.
    12. 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, Wohlschlegel JA, O'Malley RC, Ecker JR, Jacobsen SE. The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis. Proc Natl Acad Sci U S A. 2022 01 18; 119(3). PMID: 35027454; PMCID: PMC8784105.
      Citations: 6     Fields:    Translation:AnimalsCells
    13. Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC. Persistence and plasticity in bacterial gene regulation. Nat Methods. 2021 12; 18(12):1499-1505. PMID: 34824476.
      Citations: 13     Fields:    Translation:AnimalsCells
    14. Van Goethem MW, Osborn AR, Bowen BP, Andeer PF, Swenson TL, Clum A, Riley R, He G, Koriabine M, Sandor L, Yan M, Daum CG, Yoshinaga Y, Makhalanyane TP, Garcia-Pichel F, Visel A, Pennacchio LA, O'Malley RC, Northen TR. Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. Commun Biol. 2021 11 18; 4(1):1302. PMID: 34795375; PMCID: PMC8602731.
      Citations: 10     Translation:CellsPHPublic Health
    15. Huberman LB, Wu VW, Lee J, Daum C, O'Malley RC, Glass NL. Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing. mSphere. 2021 10 27; 6(5):e0056421. PMID: 34523983; PMCID: PMC8550094.
      Citations: 4     Fields:    Translation:Animals
    16. 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, Sinha N, Vogel JP, O'Malley RC, Visel A, Dickel DE. Plant single-cell solutions for energy and the environment. Commun Biol. 2021 08 12; 4(1):962. PMID: 34385583; PMCID: PMC8361165.
      Citations: 10     Translation:Animals
    17. Clum A, Huntemann M, Bushnell B, Foster B, Foster B, Roux S, Hajek PP, Varghese N, Mukherjee S, Reddy TBK, Daum C, Yoshinaga Y, O'Malley R, Seshadri R, Kyrpides NC, Eloe-Fadrosh EA, Chen IA, Copeland A, Ivanova NN. DOE JGI Metagenome Workflow. mSystems. 2021 May 18; 6(3). PMID: 34006627; PMCID: PMC8269246.
      Citations: 39     Fields:    
    18. Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao JY, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Front Microbiol. 2021; 12:632731. PMID: 34017316; PMCID: PMC8129789.
      Citations: 5     
    19. Huberman LB, Wu VW, Kowbel DJ, Lee J, Daum C, Grigoriev IV, O'Malley RC, Glass NL. DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus. Proc Natl Acad Sci U S A. 2021 03 30; 118(13). PMID: 33753477; PMCID: PMC8020665.
      Citations: 14     Fields:    Translation:Animals
    20. Meyers DJ, Leigh BA, Huntemann M, Clum A, Ritter S, Palaniappan K, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Whitman WB. Draft Genome Sequence of Yokenella regensburgei Strain WCD67, Isolated from the Boxelder Bug. Microbiol Resour Announc. 2020 Apr 09; 9(15). PMID: 32273354; PMCID: PMC7380535.
    21. Wu VW, Thieme N, Huberman LB, Dietschmann A, Kowbel DJ, Lee J, Calhoun S, Singan VR, Lipzen A, Xiong Y, Monti R, Blow MJ, O'Malley RC, Grigoriev IV, Benz JP, Glass NL. The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus. Proc Natl Acad Sci U S A. 2020 03 17; 117(11):6003-6013. PMID: 32111691; PMCID: PMC7084071.
      Citations: 42     Fields:    Translation:AnimalsCells
    22. Varoquaux N, Cole B, Gao C, Pierroz G, Baker CR, Patel D, Madera M, Jeffers T, Hollingsworth J, Sievert J, Yoshinaga Y, Owiti JA, Singan VR, DeGraaf S, Xu L, Blow MJ, Harrison MJ, Visel A, Jansson C, Niyogi KK, Hutmacher R, Coleman-Derr D, O'Malley RC, Taylor JW, Dahlberg J, Vogel JP, Lemaux PG, Purdom E. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proc Natl Acad Sci U S A. 2019 Dec 26; 116(52):27124-27132. PMID: 31806758; PMCID: PMC6936495.
      Citations: 55     Fields:    
    23. Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Göker M, Murray AE, Lindemann SR, Klenk HP, O'Malley R, Zane M, Cheng JF, Copeland A, Daum C, Singer E, Woyke T. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Sci Data. 2019 11 26; 6(1):285. PMID: 31772173; PMCID: PMC6879543.
      Citations: 48     Fields:    Translation:Cells
    24. Jaslan D, Dreyer I, Lu J, O'Malley R, Dindas J, Marten I, Hedrich R. Voltage-dependent gating of SV channel TPC1 confers vacuole excitability. Nat Commun. 2019 06 14; 10(1):2659. PMID: 31201323; PMCID: PMC6572840.
      Citations: 18     Fields:    Translation:AnimalsCells
    25. Shulse CN, Cole BJ, Ciobanu D, Lin J, Yoshinaga Y, Gouran M, Turco GM, Zhu Y, O'Malley RC, Brady SM, Dickel DE. High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types. Cell Rep. 2019 05 14; 27(7):2241-2247.e4. PMID: 31091459; PMCID: PMC6758921.
      Citations: 130     Fields:    Translation:AnimalsCells
    26. Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina Del Rio T, DeAngelis K. Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source. Microbiol Resour Announc. 2019 May 02; 8(18). PMID: 31048387; PMCID: PMC6498242.
    27. Panchy NL, Azodi CB, Winship EF, O'Malley RC, Shiu SH. Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC Evol Biol. 2019 03 13; 19(1):77. PMID: 30866803; PMCID: PMC6416927.
      Citations: 6     Fields:    Translation:Animals
    28. Vasilenko OV, Starodumova IP, Dorofeeva LV, Tarlachkov SV, Prisyazhnaya NV, Chizhov VN, Subbotin SA, Huntemann M, Clum A, Duffy K, Pillay M, Palaniappan K, Varghese N, Chen IA, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Whitman WB, Evtushenko LI. Draft Genome Sequences of New Isolates and the Known Species of the Family Microbacteriaceae Associated with Plants. Microbiol Resour Announc. 2018 Sep; 7(11). PMID: 30533634; PMCID: PMC6256657.
      Citations: 2     
    29. Handakumbura PP, Brow K, Whitney IP, Zhao K, Sanguinet KA, Lee SJ, Olins J, Romero-Gamboa SP, Harrington MJ, Bascom CJ, MacKinnon KJ, Veling MT, Liu L, Lee JE, Vogel JP, O'Malley RC, Bezanilla M, Bartley LE, Hazen SP. SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae. Plant J. 2018 11; 96(3):532-545. PMID: 30054951.
      Citations: 4     Fields:    Translation:AnimalsCells
    30. Fischer MS, Wu VW, Lee JE, O'Malley RC, Glass NL. Regulation of Cell-to-Cell Communication and Cell Wall Integrity by a Network of MAP Kinase Pathways and Transcription Factors in Neurospora crassa. Genetics. 2018 06; 209(2):489-506. PMID: 29678830; PMCID: PMC5972422.
      Citations: 19     Fields:    Translation:AnimalsCells
    31. Yoshinaga Y, Daum C, He G, O'Malley R. Genome Sequencing. Methods Mol Biol. 2018; 1775:37-52. PMID: 29876807.
      Citations: 7     Fields:    Translation:AnimalsCells
    32. 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. Nat Protoc. 2017 Aug; 12(8):1659-1672. PMID: 28726847; PMCID: PMC5576341.
      Citations: 153     Fields:    Translation:Cells
    33. 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. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2017 08; 14(8):819-825. PMID: 28650476; PMCID: PMC5564216.
      Citations: 66     Fields:    Translation:Animals
    34. 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. Plant J. 2017 Aug; 91(3):361-370. PMID: 28432803.
      Citations: 21     Fields:    Translation:Animals
    35. 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, Rank DR, Schatz MC. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 Dec; 13(12):1050-1054. PMID: 27749838; PMCID: PMC5503144.
      Citations: 823     Fields:    Translation:HumansAnimals
    36. 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. 2016 Sep 08; 166(6):1598. PMID: 27610578.
      Citations: 84     Fields:    
    37. 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, O'Neil R, O'Malley RC, Quarless DX, 1001 Genomes Consortium, Schork NJ, Nordborg M, Ecker JR, Wang C, Bemm F, Becker C, Weigel D. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 2016 Jul 14; 166(2):492-505. PMID: 27419873; PMCID: PMC5172462.
      Citations: 270     Fields:    Translation:AnimalsCells
    38. 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. 2016 May 19; 165(5):1280-1292. PMID: 27203113; PMCID: PMC4907330.
      Citations: 475     Fields:    Translation:AnimalsCells
    39. Prigge MJ, 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). 2016 05 03; 6(5):1383-90. PMID: 26976444; PMCID: PMC4856089.
      Citations: 43     Fields:    Translation:AnimalsCells
    40. O'Malley RC, Barragan CC, Ecker JR. A user's guide to the Arabidopsis T-DNA insertion mutant collections. Methods Mol Biol. 2015; 1284:323-42. PMID: 25757780; PMCID: PMC5215775.
      Citations: 48     Fields:    Translation:Animals
    41. 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, Penninger JM. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells. Cell Stem Cell. 2011 Dec 02; 9(6):563-74. PMID: 22136931; PMCID: PMC4008724.
      Citations: 133     Fields:    Translation:AnimalsCells
    42. 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. 2011 Oct 21; 334(6054):369-73. PMID: 21921155; PMCID: PMC3210014.
      Citations: 294     Fields:    Translation:AnimalsCells
    43. 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, Evans RM, Ecker JR. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011 Mar 03; 471(7336):68-73. PMID: 21289626; PMCID: PMC3100360.
      Citations: 778     Fields:    Translation:HumansCells
    44. O'Malley RC, Ecker JR. Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J. 2010 Mar; 61(6):928-40. PMID: 20409268.
      Citations: 74     Fields:    Translation:Animals
    45. 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. Dev Cell. 2008 Jun; 14(6):854-66. PMID: 18486559.
      Citations: 214     Fields:    Translation:AnimalsCells
    46. 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. 2008 May 02; 133(3):523-36. PMID: 18423832; PMCID: PMC2723732.
      Citations: 1148     Fields:    Translation:AnimalsCells
    47. 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. Nat Protoc. 2007; 2(11):2910-7. PMID: 18007627.
      Citations: 54     Fields:    Translation:Animals
    48. Binder BM, O'Malley RC, Wang W, Zutz TC, Bleecker AB. Ethylene stimulates nutations that are dependent on the ETR1 receptor. Plant Physiol. 2006 Dec; 142(4):1690-700. PMID: 17071649; PMCID: PMC1676061.
      Citations: 30     Fields:    Translation:AnimalsCells
    49. O'Malley RC, Rodriguez FI, Esch JJ, Binder BM, O'Donnell P, Klee HJ, Bleecker AB. Ethylene-binding activity, gene expression levels, and receptor system output for ethylene receptor family members from Arabidopsis and tomato. Plant J. 2005 Mar; 41(5):651-9. PMID: 15703053.
      Citations: 84     Fields:    Translation:Animals
    50. Binder BM, O'malley RC, Wang W, Moore JM, Parks BM, Spalding EP, Bleecker AB. Arabidopsis seedling growth response and recovery to ethylene. A kinetic analysis. Plant Physiol. 2004 Oct; 136(2):2913-20. PMID: 15466220; PMCID: PMC523353.
      Citations: 68     Fields:    Translation:AnimalsCells
    51. Wang W, Hall AE, O'Malley R, Bleecker AB. Canonical histidine kinase activity of the transmitter domain of the ETR1 ethylene receptor from Arabidopsis is not required for signal transmission. Proc Natl Acad Sci U S A. 2003 Jan 07; 100(1):352-7. PMID: 12509505; PMCID: PMC140975.
      Citations: 96     Fields:    Translation:AnimalsCells
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