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Ronan O’Malley

Ronan O’Malley, PhD, Sequencing Technologies Group Lead, DOE Joint Genome Institute

Ronan O’Malley, PhD, Sequencing Technologies Group Lead, DOE Joint Genome Institute

Dr. O’Malley joined the JGI in 2016 to lead the Sequencing Technologies group. In this role he manages production sequencing for community sequencing projects, and leads R&D efforts to expand the functional genomics and epigenomics capabilities of the JGI. Dr. O’Malley interest is in developing new functional genomics technologies for applications to outstanding problems in environmental and agricultural biology. His accomplishments include creating the first integrative next-generation sequencing maps of methylomes and transcriptomes in any species (Arabidopsis), and inventing DAP-seq, a rapid and low-cost annotation of most transcription factor binding sites in an organism.  Dr. O’Malley brings his expertise to the JGI to provide cutting-edge research products to the user community to understand the epigenetic and gene regulatory sequence codes in plants, microbes and fungi.

Education

  • BS in Biochemistry, University of Chicago
  • PhD in Biochemistry, University of Chicago

Publications

  1. Huberman, L. B. et al. (2021) ‘DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus’, PNAS,, 118(13). doi: 10.1073/pnas.2009501118.
  2. Wu, V. W. et al. (2020) ‘The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus’, PNAS, 117(11), pp. 6003–6013.
  3. Varoquaux, N. et al. (2019) ‘Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses’,PNAS,. doi: 10.1073/pnas.1907500116.
  4. Shulse, C. N. et al. (2019) ‘High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types’, Cell reports, 27(7), pp. 2241–2247.e4.
  5. Trigg, S. A. et al. (2017) ‘CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping’, Nature methods, 14(8), pp. 819–825.
  6. O’Malley, R. C. et al. (2016) ‘Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape’, Cell, 166(6), p. 1598.
  7. Kawakatsu, T. et al. (2016) ‘Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions’, Cell, 166(2), pp. 492–505.
  8. Chin, C.-S. et al. (2016) ‘Phased diploid genome assembly with single-molecule real-time sequencing’, Nature methods, 13(12), pp. 1050–1054.
  9. Lister, R. et al. (2008) ‘Highly integrated single-base resolution maps of the epigenome in Arabidopsis’, Cell, 133(3), pp. 523–536.