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Personal profile

Research interests

For over four decades, I have pursued the long-term research goal of understanding molecular mechanisms and evolution of gene regulation in mammals. My research has included fundamental studies of chromatin structure, developing methods for isolating molecular clones of genomic DNA from mammals (the beginnings of genomics), determining structure and developmental expression profiles of globin genes, using interspecies sequence comparisons to illuminate genome evolution and predict regulatory regions, and determining gene expression and epigenetic profiles genome-wide in search of global mechanisms of gene regulation. This diversity of projects has been enabled by excellent workers in my lab and by several long-term collaborations. I worked with Drs. Webb Miller, David Haussler, Francesca Chiaromonte, and James Taylor to generate interspecies alignments of genome sequences and predict gene regulatory function from patterns in those alignments. In collaboration with Drs. Mitch Weiss, Gerd Blobel, David Bodine, Yu Zhang, James Taylor, and Feng Yue, we apply massively parallel, short read sequencing to determine transcriptomes and to map occupancy by key transcription factors and the landscape of histone modifications during differentiation of multiple hematopoietic lineages in mouse. Importantly, the comparative genomics and epigenomic data are analyzed integratively to model and predict gene regulatory modules, always leading to experimental tests of those predictions in my laboratory. This same paradigm of data gathering, integrative analysis, and experimental tests guided our work as members of the ENCODE Project Consortium since its inception. My own laboratory produced over 100 replicated experiments released through our work in the mouse ENCODE consortium (on which I was a PI) and as a collaboration with Dr. Richard Myers at HudsonAlpha and Dr. Barbara Wold at Caltech. In summary, I bring extensive, diverse experience in biochemical, genetic, and evolutionary approaches to studies of genome function and gene regulation, all of them enabled by sophisticated bioinformatics.

Education/Academic qualification

Molecular Biology, Post-doctoral Fellow, California Institute of Technology, Pasadena, CA 91125, USA

Sep 1 1977Feb 1 1980

Award Date: Feb 1 1980

Biochemistry, Ph.D., University of Iowa

Sep 1 1973Jul 1 1977

Award Date: Jul 1 1977

Chemistry, B.A., Vanderbilt University

Sep 1 1969Jun 1 1973

Award Date: Jul 1 1973

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Projects

Genomic Architecture of LGL Leukemia

Hardison, R. C. & Loughran, T. P.

National Cancer Institute

12/1/1511/30/16

Project: Research project

  • Research Output

    An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

    Xiang, G., Keller, C. A., Heuston, E., Giardine, B. M., An, L., Wixom, A. Q., Miller, A., Cockburn, A., Sauria, M. E. G., Weaver, K., Lichtenberg, J., Göttgens, B., Li, Q., Bodine, D., Mahony, S., Taylor, J., Blobel, G. A., Weiss, M. J., Cheng, Y., Yue, F. & 4 others, Hughes, J., Higgs, D. R., Zhang, Y. & Hardison, R. C., Jan 1 2020, In : Genome research. 30, 3, p. 472-484 13 p.

    Research output: Contribution to journalArticle

    Open Access
  • S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data

    Xiang, G., Keller, C. A., Giardine, B., An, L., Li, Q., Zhang, Y. & Hardison, R. C., May 7 2020, In : Nucleic acids research. 48, 8, p. e43

    Research output: Contribution to journalArticle

    Open Access
  • 1 Scopus citations

    Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

    Hardison, R. C., Zhang, Y., Keller, C. A., Xiang, G., Heuston, E. F., An, L., Lichtenberg, J., Giardine, B. M., Bodine, D., Mahony, S., Li, Q., Yue, F., Weiss, M. J., Blobel, G. A., Taylor, J., Hughes, J., Higgs, D. R. & Göttgens, B., Jan 1 2020, In : IUBMB Life. 72, 1, p. 27-38 12 p.

    Research output: Contribution to journalReview article

    Open Access
  • Chromatin structure dynamics during the mitosis-to-G1 phase transition

    Zhang, H., Emerson, D. J., Gilgenast, T. G., Titus, K. R., Lan, Y., Huang, P., Zhang, D., Wang, H., Keller, C. A., Giardine, B., Hardison, R. C., Phillips-Cremins, J. E. & Blobel, G. A., Dec 5 2019, In : Nature. 576, 7785, p. 158-162 5 p.

    Research output: Contribution to journalArticle

  • 5 Scopus citations

    Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription

    Behera, V., Stonestrom, A. J., Hamagami, N., Hsiung, C. C., Keller, C. A., Giardine, B., Sidoli, S., Yuan, Z. F., Bhanu, N. V., Werner, M. T., Wang, H., Garcia, B. A., Hardison, R. C. & Blobel, G. A., Apr 9 2019, In : Cell Reports. 27, 2, p. 400-415.e5

    Research output: Contribution to journalArticle

    Open Access
  • 4 Scopus citations