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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

Biochemistry, Ph.D., University of Iowa

Sep 1 1973Jul 1 1977

Chemistry, B.A., Vanderbilt University

Sep 1 1969Jun 1 1973

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Projects 1980 2023

VISION: ValIdated Systematic IntegratiON of epigenomic data

Hardison, R. C., Zhang, Y., Bodine, D. M., Taylor, J. P., Blobel, G. & Weiss, M.

National Institutes of Health

7/18/165/31/21

Project: Research project

Epigenomics
Research Personnel
Regulator Genes
Hematopoietic Stem Cells
Genes

Genomic Architecture of LGL Leukemia

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

National Institutes of Health

12/1/1511/30/20

Project: Research project

Large Granular Lymphocytic Leukemia
Genome
Phenotype
Mutation
Genomic Structural Variation
Computational Biology
Aptitude
Education
training program
Genomics
Human Genome
Disease Susceptibility
Genome
National Human Genome Research Institute (U.S.)
Transcription Factors

Global Predictions and Tests of Erythroid Regulation

Zhang, Y., Chiaromonte, F., Hardison, R. C., Miller, W. C., Schuster, S., Taylor, J. P., Blobel, G., Weiss, M. & Bodine, D. M.

National Institutes of Health

2/1/048/31/15

Project: Research project

Genes
Genome
Leukemia, Erythroblastic, Acute
Sequence Alignment
Transcription Factors

Research Output 1975 2020

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
GATA Transcription Factors
Paint
Epigenomics
Genes
Chromatin

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

Phase Transition
G1 Phase
Mitosis
Chromatin
Telophase
3 Citations (Scopus)

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
Acetylation
Transcription
Histones
Chromatin
Histone Code

OnTAD: Hierarchical domain structure reveals the divergence of activity among TADs and boundaries

An, L., Yang, T., Yang, J., Nuebler, J., Xiang, G., Hardison, R. C., Li, Q. & Zhang, Y., Dec 18 2019, In : Genome biology. 20, 1, 282.

Research output: Contribution to journalArticle

Open Access
domain structure
extrusion
Chromatin
gene expression
chromatin

Systems biology in heterogenous tissues: Integrating multiple ∗omics datasets to understand hematopoietic differentiation

Lichtenberg, J., Xiang, G., Heuston, E., Giardine, B., Keller, C. A., Hardison, R. C., Bodine, D. M. & Zhang, Y., Oct 2019, Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019. Institute of Electrical and Electronics Engineers Inc., p. 240-243 4 p. 8942000. (Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Systems Biology
DNA Methylation
Histone Code
Epigenomics
Tissue