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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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Sequence Alignment Medicine & Life Sciences

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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
Genomics
Research
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 2019

1 Citation (Scopus)

Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription

Behera, V., Stonestrom, A. J., Hamagami, N., Hsiung, C. C., Keller Capone, 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

The E3 ligase adaptor molecule SPOP regulates fetal hemoglobin levels in adult erythroid cells

Lan, X., Khandros, E., Huang, P., Peslak, S. A., Bhardwaj, S. K., Grevet, J. D., Abdulmalik, O., Wang, H., Keller, C. A., Giardine, B., Baeza, J., Duffner, E. R., Demerdash, O. E., Wu, X. S., Vakoc, C. R., Garcia, B. A., Hardison, R. C., Shi, J. & Blobel, G. A., May 28 2019, In : Blood Advances. 3, 10, p. 1586-1597 12 p.

Research output: Contribution to journalArticle

Open Access
Fetal Hemoglobin
Erythroid Cells
Ubiquitin-Protein Ligases
Proteins
Clustered Regularly Interspaced Short Palindromic Repeats
5 Citations (Scopus)

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

Bartman, C. R., Hamagami, N., Keller, C. A., Giardine, B., Hardison, R. C., Blobel, G. A. & Raj, A., Feb 7 2019, In : Molecular cell. 73, 3, p. 519-532.e4

Research output: Contribution to journalArticle

RNA Polymerase II
Chromatin Immunoprecipitation
12 Citations (Scopus)

Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells

Grevet, J. D., Lan, X., Hamagami, N., Edwards, C. R., Sankaranarayanan, L., Ji, X., Bhardwaj, S. K., Face, C. J., Posocco, D. F., Abdulmalik, O., Keller Capone, C. A., Giardine, B., Sidoli, S., Garcia, B. A., Chou, S. T., Liebhaber, S. A., Hardison, R. C., Shi, J. & Blobel, G. A., Jul 20 2018, In : Science. 361, 6399, p. 285-290 6 p.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Fetal Hemoglobin
Erythroid Cells
Guide RNA
Hemoglobinopathies
4 Citations (Scopus)

Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points

Heuston, E. F., Keller Capone, C. A., Lichtenberg, J., Giardine, B., Anderson, S. M., Hardison, R. C. & Bodine, D. M., May 28 2018, In : Epigenetics and Chromatin. 11, 1, 22.

Research output: Contribution to journalArticle

Chromatin
Megakaryocytes
Hematopoiesis
Erythrocytes
Nucleic Acid Regulatory Sequences