Hiroki Yokota, Ph.D.
Associate Professor, Biomedical Engineering
Associate Professor, Anatomy and Cell Biology

Contact:
723 W. Michigan St. SL 220D
Indianapolis, IN 46202
(317)-274-2448
hyokota@iupui.edu
NIH Biosketch (*.pdf)



Education:
Ph.D. Molecular Biology, Indiana University (1993)
Ph.D. Astronautics, University of Tokyo (1983)

Postdoctoral training:
Department of Molecular Biotechnology, University of Washington School of Medicine (1993 – 1998)

Research area : Biomechanics of bones and joints using a systems-biology approach

1. Identification of the molecular mechanisms involved in mechanotransduction of bone and joint cells
2. Development of loading devices, imaging tools, and mathematical models to characterize load-induced flow and molecular events in bones and joints
3. Electromechanical characterization of bones and joints under mechanical loading
4. Formulation and evaluation of the genome-wide regulatory models involved in osteogenesis and chondrogenesis

Laboratory research and experimental methodologies

1. mechanotransduction of bone and joint cells
1. gene expression
2. molecular interactions
2. molecular imaging
1. atomic force microscopy
2. confocal fluorescence microscopy
3. bone adaptation
1. electromechanical instrumentations
2. histology
4. computational genomics and proteomics
1. modeling of genome-wide transcriptional regulation
2. modeling of molecular interactions

Selected Publications:

Liu, Y., and Yokota, H . (2004). Modelling and identification of transcription-factor binding motifs in human chondrogenesis. Systems Biol. 1:85-92.

Yokota, H ., Goldring, M.B., and Sun, H.B. (2003).  CITED2-mediated regulation of MMP-1 and MMP-13 in human chondrocytes under flow shear.  J. Biol. Chem . 278:47275-47280.

Sun, H.B., Qian, L., Yokota, H. (2001). Detection of abasic sites on individual DNA molecules using atomic force microscopy. Anal. Chem. 73:2229-2232.

Sun, H.B., Shen, J., and Yokota, H. (2000). Size-dependent positioning of human chromosomes in interphase nuclei. Biophysical J . 79:184-190.

Yokota, H., Johnson, F., Lu, H., Robinson, R., Belu, A., Garrison, M., Ratner, B., Trask, B.J., and Miller, D. (1997). A new method for straightening DNA molecules for optical restriction mapping. Nucleic Acids Research 25:1064-1070.

Yokota, H., van den Engh, G., Hearst, J.E., Sachs, R.K., and Trask, B.J. (1995). Evidence for the organization of chromatin in Mbp-sized loops arranged along a random-walk path in the human G0/G1 interphase nucleus. J. Cell Biol. 130:1239-1249.

Sachs, R.K., van den Engh, G., Trask, B.J., Yokota, H., and Hearst, J.E. (1995). A random-walk/giant-loop model for interphase chromosomes. Proc. Natl. Acad. Sci. USA 92:2710-2714.