Biomedical Engineering: Purdue School of Engineering and Technology, IUPUI

Department of Biomedical Engineering

Hiroki Yokota, Ph.D.
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

The objective of research in our group is to develop new technologies for the comprehensive analysis of regulated biological systems and to apply these technologies to the study of the signal transduction pathways involved in mechanotransduction of bone and joint cells. The focus of modern biology is shifting toward studying systems rather than the study of individual genes or proteins, since only by analyzing complete systems or subsystems can one understand the fascinating properties of cells, tissues, and organs. The analysis of biological systems requires the development of powerful new tools that permit genome-wide quantitative analysis the integration of the data. Our lab is committed to developing hardware and software tools focused on the ability to carry out global systems analyses of bones and joints. Specific areas of interest include:

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

Laboratory research and experimental methodologies

mechanotransduction of bone and joint cells

gene expression
molecular interactions

molecular imaging

atomic force microscopy
confocal fluorescence microscopy

bone adaptation

electromechanical instrumentations
histology

computational genomics and proteomics

modeling of genome-wide transcriptional regulation
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.