WIBE Profile: Dr. Xiaohua Huang joined the UCSD Department of Bioengineering in September 2002. He received his B.S. in Chemistry from Zhongshan University in China and his Ph.D. in Biophysical Chemistry from Stanford University. His graduate advisor was Prof. Steven G. Boxer. Following graduate school, he did postdoctoral work with Prof. David C Ward in the Departments of Genetics and Molecular Biochemistry and Biophysics at Yale University. Prior to his appointment in UCSD Bioengineering, Dr. Huang was a postdoctoral research fellow in the Department of Genetics at Harvard Medical School under the direction of Prof. George M. Church.
Dr. Huang is regarded as a key player in the arenas of genomics, systems biology and nano-biotechnology. Dr. Huang's appointment brings to UCSD Bioengineering expertise in genomics and systems biology and will greatly enhance our activities in these emerging interdisciplinary frontiers.
Dr. Huang's research is in the areas of genomics, systems biology and nano-biotechnology. He is particularly interested in developing the next generation of integrated bio-analytical systems, lab-on-a-chip and nano-technology based molecular devices. Developing experimental and computational tools to elucidate, model and engineer genetic regulatory networks is another area of his research interest.
The revolution in modern biology is largely due to the development of novel physicochemical and engineering methods to carry out high throughput assaying and measurements of genes and proteins. Automated DNA sequencing, polymerase chain reaction (PCR) and gene expression profiling using microarrays, to name a few, have fundamentally changed the landscape of biology and biomedical research. However, existing analytical technologies remain inadequate for many genome and proteome-scale studies due to the enormous size and complexity of many biological systems. For example, current costs associated with large-scale sequencing (estimated to be tens to hundreds of millions of dollars per mammalian genome) remain a central limiting factor for genome sequencing efforts. It is clear now that a paradigm shift in terms of methodology, scale and engineering is needed to develop more powerful enabling technologies for systems studies. One of Dr. Huang major research focus is to develop innovative integrated bioanalytical systems for ultra fast whole genome DNA sequencing, pharmacogenomics, molecular diagnostics and digital gene expression profiling. His strategy is to focus on massive parallelization, miniaturization and systems integration of biochemical reactions and detections.
Amplification of DNA by PCR is used universally to make large number of copies of DNA, a capability that has led to revolutionary advances. Dr. Huang is the pioneer of one similar high throughput technology. A novel and powerful technology for amplification called the rolling circle amplification (RCA) was recently developed by Dr. Huang and his colleagues. His recently work in Prof. Church laboratory has demonstrated the feasibility of massively parallel separation and isothermal amplification cloning of single DNA molecules on solid surfaces using RCA. Tens to hundreds of millions of single DNA molecules can be separated and cloned in situ on the functionalized surface of a glass microscopy slide. Each molecular clone on the surface can serve as an addressable nano-reactor or nano-sensor for DNA sequencing, and other biochemical reactions and detections. He has also invented a novel DNA sequencing technology. His future research will involve further development of these technologies and engineer automated integrated systems for whole genome sequencing, digital gene expression profiling and molecule diagnostics.
Another area of Dr. Huang' research concerns genetic regulatory networks. Complex genetic regulatory networks orchestrate the spatial and temporal expression of genes in response to intra- and extra-cellular signals to give rise to different cell types and tissues, stress response and other myriad of functions. Regulated expression of most genes begins with the sequence specific binding of transcription factors to the regulatory sequences of the gene. Identifying the components, structures and organizations of these networks is the first essential step towards an integrated and predictive understanding of cell cycle control, differentiation and apoptosis. Despite the availability of genome sequences of many organisms including human and mouse, the regulatory sequences of most of their gene remain unknown. Dr. Huang and his former colleagues Prof. Martha Bulyk and Prof. George Church at Harvard Medical School have developed a high throughput microarray technology to characterize DNA binding specificities of transcription factors.
This work has demonstrated that DNA microarrays can be used to accurately measure the protein-DNA binding affinity, DNA sequence binding specificities of transcription factors and therefore the feasibility of using DNA microarrays to identify putative binding sites of transcription factors in vitro on a genome scale. Dr. Huang future research in this area is to develop high throughput experimental and bioinformatics tools to identify the network components and to deconvolute, reconstruct and model these complex genetic regulatory networks. The systematic elucidation of these networks will help us better understand and interfere with cellular development and disease processes, and may lead to better tissue and organism engineering.
In the area of nano-biotechnology, Dr. Huang's future research will involve developing nano-materials for in vivo and in vitro imaging and detection of biomolecules. In addition to his experimental qualifications and abilities, Dr. Huang is computationally adept and is a paradigm researcher in the new systems biology and bioinformatics arena.
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