Jingyue Ju
Associate Professor
PhD, Bioorganic Chemistry, University of Southern California, 1993
MS, Organic Chemistry, Institute of Chemical Physics, Chinese Academy of Sciences, 1988
BS, Chemistry, Inner Mongolia University, China, 1985
812 SW Mudd Building

Professor Ju's Research Group focuses on the research and development of novel bioanalytical reagents, systems and processes using chemical science, engineering principles and experimental biological approaches to study problems of biological importance, particularly in the area of genomics. Professor Ju has pioneered the use of synthetic and analytical chemistry and fluorescence energy transfer photochemistry to construct a set of fluorescent genetic analysis reagents that overcome the inherent problems associated with the widely used 4-color fluorescent DNA sequencing and other multiplex fluorescent genetic analysis systems. This technology also facilitated the rapid development of a 96-capillary DNA sequencer with throughput of 200 million base pairs per year, an order of magnitude increase over previous sequencing technologies. The energy transfer fluorescent reagents and the high-throughput 96-capillary DNA sequencers are the major driving force for the international Human Genome Project. They provide a platform for high throughput genomic research, rapid cancer diagnostics, and generating detailed genetic information from a single cell involved in a disease for molecular therapeutics development.

We have invented a Combinatorial Fluorescent Energy Transfer (CFET) Labeling Approach that uses a limited number of fluorescent molecules to create a maximum number of fluorescent tags that have unique fluorescence signatures. We are studying the chemical and physical properties of these CFET tags using state-of-the-art instrumentation, and applying the CFET tags to multiplex DNA sequencing, SNP detection, genomewide chromosome deletion and insertion analysis, and other high-throughput multiplex genetic analysis. We have also invented a novel DNA sequencing chemistry using solid phase capturable dideoxynucleotides and mass spectrometry that obviates the use of gel electrophoresis. This method produces accurate and digital genetic sequence information with very rapid speed. We are currently developing integrated nanoscale systems to couple with the solid phase DNA sequencing chemistry for detecting disease related mutations on the genomic scale. These technologies coupled with improvements of the conventional technologies are being implemented to large-scale genomic sequencing projects and disease gene discovery and characterization projects at Columbia Genome Center, Columbia University College of Physicians & Surgeons.

Two other inventions have been conceived in the group that use photochemistry, mass spectrometry, and engineering microfabrication for high throughput parallel imaging of DNA/RNA sequences during polymerase reaction in chip and nanoscale devices. We are currently supported by a grant from the National Science Foundation Biophotonics Initiative to integrate chemical science and engineering principles for high-throughput genomics and biomedical research. We are also engaged in projects to study the fundamentals of the photochemistry of the CFET tags, as well as design and synthesize other chemical tags and biopolymer analogues that can be detected with high-sensitivity, aimed at inventing new paradigms for high-throughput research in bioscience and genomics.

Related Experience:
1999- present, Associate Professor and Head of Chemical Biology & DNA Sequencing
Department of Chemical Engineering & Columbia Genome Center, Columbia University
1998-1999, Director, Chemistry and Assay Development,
1995-1998, Senior Scientist, Incyte Genomics, Inc.
1993-1995, DOE Human Genome Distinguished Postdoctoral Fellow, University of California, Berkeley
1989-1993, Research Assistant, Department of Chemistry, University of Southern California
1988-1989, Research Assistant, Department of Chemistry and Biochemistry, University of Oklahoma
1985-1988, Researcher, Institute of Chemical Physics, Chinese Academy of Sciences

Honors and Awards:
DOE Human Genome Distinguished Postdoctoral Fellowship, 1994-1995; U.S. Biochemical Postdoctoral Fellowship, 1993;

Professional Service:
Human Genome Organization: Human Genome Meeting (DNA Sequencing Technology Session: Chair, 1997); Invited contributor and reviewer for the DNA sequencing section in Current Protocols in Molecular Biology


" 'DNA Sequencing' in Short Protocols in Molecular Biology, 4th Ed". B.E. Slatko, L.M. Albright, S. Tabor and J. Ju. (1999) eds. Ausubel, F.M. et al. (John Wiley & Sons, Inc, New York and London), pp. 7-25 to 7-37. (Book Chapter).

"Energy Transfer Fluorescent Primers: State-of-the-art in High-throughput DNA Sequencing" J. Ju, A.N. Glazer and R.A. Mathies. Genome Digest, 1997, 8-9.

"Cassette Labeling for Facile Construction of Energy Transfer Fluorescent Primers" J. Ju, A.N. Glazer and R.A. Mathies. Nucleic Acids Res., 1996, 24, 1144-1148.

"Energy Transfer Primers: A New Fluorescence Labeling Paradigm for DNA Sequencing and Analysis" J. Ju, A.N. Glazer and R.A. Mathies. Nature Medicine, 1996, 2, 246-249.

"DNA Sequencing Using a Four-Color Confocal Fluorescence Capillary Array Scanner" I. Kheterpal, J. Scherer, S. M. Clark, A. Radhakrishnan, J. Ju, C. L. Ginther, G. F. Sensabaugh and R. A. Mathies. Electrophoresis, 1996, 17, 1852-1859.

"High-Resolution Capillary Array Electrophoretic Sizing of Multiplexed Short Tandem Repeat Loci Using Energy-Transfer Fluorescent Primers" Y. Wang, J.M. Wallin, J, Ju, G.F. Sensabaugh and R.A. Mathies. Electrophoresis, 1996, 17, 1485-1490.


United States Patent 6,046,005, (2000) J. Ju, K, Konrad "Nucleic Acid Sequencing with Solid Phase Capturable Terminators Comprising a Cleavable Linking Group".

United States Patent 6,028,190, (2000) R.A. Mathies, A.N. Glazer and J. Ju "Probes Labeled with Energy Transfer Coupled Dyes".

United States Patent 5,876,936, (1999) J. Ju "Nucleic Acid Sequencing with Solid Phase Capturable Terminators".

United States Patent 5,952,180, (1999) J. Ju "Sets of Energy Transfer Fluorescent Tags and Their Use in Multi-Component Analysis".

United States Patent 5,869,255, (1999) R.A. Mathies, A.N. Glazer and J. Ju "Probes Labeled With Energy Transfer Coupled Dyes Exemplified with DNA Fragment Analysis".

United States Patent 5,804,386 and 5,814,454, (1998) J. Ju "Sets of Energy Transfer Fluorescent Tags and Their Use in Multi-Component Analysis".

United States Patent 5,707,804, (1998) R.A. Mathies, A.N. Glazer and J. Ju "Primers Labeled with Energy Transfer Coupled Dyes for DNA Sequencing".

United States Patent 5,728,528, (1998) R.A. Mathies, A.N. Glazer and J. Ju "Universal Spacer/Energy Transfer Dyes".

United States Patent 5,853,992, (1998) A.N. Glazer, S-C. Hung, R.A. Mathies, and J. Ju "Cyanine Dyes with High Absorption Cross Section as Donor Chromophores in Energy Transfer Primers".

United States Patent 5,654,419, (1997) R.A. Mathies, A.N. Glazer and J. Ju "Fluorescent Labels and Their Use in Separations".

United States Patent 5,688,648, (1997) R.A. Mathies, A.N. Glazer and J. Ju "Probes Labeled with Energy Transfer Coupled Dyes".