Driven by a scientific need or from spontaneous creativity, our group seeks to identify and then reduce to practice technology for biology and medicine.  These can include advanced instrumentation with unique, new capabilities or high-throughput versions of a process for improved speed or cost reduction.  The technological solution can sometimes be entirely equipment based, but often is a mix of instrumentation, software and biomedical content.

    Recently, focus has been in the area of Light Biology, that is the application of photons through optical components for the production of DNA chips, new light sources, immune system modulation, tissue engineering, hyperspectral imaging, microscopy and cytogenetics.  Some of our past work included the development of DNA sequencers, liquid handling and array spotting robotics, high-throughput oligo synthesizers.  Much of this work was originally inspired by the needs of the human genome project or paradigm shift from reductionist driven to data driven science in the data-rich post-genomics era.

Areas of Emphasis in Instrumentation

Digital Optical Chemistry (DOC) Hyperspectral Imaging Microscope and Scanner Development of a 3D Holographic visualization workstation/TV Nano-patterning with Light

  • Digital Optical Chemistry (DOC) - In collaboration with Texas Instruments and Affymetrix, we have developed a system to manufacture custom, dense oligonucleotide arrays for re-sequencing and expression analysis.  These are being used to advance cancer and cardiac disease research.
  • Hardware, Software and Protocols for Spotted Microarrays - In order to manufacture spotted arrays by spotting of DNA, a technique pioneered by Pat Brown at Stanford, we have developed a number of systems.  These are commercially available from Bioautomation.
  • Hyperspectral Imaging Microscope and Scanner - Several instruments have been developed where the heart of their optical detection system is a imaging spectrograph and a cooled CCD camera.  
  • Variable Spectrum Synthesizer - A digital light processing (DLP) chip from Texas Instruments have been married to an imaging spectrometer to create a new light source that can assemble hundreds of unique spectra and modify them in less than 20 microseconds.
  • Development of a 3D Holographic visualization workstation/TV - We have proven that Texas Instrument's Digital Micromirror Device (DMD) can be used to control the phase of light and thus can be used directly as a holographic medium. Three dimensional real and virtual images can be reconstructed by transcribing digital holograms to the DMD and illuminating it with coherent light.
  • Nano-patterning with Light
  • Human Genome Sequencing Automation - Within the Genome Science and Technology Center at UTSW, we have developed a number of instruments designed to accelerate the mapping and sequencing process.  This has included automated DNA prep machines, automated gel-boxes and large-scale automated robotics for PCR and cycle sequencing.
  • MerMade - The MerMade robotic system was developed for high-throughput oligonucleotide synthesis at reduced cost.  This system is currently available from Bioautomation.
  • ASTRAL - This hyperspectral imaging-based DNA sequencer was designed an built to work with flat plate sequencing or capillary gel systems.  This approach is the heart of the ABI 3700 sequencing instrument.
  • Magna Spotter - A high speed, high reliability cartisian robot was configured with a HEPA filtered, humidity controlled cabinate where nine 384 well plates are also kept cool, and custom control software.  It is used to manufacture spotted microarrays.  It is commercially available from Bioautomation.
  • Surface Plasmon Resonance Chips - In collaboration with Texas Instruments, we developed a unique coating for the system to affix DNA to the sensitive region of this miniature chip that monitors changes in index of refraction.  This chip was used to continuously monitor the level of HIV DNA within a flowed sample.
  • Optically Coupled Electronic Hybridizaton Chips - Combining the electronic hybridization properties of the Nanogen chip with the contact detection scheme of Genometrix, we have created a new type of device. This chip and associated hardware was used to detect the HIV genome within a sample.
  • Development of Protocols for the Beckman Biomek 2000 and FX liquid handling robotics systems - Both DNA sequencing and microarray clone handling have been facilitated on these general purpose pipetting systems.  We have developed a number of software configurations and custom hardware for these systems.
  • Development of Protocols for the Beckman CEQ 2000 sequencer - We have been using the CEQ sequencer for de novo genome sequencing, polymorphism discovery, quality control of microarray clone sets, and fragment analysis.  A number of our improvements to the hardware, software and protocols have been incorporated by Beckman Coulter.
  • Various other hardware and software produced for the national human geneome project