Life is the emergent physical and chemical properties of the molecular circuitry in the cells, tissues and organs of living systems. The fundamental units or components in the circuitry are the DNA, RNA and proteins molecules which are chemically synthesized by decoding the genomes through highly selective and regulated molecular interactions (protein-DNA, protein-RNA, DNA-RNA, and protein and small molecules). Logically, the deterministic understanding of human physiology and diseases requires the precise measurements of the biomolecules and the networks of their interactions. Despite the recent technological advances, our ability to determine the sequences of genomes, RNA and protein molecules, and to enumerate or measure the quantity of those molecules in cells or any biological samples remains highly inadequate.

The mission of our research is to develop the genomic and proteomic technologies that will enable the ultraaccurate sequencing and digital counting of DNA/genomes, RNA and protein molecules in single cells or any biological/clinical samples with single-molecule sensitivity. Broadly, we apply and integrate the fundamental principles and tools of molecular biology, chemistry, physics, mathematics and computer science, electrical engineering and materials science, to tackle these grand scientific and engineering challenges. We have made great strides over the past several years. Building upon the momentum, we are working towards the ultimate aim: engineering of an integrated device that is capable of sequencing the genome with close to 100% accuracy, and sequencing and counting of all RNA and protein molecules from a single cell or any biological samples very rapidly and inexpensively (say, < 1 hour @US$100). Currently, we are focusing on the following areas:

I. DNA/Genome Sequencing Technologies

1. READS Genome Technology (REAl-time DNA Sequencing)

  • It is based on high-speed single-molecule FRET (fluorescence resonant energy transfer) imaging using TIRF (total internal reflection fluorescence) microscopy.
  • Engineered DNA polymerases are used as chemo-mechanical sensors to decode DNA sequences in real time with native unlabeled dNTP's.

2. nSBS (natural Sequencing By Synthesis)

  • Only a small fraction of non-terminating fluorescently-labeled nucleotide is incorporated along with mostly native unlabeled nucleotides by using a mixture of labeled and unlabeled nucleotides.
  • Sequencing reaction is limited only by the rate of natural DNA synthesis by DNA polymerases.
  • Very long read length is feasible.

3. Ultraaacurate sequencing using nanopores

  • Engineering of new nanopore architechture for DNA sequencing;
  • Computational modeling and algorithms for sequence decoding;
  • Deep machine learning for rapid and accurate sequence decoding.

II. Microfluidic Devices and Technologies for Genomics

1. Advanced Microfluidic Processors -General Applications

  • Multi-step processing in one single microfluidic chamber;
  • Sorting, selection and capture of single cells;
  • Sorting, factionation, transport and capture of biomolecules (DNA/RNA, proteins).

2. Single-Cell Genome Sequencing

  • Sorting, selection and capture of single cells;
  • Sorting and partitioning of DNA molecules;
  • Whole genome amplification;
  • On-chip sequencing library construction;
  • Automated sample retrieval;
  • Parallel processing of multiple single cells.

3. Single-Cell mRNA Counting and Sequencing

  • Sorting, selection and capture of single cells;
  • Quantitative and rapid capture of RNA molecules;
  • Counting of RNA molecules by single-molecule fluorescence imaging;
  • Direct single-molecule RNA sequencing on chip;
  • Parallel processing of multiple single cells.

III. Proteomics Technologies

1. Protein Analysis - Using High-density Microarrays

  • Microarray facrication;
  • Facilitated assembly using magnetic or electrical fields;
  • Multiplexed encoding methods;
  • Highly multiplexed and sensitive protein detection;
  • Parallel processing of multiple samples/cells on one device.

2. Protein Analysis - Using Nanodevices and Optical Detection

  • Engineering of new nano devices and processes;
  • Theoretical studies - physical modeling;
  • Deep machine learning and algorithms for identification;
  • Single-molecule protein detection/analysis;
  • Integration of microfluidic processors and nanodevices.

3. Protein Sequencing - Nanodevice Engineering

  • Design and fabrication of novel nanodevice architectures;
  • New modalities for physical detection (optical and electrical);
  • Theoretical studies - physical modeling;
  • Deep machine learning and algorithms for sequencing decoding;
  • Ultimate demonstration of direct single-molecule protein sequencing.