Research in the Kim lab is focused on developing computer algorithms and statistical methods that enable accurate and rapid analysis of biological data, in particular sequencing data. The software systems developed in the lab include several widely used programs such as TopHat2, HISAT, TopHat-Fusion, and Centrifuge. Recently the lab released HISAT-genotype, the first and only program capable of HLA-typing, full-length HLA gene assembly, and novel HLA allele discovery using whole-genome sequencing data. HISAT-genotype has the potential to accurately analyze an individual’s genome and its >20,000 genes within a few hours on a desktop computer.

We have two other main projects:

  • Medical software development: We have been developing medical software that can enable physicians to accurately diagnose diseases. We are currently focusing on flow cytometry, immunohistochemistry (IHC) imaging, and karyotyping data analyses as they are well established and widely employed methods for diagnosing hematopoietic diseases. The programs will provide easy-to-use interfaces and AI-enabled analysis among many features.

  • Life design platform development: We have recently launched a very challenging, ambitious, long-term project to develop an in vivo synthetic biology platform, tentatively called Life Design Platform, that if successfully implemented, will enable us to create novel biochemical pathways, reprogram cells, and/or design new organisms. The output of the platform will be synthetically constructed whole genome DNA sequences, which can be transformed into a stand-alone living organism such as E. coli. Our work in part involves designing a visual programming language for writing code to represent biochemical pathways and developing a compiler program that translates a set of biochemical pathways written in the visual language to a whole genome DNA sequence in an electronic file (FASTA). Wet-lab activities encompass building and cloning synthetic DNA constructs, transfecting the constructs into cells such as E. coli, culturing and observing the cells, developing novel cloning and transformation methods, and tuning the “code” to better design organisms.

The Kim lab is located on the 4th floor of the E-building (E4.350) in the Bioinformatics Department on UT Southwestern’s South Campus.

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