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Yongwook Choi is a Staff Scientist at the J. Craig Venter Institute. Dr. Choi’s research is focused on the sequence data analysis and the development of bioinformatics algorithms and tools. He received his B.S. in Electrical Engineering and M.S. in Electrical Engineering and Computer Science from Seoul National University, and his Ph.D. in Computer Science from Purdue University.

Research Priorities

Development of bioinformatics algorithms and tools

  • Computational prediction of the functional impact of protein coding variants
  • Detection of chimeric DNA rearrangements in multiple displacement amplification process

Microbiome analysis

  • Characterization of chronic wound microbiome using 16S, metagenomics, and metatranscriptomics analysis
  • Characterization of water microbiome using 16S and metagenomics analysis

Transcriptome analysis and applications

  • Discovery of novel antimicrobial compounds through high-throughput transcriptome profile screening
  • Study of gene expression patterns of parents and progeny in plant hybrids
  • Identification of distinct response by multi-drug resistant organisms to different bacterial- confrontations


  • Genome assembly improvement using optical map and genotyping-by-sequencing map
  • Diplotype analysis of genes associated with disease
  • Comparative genome analysis


Select Publications

Co-occurrence of Anaerobes in Human Chronic Wounds.
Microbial ecology. 2018-08-23;
PMID: 30141127
Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells.
Scientific reports. 2018-06-05; 8.1: 8656.
PMID: 29872152
Comparison of phasing strategies for whole human genomes.
PLoS genetics. 2018-04-05; 14.4: e1007308.
PMID: 29621242
Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome.
Genome biology and evolution. 2017-09-01; 9.9: 2377-2394.
PMID: 28957462
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences.
Journal of neurovirology. 2017-04-01; 23.2: 171-185.
PMID: 27739035
Electrochemical detection of Pseudomonas in wound exudate samples from patients with chronic wounds.
Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society. 2016-03-01; 24.2: 366-72.
PMID: 26815644
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Bioinformatics (Oxford, England). 2015-08-15; 31.16: 2745-7.
PMID: 25851949
A maize database resource that captures tissue-specific and subcellular-localized gene expression, via fluorescent tags and confocal imaging (Maize Cell Genomics Database).
Plant & cell physiology. 2015-01-01; 56.1: e12.
PMID: 25432973
Predicting the functional effect of amino acid substitutions and indels.
PloS one. 2012-01-01; 7.3: e46688.
PMID: 23056405