Computational & Synthetic Biology Laboratory at Korea University

Research Topics Publications Members Softwares

We Seek Answers for ‘Big Questions’ by Reading Genome, Writing Genome and Editing Genome. From Molecules To Organisms, We See Everything in the Light of Evolution.

Computational Genomics

NGS

We understand living things by their genome and transcriptome

  • Sequencing is a procedure collecting the genetic code of all living things. It is the beginning of understanding the code of life. We sequence and annotate genomes (DNAseq) and transcriptomes (RNAseq) of many living organisms.
  • We are involved in the 1000 fungal genome project (1kFGP) geared by Joint Genome Institute (JGI). It is a data-driven approach.
  • We investigate Fungal Genome Universe by combining all known fungal genomes. We are specially interested in the biology of edible, medicinal and toxic mushrooms. We attempt to parse new knowledge of fungal biology by various NGS techniques.

Metagenomics & Pan-genomics are another level of sequence informatics

  • We sequence not only living organisms but also environmental samples. From antarctic soils to fermentation starters to insect guts, we explored sequence space by NGS techniques
  • We gather pan-genomic data of acetogens and probiotics (e.g. Lactobacilli)

Structural genomics

What you see is what you understand

  • We use X-ray crystallography as a magnifier to investigate bio-macromolecules at the molecular level
  • The matters in the universe are composed of a limited number of elements. The protein folds can be decomposed to the limited number of construction units. The questions is, ‘are there Structural Foldons such as protein structure alphabets that recombine to evolve molecular diversity of protein universe’?
  • Are there DNA/RNA foldons, too? (Check out later!)

Genes and Proteins

Evolutionary Genomics

  • Vast number of genes and proteins are in the protein universe. How protein structures were evolved? We explore the protein space - Protein Structure Universe where the protein structures are born, developed and innovated.
  • We examine the functionalty of protein domains and families in the pan-genome space where genes/proteins are born, developed, innovated, horizontally transferred and eventually destroyed.

Synthetic Biology

Biology is Technology

What I cannot create, I do not understand

Richard Feynman said, ‘What I cannot create, I do not understand’, which is followed by ‘Know how to solve every problem that has been solved’. This is the goal of the synthetic biology as a technology tinkering living things.

  • Construction by Design - We can construct syntheic metabolic pathway by design (e.g. iPNN - intelligent Pathway Network Navigator).
  • Learning by Construction - We can learn how nature builds ‘things’ by synthesis (e.g. PKSDS - PolyKetide Synthetase Design Suite)

iGEM $ DIYBio

Biohackers

Synthetic biology is a hacking tool for biology. Amateur and citizen scientists applying synthetic biology approach are called as ‘biohackers’. CSBL supports biohackers.

Knowledge Discovery

Engineering Principles

We learn and discover nature’s design principles for engineering biology. For instance, deconstruction of Red Algal Biomass can be accelerated by a designed pathway.

  • Agar, a recalcitrant polysaccharide, has a great potential as a renewable biomass. We have recently elucidated the details of bacterial agarolytic pathways. We have sequenced genomes (DNAseq) and transcriptomes (RNAseq) of several agarolytic microorganisms using next generation sequencing (NGS) techniques. We have identified key enzymes (e.g. beta-agarases, agarooligosaccharide beta-galactosidase - ABG, neoagarobiose hydrolase - NABH, anhydrogalactose dehydrogenase -AHGD and anhydrogalactonate cycloisomerase - ACI, etc.) in the agar metabolic pathway and determined atomic structures of key enzymes. The full understanding molecular and cellular functions of these novel agarolytic enzymes will provide the design principle of synthetic agar degradation pathways and eventually guide the construction of synthetic microorganisms converting agar into valuable chemicals.