Research

Introduction

Our bioinformatics lab, BIS Lab, was established in January 2023 at the Center for Genome Engineering (CGE), IBS, Korea. As a dedicated bioinformatics team, we are responsible for computational analyses, the development of bioinformatics tools, and actively shaping the direction of projects associated with the core research themes of CGE. We engage in both internal collaborations within CGE and external collaborations to advance genomic research.

Our lab specializes in omics research, including single-cell RNA sequencing (scRNA-seq), bulk RNA sequencing, whole-genome sequencing (WGS), and whole-exome sequencing (WES), with a primary focus on stem cells and organoids. Beyond omics, we actively develop genetic cassette systems such as SCON and Red2Onco to facilitate genetic modifications. Additionally, we are engaged in identifying and engineering novel genome-editing tools, as well as pioneering protein engineering through an approach we call "protein legolization*."

By integrating computational expertise with experimental biology, BIS Lab aims to drive innovation in genomic science and synthetic biology, contributing novel analytical frameworks and methodologies to the field.

*Protein legolization : The concept of legolization refers to generating a blueprint from the 3D model of a target object. Similarly, we propose protein legolization, which involves understanding the fundamental building blocks—such as protein folding, domains, and molecular interactions—not only within a single species but also across different species.

Organoid and Stem cell

Stem cells and organoids are valuable models for studying development, disease mechanisms, and potential therapies. Our lab uses high-throughput sequencing technologies, including scRNA-seq/bulkRNA-seq and WGS/WES/ATAC-seq, to analyze the molecular characteristics of stem cells and organoids in several species. Through bioinformatics and data analysis, we study adult|revival stem cells, gene regulation, and genetic changes involved in differentiation and disease. Our research helps improve understanding in areas such as stem cell evolution, differentiation mechanisms, regenerative medicine, drug discovery, and targeted treatments. 

#OrganoidZoo #Logitudinal PDO #Organoid Magic Growth #Epigenetic memory in stem cells #Niche independency 

#Stemness pathways

Genetic Cassettes

Genetic cassettes are crucial for precise genetic modulation and synthetic biology. BK Koo, director of the Center for Genome Engineering (CGE), developed the SCON (Short Conditional intrON) and Red2Onco systems to regulate gene expression in conditional contexts. Our lab further develops and optimizes these cassette systems to enhance their functionality for controlled gene expression and oncogenic studies.

The Red2Onco system allows us to observe how gene expression changes at the single-cell level affect not only the modified (red) cells but also their neighboring cells. To evaluate these effects based on transcriptomic reprogramming, we also handle spatial omics, bulk RNA-seq, and single-cell RNA-seq, enabling us to analyze gene expression dynamics and cellular interactions in a controlled manner. Through computational design and experimental validation, we work to refine these systems for broader applications in gene therapy and synthetic biology.

#SCON #SCON > 300 species #Red2Onco #Spatial Omics #Single cell RNA-seq

Genome Editing tools

Protein Engineering