CALL FOR PAPERS

WHY GENERATIVE GENOMICS?

Comparative Genomics has traditionally aimed to discover homologous genes and proteins from the perspective of their evolutionary relationships through alignment-based procedures. However, orphan genes have revealed the potential limitation of analyzing their origin determination. Nevertheless, the origins of orphan genes have been explored from an evolutionary perspective under the assumption that they arose either through mutational transformations of ancestral genes or as de novo genes derived from non-coding sequences. But this approach alone cannot explain the emergence conditions of taxon-restricted genes and founder genes. Another angle of Generative Genomics is using AI for the annotation of genes and biosynthesis.

HOW TO CONDUCT GENERATIVE GENOMICS RESEARCH?

Thus, we need to extend the search for the alternative origins of orphan genes beyond evolutionary origin. To this end, we conceptualized the Generative Origin and consequent Generative Genes and validate them through experiments. The functions of generative genes can be classified into two categories: Taxon-Restricted Generative Genes and Founding Generative Genes that were inherited by diverse descendants.

To validate whether an orphan gene was emerged from evolutionary origin or not, we conduct the mutational path simulation and ancestral gene validation using Protein Language Model.

Since most generative genes were not annotated yet because they were not included in the homologous group, we need research to explore the functions of generative genes with the perspective of species-specific and taxon-restricted traits. A beauty of generative gene approach is that they can be mapped with the focused species-specific traits. AI models will assist the prediction of the functions of generative genes, and will also used for the discovery and synthesis of new genes.

ILLUSTRATIVE RESEARCH TOPICS

To advance the objectives of Generative Genomics and examine its implications for health science, we propose to investigate the following research issues, as illustrated (but not limited to) by the five topics below. We believe these topics present valuable opportunities for researchers studying orphan genes and de novo genes.

1) Identification of Origins of Orphan Genes
2) Simution of mutation pathways to validate the Generative Genes
3) Identification of founder generative genes and gene networks
4) Bidirectional annotation methods by mapping generative genes with taxon-specific traits
5) Building Generative Tree of Life reconciling phenotypes and genotypes
6) Building AI Models for annotation of genes with multiomics
7) Analysis of generative genomics in species-specific disease pathway analysis
8) Design of synthetic biology using Generative Genomics Principles

Program Committee

• Chair: Jae Kyu Lee (Chair Professor, Xi’an Jiaotong University, China; Professor Emeritus, Korea Advanced Institute of Science and Technology, Korea)
• Co-chair: Ming Chen (Professor and Director of Bioinformatics Lab, College of Life Science, Zhejiang University, China)
• Dae Kyun Chung (Professor and Dean, College of Life Sciences, Kyung Hee University)
• Kyong-Tai Kim (Chair Professor and Director of Generative Genomics Lab, Handong Global University; Professor Emeritus, POSTECH)
• Wooju Kim (Professor and Director of AI Technology Research Center, Yonsei University)
• Ah-Ram Kim (Professor of Life Science & Applied AI, Handong Global University)
• Taesung Park (Professor and Director of Bioinformatics and Biostatistics Lab, Seoul National University)
• Yungang Xu (Professor of Bioinformatics and Computational Biology, Xi’an Jiaotong University)
• Chuck Yoo (Professor of Computer Science, Korea University; Former Vice President of Research, Korea University)