The National Institute of General Medical Sciences (NIGMS) awarded UTHealth School of Biomedical Informatics (SBMI) Assistant Professor Pora Kim, PhD a five-year grant worth over $1.6 million. Kim will use the funds to create bioinformatics tools to perform in-depth exploration and analysis of new genes. Her research efforts are aimed at better understanding how these genes influence the development of diseases.
During this NIGMS-funded study, Kim will perform functional annotation in order to study new genes. Functional annotation is the process of both collecting information about and describing a gene's biological identity. She will then identify potential evidence of the origin of new genes using different mechanisms of gene creation including transposable element domestication, viral integration, chromosomal rearrangements, gene duplication, and trans-splicing from human chimeric transcripts.
“The ultimate goal of my research is to understand the biological formation mechanisms and effects on diverse cellular systems of new genes in the human body,” stated Kim.
Kim’s bioinformatics research noted that there was an urgent need for a tool that could assist with systematic functional annotations of gene fusions in humans. As a result, Kim and SBMI Professor and Dr. and Mrs. Carl V. Vartian Professor in Clinical Informatics Xiaobo Zhou, PhD built FusionGDB and FGViewer. Currently, Kim and SBMI Assistant Professor Hua Tan, PhD are studying the genomic sequence features of fusion genes using a deep learning approach.
“I would like to acknowledge all members in the Center for Computational Systems Medicine (CCSM), led by Dr. Zhou. Through the CCSM, I have been able to study and try cutting-edge techniques. I understand the importance of team science between bioinformatics, machine learning, and mathematics through fostering the synergy of good science,” says Kim.
During her undergraduate studies in chemistry at Ewha Womans University in Seoul, South Korea, Kim first gained interest in the field of bioinformatics when she joined the university’s Research Center for Systems Biology. During her master’s program, she built her first database called ECgene and helped a research team as it built a gene fusion database named ChimerDB1.0. A few years later, as the next-generation sequencing field continued to blossom, she enhanced the fusion gene prediction algorithm and built an updated database – ChimerDB 2.0.
“Exploring how the origin of genes influences diseases has been a research passion of mine for many years,” Kim noted. “During my doctoral program, I applied fusion gene prediction approaches to multiple cancer types using patient data and I found several novel fusion genes with their functional roles in tumorigenesis.” When discussing her work for the new NIGMS grant, Kim stated “I will continue those same research pursuits I have worked from throughout my career and I look forward to further examining how gene fusion can be a source of creating new genes that may lead to disease.”
In order to further her research efforts, Kim is searching for two new postdoctoral researchers to join her team. The project period began on September 1 and concludes at the end of June in 2025.
published on 09/04/2020 at 12:45 p.m.