Peter S. White, PhD, Chair of the Department of Biomedical Informatics at the University of Cincinnati College of Medicine and its partner division at Cincinnati Children’s Hospital Medical Center, recently announced the addition of two new faculty members to the team: Hee Woong Lim, PhD and Jing Chen, PhD. Both are experts in computational biology.
Combining Data to Predict Disease
Jing Chen, PhD is a bioinformatician with more than 10 years’ experience in computational biology. He is currently researching methods to combine molecular, clinical, and phenotypic data to predict genes and pathogenic variants as they predispose individuals to particular pediatric diseases including childhood cancer, preterm birth and genetic diseases.
“We are delighted to welcome Dr. Chen as our newest faculty,” says Dr. White. “Jing already has a strong track record collaborating with a number of our clinicians on efforts such as the elucidation of the genetic contributors to pediatric tumor relapse and prematurity of birth. His combination of industry and academic experience in a variety of bioinformatics disciplines will positively impact many of our ongoing pediatric investigations.”
Dr. Chen earned a PhD in Bioinformatics from the University of Cincinnati. He did postdoctoral research at the University of Cincinnati’s Department of Environmental Health and Cincinnati Children’s Department of Biomedical Informatics. Dr. Chen also worked as a computational biologist at GlaxoSmithKline, the world’s sixth largest pharmaceutical company.
Under the mentorship of Bruce J. Aronow, PhD and Anil Jegga, DVM, MRes, Chen created the ToppGene suite of web applications as part of his PhD thesis. As a research scientist at the University of Cincinnati, he proposed a statistical framework to connect transcription factors with diseases and drugs based on ChIP-seq and mRNA expression. Recently he developed GDDP, a novel phenotype-disease matching method for rare genetic diseases. He has built numerous analytical pipelines for large-scale genomic data and was involved in the development of bioinformatics infrastructure and methodology in the NIH-funded LINCS program.
Dr. Chen is currently involved in several ongoing Cincinnati Children’s research projects, including efforts to develop an integrative annotation tool for personal genome variation using a graph-based approach; analysis of various maternal and fetal genetic effects on preterm birth and pregnancy outcomes; and integrative analysis of multi-omics data to target fibroblast activation in idiopathic pulmonary fibrosis.
Multi-Omics Approaches to Understand Cellular Processes
Hee Woong Lim, PhD is a computational scientist by training. His research focuses on the areas of regulatory genomics, pharmacogenomics and machine learning. Dr. Lim earned a PhD from the School of Computer Science and Engineering at Seoul National University in Korea, then switched into the field of bioinformatics and did postdoctoral research at the University of Pennsylvania (Penn).
Dr. Lim investigates transcriptional regulation of gene expression in various contexts including, but not limited to, metabolism, development, pathogenesis, and pharmacogenomics. He specifically focuses on enhancer regulation and tries to explain underlying regulatory mechanisms. To this end, he integrates various levels of genomic, epigenomic, and transcriptomic information from high-throughput data (GRO-seq, RNA-seq, ChIP-seq, ChIP-exo, etc) to understand detailed enhancer architectures and their distinct functions. View his publications here.
“Dr. Lim is a terrific addition to our already outstanding group of informaticists who use multi-omics approaches to better understand the cellular processes underlying childhood diseases,” says Dr. White. “Cincinnati Children’s investigators will be able to take advantage of his knowledge of epigenomics and nascent transcription for their own analyses. Dr. Lim is also excited to learn more from our progenitor cell group about how to better apply his ongoing work at the single-cell level.”
At the University of Pennsylvania’s Perelman School of Medicine, Dr. Lim worked with Kyoung-Jae Won, PhD and Mitchell Lazar, MD, PhD doing regulatory genomics research in metabolic systems. He was working to elucidate functional enhancer regulations in various contexts such as metabolic organ development, drug response, and physiological homeostasis in adipose tissue, liver, and pancreas.
Actively adopting global run-on sequencing (GRO-seq) in collaboration with the Lazar Lab, he developed a computational pipeline to find eRNAs and pioneered an effective way to predict and monitor transcriptionally active enhancers together with their driving transcription factors. This work enabled the team to interrogate enhancer activity directly, thereby uncovering the underlying regulatory mechanism of an anti-diabetic drug in adipocytes (paper) and discover a novel role of HDAC3 for acute adaptive thermogenesis in brown adipose tissues (paper).
He also developed a computational method to analyze chromatin immunoprecipitation with lambda exonuclease digestion followed by sequencing (ChIP-exo) data. In collaboration with Penn’s David Steger, PhD, he discovered structurally and functionally distinct binding configurations of glucocorticoid receptor in vivo (paper).
More recently in collaboration with David Hill, MD, PhD at the Children’s Hospital of Philadelphia (Lazar lab), he discovered a distinct subtype of adipose-tissue macrophage population related to inflammatory response upon diet-induced obesity using by single cell RNA-seq (paper).
Dr. Lim will be establishing an interdisciplinary laboratory that collaborates with various disciplines beyond metabolic systems at Cincinnati Children’s in both pediatric and adult medicine and will be working toward developing open-source bioinformatics tools to assist in scientific discovery. He also enjoys teaching and mentoring.