"Modern technologies are allowing us to
gain unprecedented insight into the
genetic control of cellular function,"

- Dr Emily Wong

Dr Emily Wong

Head, Regulatory Systems Laboratory

research overview

Key Research Areas

  • Genome evolution
  • Gene regulation
  • Genomics and Bioinformatics

Research Overview

Our main goal is to understand how changes in the genome sequence control transcriptional change during developmental, regenerative and evolutionary processes. By applying regulatory genomics and computational strategies, we aim to understand how genetic signals are propagated to gene expression, and how this in turn has consequences on higher biological processes. To do this, we produce high-throughput data and use statistical models but also go beyond to dry lab to generate molecular data in different organisms to address fundamental questions that have consequences in both health and disease.

research projects

There are 3 key projects underway in the Regulatory Systems Laboratory, led by Dr Emily Wong;

1. Tracing regulatory evolution
Most disease loci lie in non-coding regions of the genome and are enriched at enhancers and promoters. Enhancers are rapidly evolving and most enhancers in humans cannot be mapped to the mouse. We use novel concepts, computational and molecular approaches to identify conserved enhancers and understand their mechanism of function and mode of change. This research was recently published in Science

2. Regeneration genomics
We aim to study the systems biology of heart regeneration to better understand the restorative mechanisms of cells in damaged hearts in vertebrates. Regeneration has been studied in a range of animals but the zebrafish is the most extensively-studied vertebrate model for heart regeneration. We use quantitative strategies to understand how regulatory systems change during the repair process.

3. Regulatory variation during ageing
We are using single cell datasets to study how tissues change in ageing animals, focusing on the regulatory system.

laboratory members & collaborators


David Zheng, Research Assistant

Paola Cornejo Paramo, PhD student 

Shani Pathirana, Honours student

Qing Wang, Postdoctoral Scientist

Veronika Petrova, PhD student

Wan Hern Ching, Honours student


Dr Eileen Furlong, EMBL

Dr Tuomas Tammela, Memorial Sloan Kettering Cancer Center

Professor Bernie Degnan, University of Queensland

publication highlights

Flochay S^, Wong ES^, Zhao B^… Garfield D, Furlong E (2021) Cis-acting variation is common across regulatory layers but is often buffered in developmental programs. Genome Research 31(2):211-224  ^equal contribution

Wong ES…Francois M, Degnan B (2020) Deep conservation of the enhancer regulatory code in animals. Science 370(6517)

Friedman CE, Nguyen Q….Wong ES…Powell J, Palpant NJ (2018) Single cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation. Cell Stem Cell 23(4)

Jasinska AJ, Zelaya I, Service SK…Wong ES… Freimer N (2017) Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate. Nature Genetics doi:10.1038/ng.3959

Wong ES, Schmitt B, Thybert D, Marioni J, Ferguson-Smith A, Odom DS, Flicek P (2017) Interplay of cis and trans mechanisms driving transcription factor binding, chromatin, and gene expression evolution.  Nature Communications 8(1):1092

Wong ES, Thybert D, Schmitt B, Stefflova K, Odom DS, Flicek P (2015) Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals. Genome Research 25:167-78

Highlight by D.J. Burgess  (2015) “Decoupled transcription factor output?” Nature Reviews Genetics 16:4-5

Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL (2015) Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics 16(1):982