Dr Chan has a PhD in Genomics and Computational Biology from UQ. He underwent postdoctoral training with Professor Debashish Bhattacharya at Rutgers University (New Brunswick, New Jersey), focusing on algal genomics and evolution (phylogenomics), and the origin of plastids. His research routinely involves de novo assembly and analysis of high-throughput sequencing data.

Since his return to UQ in November 2011, Chan has been using advanced computational and database approaches to explore and develop highly scalable phylogenomic approaches, and to study genome evolution of microbes, including bacteria, algae and protists. Chan and his team relocated to ACE from UQ's Institute for Molecular Bioscience in 2020. See here for Chan's profile on UQ Researchers.

Qualifications: 
2008, Ph.D. (Genomics and Computational Biology), The University of Queensland
2003, M.Phil. with Distinction (Algal Biotechnology), University of Malaya
2001, B.Sc. (Hons I), Industrial Biology, Universiti Teknologi Malaysia
Research Interests: 
Genomics of coral symbionts and their relatives

Reef-building corals are critically sustained by the symbiosis between the coral animal and the symbiotic dinoflagellate algae. Breakdown of this symbiosis leads to coral bleaching, and if not soon re-established, coral death. The coral symbionts (in family Symbiodiniaceae) and their close relatives (i.e. the other dinoflagellates) are highly diverse, and are key primary producers in the oceans. Working with our collaborators nationally and internationally, including within the Reef Future Genomics (ReFuGe) 2020 Consortium, we are generating de novo core genome data from coral symbionts and their relatives, including symbionts isolated from the Great Barrier Reef. We are interested in genome evolution of these ecologically important species, specifically related to their evolutionary transition from free-living to symbiotic lifestyles, and its functional implications on the coral holobiont and the health of the coral reefs (e.g. via hologenomics approach).

Genome evolution and innovation

We are interested in the evolution of genomes in response to the organism's adaptation to changing environments. Using comparative genomics, we aim to identify genome features, gene content, functions, and/or pathways that are specific to distinct ecological niches. Some of the questions we are interested in include genome features unique to the coral symbionts, stress tolerance, and antibiotic resistance in bacteria. Through UQ Genomics Initiative and UQ Genome Innovation Hub, we adopt cutting-edge genomic technologies to generate high-quality genome-scale data for addressing these questions. Working with our collaborators, we adopt an experimental approach to assess microbial genome evolution in real-time, i.e. decoding the genomes across multiple generations of the microbes grown under a controlled, stress condition.

Scalable phylogenomics using alignment-free methods

Highly scalable phylogenomic approaches are needed to make evolutionary sense of the ongoing deluge of sequence data. The current standard phylogenetic/phylogenomic approach using multiple sequence alignment is based on the implicit assumption that all homologous sequences are contiguous, and can be computational expensive. We are exploring the use of alignment-free methods (specifically the use of k-mers) in large-scale phylogenomic analysis, and their sensitivity to key aspects in molecular evolution. We are expanding this approach to infer phylogenomic relationships beyond the conventional tree-like structure (i.e. as networks).

For detail about research of our team and our publications, see https://cxchan.com/

Evolutionary genomics of coral symbionts and their relatives

Reef-building corals are critically sustained by the symbiosis between the coral animal and the symbiotic dinoflagellate algae. Breakdown of this symbiosis leads to coral bleaching, and if not soon re-established, coral death. The coral symbionts (in family Symbiodiniaceae) and their close relatives (i.e. the other dinoflagellates) are highly diverse, and are key primary producers in the oceans. Working with our collaborators nationally and internationally, we are generating de novo core genome data from coral symbionts and their relatives, including symbionts isolated from the Great Barrier Reef. We are interested in genome evolution of these ecologically important species, specifically related to their evolutionary transition from free-living to symbiotic lifestyles, its functional implications on the coral holobiont and the health of the coral reefs, and how these algae diversified into some of the most ecologically successful organisms in the environment.

Evolutionary genomics of other algal symbionts in corals and plastid endosymbiosis

We are interested in the genome evolution of other algal symbionts in corals, e.g. Chromera and Ostreobium, and how it impacts adaptation of corals to changing environments.

Hologenome approach to metallophyte plant and coral microbiome

Working with our collaborators Lauren Messer and Gene Tyson (QUT), and Antony van der Ent and Peter Erskine (UQ Sustainable Minerals Institute), we are developing hologenomic approaches to investigate accumulation of heavy metals in hyperaccumulator plants (metallophytes), and to assess microbiome associated with corals. This project is funded by UQ Genome Innovation Hub collaborative projects scheme.

Hologenome and holometabolomes of Hawaiian corals

Working with our collaborators Debashish Bhattacharya (Rutgers University) and Hollie Putnam (University of Rhode Island), we are generating hologenome and holometabolome data from Hawaiian corals, to assess how distinct biotic components contribute to sustain a healthy coral holobiont (i.e. the ecological unit of multiple interacting species).

Genomics of Australian weeds

Working with our collaborators Luke Guddat, Gary Schenk and Thierry Lonhienne at UQ's School of Chemistry and Molecular Biosciences, we are assessing pesticide-resistance in multiple weed species in Australia using comparative genomic approaches.

Genomics of lignin biosynthesis in coralline red algae

Working with our collaborator Patrick Martone (University of British Columbia), we are investigating lignin biosynthesis in coralline red algae using genomic and transcriptomic approaches.

Scalable alignment-free phylogenenomics

Highly scalable phylogenomic approaches are needed to make evolutionary sense of the ongoing deluge of sequence data. The current standard phylogenetic/phylogenomic approach using multiple sequence alignment is based on the implicit assumption that all homologous sequences are contiguous, and can be computational expensive. We are exploring the use of alignment-free methods (specifically the use of k-mers) in large-scale phylogenomic analysis, and their sensitivity to key aspects in molecular evolution. We are expanding this approach to infer phylogenomic relationships beyond the conventional tree-like structure (i.e. as networks).

Address

Australian Centre for Ecogenomics
Level 5, Molecular Biosciences Bldg
University of Queensland
ST LUCIA QLD 4072
Brisbane, Australia

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