Publications

Scientific Reports
Integrative genomic, transcriptomic, and metabolomic profiling of Dillenia suffruticosa
May 2026, Vol 16

The genus Dillenia, a basal core eudicot native to Southeast Asia and the Indian Ocean islands, is prized for its wide-ranging medicinal and ornamental applications. This study generated and integrated a chromosome-scale reference genome for D. suffruticosaspanning 599 Mb with 26 chromosomes (N50:24.1 Mb) encoding 28,248 genes using organ-resolved transcriptomics and untargeted metabolomic analysis. The root metabolome is dominated by triterpenoids, including lupeol, α-/β-amyrin, and betulinic acid, whose abundance mirrors a selective cytotoxic profile against a panel of 10 cancer cell lines. Ethanol extracts were active against 7 of 10 lines (IC₅₀ = 92–194 µg mL⁻¹), while SFE extracts were active against 6 lines (IC₅₀ = 91–234 µg mL⁻¹), with limited or no activity observed in the remaining lines (IC₅₀ > 300 µg mL⁻¹). Although the specific bioactive compound(s) remain unresolved, genome annotation identified candidate oxidosqualenecyclases and downstream putative cytochrome P450 monooxygenases and UDP-glycosyltransferases, indicating the presence of genes associated with triterpenoid biosynthesis. Together, these chemogenomic resources illuminate the molecular basis of specialized metabolism in D. suffruticosa and establish a platform for future studies on its ecological functions and the discovery of plant-derived therapeutic candidates.

Read the full paper here.
 

Cell Genomics
Genomic garden: From societal and scientific impacts to biodiversity conservation
April 2025, Vol 14, Issue 3

Because of urbanization, deforestation, pollution, climate change, and natural disasters, the loss of biodiversity is a pressing concern globally. As part of our efforts toward biodiversity conservation, we propose the establishment of a genomic garden, where the genome of each plant in the garden is elucidated. Combining science, horticulture, and a digital content hub accessible with any handheld device, the genomic garden serves multiple purposes, from enhancing urban landscapes, facilitating biomedical research, and improving population health to providing entertainment and education for visitors.

Read the full paper here.
 

Cancer Discovery
Biodiversity Medicine: New Horizon and New Opportunity for Cancer
March 2024, Vol 14, Issue 3

Accessibility to standard of care remains a challenge to patients in low- and middle-income countries (LMIC), hampering efforts to alleviate the burden of cancer and to improve overall health outcomes. In response to this pressing global health care issue, we propose here a new strategy to create affordable, easily accessible, and effective therapeutic solutions to address this inequity in cancer treatment: the use of science-based biodiversity medicine as an alternative to modern drug therapy, in which we will leverage and combine high-throughput omics technologies with artificial intelligence, to study local biodiversity, their potential anticancer properties, and short- and long-term clinical response and outcomes.

Read the full paper here.
 

Communications Biology
Genome Assembly and Chemogenomic Profiling of National Flower of Singapore Papilionanthe Miss Joaquim 'Agnes' Reveals Metabolic Pathways Regulating Floral Traits
Sep 2022, Vol 5

Singapore’s National Flower, Papilionanthe (Ple.) Miss Joaquim ‘Agnes’ (PMJ) is highly prized as a horticultural flower from the Orchidaceae family. A combination of short-read sequencing, single-molecule long-read sequencing and chromatin contact mapping was used to assemble the PMJ genome, spanning 2.5 Gb and 19 pseudo-chromosomal scaffolds. Genomic resources and chemical profiling provided insights towards identifying, understanding and elucidating various classes of secondary metabolite compounds synthesized by the flower. For example, presence of the anthocyanin pigments detected by chemical profiling coincides with the expression of ANTHOCYANIN SYNTHASE (ANS), an enzyme responsible for the synthesis of the former. Similarly, the presence of vandaterosides (a unique class of glycosylated organic acids with the potential to slow skin aging) discovered using chemical profiling revealed the involvement of glycosyltransferase family enzymes candidates in vandateroside biosynthesis.

Read the full paper here. 

Cancers
Rare Occurrence of Aristolochic Acid Mutational Signatures in Oro-Gastrointestinal Tract Cancers
Jan 2022, Vol 14, Issue 3

Aristolochic acids (AAs) are a family of carcinogenic phytochemical compounds commonly found in plants of the Aristolochia and Asarum genera. Comprehensive genomic profiling of genitourinary and hepatobiliary cancers has highlighted the widespread prevalence of Aristolochic acid (AA) signatures in cancer patients across parts of Asia, particularly in Taiwan. The aim of our study was to determine in oro-gastrointestinal tract cancers (OGITCs), the prevalence, role and significance that AA plays as a driver of tumorigenesis as AA-containing products are commonly administered orally. This suggests a possible etiological relationship between OGITCs. However, in this study, the rarity of AA mutational signatures in OGITCs suggests that AA is unlikely to drive carcinogenesis in OGITCs through direct exposure. Our study is valuable because it shows that AA exposure is not an equal driver of tumorigenesis in different organs and represents an important piece of information in the field.

Read the full paper here.

Nature Genetics
The Draft Genome Of Tropical Fruit Durian (Durio Zibethinus)
Nov 2017 Issue

Durian (Durio zibethinus) is a Southeast Asian tropical plant known for its hefty, spine-covered fruit and sulfury and onion-like odor. Here we present a draft genome assembly of D. zibethinus, representing the third plant genus in the Malvales order and first in the Helicteroideae subfamily to be sequenced.

Read the full paper here.

Science Translational Medicine
Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia
Oct 2017, Vol 9, Issue 412

Aristolochic acid, an herbal compound found in many traditional medicines, had been previously linked to kidney failure, as well as cancers of the urinary tract. Because of these known toxicities, herbs containing this compound have been restricted or banned in some countries, but it is still available on the internet and in alternate formulations. By analyzing numerous samples from Taiwan and other countries in Asia and elsewhere, Ng et al. demonstrated the effects of aristolochic acid in hepatocellular carcinoma, a much more common tumor type.

The authors showed that the use of this drug remains widespread in Asia and particularly in Taiwan, and that it appears to increase the risk of multiple different cancer types.

Read the full paper here.

Science Translational Medicine
Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool
Aug 2013, Vol 5, Issue 197

Aristolochic acid (AA) is a natural compound derived from plants in the Aristolochia genus. For centuries, Aristolochia has been used throughout Asia to treat a variety of ailments as a component of traditional Chinese medicine. In recent years, however, a more sinister side of this herb has come to light when it was linked to kidney damage and cancers of the urinary tract. Now, two studies by Poon et al. and Hoang et al. present a “molecular signature” of AA-induced DNA damage, which helps to explain the mutagenic effects of AA and may also be useful as a way to detect unsuspected AA exposure as a cause of cancer.

Read the full paper here.