Artificial Intelligence to Explore and Combat Eukaryotic Pathogens

A geometric deep learning framework for genome-wide prediction of enzyme turnover number

T Pan, X Cui, HY Koh, Y Bi, X Wang, Y Zhang, S Hu, GI Webb, L Kurgan, G Zhang, J Song

2026-12-01

Background: Enzyme turnover numbers (Kcat) are fundamental kinetic constants that quantify enzymatic efficiency. Systematic studie..

Chromatin accessibility landscape of a parasitic nematode during embryogenesis

H Lu, T Campos, SB Sumanam, T Wang, Y Zheng, RB Gasser, ND Young

2026-12-01

Background: Chromatin accessibility is a fundamental determinant of genome regulation, enabling transcription factors and RNA poly..

Chromosome-scale nuclear genome and proteome of Anoplocephala perfoliata elucidate lineage-specific features of a ‘neglected’ equine tapeworm

ND Young, T Wang, CS Ang, D Lale, HP Fuehrer, SB Sumanam, PK Korhonen, BCH Chang, RB Gasser

2026-12-01

Background: Anoplocephala perfoliata is the most prevalent and pathogenic tapeworm (cestode) of horses worldwide, yet it remains m..

Genome-wide reconstruction of the intrinsic apoptosis pathway in Haemonchus contortus

Y Shen, ND Young, J Song, BE Sleebs, BCH Chang, EF Lee, WD Fairlie, RB Gasser

2026-12-01

Background: Programmed cell death (or apoptosis) is a fundamental process in metazoans, extensively characterised in mammals and o..

A practical miracidial motility assay for assessing Fasciola hepatica sensitivity to compounds in vitro

M Zheng, AC Taki, T Sukee, J Hodgkinson, TW Spithill, RB Gasser, ND Young

2026-04-01

Fasciola hepatica causes fasciolosis in livestock and humans worldwide, yet reliable tools to assess drug efficacy against the ear..

High-throughput phenotypic screening of Medicines for Malaria Venture's Hit Generation Library 1 identifies new nematocidal chemotypes

AC Taki, JJ Byrne, BCH Chang, B Laleu, TNC Wells, A Jabbar, RB Gasser

2026-04-01

Parasitic helminths impose substantial health and economic burdens on humans and livestock, and widespread resistance to existing ..

A unified framework for multiomics deconvolution

X Wang, F Li, RB Gasser, J Song

2026-03-01

The new algorithm DECODE transcends the limitations of omics-specific methods, and provides a unified framework for the deconvolut..

Chromosome-contiguous nuclear genome of Dirofilaria asiatica reveals unique molecular signatures and host interactions

ND Young, Y Zheng, AV Koehler, T Wang, SB Sumanam, U Atapattu, BCH Chang, V Colella, RB Gasser

2025-12-01

Dirofilaria asiatica is a recently described filarioid nematode of zoonotic importance whose biology, host interactions and epidem..

Comprehensive developmental somatic proteome atlas of Haemonchus contortus underpinned by a chromosome-scale genome and deep tandem mass spectrometry

T Wang, Y Zheng, ND Young, CS Ang, RB Gasser

2025-12-01

Background: Haemonchus contortus is a highly pathogenic, blood-feeding nematode that causes widespread disease and significant eco..

The developmental lipidome of Nippostrongylus brasiliensis

T Wang, MG Leeming, NA Williamson, T Bouchery, R Doolan, G Le Gros, GE Reid, NL Harris, RB Gasser

2025-12-01

Background: Nippostrongylus brasiliensis—a nematode of rodents—is commonly used as a model to study the immunobiology of parasitic..

Genome-Wide Inference of Essential Genes in Dirofilaria immitis Using Machine Learning

TL Campos, PK Korhonen, ND Young, SB Sumanam, W Bullard, JM Harrington, J Song, BCH Chang, RJ Marhöfer, PM Selzer, RB Gasser

2025-10-01

The filarioid nematode Dirofilaria immitis is the causative agent of heartworm disease, a major parasitic infection of canids, fel..

Targeted Chemical Profiling and Dereplication of Australian Plants of the Family Haemodoraceae Using a Combined HPLC-MS and HRLC(ESI)-MS Approach

L Thompson, V Chow, S Chen, P Reddy, R Brkljača, C Rix, JJ Byrne, AC Taki, RB Gasser, S Urban

2025-10-01

Australian plants of the family Haemodoraceae have been a reliable source of new secondary metabolites, particularly those of the ..

Cutaneous myiasis in a Serbian traveller returning from Kenya

S Momčilović, AV Koehler, RB Gasser

2025-09-01

Background: Cutaneous myiasis is an ectoparasitic disease caused by fly larvae. In non-endemic regions it is rare, often unfamilia..

New derivatives of benzhydroxamic acid with nematocidal activity against Haemonchus contortus and Caenorhabditis elegans

J Krátký, M Zajíčková, AC Taki, O Michel, P Matoušková, I Vokřál, K Štěrbová, O Vosála, B Lungerich, T Kurz, RB Gasser, K Harant, L Skálová

2025-08-01

Parasitic nematodes cause a wide range of diseases in animals, including humans. However, the efficacy of existing anthelmintic dr..

Anthelmintic Potential of Agelasine Alkaloids from the Australian Marine Sponge Agelas axifera

K Wijesekera, AC Taki, JJ Byrne, DC Holland, ID Jenkins, MG Ekins, AR Carroll, RB Gasser, RA Davis

2025-07-01

A recent high-throughput screening of the NatureBank marine extract library (7616 samples) identified an extract from the Australi..

Chromosome-Contiguous Reference Genome for Spirometra to Underpin Future Discovery Research

ND Young, R Malik, A Brown, T Wang, A Ash, PK Korhonen, RB Gasser

2025-07-01

Sparganosis is a neglected food- and water-borne zoonotic disease caused by members of the tapeworm genus Spirometra. More than 16..

Dirofilaria asiatica sp. nov. (Spirurida: Onchocercidae) – Defined using a combined morphological-molecular approach

V Colella, ND Young, R Manzanell, U Atapattu, SB Sumanam, LG Huggins, AV Koehler, RB Gasser

2025-07-01

Parasitic nematodes of the family Onchocercidae (superfamily Filarioidea) have evolved alongside vertebrate hosts for millions of ..

Human alveolar echinococcosis–global, regional, and national annual incidence and prevalence rates

B Lundström-Stadelmann, A Rostami, CF Frey, PR Torgerson, SM Riahi, K Bagheri, M Kaethner, A Lachenmayer, G Beldi, RB Gasser, A Hemphill

2025-07-01

Background: Alveolar echinococcosis (AE) of humans is a disease caused by the larval (metacestode) stage of the ‘fox tapeworm’ Ech..

Systems biology of Haemonchus contortus – Advancing biotechnology for parasitic nematode control

Y Zheng, ND Young, T Wang, BCH Chang, J Song, RB Gasser

2025-07-01

Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these ..

Chromosome-Contiguous Ancylostoma duodenale Reference Genome from a Single Archived Specimen Elucidates Human Hookworm Biology and Host–Parasite Interactions †

ND Young, Y Zheng, SB Sumanam, T Wang, J Song, BCH Chang, RB Gasser

2025-06-01

Soil-transmitted helminths (STHs) are parasitic nematodes that infect humans, particularly in tropical and subtropical regions, wh..

scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data

Y Liu, C Li, LC Shen, H Yan, G Wei, RB Gasser, X Hu, J Song, DJ Yu

2025-05-01

Accurate cell type annotation is fundamentally critical for single-cell sequencing (scRNA-seq) data analysis to provide insightful..

Supervised contrastive learning enhances MHC-II peptide binding affinity prediction

LC Shen, Y Liu, Z Liu, Y Zhang, Z Wang, Y Guo, J Rossjohn, J Song, DJ Yu

2025-04-15

Accurate prediction of major histocompatibility complex (MHC)-peptide binding affinity can improve our understanding of cellular i..

Advances in Anthelmintic Target Identification

HT Shanley, T Wang, AC Taki, JJ Byrne, BCH Chang, BE Sleebs, RB Gasser

2025-04-01

Parasitic nematodes pose a significant threat to human and animal health, causing widespread morbidity and substantial socioeconom..

Human dirofilariasis – A potentially significant nematode zoonosis in an era of climate change

S Momčilović, A Jovanović, RB Gasser

2025-04-01

Dirofilariasis is a mosquito-borne zoonosis caused by several species of the genus Dirofilaria. This disease can manifest as nodul..

Human Alveolar Echinococcosis—A Neglected Zoonotic Disease Requiring Urgent Attention

A Rostami, B Lundström-Stadelmann, CF Frey, G Beldi, A Lachenmayer, BCH Chang, MM Norouzian, A Hemphill, RB Gasser

2025-03-01

Alveolar echinococcosis (AE) in humans is caused by the larval (metacestode) stage of Echinococcus multilocularis, commonly known ..

Human case of diphyllobothriasis in Australia

SF Khan, AV Koehler, A Tinson, M Chinnappan, H Sheorey, RB Gasser

2025-02-17

Evaluation of Serum Supplementation on the Development of Haemonchus contortus Larvae In Vitro and on Compound Screening Results

SS Thilakarathne, AC Taki, T Wang, C Nowell, BCH Chang, RB Gasser

2025-02-01

A high-throughput platform for assessing the activity of synthetic or natural compounds on the motility and development of Haemonc..

Anthelmintic activity of selected neolignans and semisynthetic derivatives from Styrax suberifolius

K Wijesekera, AC Taki, JJ Byrne, JM White, AR Carroll, RB Gasser, RA Davis

2025-01-01

The plant metabolite, equiselignan B (2), isolated from the fruits of Styrax suberifolius was used to generate a semisynthetic lib..

Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets

AC Taki, L Kapp, RS Hall, JJ Byrne, BE Sleebs, BCH Chang, RB Gasser, A Hofmann

2025-01-01

The control of socioeconomically important parasitic roundworms (nematodes) of animals has become challenging or ineffective due t..

A phenotypic screen of the Global Health Priority Box identifies an insecticide with anthelmintic activity

HT Shanley, AC Taki, JJ Byrne, N Nguyen, TNC Wells, A Jabbar, BE Sleebs, RB Gasser

2024-12-01

Background: Infection with parasitic nematodes (helminths), particularly those of the order Strongylida (such as Haemonchus contor..

Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions

TL Campos, PK Korhonen, ND Young, BCH Chang, RB Gasser

2024-12-01

Detailed explorations of the model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have ..

SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations

T Pan, Y Bi, X Wang, Y Zhang, GI Webb, RB Gasser, L Kurgan, J Song

2024-12-01

The accurate identification of catalytic residues contributes to our understanding of enzyme functions in biological processes and..

Comparative structure activity and target exploration of 1,2-diphenylethynes in Haemonchus contortus and Caenorhabditis elegans

HT Shanley, AC Taki, N Nguyen, T Wang, JJ Byrne, CS Ang, MG Leeming, N Williamson, BCH Chang, A Jabbar, BE Sleebs, RB Gasser

2024-08-01

Infections and diseases caused by parasitic nematodes have a major adverse impact on the health and productivity of animals and hu..

The Mitogenome of the Haecon-5 Strain of Haemonchus contortus and a Comparative Analysis of Its Nucleotide Variation with Other Laboratory Strains

Y Zheng, ND Young, J Song, RB Gasser

2024-08-01

Haemonchus contortus (the barber’s pole worm)—a highly pathogenic gastric nematode of ruminants—causes significant economic losses..

Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning

TL Campos, PK Korhonen, ND Young, T Wang, J Song, R Marhoefer, BCH Chang, PM Selzer, RB Gasser

2024-07-01

Over the years, comprehensive explorations of the model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaste..

Phytochemical Profiling Studies of Alkaloids and Coumarins from the Australian Plant Geijera parviflora Lindl. (Rutaceae) and Their Anthelmintic and Antimicrobial Assessment

D Dugan, RJ Bell, R Brkljača, C Rix, AC Taki, RB Gasser, S Urban

2024-05-01

Phytochemical profiling followed by antimicrobial and anthelmintic activity evaluation of the Australian plant Geijera parviflora,..

Structure-activity relationship and target investigation of 2-aryl quinolines with nematocidal activity

HT Shanley, AC Taki, N Nguyen, T Wang, JJ Byrne, CS Ang, MG Leeming, S Nie, N Williamson, Y Zheng, ND Young, PK Korhonen, A Hofmann, BCH Chang, TNC Wells, C Häberli, J Keiser, A Jabbar, BE Sleebs, RB Gasser

2024-04-01

Within the context of our anthelmintic discovery program, we recently identified and evaluated a quinoline derivative, called ABX4..

'Bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data

Jiani Ma, Jiangning Song, Neil D Young, Bill CH Chang, Pasi K Korhonen, Tulio L Campos, Hui Liu, Robin B Gasser

2024-01-01

The identification and characterization of essential genes are central to our understanding of the core biological functions in eu..

DeepSecE: A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria

Y Zhang, J Guan, C Li, Z Wang, Z Deng, RB Gasser, J Song, HY Ou

2023-01-01

Proteins secreted by Gram-negative bacteria are tightly linked to the virulence and adaptability of these microbes to environmenta..