selected publications
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article
- Adaptive gene loss in the common bean pan-genome during range expansion and domestication. Nature Communications. 2024
- Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nature Genetics. 2024
- Delayed leaf greening involves a major shift in the expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae). Plant and Soil. 2024
- Identification and expression analysis of Phosphate Transporter 1 (PHT1) genes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae). Plant Cell and Environment. 2024
- In silico prediction and analysis of transmembrane-coiled-coil resistance gene analogues in 27 Brassicaceae species. Plant Pathology. 2024
- Approaches to increase the validity of gene family identification using manual homology search tools. Genetica. 2023
- Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs). Plant Biotechnology Journal. 2023
- DNABERT-based explainable lncRNA identification in plant genome assemblies. Computational and structural biotechnology journal. 2023
- Diversity of fatty acid biosynthesis genes across the soybean pangenome. Plant Genome. 2023
- Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus. Frontiers in Plant Science. 2023
- Legume-wide comparative analysis of pod shatter locus PDH1 reveals phaseoloid specificity, high cowpea expression and stress responsive genomic context. The Plant Journal. 2023
- Segmentation of Sandplain Lupin Weeds from Morphologically Similar Narrow-Leafed Lupins in the Field. Remote Sensing. 2023
- The conservation of gene models can support genome annotation. Plant Genome. 2023
- crosshap. Bioinformatics. 2023
- A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits. The Plant Journal. 2022
- Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. New Phytologist. 2022
- Brassica napus genes Rlm4 and Rlm7, conferring resistance to Leptosphaeria maculans, are alleles of the Rlm9 wall-associated kinase-like resistance locus. Plant Biotechnology Journal. 2022
- Copy Number Variation among Resistance Genes Analogues in Brassica napus. Genes. 2022
- Evaluating Plant Gene Models Using Machine Learning. Plants. 2022
- Expanding Gene-Editing Potential in Crop Improvement with Pangenomes. International Journal of Molecular Sciences. 2022
- Genetic and Genomic Resources for Soybean Breeding Research. Plants. 2022
- Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. Frontiers in Plant Science. 2022
- Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003. Theoretical and Applied Genetics. 2022
- In silico integration of disease resistance QTL, genes and markers with the Brassica juncea physical map. Molecular Breeding. 2022
- Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale. International Journal of Molecular Sciences. 2022
- Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction. BMC Plant Biology. 2022
- Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. Biology. 2022
- Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. International Journal of Molecular Sciences. 2022
- Pangenomics and Crop Genome Adaptation in a Changing Climate. Plants. 2022
- Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs. Plant Genome. 2022
- Plant Genotype to Phenotype Prediction Using Machine Learning. Frontiers in Genetics. 2022
- Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. Plants. 2022
- Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. Plant Genome. 2022
- The pangenome of banana highlights differences between genera and genomes. The Plant Genome. 2022
- Wheat Panache. The Plant Genome. 2022
- Whole-Genome DNA Methylation Analysis in Brassica rapa subsp. perviridis in Response to Albugo candida Infection. Frontiers in Plant Science. 2022
- Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. Plant Biotechnology Journal. 2021
- Candidate Rlm6 resistance genes against Leptosphaeria. maculans identified through a genome-wide association study in Brassica juncea (L.) Czern. Theoretical and Applied Genetics. 2021
- Current status of structural variation studies in plants. Plant Biotechnology Journal. 2021
- Daisychain. Agronomy. 2021
- Fast-forward breeding for a food-secure world. Trends in Genetics. 2021
- Genotype–Environment mismatch of kelp forests under climate change. Molecular Ecology. 2021
- Machine learning in agriculture. Plant Biotechnology Journal. 2021
- Maize Yield Prediction at an Early Developmental Stage Using Multispectral Images and Genotype Data for Preliminary Hybrid Selection. Remote Sensing. 2021
- Marine heatwaves have minimal influence on the quality of adult Sydney rock oyster flesh. Science of The Total Environment. 2021
- Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. Plant Biotechnology Journal. 2021
- QTL Genetic Mapping Study for Traits Affecting Meal Quality in Winter Oilseed Rape (Brassica Napus L.). Genes. 2021
- Resources for image-based high-throughput phenotyping in crops and data sharing challenges. Plant Physiology. 2021
- The application of pangenomics and machine learning in genomic selection in plants. Plant Genome. 2021
- Author Correction. Nature plants. 2020
- Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation. Plant Biotechnology Journal. 2020
- Climate change and the need for agricultural adaptation. Current Opinion in Plant Biology. 2020
- Effect of Leptosphaeria maculans Infection on Promoter DNA Methylation of Defence Genes in Brassica napus. Agronomy. 2020
- Frontiers in Dissecting and Managing Brassica Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes. International Journal of Molecular Sciences. 2020
- Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea. Biology. 2020
- Genome-wide identification and comparative analysis of resistance genes in Brassica juncea. Molecular Breeding. 2020
- Induced Methylation in Plants as a Crop Improvement Tool: Progress and Perspectives. Agronomy. 2020
- Pangenomics Comes of Age. Trends in Genetics. 2020
- Plant pan-genomes are the new reference. Nature plants. 2020
- Plant pangenomics. Current Opinion in Plant Biology. 2020
- Resistance gene analogs in the Brassicaceae. Plant Physiology. 2020
- Trait associations in the pangenome of pigeon pea (Cajanus cajan). Plant Biotechnology Journal. 2020
- A reference genome for pea provides insight into legume genome evolution. Nature Genetics. 2019
- Adapting legume crops to climate change using genomic approaches. Plant Cell and Environment. 2019
- Construction and comparison of three reference-quality genome assemblies for soybean. The Plant Journal. 2019
- CropSNPdb. Plant Journal. 2019
- Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics. 2019
- INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow-leafed lupin (Lupinus angustifolius L.). Plant Cell and Environment. 2019
- Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics. BMC Genomics. 2019
- Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. Plant Biotechnology Journal. 2019
- Bias in resistance gene prediction due to repeat masking. Nature plants. 2018
- Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative. Theoretical and Applied Genetics. 2018
- Genome-wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus. Crop & Pasture Science. 2018
- Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution. Journal of Experimental Botany. 2018
- Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnology Journal. 2018
- Large-scale structural variation detection in subterranean clover subtypes using optical mapping. Frontiers in Plant Science. 2018
- Shifting the limits in wheat research and breeding using a fully annotated reference genome.. Science. 2018
- The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin. Theoretical and Applied Genetics. 2018
- A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food. Plant Biotechnology Journal. 2017
- An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. Plant Biotechnology Journal. 2017
- Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnology Journal. 2017
- BioNanoAnalyst. BMC Bioinformatics. 2017
- Climate Clever Clovers. Frontiers in Plant Science. 2017
- Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus. Frontiers in Plant Science. 2017
- Improvements in Genomic Technologies. Trends in Biotechnology. 2017
- RunBNG: A software package for BioNano genomic analysis on the command line. Bioinformatics. 2017
- The pangenome of hexaploid bread wheat. Plant Journal. 2017
- An efficient approach to BAC based assembly of complex genomes. Plant Methods. 2016
- The genome of a southern hemisphere seagrass species (Zostera muelleri). Plant Physiology. 2016
- The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications. 2016
- High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics. 2015
- Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal. 2015
- Skim-based genotyping by sequencing. Methods in Molecular Biology. 2015
- Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome. Science. 2014
- Characterising diversity in the Brassica genomes. Acta Horticulturae. 2013
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chapter
- Investigating Pangenome Graphs Using Wheat Panache. Plant Genomic and Cytogenetic Databases. 2023
- An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth. Plant Comparative Genomics. 2022
- Producing High-Quality Single Nucleotide Polymorphism Data for Genome-Wide Association Studies. Methods in Molecular Biology. 2022
- Searching for Homologous Genes Using Daisychain. Plant Comparative Genomics. 2022
- High-Throughput Genotyping Technologies in Plant Taxonomy. Molecular Plant Taxonomy. 2021
- Legume pangenome construction using an iterative mapping and assembly approach. Legume Genomics. 2020
- Method for Genome-Wide Association Study. Methods in Molecular Biology. 2020
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document
- Correction to. Nature Genetics. 2024
- Correction to. Nature Communications. 2024
- Local haplotype visualization for trait association analysis with crosshap 2023
- DNABERT-based explainable lncRNA identification in plant genome assemblies 2022
- Not all pathways are the same – unique adaptations to submerged environments emerge from comparative seagrass genomics 2022
- Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data. 2021
- Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003 2021
- Yield is negatively correlated with nucleotide-binding leucine-rich repeat gene content in soybean 2021
- RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes 2020
- Association of Copy Number Variation with Qualitative and Quantitative Resistance against Leptosphaeria maculans in Brassica napus. Brassica 2016, Melbourne, Australia, 3/10/16. 2016
- The More the Merrier? Investigating Copy Number Variation in Brassica Disease Resistance. PAG ASIA 2016, Singapore, 6/06/16. 2016