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
- Epistasis and pleiotropy-induced variation for plant breeding. Plant Biotechnology Journal. 2024
- Exploring genomic feature selection. Plant Genome. 2024
- Focus on the Crop Not the Weed. Remote Sensing. 2024
- Genome-wide identification and prediction of disease resistance genes in Hirschfeldia incana. Agriculture Communications. 2024
- Genomics-based plant disease resistance prediction using machine learning. Plant Pathology. 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
- Image-based crop disease detection using machine learning. Plant Pathology. 2024
- In silico prediction and analysis of transmembrane-coiled-coil resistance gene analogues in 27 Brassicaceae species. Plant Pathology. 2024
- Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean. Plant Genome. 2024
- Multimodal Deep Learning Integration of Image, Weather, and Phenotypic Data Under Temporal Effects for Early Prediction of Maize Yield. Remote Sensing. 2024
- Plant pangenomics, current practice and future direction. Agriculture Communications. 2024
- Recent advances in the improvement of genetic resistance against disease in vegetable crops. Plant Physiology. 2024
- Technological Development and Advances for Constructing and Analyzing Plant Pangenomes. Genome Biology and Evolution. 2024
- The complex relationship between disease resistance and yield in crops. Plant Biotechnology Journal. 2024
- Unravelling inversions. Plant Biotechnology Journal. 2024
- A pangenome analysis pipeline provides insights into functional gene identification in rice. Genome Biology. 2023
- 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
- Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis. Frontiers in Sustainable Food Systems. 2023
- Diversity of Phytosterols in Leaves of Wild Brassicaceae Species as Compared to Brassica napus Cultivars: Potential Traits for Insect Resistance and Abiotic Stress Tolerance. Plants. 2023
- Diversity of fatty acid biosynthesis genes across the soybean pangenome. Plant Genome. 2023
- Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. Trends in Plant Science. 2023
- Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense Using Musa acuminata ssp. malaccensis. Pathogens. 2023
- Genetic and molecular analysis of stem rot (Sclerotinia sclerotiorum) resistance in Brassica napus (canola type). Heliyon. 2023
- Identification of a Major QTL-Controlling Resistance to the Subtropical Race 4 of Fusarium oxysporum f. sp. cubense in Musa acuminata ssp. malaccensis. Pathogens. 2023
- Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus. Frontiers in Plant Science. 2023
- Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species. Phytopathology. 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
- MCE-ST. International Journal of Applied Earth Observation and Geoinformation. 2023
- Plant genome resequencing and population genomics. Molecular Plant. 2023
- Segmentation of Sandplain Lupin Weeds from Morphologically Similar Narrow-Leafed Lupins in the Field. Remote Sensing. 2023
- Supporting crop plant resilience during climate change. Crop Science. 2023
- Teatime for pangenomics. Nature plants. 2023
- The conservation of gene models can support genome annotation. Plant Genome. 2023
- Updated guidelines for gene nomenclature in wheat.. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 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
- Advancing designer crops for climate resilience through an integrated genomics approach. Current Opinion in Plant Biology. 2022
- Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. New Phytologist. 2022
- Application of crop wild relatives in modern breeding. Frontiers in Plant Science. 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
- Capturing Wheat Phenotypes at the Genome Level.. Frontiers in Plant Science. 2022
- Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea. Plant Biotechnology Journal. 2022
- Copy Number Variation among Resistance Genes Analogues in Brassica napus. Genes. 2022
- Dissection of Genetic Effects, Heterosis, and Inbreeding Depression for Phytochemical Traits in Coriander. Plants. 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
- Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice. Frontiers in Plant Science. 2022
- Genomic prediction of preliminary yield trials in chickpea. Plant Genome. 2022
- Graph pangenomes find missing heritability. Nature Genetics. 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
- Karyology and Genome Size Analyses of Iranian Endemic Pimpinella (Apiaceae) Species. Frontiers in Plant Science. 2022
- Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction. BMC Plant Biology. 2022
- Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL. Plant Genome. 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
- SC-CAN. Remote Sensing. 2022
- Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. Plant Genome. 2022
- The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics. Plants. 2022
- The pangenome of banana highlights differences between genera and genomes. The Plant Genome. 2022
- Understanding R Gene Evolution in Brassica. Agronomy. 2022
- Use of multiple ‘omics techniques to accelerate the breeding of abiotic stress tolerant crops. Current Plant Biology. 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
- A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature. 2021
- 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
- Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding. Plant Genome. 2021
- Crop breeding for a changing climate. Theoretical and Applied Genetics. 2021
- Current status of structural variation studies in plants. Plant Biotechnology Journal. 2021
- Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies. Agronomy. 2021
- De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing. Agronomy. 2021
- Detection of Epistasis for Seed and Some Phytochemical Traits in Coriander under Different Irrigation Regimes. Agronomy. 2021
- Fast-forward breeding for a food-secure world. Trends in Genetics. 2021
- Genome structural evolution in Brassica crops. Nature plants. 2021
- Genome-Wide Identification, Expression and Functional Analysis Reveal the Involvement of FCS-Like Zinc Finger Gene Family in Submergence Response in Rice. Rice. 2021
- Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Frontiers 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
- Molecular characterization of disease resistance in Brassica juncea – The current status and the way forward. Plant Pathology. 2021
- QTL Genetic Mapping Study for Traits Affecting Meal Quality in Winter Oilseed Rape (Brassica Napus L.). Genes. 2021
- Quantitative Trait Locus Mapping of Resistance to Turnip Yellows Virus in Brassica rapa and Brassica oleracea and Introgression of These Resistances by Resynthesis Into Allotetraploid Plants for Deployment in Brassica napus.. Frontiers in Plant Science. 2021
- Rapid delivery systems for future food security. Nature Biotechnology. 2021
- Resources for image-based high-throughput phenotyping in crops and data sharing challenges. Plant Physiology. 2021
- Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain. Frontiers in Plant Science. 2021
- Status and advances in mining for blackleg (Leptosphaeria maculans) quantitative resistance (QR) in oilseed rape (Brassica napus). Theoretical and Applied Genetics. 2021
- Studying the Genetic Diversity of Yam Bean Using a New Draft Genome Assembly. Agronomy. 2021
- The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size. Molecular Biology and Evolution. 2021
- The application of pangenomics and machine learning in genomic selection in plants. Plant Genome. 2021
- Toward haplotype studies in polyploid plants to assist breeding. Molecular Plant. 2021
- Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS). F1000Research. 9:536. 2020
- A High-Performance Spectral-Spatial Residual Network for Hyperspectral Image Classification with Small Training Data. Remote Sensing. 2020
- A high-performance spectral-spatial residual network for hyperspectral image classification with small training data. Remote Sensing. 2020
- Author Correction. Nature plants. 2020
- Building a successful international research community through data sharing. F1000Research. 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
- Current status of the multinational Arabidopsis community. Plant Direct. 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
- Genetic and signalling pathways of dry fruit size. Plant Biotechnology Journal. 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
- Identification and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus. Theoretical and Applied Genetics. 2020
- Induced Methylation in Plants as a Crop Improvement Tool: Progress and Perspectives. Agronomy. 2020
- Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus. BMC Plant Biology. 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
- Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives. International Journal of Molecular Sciences. 2020
- Resistance gene analogs in the Brassicaceae. Plant Physiology. 2020
- Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate. Communications Biology. 2020
- Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement. Trends in Plant Science. 2020
- The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. Plant Biotechnology Journal. 2020
- Trait associations in the pangenome of pigeon pea (Cajanus cajan). Plant Biotechnology Journal. 2020
- Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era. Plants. 2020
- Virulence/avirulence patterns among Leptosphaeria maculans isolates determines expression of resistance, senescence and yellowing in cotyledons of Brassica napus. European Journal of Plant Pathology. 2020
- Progress in single-access information systems for wheat and rice crop improvement.. Briefings in Bioinformatics. 20:565-571. 2019
- A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference. Functional & Integrative Genomics. 2019
- 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
- Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. Plant Biotechnology Journal. 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
- Progress in single-access information systems for wheat and rice crop improvement. Briefings in Bioinformatics. 2019
- Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics. 2019
- Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. Plant Biotechnology Journal. 2019
- Wild origins of macadamia domestication identified through intraspecific chloroplast genome sequencing. Frontiers in Plant Science. 2019
- Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 361:7191. 2018
- Advances in Integrating Genomics and Bioinformatics in the Plant Breeding Pipeline. Agriculture. 2018
- Bias in resistance gene prediction due to repeat masking. Nature plants. 2018
- Bottlenecks for genome-edited crops on the road from lab to farm. Genome Biology. 2018
- Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea. Scientific Reports. 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
- Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology. 2018
- Investigating drought tolerance in chickpea using genome-wide association mapping and genomic selection based on whole-genome resequencing data. Frontiers in Plant Science. 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
- Single-Cell Genomic Analysis in Plants. Genes. 2018
- Speed breeding is a powerful tool to accelerate crop research and breeding.. Nature plants. 2018
- The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin. Theoretical and Applied Genetics. 2018
- Towards a more predictable plant breeding pipeline with CRISPR/Cas-induced allelic series to optimize quantitative and qualitative traits. Current Opinion in Plant Biology. 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
- Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. Frontiers in Plant Science. 2017
- BioNanoAnalyst. BMC Bioinformatics. 2017
- Climate Clever Clovers. Frontiers in Plant Science. 2017
- Copy number variation and disease resistance in plants. Theoretical and Applied Genetics. 2017
- Genome analysis identified novel candidate genes for ascochyta blight resistance in chickpea using whole genome re-sequencing data. Frontiers in Plant Science. 2017
- Genome editors take on crops. Science. 2017
- Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus. Frontiers in Plant Science. 2017
- Genotyping-by-sequencing approaches to characterize crop genomes. Plant Biotechnology Journal. 2017
- Improvements in Genomic Technologies. Trends in Biotechnology. 2017
- RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism. Bioresource Technology. 2017
- RunBNG: A software package for BioNano genomic analysis on the command line. Bioinformatics. 2017
- SNP discovery using a pangenome. Biology. 2017
- The pangenome of hexaploid bread wheat. Plant Journal. 2017
- Towards CRISPR/Cas crops - bringing together genomics and genome editing. New Phytologist. 2017
- Databases for Wheat Genomics and Crop Improvement.. Methods in Molecular Biology. 1679:277-291. 2017
- A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. Theoretical and Applied Genetics. 2016
- Advances in genomics for adapting crops to climate change. Current Plant Biology. 2016
- An efficient approach to BAC based assembly of complex genomes. Plant Methods. 2016
- Analytical and Decision Support Tools for Genomics-Assisted Breeding. Trends in Plant Science. 2016
- Chloroplast genomics. Current Plant Biology. 2016
- Development and Validation of Thinopyrum elongatum–Expressed Molecular Markers Specific for the Long Arm of Chromosome 7E. Crop Science. 2016
- Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola. Frontiers in Plant Science. 2016
- Global agricultural intensification during climate change: a role for genomics.. Plant Biotechnology Journal. 2016
- Plant Bioinformatics Methods and Protocols Preface. PLANT BIOINFORMATICS: METHODS AND PROTOCOLS, 2ND EDITION. 2016
- SNP analysis of Macadamia integrifolia chloroplast genomes to determine the genetic structure of wild populations. Acta Horticulturae. 2016
- The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Current Opinion in Plant Biology. 2016
- The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses. Functional & Integrative Genomics. 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
- Towards plant pangenomics. Plant Biotechnology Journal. 2016
- A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics. 2015
- Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Frontiers in Plant Science. 2015
- BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal. 2015
- Bioinformatics: Identifi cation of markers from Next-Generation sequence data. Methods in Molecular Biology. 2015
- Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene. Theoretical and Applied Genetics. 2015
- CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database. 2015
- Gene loss in the fungal canola pathogen Leptosphaeria maculans. Functional & Integrative Genomics. 2015
- Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany. 2015
- 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
- High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources. 2015
- Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal. 2015
- Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L.var. capitata L.). Molecular Breeding. 2015
- Molecular Marker Databases. Methods in Molecular Biology. 2015
- Population diversity of Leptosphaeria maculans in Australia. International Journal of Biology. 2015
- Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports. 2015
- Scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis. G3: Genes, Genomes, Genetics. 2015
- Skim-based genotyping by sequencing. Methods in Molecular Biology. 2015
- Transcriptomic changes in coral holobionts provide insights into physiological challenges of future climate and ocean change. PLOS ONE. 2015
- Unfolding the secrets of coral-Algal symbiosis. ISME Journal. 2015
- A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal. 2014
- A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.. Science. 2014
- A complex recombination pattern in the genome of allotetraploid Brassica napusas revealed by a high-density genetic map. PLOS ONE. 2014
- A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Functional & Integrative Genomics. 2014
- Ancient hybridizations among the ancestral genomes of bread wheat.. Science. 2014
- Comparative analysis of Stowaway-like miniature inverted repeat transposable elements in wheat group 7 chromosomes: Abundance, composition, and evolution. Journal of Systematics and Evolution. 2014
- Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. Plant Molecular Biology Reporter. 2014
- Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome. Science. 2014
- Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics. 2014
- Erratum: Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome (Science (2014) 345:6199 (950-953)). Science. 2014
- Genome interplay in the grain transcriptome of hexaploid bread wheat. Science. 2014
- Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLOS ONE. 2014
- New technologies for ultrahigh-throughput genotyping in plant taxonomy. Methods in Molecular Biology. 2014
- SNP markers-based map construction and genome-wide linkage analysis in Brassica napus. Plant Biotechnology Journal. 2014
- Structural variations in plant genomes. Briefings in Functional Genomics. 2014
- The brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications. 2014
- The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment. Genome Biology. 2014
- Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology. 2014
- A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: Applications in genetic dissection of qualitative and quantitative traits. BMC Genomics. 2013
- Accessing complex crop genomes with next-generation sequencing. Theoretical and Applied Genetics. 2013
- Characterising diversity in the Brassica genomes. Acta Horticulturae. 2013
- Characterising diversity in the Brassica genomes. Acta Horticulturae. 2013
- Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal. 2013
- Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology. 2013
- Functional genomics to study stress responses in crop legumes: Progress and prospects. Functional Plant Biology. 2013
- Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). Theoretical and Applied Genetics. 2013
- Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. Functional & Integrative Genomics. 2013
- Next generation characterisation of cereal genomes for marker discovery. Biology. 2013
- Predicting polymorphic EST-SSRs in silico. Molecular Ecology Resources. 2013
- Next-generation sequencing applications for wheat crop improvement.. American Journal of Botany. 99:365-371. 2012
- Advances in DNA sequencing accelerating plant biotechnology. Plant Biotechnology Journal. 2012
- Bioinformatics tools and databases for analysis of next-generation sequence data. Briefings in Functional Genomics. 2012
- Bread matters. Plant Biotechnology Journal. 2012
- Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata. PLOS ONE. 2012
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Coverage-based consensus calling (C
B CC) of short sequence reads and comparison of CB CC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. American Journal of Botany. 2012 - Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. American Journal of Botany. 2012
- Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology. 2012
- Genetic, Biochemical, and Morphological Diversity of the Legume Biofuel Tree Pongamia pinnata. Journal of Plant Genome Sciences. 2012
- Genomic advances will herald new insights into the Brassica: Leptosphaeria maculans pathosystem. Plant Biology. 2012
- Genomic databases for crop improvement. Agronomy. 2012
- Identification and characterization of candidate Rlm4 blackleg resistance genes in Brassica napus using next-generation sequencing. Plant Biotechnology Journal. 2012
- Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway. Plant Biotechnology Journal. 2012
- Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.). Theoretical and Applied Genetics. 2012
- Next-generation sequencing applications for wheat crop improvement. American Journal of Botany. 2012
- SNP discovery and applications in Brassica napus. Journal of Plant Biotechnology. 2012
- Second-generation sequencing for gene discovery in the Brassicaceae. Plant Biotechnology Journal. 2012
- Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theoretical and Applied Genetics. 2012
- Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnology Journal. 2012
- Transient Nod factor-dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots. Plant Biotechnology Journal. 2012
- WheatGenome.info. Plant and Cell Physiology. 2012
- Next-generation sequencing applications for wheat crop improvement. Science & Engineering Faculty. 2012
- Rapid divergence of repetitive DNAs in Brassica relatives. Genomics. 2011
- Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal. 2011
- The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics. 2011
- CMap3D: A 3D visualization tool for comparative genetic maps. Bioinformatics. 2010
- Future tools for association mapping in crop plants. Genome. 2010
- Plant genome sequencing: Applications for crop improvement. Plant Biotechnology Journal. 2010
- Sequence and structure of Brassica rapa chromosome A3. Genome Biology. 2010
- Sequence and structure of Brassica rapa chromosome A3.. Genome Biology. 2010
- Targeted identification of genomic regions using TAGdb. Plant Methods. 2010
- AutoSNPdb: An annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Research. 2009
- De novo sequencing of plant genomes using second-generation technologies. Briefings in Bioinformatics. 2009
- Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnology Journal. 2009
- Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. Theoretical and Applied Genetics. 2009
- Genetic maps and the use of synteny. Methods in Molecular Biology. 2009
- Genome sequence data: Management, storage, and visualization. BioTechniques. 2009
- Genome sequencing approaches and successes. Methods in Molecular Biology. 2009
- Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree. Methods in Molecular Biology. 2009
- Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation. Current Bioinformatics. 2009
- New technologies for ultra-high throughput genotyping in plants. Methods in Molecular Biology. 2009
- Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotechnology Journal. 2009
- A comparative map viewer integrating genetic maps for Brassica and Arabidopsis. BMC Plant Biology. 2007
- Accessing integrated Brassica genetic and genomic data using the BASC server. Methods in Molecular Biology. 2007
- Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers. Methods in Molecular Biology. 2007
- BASC: An integrated bioinformatics system for Brassica research. Nucleic Acids Research. 2007
- Characterization of simple sequence repeat markers derived in silico from Brassica rapa bacterial artificial chromosome sequences and their application in Brassica napus. Molecular Ecology Notes. 2007
- Genomic distribution of simple sequence repeats in Brassica rapa. Molecules and Cells. 2007
- Genomic distribution of simple sequence repeats in Brassica rapa. Molecules and Cells. 2007
- Identification and characterization of simple sequence repeat markers from Brassica napus expressed sequences. Molecular Ecology Notes. 2007
- Modification of nitrogen remobilization, grain fill and leaf senescence in maize (Zea mays) by transposon insertional mutagenesis in a protease gene. New Phytologist. 2007
- Plant Bioinformatics - Methods and Protocols: Preface. Methods in Molecular Biology. 2007
- Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. Molecular Ecology Notes. 2007
- The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theoretical and Applied Genetics. 2007
- A survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana. Molecules and Cells. 2006
- A survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana. Molecules and Cells. 2006
- An assessment of genetic diversity within and between Brassica napus and Brassica juncealines from international germplasm collections. Acta Horticulturae. 2006
- Analysis of the Brassica 'A' and 'C' genomes and comparison with the genome of Arabidopsis thaliana. Acta Horticulturae. 2006
- Comparison of transcription of multiple genes at three developmental stages of the plant pathogen Sclerotinia sclerotiorum. Fems Microbiology Letters. 2006
- Identification and characterization of simple sequence repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. Molecular Ecology Notes. 2006
- Identification and characterization of simple sequence repeat (SSR) markers from Fragaria x ananassa expressed sequences. Molecular Ecology Notes. 2006
- Integrating and interrogating diverse Brassica data within an EnsEMBL structured database. Acta Horticulturae. 2006
- SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery. Nucleic Acids Research. 2006
- The auxin-induced K+ channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development. Plant Molecular Biology. 2006
- Transcriptome analysis of Neotyphodium and Epichloe grass endophytes. Fungal Genetics and Biology. 2006
- Brassica ASTRA: An integrated database for Brassica genomic research. Nucleic Acids Research. 2005
- SNPServer: A real-time SNP discovery tool. Nucleic Acids Research. 2005
- A transcriptomics resource for wheat functional genomics. Plant Biotechnology Journal. 2004
- New computational tools for Brassica genome research. Comparative and Functional Genomics. 2004
- Plant bioinformatics: From genome to phenome. Trends in Biotechnology. 2004
- Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics. 2004
- A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. Molecular Breeding. 2003
- Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiology. 2003
- Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics. 2003
- Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. BioTechniques. 2002
- Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. BioTechniques. 2002
- Characterization of the flanking regions of Zea mays microsatellites reveals a large number of useful sequence polymorphisms. Theoretical and Applied Genetics. 2002
- Identification of transposon-tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. Plant Journal. 2000
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book
- Plant Genomics and Climate Change 2016
- The impact of genomics technology on adapting plants to climate change 2016
- Next Generation Sequencing and Germplasm Resources 2014
- Sequence based DNA markers and genotyping for cereal genomics and breeding 2014
- Bioinformatics Tools to Assist Breeding for Climate Change 2013
- Bioinformatics 2009
- Bioinformatics and Plant Genomics for Staple Crops Improvement 2008
- Gene Discovery and Microarray-Based Transcfuptome Analysis of the Grass-Endophyte Association 2008
- Bioinformatics 2007
- DNA sequence databases 2007
- Molecular marker discovery and genetic map visualisation 2007
- A high-throughput gene silencing approach for studying the interaction between perennial ryegrass (Lolium perenne) and the fungal endophyte Neotyphodium lolii 2005
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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
- Application of pangenomics for wheat molecular breeding. Molecular Breeding in Wheat, Maize and Sorghum. 2021
- High-Throughput Genotyping Technologies in Plant Taxonomy. Molecular Plant Taxonomy. 2021
- Bioinformatics and plant breeding. Quantitative genetics, genomics and plant breeding. 2020
- Legume pangenome construction using an iterative mapping and assembly approach. Legume Genomics. 2020
- Method for Genome-Wide Association Study. Methods in Molecular Biology. 2020
- Using genomics to adapt crops to climate change. Sustainable Solutions for Food Security. 2019
- Revolution in genotyping platforms for crop improvement. Advances in Biochemical Engineering/Biotechnology. 2018
- Sequencing the Chickpea Genome. The Chickpea Genome. 2017
- Preface. Plant Genomics and Climate Change. 2016
- Genomic databases for crop improvement. The role of bioinformatics in agriculture. 2014
- Genome Sequencing Initiatives. Genetics, Genomics and Breeding of Oilseed Brassicas. 2012
- Role of Bioinformatics as a Tool for Oilseed Brassica Species. Genetics, Genomics and Breeding of Oilseed Brassicas. 2012
- Role of bioinformatics as a tool for vegetable Brassica species. Genetics, Genomics and Breeding of Vegetable Brassicas. 2011
- Accessing integrated Brassica genetic and genomic data using the BASC server. Plant Bioinformatics - Methods and Protocols. 2007
- Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers. Plant Bioinformatics - Methods and Protocols. 2007
- Plant Bioinformatics - Methods and Protocols. Plant Bioinformatics - Methods and Protocols. 2007
- Preface. Bioinformatics. 2007
- A proposal for an international transcriptome initiative for forage and turf. Molecular Breeding for The Genetic Improvement of Forage Crops and Turf. 2005
- Clover ASTRA. Molecular Breeding for The Genetic Improvement of Forage Crops and Turf. 2005
- Endophyte ASTRA. Molecular Breeding for The Genetic Improvement of Forage Crops and Turf. 2005
- Ryegrass ASTRA. Molecular Breeding for The Genetic Improvement of Forage Crops and Turf. 2005
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abstract
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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
- Author Correction. Nature. 2022
- 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
- Preface. Methods in Molecular Biology. 2022
- Draft Genome Assembly and Transcriptome Dataset for European Turnip (Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance. Frontiers in Genetics. 2021
- 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
- Current biology special issue. Current Plant Biology. 2020
- Editorial overview. Current Opinion in Plant Biology. 2020
- Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction inBrassica napus 2020
- RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes 2020
- Editorial overview. Current Opinion in Plant Biology. 2018
- Speed breeding: A powerful tool to accelerate crop research and breeding 2017
- 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
- An assessment of genetic diversity within and between Brassica napus and Brassica juncealines from international germplasm collections. Proceedings of the Joint Meeting of the XIVth Crucifer Genetics Workshop and IVth ISHS Symposium on Brassicas. 2006
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edited book
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external to wheat