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ACMGA: a reference-free multiple-genome alignment pipeline for plant species

BMC genomics, 2024-05, Vol.25 (1), p.515-515

2024

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Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test

PLoS genetics, 2018-10, Vol.14 (10), p.e1007699

2018

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Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance

Genome Biology, 2021-06, Vol.22 (1), p.185-185, Article 185

2021

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Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization

PloS one, 2014-03, Vol.9 (3), p.e89323-e89323

2014

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Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

PLoS genetics, 2023-12, Vol.19 (12), p.e1011086-e1011086

2023

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Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides

Nature communications, 2023-09, Vol.14 (1), p.6072-6072, Article 6072

2023

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Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species

The Plant cell, 2021-07, Vol.33 (6), p.1863-1887

2021

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A role for heritable transcriptomic variation in maize adaptation to temperate environments

Genome Biology, 2023-03, Vol.24 (1), p.55-55, Article 55

2023

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Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers

Frontiers in plant science, 2022-09, Vol.13, p.1004387-1004387

2022

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Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy

Frontiers in genetics, 2019-11, Vol.10, p.1046-1046

2019

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A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

The plant genome, 2022-06, Vol.15 (2), p.e20204-n/a

2022

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MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison

PloS one, 2012-11, Vol.7 (11), p.e48998-e48998

2012

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New whole-genome alignment tools are needed for tapping into plant diversity

Trends in plant science, 2024-03, Vol.29 (3), p.355-369

2024

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Prediction and characterization of protein-protein interaction networks in swine

Proteome science, 2012-01, Vol.10 (1), p.2-2, Article 2

2012

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Transcriptome profiling analysis of tea plant (Camellia sinensis) using Oxford Nanopore long-read RNA-Seq technology

Gene, 2021-02, Vol.769, p.145247-145247, Article 145247

2021

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Applying AnchorWave to Address Plant Genome Alignment

Bio-protocol, 2023-10, Vol.13 (19)

2023

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Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.)

The New phytologist, 2024-06, Vol.242 (5), p.2115-2131

2024

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AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

Proceedings of the National Academy of Sciences - PNAS, 2022-01, Vol.119 (1)

2022

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Meta-Mesh: metagenomic data analysis system

Shengwu gongcheng xuebao, 2014-01, Vol.30 (1), p.6

2014

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Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition[OPEN]

The Plant cell, 2020-05, Vol.32 (5), p.1479-1500

2020

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Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy

Plant physiology (Bethesda), 2016-08, Vol.171 (4), p.2659-2670

2016

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Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Cell, 2023-05, Vol.186 (11), p.2313-2328.e15

2023

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Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy1[OPEN]

Plant physiology (Bethesda), 2016-06, Vol.171 (4), p.2659-2670

2016

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QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes

Horticulture research, 2022-01, Vol.9

2022

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ACMGA: a reference-free multiple-genome alignment pipeline for plant species

Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test

Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides

Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species

A role for heritable transcriptomic variation in maize adaptation to temperate environments

Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns

Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers

Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison

New whole-genome alignment tools are needed for tapping into plant diversity

Prediction and characterization of protein-protein interaction networks in swine

Transcriptome profiling analysis of tea plant (Camellia sinensis) using Oxford Nanopore long-read RNA-Seq technology

Applying AnchorWave to Address Plant Genome Alignment

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.)

AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

Meta-Mesh: metagenomic data analysis system

Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition[OPEN]

Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy1[OPEN]

QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes

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