Pankaj Jaiswal
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View article: The PanOryza pangene catalog of Asian cultivated rice
The PanOryza pangene catalog of Asian cultivated rice Open
The rice genome underpins fundamental research and breeding, but the Nipponbare ( japonica ) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was develo…
View article: Energy transfer dynamics and spectrally resolved upconversion emission in Er3+-Yb3+ activated sodium yttrium molybdate
Energy transfer dynamics and spectrally resolved upconversion emission in Er3+-Yb3+ activated sodium yttrium molybdate Open
View article: A pan-gene catalogue of Asian cultivated rice
A pan-gene catalogue of Asian cultivated rice Open
The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was develope…
View article: Post-GWAS Prioritization of Genome–Phenome Association in Sorghum
Post-GWAS Prioritization of Genome–Phenome Association in Sorghum Open
Genome-wide association studies (GWAS) are widely used to infer the genetic basis of traits in organisms; however, selecting appropriate thresholds for analysis remains a significant challenge. In this study, we introduce the Sequential SN…
View article: Post-GWAS Prioritization of Genome–Phenome Association in Sorghum
Post-GWAS Prioritization of Genome–Phenome Association in Sorghum Open
Genome-wide association studies (GWAS) are widely used to infer the genetic basis of traits in organisms; however, selecting appropriate thresholds for analysis remains a significant challenge. In this study, we introduce the Sequential SN…
View article: Correction: Gupta, P.; Jaiswal, P. Transcriptional Modulation During Photomorphogenesis in Rice Seedlings. Genes 2024, 15, 1072
Correction: Gupta, P.; Jaiswal, P. Transcriptional Modulation During Photomorphogenesis in Rice Seedlings. Genes 2024, 15, 1072 Open
In the original publication [...]
View article: Transcriptional Modulation During Photomorphogenesis in Rice Seedlings
Transcriptional Modulation During Photomorphogenesis in Rice Seedlings Open
Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome a…
View article: Reference genome of the nutrition-rich orphan crop chia (Salvia hispanica) and its implications for future breeding
Reference genome of the nutrition-rich orphan crop chia (Salvia hispanica) and its implications for future breeding Open
Chia ( Salvia hispanica L. ) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. I…
View article: Post-GWAS Prioritization of Genome-Phenome Association in Sorghum
Post-GWAS Prioritization of Genome-Phenome Association in Sorghum Open
Genome-Wide Association Studies (GWAS) are widely used to infer the genetic basis of traits in organisms, yet selecting appropriate thresholds for analysis remains a significant challenge. In this study, we developed the Sequential SNP Pri…
View article: Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology
Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology Open
The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and…
View article: Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis
Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis Open
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 addit…
View article: Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes
Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes Open
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of c…
View article: Transcriptional modulation during photomorphogenesis in rice seedlings
Transcriptional modulation during photomorphogenesis in rice seedlings Open
Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome a…
View article: Njobvu-AI: An open-source tool for collaborative image labeling and implementation of computer vision models
Njobvu-AI: An open-source tool for collaborative image labeling and implementation of computer vision models Open
Practitioners interested in using computer vision models lack user-friendly and open-source software that combines features to label training data, allow multiple users, train new algorithms, review output, and implement new models. Labeli…
View article: Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance
Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance Open
Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10–30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs…
View article: Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation
Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation Open
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pangenomes of several crops. The pan-genomes of cr…
View article: Comparative Analysis of Salinity Response Transcriptomes in Salt-Tolerant Pokkali and Susceptible IR29 Rice
Comparative Analysis of Salinity Response Transcriptomes in Salt-Tolerant Pokkali and Susceptible IR29 Rice Open
Rice is a major cereal crop responsible for feeding the world’s population. To improve grain yield and quality, meet growing demand, and face the challenges posed by abiotic and biotic stress, it is imperative to explore genetic diversity …
View article: Using knowledge graphs to infer gene expression in plants
Using knowledge graphs to infer gene expression in plants Open
Introduction Climate change is already affecting ecosystems around the world and forcing us to adapt to meet societal needs. The speed with which climate change is progressing necessitates a massive scaling up of the number of species with…
View article: Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)
Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa) Open
Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tole…
View article: Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome
Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome Open
View article: The Gene Ontology knowledgebase in 2023
The Gene Ontology knowledgebase in 2023 Open
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life…
View article: Using knowledge graphs to infer gene expression in plants
Using knowledge graphs to infer gene expression in plants Open
Climate change is already affecting ecosystems around the world and forcing us to adapt to meet societal needs. The speed with which climate change is progressing necessitates a massive scaling up of the number of species with unde…
View article: Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability
Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability Open
Plant genetic resources are source genetic material for conducting research and breeding. The use of this material is subject to international and national regulations on access and benefit-sharing (ABS). With modern genetic technologies g…
View article: Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of <i>Populus trichocarpa</i>
Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of <i>Populus trichocarpa</i> Open
Understanding gene expression and regulation requires insights into RNA transcription, processing, modification, and translation. However, the relationship between the epitranscriptome and the proteome under drought stress remains undeterm…
View article: Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates Open
Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present g…
View article: Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development
Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development Open
Chia ( Salvia hispanica L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information av…
View article: PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses
PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses Open
Populus trichocarpa ( P. trichocarpa ) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa . However, no comprehensive dat…
View article: Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”
Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities” Open
Author(s): Vangay, Pajau; Burgin, Josephine; Johnston, Anjanette; Beck, Kristen L; Berrios, Daniel C; Blumberg, Kai; Canon, Shane; Chain, Patrick; Chandonia, John-Marc; Christianson, Danielle; Costes, Sylvain V; Damerow, Joan; Duncan, Will…
View article: Peer Review #2 of "Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily (v0.2)"
Peer Review #2 of "Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily (v0.2)" Open
The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locusReceptor Kinase (SRK) from Brassica that acts as the female…
View article: Peer Review #1 of "Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily (v0.1)"
Peer Review #1 of "Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily (v0.1)" Open
The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locusReceptor Kinase (SRK) from Brassica that acts as the female…