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BioCIDER: a Contextualisation InDEx for biological Resources discovery
The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate... -
Multilocus Analysis Resolves the European Finch Epidemic Strain of Trichomona...
Abstract In Europe, Trichomonas gallinae recently emerged as a cause of epidemic disease in songbirds. A clonal strain of the parasite, first found in the United Kingdom, has... -
Coordinated circadian timing through the integration of local inputs in Arabi...
Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple... -
Spatially resolved transcriptomics reveals plant host responses to pathogens
Background Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with... -
Targeted interplay between bacterial pathogens and host autophagy
Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert it. Despite previous key findings of... -
Probing the 3D architecture of the plant nucleus with microscopy approaches: ...
The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing... -
Phytoplasma SAP11 effector destabilization of TCP transcription factors diffe...
Phytoplasmas are insect-transmitted bacterial pathogens that colonize a wide range of plant species, including vegetable and cereal crops, and herbaceous and woody ornamentals.... -
Exploring gene networks in two sunflower lines with contrasting leaf senescen...
Background Leaf senescence is a complex process, controlled by multiple genetic and environmental variables. In sunflower, leaf senescence is triggered abruptly following... -
Genetic Diversity and Gene Family Expansions in Members of the Genus Entamoeba
Amoebiasis is the third-most common cause of mortality worldwide from a parasitic disease. Although the primary etiological agent of amoebiasis is the obligate human parasite... -
Leveraging multiple transcriptome assembly methods for improved gene structur...
The performance of RNA-Seq aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Here we... -
A modified sequence capture approach allowing standard and methylation analys...
Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing... -
A world of opportunities with nanopore sequencing
Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase... -
MinION Analysis and Reference Consortium: Phase 2 data release and analysis o...
Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop,... -
Comparison of the human gastric microbiota in hypochlorhydric states arising ...
Several conditions associated with reduced gastric acid secretion confer an altered risk of developing a gastric malignancy. Helicobacter pylori-induced atrophic gastritis... -
Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases...
Molecular tools adapted from bacterial CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) systems for adaptive immunity have become widely used for plant genome... -
CropSight: a scalable and open-source information management system for distr...
High-quality plant phenotyping and climate data lay the foundation for phenotypic analysis and genotype-environment interaction, providing important evidence not only for plant... -
Integrating a newly developed BAC-based physical mapping resource for Lolium ...
Lolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic... -
Aequatus: an open-source homology browser
Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral... -
ReGaTE: Registration of Galaxy Tools in Elixir
Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives.... -
Introducing the Brassica Information Portal: Towards integrating genotypic an...
The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted...
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