A5000499457- Single-cell and spatial transcriptomics
- Chromosomal and Genetic Variations
- Plant Disease Resistance and Genetics
- Advanced biosensing and bioanalysis techniques
- Plant Pathogens and Resistance
- CRISPR and Genetic Engineering
- Molecular Biology Techniques and Applications
- Immune cells in cancer
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Cell Image Analysis Techniques
- RNA Research and Splicing
European Bioinformatics Institute
2023-2024
National Institute of Biology
2023-2024
Wageningen University & Research
2021
Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene protein expression localisation in bulk at single cell level. These resources aim to allow users investigate their normal tissue (baseline) or response perturbations such as disease changes genotype (differential) across multiple species. Users invited search genes metadata terms species biological conditions a standardised consistent interface....
Cell-type deconvolution methods aim to infer cell composition from bulk transcriptomic data. The proliferation of developed coupled with inconsistent results obtained in many cases, highlights the pressing need for guidance selection appropriate methods. Additionally, growing accessibility single-cell RNA sequencing datasets, often accompanied by expression related samples enable benchmark existing
RNA-guided genomic transcriptional regulation tools, namely Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for the field of functional genomics. Deriving from CRISPR/Cas9 system, both systems comprise catalytically dead Cas9 (dCas9) single guide RNA (sgRNA). This type dCas9 is incapable cleaving DNA but retains its ability to specifically bind DNA. The binding dCas9/sgRNA complex target...
Abstract Cell-type deconvolution methods aim to infer cell composition from bulk transcriptomic data. The proliferation of developed methods, coupled with inconsistent results obtained in many cases, highlights the pressing need for guidance selection appropriate methods. Additionally, growing accessibility single-cell RNA sequencing datasets, often accompanied by expression related samples, enable benchmark existing In this study, we conduct a comprehensive assessment 31 utilising...
Potato ( Solanum tuberosum ) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, despite frequent updates, they are not unified. This hinders comparison across versions, limits ability to reuse experimental data without significant re-analysis, leads missing or wrongly annotated genes. Here, we unify recent double monoploid v4 v6 by developing an automated merging protocol, resulting in Unified poTato genome (UniTato). We subsequently established...
Abstract Potato ( Solanum tuberosum ) is the most popular tuber crop and model organism. Though its gene models are frequently updated, they not unified, leading to missing or wrongly annotated genes. Here, we thus unify recent potato double monoploid v4 v6 by automatic merging. We established an Apollo web server that enables access Unified poTato genome annotation database (UniTato) as well further community-based manual curation at unitato.nib.si . demonstrate how interface can help...