A5030007324- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Ubiquitin and proteasome pathways
- Microbial Community Ecology and Physiology
- Tissue Engineering and Regenerative Medicine
- Immune cells in cancer
- Advanced Biosensing Techniques and Applications
- Single-cell and spatial transcriptomics
- Enzyme Structure and Function
- Advanced biosensing and bioanalysis techniques
- Bioinformatics and Genomic Networks
- Protist diversity and phylogeny
- Marine Bivalve and Aquaculture Studies
- S100 Proteins and Annexins
- Antioxidant Activity and Oxidative Stress
- Plant Molecular Biology Research
- Signaling Pathways in Disease
- Mechanisms of cancer metastasis
- Mesenchymal stem cell research
- Photosynthetic Processes and Mechanisms
King Abdullah University of Science and Technology
2014-2024
Wellcome Sanger Institute
2008
University College London
2008
Université Claude Bernard Lyon 1
2008
Centre National de la Recherche Scientifique
2008
Georgetown University
2008
University Hospital Heidelberg
2008
SIB Swiss Institute of Bioinformatics
2008
European Bioinformatics Institute
2008
Heidelberg University
2008
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY TIGRFAMs. Integration is performed manually approximately half of the total 58,000 signatures available in databases belong to an entry. Recently, we have started also display remaining un-integrated via our web...
Understanding and exploiting genetic diversity is a key factor for the productive stable production of rice. Here, we utilize 73 high-quality genomes that encompass subpopulation structure Asian rice (Oryza sativa), plus two wild relatives (O. rufipogon O. punctata), to build pan-genome inversion index 1769 non-redundant inversions span an average ~29% sativa cv. Nipponbare reference genome sequence. Using this index, estimate rate ~700 per million years in rice, which 16 50 times higher...
Abstract Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand response are urgently needed order develop strategies cope with effects of change. Because Physcomitrella patens holds a key evolutionary position bridging gap between green algae higher plants because it exhibits well-developed tolerance, is an excellent model for exploration. Here, we have...
The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) found to be blue pigmented. In present study, we focused on understanding metabolic genetic basis observed phenotype functional equivalence between blue-pigmented organisms from phylum Arthropoda, subclass Copepoda (Acartia fossae) Chordata, class...
Abstract Background Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one SNP calling software publicly available, but unfortunately, high-performance computing versions this tool have yet become available affordable. Results Here we report an open-source variant workflow...
While programmed cell death receptor 1 (PD-1) blockade treatment has revolutionized of patients with melanoma, clinical outcomes are highly variable, and only a fraction show durable responses. Therefore, there is clear need for predictive biomarkers to select who will benefit from the treatment.To identify potential markers response PD-1 checkpoint immunotherapy, we conducted single-cell RNA sequencing analyses peripheral blood mononuclear cells (PBMC) (n=8), as well an in-depth immune...
In mammals, LINE-1 (L1) retrotransposons constitute between 15% and 20% of the genome. Although only a few copies have retained ability to retrotranspose, evidence in brain differentiating pluripotent cells indicates that L1 retrotransposition occurs creates mosaics normal somatic tissues. The function de novo insertions remains be understood. transdifferentiation mouse embryonic fibroblasts dopaminergic neuronal fate provides suitable model for studying dynamics defined genomic unaltered...
Abstract Summary: The development of computational resources to visualize and explore data from combined genome-wide expression linkage studies is essential for the testable hypotheses. eQTL Explorer stores profiles, information external sources in a relational database enables simultaneous visualization intuitive interpretation via Java graphical interface. provides new powerful tool interrogate these very large complex datasets. Availability: application freely available non-commercial...
Oryza is remarkable genus - with two domesticated (i.e. Asian and African rice) 25 diploid tetraploid wild species, 11 extant genome types, a ~3.4-fold size variation that possesses virtually untapped reservoir of genes can be used for crop improvement. Here we unveil interrogate new chromosome-level assemblies nine species in the context ~15 million years evolution genus. We show core (sub)genome across all types only ~200 Mb largely syntenic, while remaining nuclear fractions, spanning...
Abstract Background Despite considerable efforts within the microarray community for standardising data format, content and description, technologies present major challenges in managing, sharing, analysing re-using large amount of generated locally or internationally. Additionally, it is recognised that inconsistent low quality experimental annotation public repositories significantly compromises re-use meta-analysis. MiMiR, Mi croarray ning R esource was designed to tackle some these...
Abstract The neuston layer in tropical seas provides a good model to study the effects of increased levels different stressors (e.g., temperature, ultraviolet radiation and Trichodesmium blooms). Here, we use comparative situ metatranscriptomics approach reveal functional genomic composition metabolically active neustonic mesozooplankton community response summer conditions Red Sea. population exhibited changes abundance with significant decline copepods appendicularia July, when cells were...
BACKGROUND: Merging stem cells with biomimetic materials represent an attractive approach to tissue engineering. The development of alternative scaffold the ability mimic extracellular matrix, and 3D gradient preventing any alteration in cell metabolism or their gene expression patterns, would have many medical applications. OBJECTIVE: In this study, we introduced use RGD (Arg-Gly-Asp) bio-conjugated cotton promote growth proliferation mesenchymal (MSCs). METHODS: We measured markers...
Abstract A high-performance computing genome variant calling workflow was designed to run GATK on HPC platforms. This efficiently called an average of 27.3 M, 32.6 168.9 and 16.2 M SNPs for rice, sorghum, maize, soybean, respectively, the most recently released high-quality reference sequences. Analysis a rice pan-genome panel revealed 2.1 novel that have yet be publicly released.
Abstract Aside from their roles in the cytoplasm, RNA-interference components have been reported to localize also nucleus of human cells. In particular, AGO1 associates with active chromatin and appears influence global gene expression. However, mechanistic aspects remain elusive. Here, we identify as a paraspeckle component that combination NEAT1 lncRNA maintains 3D genome architecture. We demonstrate interacts its depletion affects expression formation paraspeckles. By Hi-C analysis...
Abstract Understanding and exploiting genetic diversity is a key factor for the productive stable production of rice. Utilizing 16 high-quality genomes that represent subpopulation structure Asian rice ( O. sativa ), plus two close relatives rufipogon punctata we built pan-genome inversion index 1,054 non-redundant inversions span an average ∼ 14% cv. Nipponbare reference genome sequence. Using this estimated rate 1,100 per million years in rice, which 37 to 73 times higher than previously...