A5080808086- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Marine Biology and Environmental Chemistry
- Evolution and Genetic Dynamics
- Marine Ecology and Invasive Species
- Cell Image Analysis Techniques
- RNA and protein synthesis mechanisms
- Genetics, Aging, and Longevity in Model Organisms
- RNA modifications and cancer
- AI in cancer detection
- Mesenchymal stem cell research
- Morphological variations and asymmetry
- Developmental Biology and Gene Regulation
- Neonatal Respiratory Health Research
- Genetic diversity and population structure
- Immune cells in cancer
- Spaceflight effects on biology
- vaccines and immunoinformatics approaches
- Molecular Biology Techniques and Applications
- Evolutionary Game Theory and Cooperation
- Animal Behavior and Reproduction
- Coral and Marine Ecosystems Studies
- Acute Myeloid Leukemia Research
- Advanced Vision and Imaging
- Environmental DNA in Biodiversity Studies
Centro Nacional de Análisis Genómico
2023-2025
Centre for Genomic Regulation
2023-2024
University College London
2018-2023
Centre for Life
2018-2023
Universitat Autònoma de Barcelona
2023
University of Helsinki
2015-2019
Cell lineages provide the framework for understanding how cell fates are decided during development. Describing in most organisms is challenging; even a fruit fly larva has ~50,000 cells and small mammal >1 billion cells. Recently, idea of applying CRISPR to induce mutations development, be used as heritable markers lineage reconstruction, been proposed by several groups. While an attractive idea, its practical value depends on accuracy that can generated. Here, we use computer simulations...
The recent advent of CRISPR and other molecular tools enabled the reconstruction cell lineages based on induced DNA mutations promises to solve ones more complex organisms. To date, no lineage algorithms have been rigorously examined for their performance robustness across dataset types number cells. benchmark such methods, we decided organize a DREAM challenge using in vitro experimental intMEMOIR recordings silico data C. elegans tree about 1,000 cells Mus musculus 10,000 Some 22...
Pelagic larval stages are widespread across animals, yet it is unclear whether larvae were present in the last common ancestor of animals or they evolved multiple times due to selective pressures. Many marine at least superficially similar; small, swim through beating bands cilia, and sense environment with an apical organ. To understand these similarities, we have generated single-cell atlases for from two animal phyla compared their cell types. We found clear similarities among ciliary...
Abstract In some eukaryotes, a ‘hidden break’ has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break common protostome animals (arthropods, molluscs, annelids etc.), but also reported vertebrates and non-metazoan eukaryotes. We present new computational approach to determine presence of hidden rRNAs using mapping RNA-Seq data. find homologous across protostomes although it lost small number taxa. show that rare breaks vertebrate are not break. A...
We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns, and development with the aim mapping adaptation over entire embryo's map is based on analyzing information for 5,969 genes (from text-based annotations in situ hybridization data directly from BDGP database, Tomancak et al. 2007) polymorphism divergence these project DGRP, Mackay 2012). The proportion nonsynonymous substitutions that...
Previous studies of the evolution genes expressed at different life-cycle stages Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data D. and divergence between yakuba. For set melanogaster, as reported in modENCODE, estimate ratio relative synonymous sites (α) then α is discomposed into (ωa) (ωna) substitutions. We find that mid-...
Abstract Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking divisions using live microscopy, or deducing history of cells molecular recorders. A lineage on its own, however, is simply a description as branching events. major goal current research integrate this relationships with information about spatial distribution identities those produce. Visualizing, interpreting exploring these complex data an intuitive manner requires...
Abstract Pelagic larval stages are widespread across animals, yet it is unclear if larvae were present in the last common ancestor of animals or whether they evolved multiple times due to selective pressures. Many marine at least superficially similar, small, swim through beating ciliated bands and sense environment with an apical organ structure. To understand these similarities, we have generated single cell atlases for from two animal phyla compared their types. We found clear...
ABSTRACT In some eukaryotes, a ‘hidden break’ has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break common protostome animals (arthropods, molluscs, annelids etc.) but also reported vertebrates and non-metazoan eukaryotes. We present new computational approach to determine presence of hidden rRNAs using mapping RNA-Seq data. find homologous across protostomes although lost small number taxa. show that rare breaks vertebrate are not break. A found...
Abstract The cellular complexity of the endochondral bone underlies its essential and pleiotropic roles during organismal life. While adult has received significant attention, we still lack a deep understanding perinatal cellulome. Here, have profiled full composition murine at single‐cell level transition from fetal to newborn life in comparison with tissue, particular emphasis on mesenchymal compartment. contains different fibroblastic clusters blastema‐like characteristics organizing...
We introduce Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP), a scalable profiling approach of individual cells. Leveraging transcriptomics proteomics imaging platforms, STAMP eliminates sequencing costs, to enable single-cell genomics from hundreds millions cells at an unprecedented low cost. Stamping in suspension onto slides, supports single-modal (RNA or protein) multimodal flexible, ultra-high-throughput formats. allows the analysis single multiple samples within...
Human immune cells are under constant evolutionary pressure, primarily through their role as first line of defence against pathogens. Most studies on adaptation are, however, based protein-coding genes without considering cellular context. Here, using data from the Cell Atlas, we infer gene rate human landscape at resolution. We find abundant cell types, like progenitor during development and adult in barrier tissues, to harbour significantly increased rates. confirm tissue-resident T NK...
Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking divisions using live microscopy, or deducing history of cells molecular recorders. A lineage on its own, however, is simply a description as branching events. major goal current research integrate this relationships with information about spatial distribution identities those produce. Visualising, interpreting exploring these complex data an intuitive manner requires...