Carlos Talavera‐López
A5081891785- Single-cell and spatial transcriptomics
- Trypanosoma species research and implications
- Insect symbiosis and bacterial influences
- Iron Metabolism and Disorders
- Research on Leishmaniasis Studies
- Malaria Research and Control
- Gene Regulatory Network Analysis
- Neuroinflammation and Neurodegeneration Mechanisms
- Cell Image Analysis Techniques
- Helminth infection and control
- Cancer Genomics and Diagnostics
- T-cell and B-cell Immunology
- Complement system in diseases
- Cancer Cells and Metastasis
- COVID-19 Clinical Research Studies
- Neurogenesis and neuroplasticity mechanisms
- X-ray Diffraction in Crystallography
- SARS-CoV-2 and COVID-19 Research
- Parasites and Host Interactions
- Mosquito-borne diseases and control
- Crystallization and Solubility Studies
- Extracellular vesicles in disease
- Receptor Mechanisms and Signaling
- Congenital heart defects research
- Supramolecular Chemistry and Complexes
University of Würzburg
2023-2025
Helmholtz Zentrum München
2022-2024
Technical University of Munich
2024
Wellcome Sanger Institute
2019-2022
Karolinska Institutet
2013-2022
Ludwig-Maximilians-Universität München
2022
European Bioinformatics Institute
2019-2021
The Francis Crick Institute
2016-2021
Universitat de les Illes Balears
2012-2019
Fundació Universitat-Empresa de les Illes Balears
2016
Conifers have dominated forests for more than 200 million years and are of huge ecological economic importance. Here we present the draft assembly 20-gigabase genome Norway spruce (Picea abies), first available any gymnosperm. The number well-supported genes (28,354) is similar to >100 times smaller Arabidopsis thaliana, there no evidence a recent whole-genome duplication in gymnosperm lineage. Instead, large size seems result from slow steady accumulation diverse set long-terminal repeat...
Abstract Cardiovascular disease is the leading cause of death worldwide. Advanced insights into mechanisms and therapeutic strategies require a deeper understanding molecular processes involved in healthy heart. Knowledge full repertoire cardiac cells their gene expression profiles fundamental first step this endeavour. Here, using state-of-the-art analyses large-scale single-cell single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight...
Abstract Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources compiles data on the abundance localisation of RNA proteins in various biological systems contexts provides open access to this research community. With increased availability single cell RNA-Seq datasets public archives, we have now extended with a new added-value service display expression cells. Single Cell was launched 2018 currently includes 123 studies from 12 species. The website can be...
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations individual the variability present in population. Here we integrated Human Lung Cell Atlas (HLCA), combining 49 respiratory system into single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents consensus re-annotation with...
ABSTRACT The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) associated proteases, transmembrane protease serine (TMPRSS2) Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess cell type-specific RNA expression ACE2 , TMPRSS2 CTSL through integrated...
The function of a cell is defined by its intrinsic characteristics and niche: the tissue microenvironment in which it dwells. Here we combine single-cell spatial transcriptomics data to discover cellular niches within eight regions human heart. We map cells microanatomical locations integrate knowledge-based unsupervised structural annotations. also profile cardiac conduction system
ABSTRACT Organ- and body-scale cell atlases have the potential to transform our understanding of human biology. To capture variability present in population, these must include diverse demographics such as age ethnicity from both healthy diseased individuals. The growth size number single-cell datasets, combined with recent advances computational techniques, for first time makes it possible generate comprehensive large-scale through integration multiple datasets. Here, we integrated Human...
Abstract The increasing availability of large-scale single-cell atlases has enabled the detailed description cell states. In parallel, advances in deep learning allow rapid analysis newly generated query datasets by mapping them into reference atlases. However, existing data transformations learned to map are not easily explainable using biologically known concepts such as genes or pathways. Here we propose expiMap, a informed deep-learning architecture that enables mapping. ExpiMap learns...
Abstract Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome Iberian ribbed newt Pleurodeles waltl , a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b mir-427/430/302, as well Harbinger DNA transposons carrying Myb -like...
A bstract Probabilistic models have provided the underpinnings for state-of-the-art performance in many single-cell omics data analysis tasks, including dimensionality reduction, clustering, differential expression, annotation, removal of unwanted variation, and integration across modalities. Many being deployed are amenable to scalable stochastic inference techniques, accordingly they able process datasets realistic growing sizes. However, community-wide adoption probabilistic approaches is...
Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI–TcVI. CL Brener, reference strain T. cruzi genome project, a hybrid with assembled 41 putative chromosomes. Gene copy number variation (CNV) well documented as an important mechanism to enhance gene expression and variability in cruzi. Chromosomal CNV (CCNV) another level which whole blocks genes are expanded simultaneously. Although karyotype not defined, several...
Background Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild domestic mammals across Central South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas cruzi. We have sequenced T. genome to provide new tools elucidating distinct intriguing biology this species key pathways related interaction with its arthropod mammalian hosts. Methodology/Principal Findings The haploid ∼24 Mb in length, smallest least...
Adult neural stem cells, located in discrete brain regions, generate new neurons throughout life. These cells are specialized astrocytes, but astrocytes other regions do not under physiological conditions. After stroke, however, striatal undergo neurogenesis mice, triggered by decreased Notch signaling. We used single-cell RNA sequencing to characterize Notch-depleted vivo. Striatal were upstream of the neuronal lineage. As initiated neurogenesis, they became transcriptionally very similar...
, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having very plastic, repetitive and complex genome, parasite displays highly diverse repertoire surface molecules, with pivotal roles in cell invasion, immune evasion pathogenesis. Before 2016, complexity genomic regions containing these genes impaired assembly genome at chromosomal level, making it impossible to study structure function several thousand encoding molecules...
Spatial omics allow us to identify and analyze communities of cells coordinating specific functions within a tissue. While these communities, defined as cell niches, are fundamentally shaped by interactions between spatially neighboring cells, we lack computational frameworks that can leverage spatial data quantitatively characterize niches based on interaction events. To address this, introduce NicheCompass, graph deep learning method designed the principles cellular communication....
Trypanosoma cruzi marinkellei is a bat-associated parasite of the subgenus Schizotrypanum and it regarded as T. subspecies. Here we report draft genome sequence c. comparison with cruzi. Our aims were to identify unique sequences genomic features, which may relate their distinct niches. The was found be ~11% smaller than that human-derived Sylvio X10. size difference attributed copy number variation coding non-coding sequences. divergence in regions ~7.5% between A acetyltransferase gene...
Abstract Cerebral malaria is a pathology involving inflammation in the brain. There are many immune cell types activated during this process, but there little information on response of microglia, severe complication. We examined microglia by genome wide transcriptomic analysis model experimental cerebral (ECM), which C57BL/6 mice infected with Plasmodium berghei ANKA. Thousands transcripts were differentially expressed at two different time points infection. Proliferation was dominant...
Abstract Spatial omics enable the characterization of colocalized cell communities that coordinate specific functions within tissues. These communities, or niches, are shaped by interactions between neighboring cells, yet existing computational methods rarely leverage such for their identification and characterization. To address this gap, here we introduce NicheCompass, a graph deep-learning method models cellular communication to learn interpretable embeddings encode signaling events,...
Trypanosoma cruzi affects millions of people worldwide. Clinical variability Chagas disease can be due to the genetic this parasite, requiring further genome studies. Here we report sequence T. Dm28c clone (TcI), a strain related sylvatic cycle parasite.