A5072996052- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Genetic Mapping and Diversity in Plants and Animals
- Insect symbiosis and bacterial influences
- Genetic and phenotypic traits in livestock
- Bacteriophages and microbial interactions
- Immune cells in cancer
- T-cell and B-cell Immunology
- Genetic Associations and Epidemiology
- vaccines and immunoinformatics approaches
- Immune Cell Function and Interaction
- Evolutionary Algorithms and Applications
- Genomics and Rare Diseases
- Genomic variations and chromosomal abnormalities
University of Arizona
2022-2024
Universitat Autònoma de Barcelona
2018-2022
Abstract Drosophila melanogaster is a leading model in population genetics and genomics, growing number of whole-genome data sets from natural populations this species have been published over the last years. A major challenge integration disparate sets, often generated using different sequencing technologies bioinformatic pipelines, which hampers our ability to address questions about evolution species. Here we these issues by developing bioinformatics pipeline that maps pooled (Pool-Seq)...
Abstract The McDonald and Kreitman test (MKT) is one of the most powerful widely used methods to detect quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative test), a novel web-based service performing four distinct MKT types. It allows detection estimation different regimes −adaptive, neutral, strongly deleterious weakly deleterious− acting on any genomic sequence. can analyze both user's own population data pre-loaded Drosophila...
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges have left signatures in landscape of genetic variation and we can identify today's genomes. Here, (i) perform an outlier approach on eight different population statistics for 22 non-admixed human populations Phase III 1000 Genomes Project detect selective sweeps at historical ages, as well events recurrent positive selection lineage; (ii) create PopHumanScan, online catalog compiles...
Inferring the effects of positive selection on genomes remains a critical step in characterizing ultimate and proximate causes adaptation across species, quantifying challenge due to confounding many other evolutionary processes. Robust efficient approaches for inference could help characterize rate strength nonmodel species which demographic history, mutational processes, recombination patterns are not currently well-described. Here, we introduce an user-friendly extension McDonald-Kreitman...
Abstract Inferring the effects of positive selection on genomes remains a critical step in characterizing ultimate and proximate causes adaptation across species, quantifying challenge due to confounding many other evolutionary processes. Robust efficient approaches for inference could help characterize rate strength non-model species which demographic history, mutational processes, recombination patterns are not currently well-described. Here, we introduce an user-friendly extension...
Abstract Pathogens were a major driver of genetic adaptation during human evolution. Viruses in particular dominant the thousands proteins that physically interact with viruses (VIPs for Virus-Interacting Proteins). This however poses conundrum. The best understood cases virus-driven specialized immune antiviral factors or host viral receptors are numerically vastly insufficient to explain abundant adaptations VIPs. What adaptive mechanisms can then at least partly close this gap? VIPs tend...
Abstract Drosophila melanogaster is a leading model in population genetics and genomics, growing number of whole-genome datasets from natural populations this species have been published over the last 20 years. A major challenge integration these disparate datasets, often generated using different sequencing technologies bioinformatic pipelines, which hampers our ability to address questions about evolution structure species. Here we issues by developing bioinformatics pipeline that maps...
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...
Adaptive challenges that humans faced as they expanded across the globe left specific molecular footprints can be decoded in our today's genomes. Different sets of metrics are used to identify genomic regions have undergone selection. However, there fewer methods capable pinpointing allele ultimately responsible for this Here, we present PopHumanVar, an interactive online application is designed facilitate exploration and thorough analysis candidate by integrating both functional population...
Abstract The human immune system is under constant evolutionary pressure, primarily through its role as first line of defence against pathogens. Accordingly, population genomics studies have shown that immune-related genes a high rate adaptive evolution. These studies, however, are mainly based on protein-coding without cellular context, leaving the cell types and states uncharted. Inferring adaptation in developing adult cells at resolution, we found from both lymphoid myeloid compartments...