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McLaren Paul J, Gawanbacht Ali, Pyndiah Nitisha, Krapp Christian, Hotter Dominik, Kluge Silvia F, Götz Nicola, Heilmann Jessica, Mack Katharina, Sauter Daniel, Thompson Danielle, Perreaud Jérémie, Rausell Antonio, Munoz Miguel, Ciuffi Angela, Kirchhoff Frank, Telenti Amalio (2015), Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses., in
Retrovirology, 12, 41-41.
McLaren Paul J, Gawanbacht Ali, Pyndiah Nitisha, Krapp Christian, Hotter Dominik, Kluge Silvia F, Götz Nicola, Heilmann Jessica, Mack Katharina, Sauter Daniel, Thompson Danielle, Perreaud Jérémie, Rausell Antonio, Munoz Miguel, Ciuffi Angela, Kirchhoff Frank, Telenti Amalio (2015), Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses., in
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Juliá Miguel, Telenti Amalio, Rausell Antonio (2015), Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq., in
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Bioinformatics (Oxford, England).
Intracellular defense against pathogens is a fundamental component of human innate immunity. However, the numbers of genes defined as being part of innate immunity is large, and there is a need for better criteria to identify the subset of genes acting as intracellular effectors. In this proposal we explore and advance tools and functional approaches that can assist re-defining subsets of innate immunity and interpreting variation in the human genome. We place emphasis on the identification of components of the intracellular defense against pathogens using HIV infection as a model. Three research groups converge on this goal:1. Evolutionary genomics (Zdobnov laboratory)?Identification of evolutionary signatures that characterize different sets of genes of the innate immunity.?Identification of non-annotated genes that share the characteristics of specific subsets of genes of the innate immunity.2. Human genomics (Fellay laboratory)?Accessing population-level human genome sequence data and cataloguing genetic variation.?Identification of genomic signatures that characterize different sets of genes of the innate immunity.?Assessment of impact of variation in innate immunity genes on infection phenotypes in human patient populations3. Functional genomics (Telenti laboratory)?Development of the concept of permissive cells (HIV model) as a tool for the identification of effector genes.?Single cell analysis to identify the basis of cell-to-cell heterogeneity in permissiveness.The expected outcome of the project is the generation of signatures of a subset of genes of the innate immunity with effector capacities, their testing in in vitro systems, and the identification of human variation within these genes with possible phenotypic consequences.