Santiago Carmona

Publications

• Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses
• STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data
• Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting
• UCell: robust and scalable single-cell gene signature scoring
• APRANK: computational prioritization of antigenic proteins and peptides from complete pathogen proteomes
• Interpretation of T cell states from single-cell transcriptomics data using reference atlases
• Super-cells untangle large and complex single-cell transcriptome networks
• A single-cell reference atlas delineates CD4+ T cell subtype-specific adaptation during acute and chronic viral infections
• Novel biotechnological platform based on baculovirus occlusion bodies carrying Babesia bovis small antigenic peptides for the design of a diagnostic enzyme-linked immunosorbent assay (ELISA).
• Deciphering the evolution of vertebrate immune cell types with single-cell RNA-seq
• Molecular and antigenic characterization of Trypanosoma cruzi TolT proteins.
• Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy.
• MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma
• Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq
• Deciphering the evolution of vertebrate immune cell types with single-cell RNA-seq
• Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq
• Enhanced Phenotype Definition for Precision Isolation of Precursor Exhausted Tumor-Infiltrating CD8 T Cells
• STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data
• Diagnostic Peptide Discovery: Prioritization of Pathogen Diagnostic Markers Using Multiple Features
• Mapping antigenic motifs in the trypomastigote small surface antigen from Trypanosoma cruzi
• Towards high-throughput immunomics for infectious diseases: Use of next-generation peptide microarrays for rapid discovery and mapping of antigenic determinants
• Characterization of Toxoplasma gondii subtelomeric-like regions: Identification of a long-range compositional bias that is also associated with gene-poor regions
• Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes
• Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types
• E-MTAB-4617 - Single-cell RNA sequencing of spleen-derived LCK-expressing cells from adult zebrafish
• Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes.
• High-resolution profiling of linear B-cell epitopes from mucin-associated surface proteins (MASPs) of Trypanosoma cruzi during human infections.
• Identification of innate lymphoid cells in single-cell RNA-Seq data
• TDR targets: A chemogenomics resource for neglected diseases
• Genomic-scale prioritization of drug targets: The TDR Targets database
• Identification of attractive drug targets in neglected- disease pathogens using an in Silico approach
• TcSNP: A database of genetic variation in Trypanosoma cruzi
• Integrating and Mining Helminth Genomes to Discover and Prioritize Novel Therapeutic Targets
• A computational pipeline for diagnostic biomarker discovery in the human pathogen Trypanosoma cruzi
• Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens
• SPICA: Swiss portal for immune cell analysis
• scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets
• Orthogonal Gene Engineering Enables CD8+ T Cells to Control Tumors through a Novel PD-1+TOX-indifferent Synthetic Effector State
• Characterization of ADAT2/3 molecules in Trypanosoma cruzi and regulation of mucin gene expression by tRNA editing
• Metacells untangle large and complex single-cell transcriptome networks
• Low-Dose Radiotherapy Reverses Tumor Immune Desertification and Resistance to Immunotherapy
• Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation
• APRANK: Computational Prioritization of Antigenic Proteins and Peptides From Complete Pathogen Proteomes
• UCell: Robust and scalable single-cell gene signature scoring
• A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections
• Supplementary Table S2 from MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma
• Supplementary Table S2 from MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma
• Supplementary Figures and Table 1 from MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma
• Supplementary Figures and Table 1 from MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma
• Data from MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma
• Data from MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma
• Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8+ T cells
• Semi-supervised integration of single-cell transcriptomics data
• Wounding triggers invasive progression in human basal cell carcinoma
• ECM Signatures Reveal Quiescent Stem Cell Diversity in the Colonic Niche
• Metabolic reinvigoration of NK cells by IL-21 enhances immunotherapy against MHC-I deficient solid tumors