Johan Ankarklev
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View article: Deep Integrated Network Analysis – a data-driven tool to discover and characterize disease pathways in the liver
Deep Integrated Network Analysis – a data-driven tool to discover and characterize disease pathways in the liver Open
Background & Aims An extensive number of studies have utilized transcriptomic profiling as a valuable tool for uncovering genes related to diseases and physiological processes of the liver. Here we combine this wealth of information to pro…
View article: Genome-wide profiling of tRNA modifications reveal the presence of divergent signatures in <i>Plasmodium falciparum</i>
Genome-wide profiling of tRNA modifications reveal the presence of divergent signatures in <i>Plasmodium falciparum</i> Open
tRNAs are known to be extensively decorated with various nucleotide modifications, which can modulate the biological properties of tRNAs, such as promoting translation efficiency or fidelity, influencing codon preference and stabilizing te…
View article: tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation in Plasmodium falciparum
tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation in Plasmodium falciparum Open
Summary: An adaptive feature of malaria-causing parasites is the digestion of host hemoglobin (HB) to acquire amino acids (AAs). Here, we describe a link between nutrient availability and translation dependent regulation of gene expression…
View article: Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution
Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution Open
Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The coordination of host responses across the complex liver tissue during mala…
View article: Host-Pathogen Interactions in the<i>Plasmodium</i>-Infected Mouse Liver at Spatial and Single-Cell Resolution
Host-Pathogen Interactions in the<i>Plasmodium</i>-Infected Mouse Liver at Spatial and Single-Cell Resolution Open
Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The spatial coordination of factors regulating immune responses and metabolic …
View article: Single-cell sequencing of tumor-associated macrophages in a Drosophila model
Single-cell sequencing of tumor-associated macrophages in a Drosophila model Open
Introduction Tumor-associated macrophages may act to either limit or promote tumor growth, yet the molecular basis for either path is poorly characterized. Methods We use a larval Drosophila model that expresses a dominant-active version o…
View article: A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration
A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration Open
Dataset created in the study "A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration" Structure ST_berghei_liver contains data generated du…
View article: Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution
Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution Open
Dataset created in the study "A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration" Structure ST_berghei_liver contains data generated du…
View article: Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution
Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution Open
Dataset created in the study "A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration" Structure ST_berghei_liver contains data generated du…
View article: scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics
scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics Open
Dendritic cells and macrophages are integral parts of the innate immune system and gatekeepers against infection. The protozoan pathogen, Toxoplasma gondii , is known to hijack host immune cells and modulate their immune response, making i…
View article: Single-cell sequencing of tumor-associated macrophages in a<i>Drosophila</i>model
Single-cell sequencing of tumor-associated macrophages in a<i>Drosophila</i>model Open
Introduction Tumor-associated macrophages may act to either limit or promote tumor growth, yet the molecular basis for either path is poorly characterized. Methods We use a larval Drosophila model that expresses a dominant-active version o…
View article: Single-cell sequencing of tumor-associated macrophages in a Drosophila model
Single-cell sequencing of tumor-associated macrophages in a Drosophila model Open
Abstract Tumor-associated macrophages may act to either limit or promote tumor growth, yet the molecular basis for either path is poorly characterized. Using a Drosophila model for dysplastic growth during tumor early progression in combin…
View article: Amino acid usage and tRNA expression underlies proteome adaptation in<i>Plasmodium falciparum</i>
Amino acid usage and tRNA expression underlies proteome adaptation in<i>Plasmodium falciparum</i> Open
Parasites often depend on metabolic adaptation to the host environment. An adaptive feature of malaria-causing parasites is digestion of hemoglobin (HB) to acquire amino acids (AAs). Here we describe a link between nutrient availability an…
View article: Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut
Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut Open
The malaria parasite Plasmodium falciparum causes more than half a million deaths per year. The current treatment regimen targets the symptom-causing blood stage inside the human host.
View article: scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics
scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics Open
Abstract Host-parasite interactions include complex interplays between an invading and a defending organism, each continuously adapting to gain the upper hand. The protozoan parasite, Toxoplasma gondii, can invade every nucleated cell type…
View article: scDual-Seq of<i>Toxoplasma gondii</i>-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics
scDual-Seq of<i>Toxoplasma gondii</i>-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics Open
SUMMARY Host-parasite interactions include complex interplays between an invading and a defending organism, each continuously adapting to gain the upper hand. The protozoan parasite, Toxoplasma gondii , can invade every nucleated cell type…
View article: scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics
scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics Open
Abstract Host-parasite interactions include complex interplays between an invading and a defending organism, each continuously adapting to gain the upper hand. The protozoan parasite, Toxoplasma gondii, can invade every nucleated cell type…
View article: Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut
Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut Open
Abstract: Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for no…
View article: Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut
Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut Open
Abstract: Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for no…
View article: Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut
Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut Open
Abstract: Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for no…
View article: Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections
Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections Open
Identification of host factors affecting individual SARS-CoV-2 susceptibility will provide a better understanding of the large variations in disease severity and will identify potential factors that can be used, or targeted, in antiviral d…
View article: Single-cell transcriptomics to define<i>Plasmodium falciparum</i>stage-transition in the mosquito midgut
Single-cell transcriptomics to define<i>Plasmodium falciparum</i>stage-transition in the mosquito midgut Open
Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory vector mosquito provides a promising target for novel contro…
View article: Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation
Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation Open
Mosquito immune cells, known as hemocytes, are integral to cellular and humoral responses that limit pathogen survival and mediate immune priming. However, without reliable cell markers and genetic tools, studies of mosquito immune cells h…
View article: Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver
Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver Open
Reconstruction of heterogeneity through single-cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remai…
View article: Additional file 2 of Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate
Additional file 2 of Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate Open
Additional file 2: Specific genes, shared genes and disrupted open reading frames. Contains lists of isolate specific genes, genes shared between two isolates and putative pseudogenes. A list of artificially disrupted open reading frames i…