Bishwa Ghimire
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View article: COVID-19 vaccine type controls stromal reprogramming in draining lymph nodes
COVID-19 vaccine type controls stromal reprogramming in draining lymph nodes Open
Lymph node (LN) stromal cells are critical regulators of immune reactions, yet their responses to different SARS-CoV-2 vaccines remain unexplored. Here, we immunized mice with clinically approved gene- and protein-based COVID-19 vaccines t…
View article: Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview
Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview Open
Molecular characterization of a biological sample, e.g., with omics approaches, is fundamental for the development and implementation of personalized and precision medicine approaches. In this context, quality assessment is one of the most…
View article: Nextpie: a web-based reporting tool and database for reproducible nextflow pipelines
Nextpie: a web-based reporting tool and database for reproducible nextflow pipelines Open
Motivation High-throughput genomic data analysis consists of the inexorably intertwined inputs and outputs of a vast array of bioinformatic analysis tools. To guarantee streamlined and reproducible analyses, the often complex data analysis…
View article: Oxidative Stress and Inflammation-Related mRNAs Are Elevated in Serum of a Finnish Wet AMD Cohort
Oxidative Stress and Inflammation-Related mRNAs Are Elevated in Serum of a Finnish Wet AMD Cohort Open
Differentially expressed systemic mRNAs that are linked to mitochondrial function, oxidative stress, and inflammation may have a role in the pathology of wAMD. Our observations provide new data for the understanding of the progression of w…
View article: Comprehensive multi-omics profiling of a healthy human cohort
Comprehensive multi-omics profiling of a healthy human cohort Open
Multi-omics investigations hold promise for uncovering biomarker profiles crucial for disease diagnosis, prognosis, and monitoring interventions. However, these profiles are susceptible to technical and biological variation. Capturing biol…
View article: Hepatocyte-specific loss of melanocortin 1 receptor disturbs fatty acid metabolism and promotes adipocyte hypertrophy
Hepatocyte-specific loss of melanocortin 1 receptor disturbs fatty acid metabolism and promotes adipocyte hypertrophy Open
View article: Generation and characterisation of scalable and stable human pluripotent stem cell-derived microvascular-like endothelial cells for cardiac applications
Generation and characterisation of scalable and stable human pluripotent stem cell-derived microvascular-like endothelial cells for cardiac applications Open
View article: Hepatocyte-specific loss of melanocortin 1 receptor disturbs fatty acid metabolism and promotes adipocyte hypertrophy
Hepatocyte-specific loss of melanocortin 1 receptor disturbs fatty acid metabolism and promotes adipocyte hypertrophy Open
Background/objectives Melanocortins mediate their biological functions via five different melanocortin receptors (MC1R - MC5R). MC1R is expressed in the skin and leukocytes, where it regulates skin pigmentation and inflammatory responses. …
View article: α-Melanocyte-stimulating hormone alleviates pathological cardiac remodeling via melanocortin 5 receptor
α-Melanocyte-stimulating hormone alleviates pathological cardiac remodeling via melanocortin 5 receptor Open
α-Melanocyte-stimulating hormone (α-MSH) regulates diverse physiological functions by activating melanocortin receptors (MC-R). However, the role of α-MSH and its possible target receptors in the heart remain completely unknown. Here we in…
View article: Generation and characterization of scalable and stable human pluripotent stem cell-derived microvascular-like endothelial cells for cardiac applications
Generation and characterization of scalable and stable human pluripotent stem cell-derived microvascular-like endothelial cells for cardiac applications Open
Cardiac microvascular disease (CMD) and its progression towards major adverse coronary events pose a significant health challenge. Accurate in vitro investigation of CMD requires a robust cell model that faithfully represents the cells wit…
View article: Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers
Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers Open
Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell…
View article: Multi-omics Quality Assessment in Personalized Medicine through EATRIS
Multi-omics Quality Assessment in Personalized Medicine through EATRIS Open
Molecular characterization of a biological sample, e.g., with omics approaches, is fundamental for the development and implementation of personalized and precision medicine approaches. In this context, quality assessment is one of the most…
View article: Melanocortin 1 receptor regulates cholesterol and bile acid metabolism in the liver
Melanocortin 1 receptor regulates cholesterol and bile acid metabolism in the liver Open
Melanocortin 1 receptor (MC1-R) is widely expressed in melanocytes and leukocytes and is thus strongly implicated in the regulation of skin pigmentation and inflammation. MC1-R has also been found in the rat and human liver, but its functi…
View article: Author response: Melanocortin 1 receptor regulates cholesterol and bile acid metabolism in the liver
Author response: Melanocortin 1 receptor regulates cholesterol and bile acid metabolism in the liver Open
Full text Figures and data Side by side Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Abstract Melanocortin 1 …
View article: α-Melanocyte-Stimulating Hormone Regulates Pathological Cardiac Remodeling by Activating Melanocortin 5 Receptor in Cardiomyocytes
α-Melanocyte-Stimulating Hormone Regulates Pathological Cardiac Remodeling by Activating Melanocortin 5 Receptor in Cardiomyocytes Open
Background α-Melanocyte-stimulating hormone (α-MSH) regulates diverse physiological functions by activating melanocortin receptors (MC-R). α-MSH is predominantly expressed in the pituitary gland, but it is also found in several peripheral …
View article: 1006 Single-cell functional genomics of natural killer cell evasion in blood cancers
1006 Single-cell functional genomics of natural killer cell evasion in blood cancers Open
Background Natural killer (NK) cells are emerging as a promising therapeutic option in cancer. To better understand how cancer cells evade NK cells, we studied interacting NK and blood cancer cells using single-cell and genome-scale functi…
View article: Single-cell functional genomics of natural killer cell evasion in blood cancers
Single-cell functional genomics of natural killer cell evasion in blood cancers Open
SUMMARY Natural killer (NK) cells are emerging as a promising therapeutic option in cancer. To better understand how cancer cells evade NK cells, we studied interacting NK and blood cancer cells using single-cell and genome-scale functiona…
View article: Umbilical cord blood DNA methylation in children who later develop type 1 diabetes
Umbilical cord blood DNA methylation in children who later develop type 1 diabetes Open
View article: Human pluripotent stem cell-derived cells endogenously expressing follicle-stimulating hormone receptors: modeling the function of an inactivating receptor mutation
Human pluripotent stem cell-derived cells endogenously expressing follicle-stimulating hormone receptors: modeling the function of an inactivating receptor mutation Open
Follicle-stimulating hormone (FSH) is crucial in the development and regulation of reproductive functions. The actions of human FSH and its receptor (FSHR) and mutations therein have mainly been studied using in vivo models, primary cells,…
View article: Analysis of human brain tissue derived from DBS surgery
Analysis of human brain tissue derived from DBS surgery Open
Background Transcriptomic and proteomic profiling of human brain tissue is hindered by the availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the…
View article: A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development
A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development Open
View article: Additional file 1 of Analysis of human brain tissue derived from DBS surgery
Additional file 1 of Analysis of human brain tissue derived from DBS surgery Open
Additional file 1. Proteomics dataset, quantified proteins
View article: Additional file 2 of Analysis of human brain tissue derived from DBS surgery
Additional file 2 of Analysis of human brain tissue derived from DBS surgery Open
Additional file 2. GO and KEGG pathway enrichment analysis for proteomics data and lists of Uniprot identifiers used for enrichment analysis
View article: Additional file 3 of Analysis of human brain tissue derived from DBS surgery
Additional file 3 of Analysis of human brain tissue derived from DBS surgery Open
Additional file 3. SynGO enrichment analysis for RNA-seq data, filtered gene list and enrichment analysis
View article: Additional file 4 of Analysis of human brain tissue derived from DBS surgery
Additional file 4 of Analysis of human brain tissue derived from DBS surgery Open
Additional file 4. RNA-seq dataset, feature counts in each analyzed sample
View article: Analysis of human brain tissue derived from DBS surgery
Analysis of human brain tissue derived from DBS surgery Open
Background Transcriptomic and proteomic profiling of human brain tissue is hindered by availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the pos…
View article: STAT3 activation in large granular lymphocyte leukemia is associated with cytokine signaling and DNA hypermethylation
STAT3 activation in large granular lymphocyte leukemia is associated with cytokine signaling and DNA hypermethylation Open
View article: Umbilical Cord Blood DNA Methylation in Children Who Later Develop Type 1 Diabetes
Umbilical Cord Blood DNA Methylation in Children Who Later Develop Type 1 Diabetes Open
Distinct DNA methylation patterns have recently been observed to precede type 1 diabetes in whole blood collected from young children. Our aim was to determine, whether perinatal DNA methylation could be associated with later progression t…
View article: Patient-tailored design for selective co-inhibition of leukemic cell subpopulations
Patient-tailored design for selective co-inhibition of leukemic cell subpopulations Open
Machine learning and single-cell data inform personalized drug combinations that selectively co-inhibit cancer cell populations.
View article: Immunogenomic Landscape of Hematological Malignancies
Immunogenomic Landscape of Hematological Malignancies Open