Daniel Dimitrov
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View article: OmniPath: integrated knowledgebase for multi-omics analysis
OmniPath: integrated knowledgebase for multi-omics analysis Open
Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath ( https://…
View article: RIDDEN: Data-driven inference of receptor activity from transcriptomic data
RIDDEN: Data-driven inference of receptor activity from transcriptomic data Open
Intracellular signaling initiated from ligand-bound receptors plays a fundamental role in both physiological regulation and development of disease states, making receptors one of the most frequent drug targets. Systems level analysis of re…
View article: RIDDEN: Data-driven inference of receptor activity from transcriptomic data
RIDDEN: Data-driven inference of receptor activity from transcriptomic data Open
Intracellular signaling initiated from ligand bound receptors plays a fundamental role in both physiological regulation and development of disease states, making receptors one of the most frequent drug targets. Systems level analysis of re…
View article: Unraveling the influence of Indoxyl Sulfate and apixaban in drug metabolism and elimination: Is sex a major player?
Unraveling the influence of Indoxyl Sulfate and apixaban in drug metabolism and elimination: Is sex a major player? Open
Chronic Kidney Disease (CKD) is associated with heightened risk of thrombosis. Prescription of anticoagulants is key to manage it; however, CKD patients have shown an increased risk of bleeding under anticoagulation therapy compared to non…
View article: VIB Hackathon on spatial omics tools and methods
VIB Hackathon on spatial omics tools and methods Open
During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The topics were organized in five workgroups and included benchmarking, pipelines, spatial transcriptomics, spatial proteom…
View article: LIANA+_Integrating_MultiOmics_Data v1
LIANA+_Integrating_MultiOmics_Data v1 Open
A Protocol describing the application of LIANA+ on a spatially-resolved metabolite-transcriptome dataset from a recent murine Parkinson’s disease model Vicari et al., 2023. We demonstrate LIANA+’s utility in harmonizing spatially-resolved …
View article: MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions Open
From the catalytic breakdown of nutrients to signaling, interactions between metabolites and proteins play an essential role in cellular function. An important case is cell–cell communication, where metabolites, secreted into the microenvi…
View article: Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples
Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples Open
In recent years, data-driven inference of cell-cell communication has helped reveal coordinated biological processes across cell types. Here, we integrate two tools, LIANA and Tensor-cell2cell, which, when combined, can deploy multiple exi…
View article: Clarifying the murk: unveiling bacterial dynamics in response to crude oil pollution, Corexit-dispersant, and natural sunlight in the Gulf of Mexico
Clarifying the murk: unveiling bacterial dynamics in response to crude oil pollution, Corexit-dispersant, and natural sunlight in the Gulf of Mexico Open
The 2010 Deepwater Horizon (DwH) Oil spill released an enormous volume of oil into the Gulf of Mexico (GoM), prompting the widespread use of chemical dispersants like Corexit ® EC9500A. The ecological consequences of this treatment, especi…
View article: MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions Open
Interactions between proteins and metabolites are key for cellular function, from the catalytic breakdown of nutrients to signaling. An important case is cell-cell communication, where cellular metabolites are secreted into the microenviro…
View article: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease Open
Biomedical single-cell atlases describe disease at the cellular level. However, analysis of this data commonly focuses on cell-type-centric pairwise cross-condition comparisons, disregarding the multicellular nature of disease processes. H…
View article: Author response: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Author response: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease 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 Metrics Abstract Biomedi…
View article: SingleCellExperiment Object for Kang et al., 2018 PBMCs data
SingleCellExperiment Object for Kang et al., 2018 PBMCs data Open
Kang et al., 2018 lupus PBMC data as SingleCellExperiment; also available under https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96583. Converted from an AnnData object from https://github.com/theislab/pertpy
View article: SingleCellExperiment Object for Kang et al., 2018 PBMCs data
SingleCellExperiment Object for Kang et al., 2018 PBMCs data Open
Kang et al., 2018 lupus PBMC data as SingleCellExperiment; also available under https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96583. Converted from an AnnData object from https://github.com/theislab/pertpy
View article: LIANA+: an all-in-one cell-cell communication framework
LIANA+: an all-in-one cell-cell communication framework Open
The growing availability of single-cell and spatially-resolved transcriptomics has led to the rapidly growing popularity of methods to infer cell-cell communication. Many approaches have emerged, each capturing only a partial view of the c…
View article: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease Open
Collection of auxiliary data to reproduce the results from "Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease". Source code is available at: https://github.com/saezlab/MOFAcell Exceptions: Spat…
View article: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease Open
Collection of auxiliary data to reproduce the results from "Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease". Source code is available at: https://github.com/saezlab/MOFAcell Exceptions: Spat…
View article: Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples
Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples Open
In recent years, data-driven inference of cell-cell communication has helped reveal coordinated biological processes across cell types. While multiple cell-cell communication tools exist, results are specific to the tool of choice, due to …
View article: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease Open
Single-cell atlases across conditions are essential in the characterization of human disease. In these complex experimental designs, patient samples are profiled across distinct cell-types and clinical conditions to describe disease proces…
View article: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease Open
Collection of auxiliary data to reproduce the results from "Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease". Source code is available at: https://github.com/saezlab/MOFAcell Exceptions: Spat…
View article: Seurat Object
Seurat Object Open
single-cell COVID-19 data (Silvin, 2020), converted to Seurat Silvin, A., Chapuis, N., Dunsmore, G., Goubet, A.G., Dubuisson, A., Derosa, L., Almire, C., Hénon, C., Kosmider, O., Droin, N. and Rameau, P., 2020. Elevated calprotectin and a…
View article: TNBC Data from Wu et al, 2021
TNBC Data from Wu et al, 2021 Open
Anndata format of the TNBC data set generated by Wu et al, 2021, together with inferred cytokine activity, as described in Dimitrov et al, 2022. Wu, S.Z., Al-Eryani, G., Roden, D.L., Junankar, S., Harvey, K., Andersson, A., Thennavan, A.…
View article: TNBC Data from Wu et al, 2021
TNBC Data from Wu et al, 2021 Open
Anndata format of the TNBC data set generated by Wu et al, 2021, together with inferred cytokine activity, as described in Dimitrov et al, 2022. Wu, S.Z., Al-Eryani, G., Roden, D.L., Junankar, S., Harvey, K., Andersson, A., Thennavan, A.…