Simone G. Riva
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View article: CREST-GV: Cell types Ranking and Enrichment Score for selecTive Genetic Variants
CREST-GV: Cell types Ranking and Enrichment Score for selecTive Genetic Variants Open
Genome-Wide Association Studies (GWAS) have transformed our understanding of genetic traits and diseases since 2005 by analysing genetic variants across the human genome. Whilst they have successfully identified thousands of genetic locati…
View article: REnformer, a single-cell ATAC-seq predicting model to investigate open chromatin sites
REnformer, a single-cell ATAC-seq predicting model to investigate open chromatin sites Open
Genome regulatory elements are fundamental to cellular identity and cell type specific gene expression. Understanding how the underlying genetic code is differentially utilised by different cell types is central to understanding human heal…
View article: GENESIS: Generating scRNA-Seq data from Multiome Gene Expression
GENESIS: Generating scRNA-Seq data from Multiome Gene Expression Open
Single-cell technologies have significantly advanced our understanding of cellular heterogeneity by allowing the examination of individual cells at high resolution. Traditional single-cell RNA sequencing (scRNA-Seq) methods, which utilise …
View article: Active regulatory elements recruit cohesin to establish cell specific chromatin domains
Active regulatory elements recruit cohesin to establish cell specific chromatin domains Open
As the 3D structure of the genome is analysed at ever increasing resolution it is clear that there is considerable variation in the 3D chromatin architecture across different cell types. It has been proposed that this may, in part, be due …
View article: Constructing a Computational Workflow for the Identification of Novel Cellular and Molecular Drivers of Human Granulopoiesis
Constructing a Computational Workflow for the Identification of Novel Cellular and Molecular Drivers of Human Granulopoiesis Open
Neutrophils are crucial immune cells with complex and heterogeneous transcriptional programs. To understand the dynamic changes governing human granulopoiesis, we previously developed an ex vivo myeloid cell differentiation assay using hum…
View article: Deciphering cis-regulatory elements using REgulamentary
Deciphering cis-regulatory elements using REgulamentary Open
With the boom in Genome-Wide Association Studies (GWAS), it has become apparent that many disease-associated genetic variants lie in the non-coding regions of the genome. In order to prioritise these variants and disentangle their function…
View article: Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases Open
Background Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly…
View article: Active regulatory elements recruit cohesin to establish cell-specific chromatin domains
Active regulatory elements recruit cohesin to establish cell-specific chromatin domains Open
As the structure of the genome is analysed at ever increasing resolution it is becoming clear that there is considerable variation in the 3D chromatin architecture across different cell types. It has been proposed that this may, in part, b…
View article: MAGNETO: Cell type marker panel generator from single-cell transcriptomic data
MAGNETO: Cell type marker panel generator from single-cell transcriptomic data Open
Single-cell RNA sequencing experiments produce data useful to identify different cell types, including uncharacterized and rare ones. This enables us to study the specific functional roles of these cells in different microenvironments and …
View article: CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data
CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data Open
Assay for transposase-accessible chromatin (ATAC) and chromatin immunoprecipitation (ChIP), coupled with next-generation sequencing (NGS), have revolutionized the study of gene regulation. A lack of standardization in the analysis of the h…
View article: <i>IRX3</i> Oncogene Activation in T-ALL through Enhancer Hijacking Caused By <i>fto</i> Intron 8 Deletions
<i>IRX3</i> Oncogene Activation in T-ALL through Enhancer Hijacking Caused By <i>fto</i> Intron 8 Deletions Open
status: Published
View article: SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks
SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks Open
Several software tools for the simulation and analysis of biochemical reaction networks have been developed in the last decades; however, assessing and comparing their computational performance in executing the typical tasks of computation…
View article: SMGen: A generator of synthetic models of biochemical reaction networks
SMGen: A generator of synthetic models of biochemical reaction networks Open
Several software tools for the simulation and analysis of biochemical reaction networks have been developed in the last decades; however, assessing and comparing their computational performance in executing the typical tasks of Computation…
View article: <tt>SMaSH:</tt>A scalable, general marker gene identification framework for single-cell RNA sequencing and Spatial Transcriptomics
SMaSH:A scalable, general marker gene identification framework for single-cell RNA sequencing and Spatial Transcriptomics Open
Spatial transcriptomics is revolutionising the study of single-cell RNA and tissue-wide cell heterogeneity, but few robust methods connecting spatially resolved cells to so-called marker genes from single-cell RNA sequencing, which generat…
View article: Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis Open
Regulation of hematopoiesis during human development remains poorly defined. Here we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to over 8,000 human immu…