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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: scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq
scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq Open
Bulk ATAC-seq assays have been used to map and profile the chromatin accessibility of regulatory elements such as enhancers, promoters, and insulators. This has provided great insight into the regulation of gene expression in many cell typ…
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: 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: Developing a computational high-resolution scATAC-seq platform to prioritize non-coding genetic variants
Developing a computational high-resolution scATAC-seq platform to prioritize non-coding genetic variants Open
A genome-wide association study (GWAS) is a standard approach for understanding the relationship between genetic variants and disease, resulting in a better understanding of disease mechanisms. However, despite the vast contribution of GWA…
View article: Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey
Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey Open
The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in comput…
View article: The Refractive Periscope – a Novel Concept
The Refractive Periscope – a Novel Concept Open
A periscope is an optical device whose function is to allow sighting of objects that are not in direct line of sight with the observer Eye/Screen/Detector. The concept behind the periscope is tilting the optical axis by breaking the rays o…
View article: Author Correction: Non-Invasive Imaging Through Scattering Medium by Using a Reverse Response Wavefront Shaping Technique
Author Correction: Non-Invasive Imaging Through Scattering Medium by Using a Reverse Response Wavefront Shaping Technique Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Image nonlinearity and non-uniformity corrections using Papoulis - Gerchberg algorithm in gamma imaging systems
Image nonlinearity and non-uniformity corrections using Papoulis - Gerchberg algorithm in gamma imaging systems Open
In this paper, the authors describe a novel technique for image nonlinearity and non-uniformity corrections in imaging systems based on gamma detectors. The limitation of the gamma detector prevents the producing of high quality images due…