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Analysis of endothelial-to-haematopoietic transition at the single cell level identifies cell cycle regulation as a driver of differentiation

Wed, 01/07/2020 - 5:30am
Haematopoietic stem cells (HSCs) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematop...
Categories: Bioinformatics Trends

Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data

Wed, 01/07/2020 - 5:30am
The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methyla...
Categories: Bioinformatics Trends

Computational inference of cancer-specific vulnerabilities in clinical samples

Mon, 29/06/2020 - 5:30am
Systematic in vitro loss-of-function screens provide valuable resources that can facilitate the discovery of drugs targeting cancer vulnerabilities.
Categories: Bioinformatics Trends

Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

Mon, 29/06/2020 - 5:30am
Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in norm...
Categories: Bioinformatics Trends

Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer

Wed, 24/06/2020 - 5:30am
Malignant transformation and progression of cancer are driven by the co-evolution of cancer cells and their dysregulated tumor microenvironment (TME). Recent studies on immunotherapy demonstrate the efficacy i...
Categories: Bioinformatics Trends

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients

Mon, 22/06/2020 - 5:30am
Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heteroge...
Categories: Bioinformatics Trends

Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study

Fri, 19/06/2020 - 5:30am
Despite the success and fast adaptation of deep learning models in biomedical domains, their lack of interpretability remains an issue. Here, we introduce Enhanced Integrated Gradients (EIG), a method to ident...
Categories: Bioinformatics Trends

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Thu, 18/06/2020 - 5:30am
Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of ...
Categories: Bioinformatics Trends

The two languages of science

Wed, 17/06/2020 - 5:30am
Categories: Bioinformatics Trends

KAML: improving genomic prediction accuracy of complex traits using machine learning determined parameters

Wed, 17/06/2020 - 5:30am
Advances in high-throughput sequencing technologies have reduced the cost of genotyping dramatically and led to genomic prediction being widely used in animal and plant breeding, and increasingly in human gene...
Categories: Bioinformatics Trends

Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

Wed, 17/06/2020 - 5:30am
At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fr...
Categories: Bioinformatics Trends

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis

Tue, 16/06/2020 - 5:30am
Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and ...
Categories: Bioinformatics Trends

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize

Tue, 16/06/2020 - 5:30am
Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of...
Categories: Bioinformatics Trends

Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life

Tue, 16/06/2020 - 5:30am
Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown.
Categories: Bioinformatics Trends

SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds

Tue, 16/06/2020 - 5:30am
We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deamina...
Categories: Bioinformatics Trends

Dynamic rewiring of the human interactome by interferon signaling

Mon, 15/06/2020 - 5:30am
The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulate...
Categories: Bioinformatics Trends

SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

Fri, 12/06/2020 - 5:30am
Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of da...
Categories: Bioinformatics Trends

Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

Tue, 09/06/2020 - 5:30am
Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely rema...
Categories: Bioinformatics Trends

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Mon, 08/06/2020 - 5:30am
Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been...
Categories: Bioinformatics Trends

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July 2020