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Updated: 21 hours 37 min ago

CHOP: haplotype-aware path indexing in population graphs

Wed, 11/03/2020 - 5:30am
The practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of in...
Categories: Bioinformatics Trends

Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium

Wed, 11/03/2020 - 5:30am
How intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly und...
Categories: Bioinformatics Trends

High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life

Mon, 09/03/2020 - 5:30am
mRNA can form local secondary structure within the protein-coding sequence, and the strength of this structure is thought to influence gene expression regulation. Previous studies suggest that secondary struct...
Categories: Bioinformatics Trends

A benchmark of algorithms for the analysis of pooled CRISPR screens

Mon, 09/03/2020 - 5:30am
Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guid...
Categories: Bioinformatics Trends

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons

Mon, 09/03/2020 - 5:30am
Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson’s disease (PD), but its molecular determinants are unknown. Here, we ident...
Categories: Bioinformatics Trends

The genome evolution and domestication of tropical fruit mango

Fri, 06/03/2020 - 5:30am
Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other g...
Categories: Bioinformatics Trends

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9

Thu, 05/03/2020 - 5:30am
The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinyl...
Categories: Bioinformatics Trends

WhatsGNU: a tool for identifying proteomic novelty

Thu, 05/03/2020 - 5:30am
To understand diversity in enormous collections of genome sequences, we need computationally scalable tools that can quickly contextualize individual genomes based on their similarities and identify features o...
Categories: Bioinformatics Trends

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Thu, 05/03/2020 - 5:30am
Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s n...
Categories: Bioinformatics Trends

NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing

Tue, 03/03/2020 - 5:30am
The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are sti...
Categories: Bioinformatics Trends

Longitudinal survey of microbiome associated with particulate matter in a megacity

Tue, 03/03/2020 - 5:30am
While the physical and chemical properties of airborne particulate matter (PM) have been extensively studied, their associated microbiome remains largely unexplored. Here, we performed a longitudinal metagenom...
Categories: Bioinformatics Trends

Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS

Tue, 03/03/2020 - 5:30am
We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. Compati...
Categories: Bioinformatics Trends

gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection

Mon, 02/03/2020 - 5:30am
Pooled CRISPR screens are a powerful tool to probe genotype-phenotype relationships at genome-wide scale. However, criteria for optimal design are missing, and it remains unclear how experimental parameters af...
Categories: Bioinformatics Trends

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility

Thu, 27/02/2020 - 5:30am
Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contr...
Categories: Bioinformatics Trends

A rare codon-based translational program of cell proliferation

Thu, 27/02/2020 - 5:30am
The speed of translation elongation is primarily determined by the abundance of tRNAs. Thus, the codon usage influences the rate with which individual mRNAs are translated. As the nature of tRNA pools and modi...
Categories: Bioinformatics Trends

Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides

Wed, 26/02/2020 - 5:30am
CRISPR-Cas9 has been developed as a therapeutic agent for various infectious and genetic diseases. In many clinically relevant applications, constitutively active CRISPR-Cas9 is delivered into human cells with...
Categories: Bioinformatics Trends

Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Tue, 25/02/2020 - 5:30am
Following publication of the original paper [1], an error was reported in the third paragraph in the section “Analysis of GMB composition and its correlates” (page 3 of the PDF). The first sentence of the text sh...
Categories: Bioinformatics Trends

Linked optical and gene expression profiling of single cells at high-throughput

Mon, 24/02/2020 - 5:30am
Single-cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through changes in gene expression. Linking sequencing with optical analys...
Categories: Bioinformatics Trends

ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

Mon, 24/02/2020 - 5:30am
Recently, several non-classical functions of histone modification regulators (HMRs), independent of their known histone modification substrates and products, have been reported to be essential for specific cel...
Categories: Bioinformatics Trends

Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads

Mon, 24/02/2020 - 5:30am
Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited ...
Categories: Bioinformatics Trends

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