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Most Recent Articles: Genome Biology
Updated: 20 hours 39 min ago

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

Tue, 07/01/2020 - 5:30am
CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conse...
Categories: Bioinformatics Trends

Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis

Tue, 31/12/2019 - 5:30am
Tumor-reactive CD8+ tumor-infiltrating lymphocytes (TILs) represent a subtype of T cells that can recognize and destroy tumor specifically. Understanding the regulatory mechanism of tumor-reactive CD8+ T cells...
Categories: Bioinformatics Trends

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

Tue, 31/12/2019 - 5:30am
The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However,...
Categories: Bioinformatics Trends

mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity

Mon, 30/12/2019 - 5:30am
The RNA helicase eIF4A1 is a key component of the translation initiation machinery and is required for the translation of many pro-oncogenic mRNAs. There is increasing interest in targeting eIF4A1 therapeutica...
Categories: Bioinformatics Trends

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

Sat, 28/12/2019 - 5:30am
Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative...
Categories: Bioinformatics Trends

The somatic mutation landscape of the human body

Tue, 24/12/2019 - 5:30am
Somatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet they remain largely uncharacterized.
Categories: Bioinformatics Trends

A comparison framework and guideline of clustering methods for mass cytometry data

Mon, 23/12/2019 - 5:30am
With the expanding applications of mass cytometry in medical research, a wide variety of clustering methods, both semi-supervised and unsupervised, have been developed for data analysis. Selecting the optimal ...
Categories: Bioinformatics Trends

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Mon, 23/12/2019 - 5:30am
Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to technical factors, including the number of molecules detected in each cell, which can confound biological heterogeneity w...
Categories: Bioinformatics Trends

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model

Mon, 23/12/2019 - 5:30am
Single-cell RNA-Seq (scRNA-Seq) profiles gene expression of individual cells. Recent scRNA-Seq datasets have incorporated unique molecular identifiers (UMIs). Using negative controls, we show UMI counts follow...
Categories: Bioinformatics Trends

RADAR: differential analysis of MeRIP-seq data with a random effect model

Mon, 23/12/2019 - 5:30am
Epitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially...
Categories: Bioinformatics Trends

tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies

Mon, 23/12/2019 - 5:30am
Untangling the complex variations of microbiome associated with large-scale host phenotypes or environment types challenges the currently available analytic methods. Here, we present tmap, an integrative framewor...
Categories: Bioinformatics Trends

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

Fri, 20/12/2019 - 5:30am
We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell typ...
Categories: Bioinformatics Trends

Paragraph: a graph-based structural variant genotyper for short-read sequence data

Thu, 19/12/2019 - 5:30am
Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an a...
Categories: Bioinformatics Trends

Genotype-free demultiplexing of pooled single-cell RNA-seq

Thu, 19/12/2019 - 5:30am
A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We intr...
Categories: Bioinformatics Trends

What is the question?

Thu, 19/12/2019 - 5:30am
Categories: Bioinformatics Trends

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads

Wed, 18/12/2019 - 5:30am
Single-molecule long-read sequencing has been used to improve mRNA isoform identification. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and sequencing...
Categories: Bioinformatics Trends

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Wed, 18/12/2019 - 5:30am
Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogene...
Categories: Bioinformatics Trends

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Wed, 18/12/2019 - 5:30am
The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of so...
Categories: Bioinformatics Trends

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Wed, 18/12/2019 - 5:30am
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembl...
Categories: Bioinformatics Trends

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April 2020