Jump to Navigation
Subscribe to Genome Biology feed
Most Recent Articles: Genome Biology
Updated: 19 hours 55 min ago

scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles

Mon, 03/02/2020 - 5:30am
Simultaneous measurements of transcriptomic and epigenomic profiles in the same individual cells provide an unprecedented opportunity to understand cell fates. However, effective approaches for the integrative...
Categories: Bioinformatics Trends

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Mon, 03/02/2020 - 5:30am
Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques,...
Categories: Bioinformatics Trends

Host-associated microbiomes are predicted by immune system complexity and climate

Mon, 03/02/2020 - 5:30am
Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolis...
Categories: Bioinformatics Trends

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis

Mon, 03/02/2020 - 5:30am
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the m...
Categories: Bioinformatics Trends

The Deep Genome Project

Mon, 03/02/2020 - 5:30am
Categories: Bioinformatics Trends

CUBIC: an atlas of genetic architecture promises directed maize improvement

Fri, 24/01/2020 - 5:30am
Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we presen...
Categories: Bioinformatics Trends

scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens

Fri, 24/01/2020 - 5:30am
We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. sc...
Categories: Bioinformatics Trends

Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Fri, 24/01/2020 - 5:30am
Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF...
Categories: Bioinformatics Trends

Gene content evolution in the arthropods

Thu, 23/01/2020 - 5:30am
Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recor...
Categories: Bioinformatics Trends

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

Wed, 22/01/2020 - 5:30am
Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes.
Categories: Bioinformatics Trends

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing

Mon, 20/01/2020 - 5:30am
Principal component analysis (PCA) is an essential method for analyzing single-cell RNA-seq (scRNA-seq) datasets, but for large-scale scRNA-seq datasets, computation time is long and consumes large amounts of ...
Categories: Bioinformatics Trends

Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads

Fri, 17/01/2020 - 5:30am
The error-prone third-generation sequencing (TGS) long reads can be corrected by the high-quality second-generation sequencing (SGS) short reads, which is referred to as hybrid error correction. We here invest...
Categories: Bioinformatics Trends

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Fri, 17/01/2020 - 5:30am
Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is hig...
Categories: Bioinformatics Trends

Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes

Fri, 17/01/2020 - 5:30am
RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, w...
Categories: Bioinformatics Trends

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells

Thu, 16/01/2020 - 5:30am
Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions play important roles in condensing super-enhancer regions into a ...
Categories: Bioinformatics Trends

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

Thu, 16/01/2020 - 5:30am
Large-scale single-cell transcriptomic datasets generated using different technologies contain batch-specific systematic variations that present a challenge to batch-effect removal and data integration. With c...
Categories: Bioinformatics Trends

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

Tue, 14/01/2020 - 5:30am
Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C’s resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces...
Categories: Bioinformatics Trends

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

Tue, 14/01/2020 - 5:30am
Although scRNA-seq is now ubiquitously adopted in studies of intratumor heterogeneity, detection of somatic mutations and inference of clonal membership from scRNA-seq is currently unreliable. We propose DENDR...
Categories: Bioinformatics Trends

Chromatin interactome mapping at 139 independent breast cancer risk signals

Tue, 07/01/2020 - 5:30am
Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elem...
Categories: Bioinformatics Trends

Non-coding RNAs underlie genetic predisposition to breast cancer

Tue, 07/01/2020 - 5:30am
Genetic variants identified through genome-wide association studies (GWAS) are predominantly non-coding and typically attributed to altered regulatory elements such as enhancers and promoters. However, the con...
Categories: Bioinformatics Trends

Pages

Calendar

Mon
Tue
Wed
Thu
Fri
Sat
Sun
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
 
April 2020