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Most Recent Articles: Genome Biology
Updated: 20 hours 58 min ago

Lamina-associated domains: peripheral matters and internal affairs

Thu, 02/04/2020 - 5:30am
At the nuclear periphery, associations of chromatin with the nuclear lamina through lamina-associated domains (LADs) aid functional organization of the genome. We review the organization of LADs and provide ev...
Categories: Bioinformatics Trends

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

Thu, 02/04/2020 - 5:30am
We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples. TADsplimer recaptures splits and m...
Categories: Bioinformatics Trends

Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome

Wed, 01/04/2020 - 5:30am
Epigenetic modifications, including DNA methylation, play an important role in gene silencing and genome stability. Consequently, epigenetic dysregulation can cause several diseases, such as cancer, obesity, d...
Categories: Bioinformatics Trends

CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma

Tue, 31/03/2020 - 5:30am
Long non-coding RNAs (lncRNAs) exhibit highly cell type-specific expression and function, making this class of transcript attractive for targeted cancer therapy. However, the vast majority of lncRNAs have not ...
Categories: Bioinformatics Trends

Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

Mon, 30/03/2020 - 5:30am
Recent efforts to describe the human epigenome have yielded thousands of epigenomic and transcriptomic datasets. However, due primarily to cost, the total number of such assays that can be performed is limited...
Categories: Bioinformatics Trends

Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

Mon, 30/03/2020 - 5:30am
The human epigenome has been experimentally characterized by thousands of measurements for every basepair in the human genome. We propose a deep neural network tensor factorization method, Avocado, that compre...
Categories: Bioinformatics Trends

Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts

Thu, 26/03/2020 - 5:30am
Osteoporosis is a complex disease with a strong genetic contribution. A recently published genome-wide association study (GWAS) for estimated bone mineral density (eBMD) identified 1103 independent genome-wide...
Categories: Bioinformatics Trends

DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure

Thu, 26/03/2020 - 5:30am
Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insu...
Categories: Bioinformatics Trends

Diverse genetic mechanisms underlie worldwide convergent rice feralization

Thu, 26/03/2020 - 5:30am
Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies worldwide and aggressively outcompetes cultivated varietie...
Categories: Bioinformatics Trends

A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing

Wed, 25/03/2020 - 5:30am
AsCas12a and LbCas12a nucleases are reported to be promising tools for genome engineering with protospacer adjacent motif (PAM) TTTV as the optimal. However, the C-containing PAM (CTTV, TCTV, TTCV, etc.) recog...
Categories: Bioinformatics Trends

High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

Tue, 24/03/2020 - 5:30am
DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromat...
Categories: Bioinformatics Trends

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection

Mon, 23/03/2020 - 5:30am
CTCF is a key insulator-binding protein, and mammalian genomes contain numerous CTCF sites, many of which are organized in tandem.
Categories: Bioinformatics Trends

Obstacles to detecting isoforms using full-length scRNA-seq data

Mon, 23/03/2020 - 5:30am
Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk R...
Categories: Bioinformatics Trends

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

Mon, 23/03/2020 - 5:30am
The three-dimensional conformation of a genome can be profiled using Hi-C, a technique that combines chromatin conformation capture with high-throughput sequencing. However, structural variations often yield f...
Categories: Bioinformatics Trends

Decode-seq: a practical approach to improve differential gene expression analysis

Mon, 23/03/2020 - 5:30am
Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of ...
Categories: Bioinformatics Trends

VALOR2: characterization of large-scale structural variants using linked-reads

Thu, 19/03/2020 - 5:30am
Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic...
Categories: Bioinformatics Trends

Benchmarking of computational error-correction methods for next-generation sequencing data

Tue, 17/03/2020 - 5:30am
Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors pres...
Categories: Bioinformatics Trends

BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty

Mon, 16/03/2020 - 5:30am
Alternative splicing is a biological process during gene expression that allows a single gene to code for multiple proteins. However, splicing patterns can be altered in some conditions or diseases. Here, we p...
Categories: Bioinformatics Trends

Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing

Sat, 14/03/2020 - 5:30am
Hybrid genome assembly has emerged as an important technique in bacterial genomics, but cost and labor requirements limit large-scale application. We present Ultraplexing, a method to improve per-sample sequen...
Categories: Bioinformatics Trends



April 2020