Jump to Navigation
Subscribe to Genome Biology feed
Most Recent Articles: Genome Biology
Updated: 21 hours 16 min ago

When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data

Fri, 13/09/2019 - 5:30am
Considerable advances in genomics over the past decade have resulted in vast amounts of data being generated and deposited in global archives. The growth of these archives exceeds our ability to process their ...
Categories: Bioinformatics Trends

Quantitative MNase-seq accurately maps nucleosome occupancy levels

Fri, 13/09/2019 - 5:30am
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, its aggressive endo-/exo-nuclease activities make MNase-seq unreliable for determining nucleosome occupancies, because cleavages within ...
Categories: Bioinformatics Trends

The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance

Thu, 12/09/2019 - 5:30am
Robustness and evolutionary stability of gene expression in the human genome are established by an array of redundant enhancers.
Categories: Bioinformatics Trends

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

Tue, 10/09/2019 - 5:30am
Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the dive...
Categories: Bioinformatics Trends

A comparison of automatic cell identification methods for single-cell RNA sequencing data

Mon, 09/09/2019 - 5:30am
Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotati...
Categories: Bioinformatics Trends

scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data

Mon, 09/09/2019 - 5:30am
Technical variation in feature measurements, such as gene expression and locus accessibility, is a key challenge of large-scale single-cell genomic datasets. We show that this technical variation in both scRNA...
Categories: Bioinformatics Trends

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis

Mon, 09/09/2019 - 5:30am
We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cl...
Categories: Bioinformatics Trends

TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis

Wed, 04/09/2019 - 5:30am
In the analysis of high-throughput data from complex samples, cell composition is an important factor that needs to be accounted for. Except for a limited number of tissues with known pure cell type profiles, ...
Categories: Bioinformatics Trends

Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency

Tue, 03/09/2019 - 5:30am
Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and t...
Categories: Bioinformatics Trends

Correction to: Spatial chromatin architecture alteration by structural variations in human genomes at the population scale

Tue, 03/09/2019 - 5:30am
Following publication of the original article [1], it was noticed that the incorrect Fig. 2 and Fig. 3. were processed during production. It was also noticed that Fig. 4a was processed with a superfluous “1e7”...
Categories: Bioinformatics Trends

MITRE: inferring features from microbiota time-series data linked to host status

Mon, 02/09/2019 - 5:30am
Longitudinal studies are crucial for discovering causal relationships between the microbiome and human disease. We present MITRE, the Microbiome Interpretable Temporal Rule Engine, a supervised machine learnin...
Categories: Bioinformatics Trends

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

Mon, 02/09/2019 - 5:30am
Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing pat...
Categories: Bioinformatics Trends

Correction to: Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

Mon, 02/09/2019 - 5:30am
Following publication of the original article [1], the authors reported that Additional file 4, “Table S5. Parent-of-origin RNAseq dataset of 4 DAP INTACT-purified endosperm of Col × Ler reciprocal crosses” had t...
Categories: Bioinformatics Trends

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

Thu, 29/08/2019 - 5:30am
Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night.
Categories: Bioinformatics Trends

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types

Wed, 28/08/2019 - 5:30am
Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the ...
Categories: Bioinformatics Trends

Night science

Wed, 28/08/2019 - 5:30am
Categories: Bioinformatics Trends

The changing landscape of research funding: challenges for mid-career researchers

Wed, 28/08/2019 - 5:30am
Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...
Categories: Bioinformatics Trends

Funding research, a Chinese perspective

Wed, 28/08/2019 - 5:30am
Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...
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
 
September 2019