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Method
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation ch...
Genome Biology 2017 18:141
Published on: 27 July 2017
Research
The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence show...
Genome Biology 2017 18:142
Published on: 27 July 2017
Method
Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequen...
Genome Biology 2017 18:140
Published on: 27 July 2017
Method
Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of singl...
Genome Biology 2017 18:138
Published on: 24 July 2017
Research
While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...
Genome Biology 2017 18:137
Published on: 21 July 2017
Research
Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are charact...
Genome Biology 2017 18:136
Published on: 21 July 2017
Research Highlight
Three recent studies analyzing large-scale collections of human induced pluripotent stem cell lines provide valuable insight into how genetic regulatory variation affects cellular and molecular traits.
Genome Biology 2017 18:135
Published on: 20 July 2017
Research
The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the eme...
Genome Biology 2017 18:130
Published on: 20 July 2017
Meeting report
A report on the Second Aegean International Conference on the Long and the Short of Non-Coding RNAs, held in Heraklion, Greece, 9–14 June 2017.
Genome Biology 2017 18:133
Published on: 7 July 2017
Research
Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanism...
Genome Biology 2017 18:134
Published on: 7 July 2017
Editorial
Genome Biology 2017 18:132
Published on: 6 July 2017
Research
Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we ...
Genome Biology 2017 18:131
Published on: 6 July 2017
Correspondence
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...
Genome Biology 2017 18:128
Published on: 5 July 2017
Correspondence
Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Bio...
Genome Biology 2017 18:129
Published on: 5 July 2017
Correspondence
Genome Biology 2017 18:127
Published on: 5 July 2017
Research
The mapping resolution of genome-wide association studies (GWAS) is limited by historic recombination events and effects are often assigned to haplotype blocks rather than individual SNPs. It is not clear how ...
Genome Biology 2017 18:126
Published on: 3 July 2017
Method
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell...
Genome Biology 2017 18:122
Published on: 28 June 2017
Review
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA ...
Genome Biology 2017 18:124
Published on: 27 June 2017
Method
Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity in transcription, but the limitations of the technology have prevented its application to dissect variability in RNA proces...
Genome Biology 2017 18:123
Published on: 27 June 2017
Method
Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, i...
Genome Biology 2017 18:125
Published on: 27 June 2017
Research
Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere posit...
Genome Biology 2017 18:121
Published on: 21 June 2017
Research Highlight
A distinct chromatin mark, H3K36me3, has been found to engage in temperature-dependent alternative splicing and ambient temperature-dependent flowering-time control in Arabidopsis.
Genome Biology 2017 18:119
Published on: 19 June 2017
Research Highlight
Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication a...
Genome Biology 2017 18:117
Published on: 19 June 2017
Research Highlight
Fine-mapping to identify causal variants in genome-wide association studies remains challenging. A recent study provides guidance for future research.
Genome Biology 2017 18:118
Published on: 19 June 2017
Review
Studies on genetic–epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in ...
Genome Biology 2017 18:120
Published on: 19 June 2017
Impact Factor: 11.908
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