Erratum
Genome Biology 2017 18:154
Published on: 15 August 2017
The original article was published in Genome Biology 2017 18:7
Articles
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Research
Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance
Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characteriz...
Genome Biology 2017 18:153
Published on: 11 August 2017
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Method
A tandem simulation framework for predicting mapping quality
Read alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is ...
Genome Biology 2017 18:152
Published on: 10 August 2017
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Method
A statistical framework for analyzing deep mutational scanning data
Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error est...
Genome Biology 2017 18:150
Published on: 7 August 2017
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Method
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene leve...
Genome Biology 2017 18:151
Published on: 7 August 2017
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Research
Large scale genomic reorganization of topological domains at the HoxD locus
The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activat...
Genome Biology 2017 18:149
Published on: 7 August 2017
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Method
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTran...
Genome Biology 2017 18:148
Published on: 4 August 2017
The Erratum to this article has been published in Genome Biology 2017 18:160
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Meeting report
Searching for cancer vulnerabilities amid genetic chaos
A meeting report on the Third European Association for Cancer Research Conference on Cancer Genomics, held at Churchill College, Cambridge, UK, 25–28 June 2017.
Genome Biology 2017 18:147
Published on: 3 August 2017
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Research
An interaction map of circulating metabolites, immune gene networks, and their genetic regulation
Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic ...
Genome Biology 2017 18:146
Published on: 1 August 2017
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Research Highlight
Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation
Using a powerful machine learning approach, a recent study of human genomes has revealed widespread footprints of recent positive selection on standing genetic variation.
Genome Biology 2017 18:139
Published on: 1 August 2017
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Research
The three-dimensional genome organization of Drosophila melanogaster through data integration
Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate a...
Genome Biology 2017 18:145
Published on: 31 July 2017
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Research
A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)-creating mutation
Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations as...
Genome Biology 2017 18:144
Published on: 28 July 2017
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Research
Population and allelic variation of A-to-I RNA editing in human transcriptomes
A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism f...
Genome Biology 2017 18:143
Published on: 28 July 2017
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Method
ReMixT: clone-specific genomic structure estimation in cancer
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
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Research
Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis
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
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Method
Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network
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
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Method
MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics
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
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Research
Characterization of background noise in capture-based targeted sequencing data
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
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Research
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
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
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Research
Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice
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
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Research Highlight
Understanding the genetics behind complex human disease with large-scale iPSC collections
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
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Research
Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding
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
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Meeting report
Canonical mRNA is the exception, rather than the rule
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
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Research
MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity
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
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Editorial
Genome Biology 2017 18:132
Published on: 6 July 2017
