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Research
One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classif...
Genome Biology 2017 18:182
Published on: 21 September 2017
Method
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin ...
Genome Biology 2017 18:181
Published on: 21 September 2017
Research
The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA poly...
Genome Biology 2017 18:180
Published on: 20 September 2017
Method
Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infin...
Genome Biology 2017 18:178
Published on: 19 September 2017
Research Highlight
Inheritance of DNA methylation states from gametes determines genomic imprinting in mammals. A new study shows that repressive chromatin in oocytes can also confer imprinting.
Genome Biology 2017 18:177
Published on: 19 September 2017
Research
DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global pa...
Genome Biology 2017 18:176
Published on: 18 September 2017
Research
Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming ...
Genome Biology 2017 18:171
Published on: 15 September 2017
Research
Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of input...
Genome Biology 2017 18:172
Published on: 15 September 2017
Research
Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases.
Genome Biology 2017 18:170
Published on: 14 September 2017
Open Letter
Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. We show that this information is essential to...
Genome Biology 2017 18:175
Published on: 14 September 2017
Method
As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current...
Genome Biology 2017 18:174
Published on: 12 September 2017
Editorial
Genome Biology 2017 18:173
Published on: 12 September 2017
Method
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-...
Genome Biology 2017 18:169
Published on: 8 September 2017
Research
The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the divers...
Genome Biology 2017 18:167
Published on: 6 September 2017
Research Highlight
Genome Biology 2017 18:168
Published on: 6 September 2017
Research
Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most i...
Genome Biology 2017 18:166
Published on: 5 September 2017
Software
Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cell...
Genome Biology 2017 18:164
Published on: 4 September 2017
Research
Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4+ T cells. Linking such regulatory regions to gene promoters in disease-relevant cell context...
Genome Biology 2017 18:165
Published on: 4 September 2017
Research
Whole-genome bisulfite sequencing (WGBS) is the gold standard for studying landscape DNA methylation. Current computational methods for WGBS are mainly designed for gene regulatory regions with multiple under-...
Genome Biology 2017 18:163
Published on: 31 August 2017
Research
Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential sourc...
Genome Biology 2017 18:162
Published on: 30 August 2017
Research
Soybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both corr...
Genome Biology 2017 18:161
Published on: 24 August 2017
Research Highlight
New methods for simultaneously quantifying protein and gene expression at the single-cell level have the power to identify cell types and to classify cell populations.
Genome Biology 2017 18:159
Published on: 24 August 2017
Erratum
Genome Biology 2017 18:160
Published on: 24 August 2017
The original article was published in Genome Biology 2017 18:148
Research
As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. Ho...
Genome Biology 2017 18:158
Published on: 23 August 2017
Research
The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation...
Genome Biology 2017 18:157
Published on: 22 August 2017
