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The interplay of demography and selection during maize domestication and expansion

Mon, 13/11/2017 - 5:30am
The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay be...
Categories: Bioinformatics Trends

Correction to: Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

Wed, 08/11/2017 - 5:30am
Upon publication of the original article [1], it was noted that references 11 and 22 were miscited in the reference list.
Categories: Bioinformatics Trends

Depletion of somatic mutations in splicing-associated sequences in cancer genomes

Tue, 07/11/2017 - 5:30am
An important goal of cancer genomics is to identify systematically cancer-causing mutations. A common approach is to identify sites with high ratios of non-synonymous to synonymous mutations; however, if synon...
Categories: Bioinformatics Trends

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq

Tue, 07/11/2017 - 5:30am
Single-cell RNA-sequencing (scRNA-seq) allows studying heterogeneity in gene expression in large cell populations. Such heterogeneity can arise due to technical or biological factors, making decomposing source...
Categories: Bioinformatics Trends

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

Wed, 01/11/2017 - 5:30am
Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-r...
Categories: Bioinformatics Trends

The influence of microRNAs and poly(A) tail length on endogenous mRNA–protein complexes

Tue, 31/10/2017 - 5:30am
All mRNAs are bound in vivo by proteins to form mRNA–protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, ...
Categories: Bioinformatics Trends

Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7

Tue, 31/10/2017 - 5:30am
Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding land...
Categories: Bioinformatics Trends

Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation

Tue, 31/10/2017 - 5:30am
Polycomb Repressive Complexes 2 (PRC2) are multi-protein chromatin modifiers that are evolutionarily conserved among eukaryotes and play key roles in the regulation of gene expression, notably through the trim...
Categories: Bioinformatics Trends

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Mon, 30/10/2017 - 5:30am
Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of protein variants or to the regulation of gene expression via nonsense-mediated messenger RNA (mRNA) dec...
Categories: Bioinformatics Trends

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses

Fri, 27/10/2017 - 5:30am
Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5′ cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with indi...
Categories: Bioinformatics Trends

The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element

Fri, 27/10/2017 - 5:30am
It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long non-coding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and s...
Categories: Bioinformatics Trends

scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing

Fri, 27/10/2017 - 5:30am
The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method, scDual-Seq, that simultaneously...
Categories: Bioinformatics Trends

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

Thu, 26/10/2017 - 5:30am
Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning a...
Categories: Bioinformatics Trends

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Tue, 24/10/2017 - 5:30am
Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted fr...
Categories: Bioinformatics Trends

Epitranscriptomic influences on development and disease

Mon, 23/10/2017 - 5:30am
RNA contains over 150 types of chemical modifications. Although many of these chemical modifications were discovered several decades ago, their functions were not immediately apparent. Discoveries of RNA demet...
Categories: Bioinformatics Trends

Systematic identification of regulatory variants associated with cancer risk

Mon, 23/10/2017 - 5:30am
Most cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically...
Categories: Bioinformatics Trends

Editing inducer elements increases A-to-I editing efficiency in the mammalian transcriptome

Mon, 23/10/2017 - 5:30am
Adenosine to inosine (A-to-I) RNA editing has been shown to be an essential event that plays a significant role in neuronal function, as well as innate immunity, in mammals. It requires a structure that is lar...
Categories: Bioinformatics Trends

Promoting RNA editing by ADAR attraction

Mon, 23/10/2017 - 5:30am
Concentration is important and not only while driving; a new study indicates how an adjacent genomic element helps to increase the efficiency of a specific adenosine to inosine RNA editing reaction, by providi...
Categories: Bioinformatics Trends

Evidence of reduced recombination rate in human regulatory domains

Fri, 20/10/2017 - 5:30am
Recombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, ...
Categories: Bioinformatics Trends

Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage

Fri, 06/10/2017 - 5:30am
The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of...
Categories: Bioinformatics Trends

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