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Precise genome-wide mapping of single nucleosomes and linkers in vivo

Fri, 09/02/2018 - 5:30am
We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our ...
Categories: Bioinformatics Trends

Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys

Thu, 08/02/2018 - 5:30am
Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large ...
Categories: Bioinformatics Trends

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

Wed, 07/02/2018 - 5:30am
Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching ap...
Categories: Bioinformatics Trends

Correction to: A statistical framework for analyzing deep mutational scanning data

Wed, 07/02/2018 - 5:30am
After publication of our article [1] it was brought to our attention that a line of code was missing from our program to combine the within-replicate variance and between-replicate variance. This led to an ove...
Categories: Bioinformatics Trends

Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale

Tue, 06/02/2018 - 5:30am
Accurately selecting relevant alleles in large sequencing experiments remains technically challenging. Bystro (https://bystro.io/) is the first online, cloud...
Categories: Bioinformatics Trends

SCANPY: large-scale single-cell gene expression data analysis

Tue, 06/02/2018 - 5:30am
Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing,...
Categories: Bioinformatics Trends

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Wed, 31/01/2018 - 5:30am
On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challe...
Categories: Bioinformatics Trends

Focus on African diversity confirms complexity of skin pigmentation genetics

Wed, 31/01/2018 - 5:30am
Renewed focus on African populations confirms the complexity of skin pigmentation genetics, and suggests future directions for pigmentation research.
Categories: Bioinformatics Trends

A panoramic view of RNA modifications: exploring new frontiers

Tue, 30/01/2018 - 5:30am
Meeting report on the Cold Spring Harbor Asia conference on RNA Modifications and Epitranscriptomics, held in Suzhou, China, 13–17 November, 2017.
Categories: Bioinformatics Trends

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

Mon, 29/01/2018 - 5:30am
Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protec...
Categories: Bioinformatics Trends

Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha

Thu, 25/01/2018 - 5:30am
In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur d...
Categories: Bioinformatics Trends

Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline

Wed, 24/01/2018 - 5:30am
The 3′ untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produce...
Categories: Bioinformatics Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

Tue, 23/01/2018 - 5:30am
The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli throu...
Categories: Bioinformatics Trends

SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells

Fri, 19/01/2018 - 5:30am
Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential fo...
Categories: Bioinformatics Trends

FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations

Wed, 17/01/2018 - 5:30am
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate ...
Categories: Bioinformatics Trends

Antisense suppression of the nonsense mediated decay factor Upf3b as a potential treatment for diseases caused by nonsense mutations

Mon, 15/01/2018 - 5:30am
About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncate...
Categories: Bioinformatics Trends

Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells

Mon, 15/01/2018 - 5:30am
Canonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mammalian epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well chara...
Categories: Bioinformatics Trends

RNA virus interference via CRISPR/Cas13a system in plants

Thu, 04/01/2018 - 5:30am
CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleav...
Categories: Bioinformatics Trends

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

Thu, 28/12/2017 - 5:30am
The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the...
Categories: Bioinformatics Trends

Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers

Thu, 28/12/2017 - 5:30am
Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhanc...
Categories: Bioinformatics Trends

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February 2018