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ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

Mon, 24/02/2020 - 5:30am
Recently, several non-classical functions of histone modification regulators (HMRs), independent of their known histone modification substrates and products, have been reported to be essential for specific cel...
Categories: Bioinformatics Trends

Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads

Mon, 24/02/2020 - 5:30am
Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited ...
Categories: Bioinformatics Trends

Author Correction: 547 transcriptomes from 44 brain areas reveal features of the aging brain in non-human primates

Mon, 24/02/2020 - 5:30am
Following publication of the original paper [1], the authors reported an error in the affiliation of Xin-Tian Hu, who is also affiliated with “Kunming Primate Research Center, Kunming Institute of Zoology, Chi...
Categories: Bioinformatics Trends

Histone H3K27 acetylation is dispensable for enhancer activity in mouse embryonic stem cells

Fri, 21/02/2020 - 5:30am
H3K27ac is well recognized as a marker for active enhancers and a great indicator of enhancer activity. However, its functional impact on transcription has not been characterized. By substituting lysine 27 in ...
Categories: Bioinformatics Trends

Comprehensive assessment of computational algorithms in predicting cancer driver mutations

Thu, 20/02/2020 - 5:30am
The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations...
Categories: Bioinformatics Trends

A framework for transcriptome-wide association studies in breast cancer in diverse study populations

Thu, 20/02/2020 - 5:30am
The relationship between germline genetic variation and breast cancer survival is largely unknown, especially in understudied minority populations who often have poorer survival. Genome-wide association studie...
Categories: Bioinformatics Trends

Author Correction: Interaction between the microbiome and TP53 in human lung cancer

Thu, 20/02/2020 - 5:30am
Following publication of the original paper [1], the authors submitted a new Additional file 5 to replace the one containing formatting issues. The updated Additional file 5 is published in this correction.
Categories: Bioinformatics Trends

Publisher Correction: Host-associated microbiomes are predicted by immune system complexity and climate

Thu, 20/02/2020 - 5:30am
Following publication of the original paper [1], it was reported that an error in the processing of Fig. 8 occurred. In the online HTML version of the article, Fig. 8 was presented as a duplication of Fig. 7. ...
Categories: Bioinformatics Trends

Protein velocity and acceleration from single-cell multiomics experiments

Tue, 18/02/2020 - 5:30am
The simultaneous quantification of protein and RNA makes possible the inference of past, present, and future cell states from single experimental snapshots. To enable such temporal analysis from multimodal sin...
Categories: Bioinformatics Trends

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Fri, 14/02/2020 - 5:30am
Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian s...
Categories: Bioinformatics Trends

Mutational signatures: experimental design and analytical framework

Fri, 14/02/2020 - 5:30am
Mutational signatures provide a powerful alternative for understanding the pathophysiology of cancer. Currently, experimental efforts aimed at validating and understanding the etiologies of cancer-derived muta...
Categories: Bioinformatics Trends

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

Wed, 12/02/2020 - 5:30am
Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle poss...
Categories: Bioinformatics Trends

Genotyping structural variants in pangenome graphs using the vg toolkit

Wed, 12/02/2020 - 5:30am
Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide a...
Categories: Bioinformatics Trends

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Wed, 12/02/2020 - 5:30am
Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty aci...
Categories: Bioinformatics Trends

A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells

Mon, 10/02/2020 - 5:30am
Quiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcript...
Categories: Bioinformatics Trends

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

Fri, 07/02/2020 - 5:30am
We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP...
Categories: Bioinformatics Trends

Opportunities and challenges in long-read sequencing data analysis

Fri, 07/02/2020 - 5:30am
Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long...
Categories: Bioinformatics Trends

Admixture-enabled selection for rapid adaptive evolution in the Americas

Fri, 07/02/2020 - 5:30am
Admixture occurs when previously isolated populations come together and exchange genetic material. We hypothesize that admixture can enable rapid adaptive evolution in human populations by introducing novel ge...
Categories: Bioinformatics Trends

Publisher Correction: Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Fri, 07/02/2020 - 5:30am
Following publication of the original paper [1], an error was reported in the processing of Fig. 2. The correct Fig. 2 is supplied below and the original article [1] has been corrected. The publishers apologiz...
Categories: Bioinformatics Trends

Systematic functional identification of cancer multi-drug resistance genes

Fri, 07/02/2020 - 5:30am
Drug resistance is a major obstacle in cancer therapy. To elucidate the genetic factors that regulate sensitivity to anti-cancer drugs, we performed CRISPR-Cas9 knockout screens for resistance to a spectrum of...
Categories: Bioinformatics Trends

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February 2020