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| Open AccessPoor sleep and shift work associate with increased blood pressure and inflammation in UK Biobank participants
Circadian disruption is linked to increased blood pressure and heart disease risk. Here, the authors show a positive association between circadian disruption and blood pressure (SBP/DBP) regulation in males and females irrespective of age, weight and inflammatory status.
- Monica Kanki
- , Artika P. Nath
- & Morag J. Young
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| Open AccessSimulation of undiagnosed patients with novel genetic conditions
Rare Mendelian disorders pose a major diagnostic challenge, but evaluation of automated tools that aim to uncover causal genes tools is limited. Here, the authors present a computational pipeline that simulates realistic clinical datasets to address this deficit.
- Emily Alsentzer
- , Samuel G. Finlayson
- & Isaac S. Kohane
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Article
| Open AccessExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species
RNA-sequencing data analysis is difficult for non-model species that have no reference genome. ExpressAnalyst enables RNA-sequencing analysis for any eukaryotic species in less than 24 h, on a laptop, and without any programming.
- Peng Liu
- , Jessica Ewald
- & Jianguo Xia
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Article
| Open AccessBladder cancer organoids as a functional system to model different disease stages and therapy response
Bladder cancer heterogeneity can limit treatment efficacy in individual patients. Here, the authors use patient derived organoids to develop a drug screening pipeline and identify markers of treatment response.
- Martina Minoli
- , Thomas Cantore
- & Marianna Kruithof-de Julio
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| Open AccessSex differences in allometry for phenotypic traits in mice indicate that females are not scaled males
Research aimed at improving healthcare has largely focused on male animals and cells. Here, the authors use data from the International Mouse Phenotyping Consortium to show that body weight does not account for all phenotypic differences between male and female mice, supporting more female-focused research.
- Laura A. B. Wilson
- , Susanne R. K. Zajitschek
- & Shinichi Nakagawa
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Article
| Open AccessTranscriptomic architecture of nuclei in the marmoset CNS
Studies of cell heterogeneity in white matter in primates have been limited to date. Here the authors describe a marmoset brain cell atlas that bridges rodent and human data, revealing strong gray-white matter glial segregation.
- Jing-Ping Lin
- , Hannah M. Kelly
- & Daniel S. Reich
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Article
| Open AccessChIP-Hub provides an integrative platform for exploring plant regulome
A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.
- Liang-Yu Fu
- , Tao Zhu
- & Dijun Chen
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Article
| Open AccessThe 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
This paper describes the ‘4DN Data Portal’ that hosts data generated by the 4D Nucleome network, including Hi-C and other chromatin conformation capture assays, as well as various sequencing-based and imaging-based assays. Raw data have been uniformly processed to increase comparability and the portal is implemented with visualization tools to browse the data without download.
- Sarah B. Reiff
- , Andrew J. Schroeder
- & Peter J. Park
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| Open AccessKnowledge integration and decision support for accelerated discovery of antibiotic resistance genes
Here the authors present KIDS, a knowledge graph integration and phenotypic prediction framework. When applied on antibiotic data, it identifies 6 novel antibiotic resistant E. coli genes that the authors subsequently validate.
- Jason Youn
- , Navneet Rai
- & Ilias Tagkopoulos
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| Open AccessMultilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation
Ensuring international benefit-sharing from sequence data without jeopardising open sharing is a major obstacle for the Convention on Biological Diversity and other UN negotiations. Here, the authors propose a solution to address the concerns of both developing countries and life scientists.
- Amber Hartman Scholz
- , Jens Freitag
- & Jörg Overmann
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Article
| Open AccessThe molecular basis, genetic control and pleiotropic effects of local gene co-expression
Local gene co-expression is found throughout the genome, but systematic analysis of these co-expressed genes is needed. Here, the authors identify local co-expressed genes in 49 tissues and characterize the genetic variants which may affect their expression and contribute to disease.
- Diogo M. Ribeiro
- , Simone Rubinacci
- & Olivier Delaneau
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Article
| Open AccessLandscape of allele-specific transcription factor binding in the human genome
Single-nucleotide variants in enhancers or promoters may affect gene transcription by altering transcription factor binding sites. Here the authors present a meta-analysis empowered by a new statistical method covering thousands of ChIP-Seq experiments resulting in the identification of more than 500 thousand allele-specific binding (ASB) events in the human genome.
- Sergey Abramov
- , Alexandr Boytsov
- & Ivan V. Kulakovskiy
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Article
| Open AccessRetrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.
- Matthew H. Bailey
- , William U. Meyerson
- & Christian von Mering
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| Open AccessDifferent scaling of linear models and deep learning in UKBiobank brain images versus machine-learning datasets
Schulz et al. systematically benchmark performance scaling with increasingly sophisticated prediction algorithms and with increasing sample size in reference machine-learning and biomedical datasets. Complicated nonlinear intervariable relationships remain largely inaccessible for predicting key phenotypes from typical brain scans.
- Marc-Andre Schulz
- , B. T. Thomas Yeo
- & Danilo Bzdok
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| Open AccessA machine-compiled database of genome-wide association studies
Most databases of genotype-phenotype associations are manually curated. Here, Kuleshov et al. describe a machine curation system that extracts such relationships from the GWAS literature and synthesizes them into a structured knowledge base called GWASkb that can complement manually curated databases.
- Volodymyr Kuleshov
- , Jialin Ding
- & Michael Snyder
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| Open AccessFDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
To be able to use infectious disease next generation sequencing as a diagnostic tool, appropriate reference datasets are required. Here, Sichtig et al. describe FDA-ARGOS, a reference database for high-quality microbial reference genomes, and demonstrate its utility on the example of two use cases.
- Heike Sichtig
- , Timothy Minogue
- & Uwe Scherf
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Article
| Open AccessCapturing variation impact on molecular interactions in the IMEx Consortium mutations data set
Genetic variants might exert their functional effects via influencing molecular interaction. Here, the authors present a resource featuring almost 28,000 annotations describing the effect of small sequence changes on physical protein interactions, curated by IMEx Consortium curators.
- J. Khadake
- , B. Meldal
- & P. Porras
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Article
| Open AccessA reference haplotype panel for genome-wide imputation of short tandem repeats
Short-tandem repeats (STR), similar to single nucleotide polymorphisms (SNP), contribute to complex traits, but their ascertainment by next-generation sequencing is costly. Here, Saini et al. provide a SNP+STR haplotype reference panel that allows imputation of STRs from SNP array data.
- Shubham Saini
- , Ileena Mitra
- & Melissa Gymrek
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| Open AccessInformation recovery from low coverage whole-genome bisulfite sequencing
Here, Libertini and colleagues devise a computation tool that can analyze whole-genome bisulfite sequencing (WGBS) data to recover of ∼30% of the lost differential methylation position information. They use COMETgazer and COMETvintage to analyze 13 diffferent methylome data to demonstrate their performance.
- Emanuele Libertini
- , Simon C. Heath
- & Stephan Beck