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| Open AccessBayesian association scan reveals loci associated with human lifespan and linked biomarkers
Along with various environmental factors, a complex genetic architecture influences human lifespan. Here, McDaid and colleagues reveal novel loci associated with human lifespan and linked biomarkers by Bayesian association scan.
- Aaron F. McDaid
- , Peter K. Joshi
- & Zoltán Kutalik
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Article
| Open AccessAn analytic approximation of the feasible space of metabolic networks
Large-scale metabolic models of organisms from microbes to mammals can provide great insight into cellular function, but their analysis remains challenging. Here, the authors provide an approximate analytic method to estimate the feasible solution space for the flux vectors of metabolic networks, enabling more accurate analysis under a wide range of conditions of interest.
- Alfredo Braunstein
- , Anna Paola Muntoni
- & Andrea Pagnani
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| Open AccessDpath software reveals hierarchical haemato-endothelial lineages of Etv2 progenitors based on single-cell transcriptome analysis
Single-cell RNA sequencing has enabled great advances in understanding developmental biology but reconstructing cellular lineages from this data remains challenging. Here the authors develop an algorithm,dpath, which models the lineage relationships of underlying single cells based on single cell RNA seq data and apply it to study lineage progression of Etv2 expressing progenitors.
- Wuming Gong
- , Tara L. Rasmussen
- & Daniel J. Garry
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| Open AccessA principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape
Past genome-wide associate studies have identified hundreds of genetic loci that influence body size and shape when examined one trait at a time. Here, Jeff and colleagues develop an aggregate score of various body traits, and use meta-analysis to find new loci linked to body shape.
- Janina S. Ried
- , Janina Jeff M.
- & Ruth J. F. Loos
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| Open AccessSequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
Plasticity and clonal population structure in bacterial genomes can hinder traditional SNP-based genetic association studies. Here, Corander and colleagues present a method to identify variable-length sequence elements enriched in a phenotype of interest, and demonstrate its use in human pathogens.
- John A. Lees
- , Minna Vehkala
- & Jukka Corander
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| Open AccessreChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells
Co-localizing chromatin modifications and regulators can exert a combinatorial effect on chromatin structure and function. Here the authors describe reChIP-seq and normR to identify co-localizing proteins in an unbiased genome-wide manner.
- Sarah Kinkley
- , Johannes Helmuth
- & Ho-Ryun Chung
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Article
| Open AccessSURVIV for survival analysis of mRNA isoform variation
Clinical RNA-seq datasets can predict clinical outcomes. Here, Shen et al. report a statistical method for survival analysis of mRNA isoform variation using clinical RNA-seq datasets, and the identified isoform based survival predictors outperform gene expression based survival predictors using TCGA data on six cancer types.
- Shihao Shen
- , Yuanyuan Wang
- & Yi Xing
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Article
| Open AccessCox process representation and inference for stochastic reaction–diffusion processes
Stochastic reaction-diffusion systems are used for modelling spatial dynamics in many disciplines, but parameter inference and model selection remain challenging. Here the authors offer a solution enabled by a connection between reaction-diffusion and the well-studied spatio-temporal Cox processes.
- David Schnoerr
- , Ramon Grima
- & Guido Sanguinetti
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| Open AccessIdentifying genetically driven clinical phenotypes using linear mixed models
Use of general linear mixed models (GLMMs) in genetic variance analysis can quantify the relative contribution of additive effects from genetic variation on a given trait. Here, Jonathan Mosley and colleagues apply GLMM in a phenome-wide analysis and show that genetic variations in the HLA region are associated with 44 phenotypes, 5 phenotypes which were not previously reported in GWASes.
- Jonathan D. Mosley
- , John S. Witte
- & Joshua C. Denny
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| Open AccessUsing food-web theory to conserve ecosystems
The influence of species conservation on food webs is less well understood than the effects of species loss. Here, the authors test several indices against optimal food web management and find no current metrics are reliably effective at identifying species conservation priorities.
- E. McDonald-Madden
- , R. Sabbadin
- & H. P. Possingham
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Article
| Open AccessBayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability
Das et al. present a novel Bayesian approach called expression Quantitative Trait enhancer Loci (eQTeL), which effectively integrates genetic and epigenetic information to identify combination of regulatory genomic variants underlying expression variance. Using various functional data, the authors show the variants identified by eQTeL are likely to be causal.
- Avinash Das
- , Michael Morley
- & Sridhar Hannenhalli
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Article |
The statistical geometry of transcriptome divergence in cell-type evolution and cancer
Body plan complexity is associated with the number of different cell types, yet the processes that create this diversity are unclear. Here the authors use transcriptomics to test the hypothesis that unlike cancer cells, novel normal cell types arise through sub-specialization of an ancestral cell type.
- Cong Liang
- , Alistair R.R. Forrest
- & Günter P. Wagner