Bioinformatics articles within Nature Communications

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  • Article
    | Open Access

    Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.

    • Cyril Matthey-Doret
    • , Lyam Baudry
    •  & Axel Cournac

  • Article
    | Open Access

    Here, the authors tailor an acetylated galactoglucomannan (AcGGM) fibre from spruce wood to specifically enrich Roseburia and Faecalibacterium - beneficial species which have the enzymatic machinery to breakdown the fibre and generate butyrate. They subsequently perform a piglet feeding trial, metagenomics and metaproteomics, together showing that AcGGM-fed pigs exhibit not only increased Roseburia and Faecalibacterium populations with AcGGM-specific mannan-specific esterases, but also secondary metabolic pathways.

    • Leszek Michalak
    • , John Christian Gaby
    •  & Bjørge Westereng

  • Article
    | Open Access

    Current cell segmentation methods for Saccharomyces cerevisiae face challenges under a variety of standard experimental and imaging conditions. Here the authors develop a convolutional neural network for accurate, label-free cell segmentation.

    • Nicola Dietler
    • , Matthias Minder
    •  & Sahand Jamal Rahi

  • Article
    | Open Access

    The mechanisms regulating stem cells to give rise to human interfollicular epidermis are unclear. Here, the authors use single cell RNA sequencing to identify heterogeneity within the human neonatal interfollicular epidermis and distinct spatial positioning of at least four basal stem cell populations.

    • Shuxiong Wang
    • , Michael L. Drummond
    •  & Scott X. Atwood

  • Article
    | Open Access

    Droplet-based high throughput single cell sequencing techniques can often lose information on transcript splicing and heterogenity. Here the authors introduce ScNaUmi-seq, which uses Oxford Nanopore sequencing and barcoding to generate high accuracy full length sequences.

    • Kevin Lebrigand
    • , Virginie Magnone
    •  & Rainer Waldmann

  • Article
    | Open Access

    To investigate the molecular foundation of sporadic Alzheimer’s disease (AD), Beckmann et al. constructed multiscale causal networks on a large human AD multi-omics dataset, detecting AD-associated networks and their top predicted regulator, VGF, with extensive validation in the 5xFAD mouse model.

    • Noam D. Beckmann
    • , Wei-Jye Lin
    •  & Eric E. Schadt

  • Article
    | Open Access

    Glucocorticoids (GC) are commonly used to suppress undesirable inflammatory responses. Here the authors show, using hi-dimensional flow cytometry data, that GC treatment following major surgeries alters adaptive immunity without significant modulation of innate immune responses or pain/functional impairment.

    • Edward A. Ganio
    • , Natalie Stanley
    •  & Brice Gaudilliere

  • Article
    | Open Access

    During nuclear surveillance in yeast and human cells, the RNA exosome functions together with the TRAMP complexes. Here, the authors defined the protein composition of the TRAMP complexes and identified specific RNA binding sites for the different TRAMP components.

    • Clémentine Delan-Forino
    • , Christos Spanos
    •  & David Tollervey

  • Article
    | Open Access

    The complexity of structural variation (SV) and short tandem repeats (STRs) makes it necessary to apply different calling and filtering strategies to sequencing datasets. Here, Jakubosky et al. report a comprehensive SV and STR callset from whole-genome sequencing of 477 individuals from iPSCORE and HipSci using five algorithms.

    • David Jakubosky
    • , Erin N. Smith
    •  & Kelly A. Frazer

  • Article
    | Open Access

    Traditional methods for determining cell type composition lack scalability, while single-cell technologies remain costly and noisy compared to bulk RNA-seq. Here, the authors present a highly efficient tool to measure cellular heterogeneity in bulk expression through robust integration of single-cell information.

    • Shaoheng Liang
    • , Fang Wang
    •  & Ken Chen

  • Article
    | Open Access

    Horizontal transfer (HT) and evolution of transposable elements (TEs) has rarely been quantified on a large scale. Here, the authors screen 307 vertebrate genomes and infer 975 HT events (93% in ray-finned fishes); all TEs involved in HT evolve within genomes under purifying selection, as do most retrotransposons.

    • Hua-Hao Zhang
    • , Jean Peccoud
    •  & Clément Gilbert

  • Article
    | Open Access

    The surface nanotopography of biomaterials direct cell behavior, but screening for desired effects is inefficient. Here, the authors introduce a platform that enables prediction of nanotopography-induced gene expression changes from changes in cell morphology, including in co-culture environments.

    • Marie F. A. Cutiongco
    • , Bjørn Sand Jensen
    •  & Nikolaj Gadegaard

  • Article
    | Open Access

    Reference databases are essential for studies on host-microbiota interactions. Here, the authors present the construction of VIRGO, a human vaginal non-redundant gene catalog, which represents a comprehensive resource for taxonomic and functional profiling of vaginal microbiomes from metagenomic and metatranscriptomic datasets.

    • Bing Ma
    • , Michael T. France
    •  & Jacques Ravel

  • Article
    | Open Access

    Although most are silenced, certain transposable elements (TEs) have been co-opted by the host. Here, the authors quantify the epigenomic status of TEs using data from the Roadmap Epigenomics Project, provide a systematic profile of TE activity across normal human tissues and development, finding that TEs encompass a quarter of the human regulatory epigenome, with 47% of TEs in regulatory states.

    • Erica C. Pehrsson
    • , Mayank N. K. Choudhary
    •  & Ting Wang

  • Article
    | Open Access

    Allele-specific expression at single-cell resolution can reveal stochastic and dynamic features of gene expression in greater detail. The authors propose scBASE, a soft zero-and-one inflated model that improves estimation of cellular allelic proportions by pooling information across cells.

    • Kwangbom Choi
    • , Narayanan Raghupathy
    •  & Gary A. Churchill

  • Article
    | Open Access

    Anatomical brain atlases elucidate the anatomical and functional organisation across species but different atlases have conflicting anatomical border and 3D coordinates. The authors integrated two atlases into a unified and highly segmented anatomical labelling system of the mouse brain.

    • Uree Chon
    • , Daniel J. Vanselow
    •  & Yongsoo Kim

  • Article
    | Open Access

    Atopic dermatitis (AD) and psoriasis (PSO) are associated with dysbiosis. Here, by analyses of skin microbiome and host transcriptome of AD and PSO patients, the authors find distinct microbial and disease-related gene transcriptomic signatures that differentiate both diseases.

    • Nanna Fyhrquist
    • , Gareth Muirhead
    •  & Harri Alenius

  • Article
    | Open Access

    Squamous cell lung cancer has dismal prognosis due to the dearth of effective treatments. Here, the authors perform an integrated proteogenomic analysis of the disease, revealing three proteomics-based subtypes and suggesting potential therapeutic opportunities.

    • Paul A. Stewart
    • , Eric A. Welsh
    •  & Eric B. Haura

  • Article
    | Open Access

    The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.

    • Zhen-Lin Chen
    • , Jia-Ming Meng
    •  & Si-Min He

  • Article
    | Open Access

    Single-cell CRISPR screening combines pooled CRISPR screening with scRNA-seq analysis to expand the resolution power of genetic screening. Here, the authors develop MUSIC, a computational pipeline for analyzing single-cell CRISPR screening data.

    • Bin Duan
    • , Chi Zhou
    •  & Qi Liu

  • Article
    | Open Access

    Untargeted metabolomics detects large numbers of metabolites but their annotation remains challenging. Here, the authors develop a metabolic reaction network-based recursive algorithm that expands metabolite annotation by taking advantage of the mass spectral similarity of reaction-paired neighbor metabolites.

    • Xiaotao Shen
    • , Ruohong Wang
    •  & Zheng-Jiang Zhu

  • Article
    | Open Access

    Accurate and actionable biomarkers that integrate diverse molecular, functional and clinical information hold great promise in precision medicine. Here, the authors develop SIMMS, a method for pathway-based cross-disease biomarker discovery.

    • Syed Haider
    • , Cindy Q. Yao
    •  & Paul C. Boutros

  • Article
    | Open Access

    The specific glycosylation patterns of biological drugs often impact the efficacy and safety of the therapeutic product. Here the authors describe a native mass spectrometry approach that allows the resolution of highly complex glycosylation patterns on large proteins, which they apply to the therapeutic Fc-fusion protein Etanercept.

    • Therese Wohlschlager
    • , Kai Scheffler
    •  & Christian G. Huber

  • Article
    | Open Access

    Single cell messenger RNAseq allows the study of heterogeneity in tissue samples. Here the authors present BEARscc, a tool that uses RNA spike-in controls to simulate experiment-specific technical replicates to estimate the robustness of computational predictions of subpopulations of cells.

    • D. T. Severson
    • , R. P. Owen
    •  & B. Schuster-Böckler

  • Article
    | Open Access

    Data sharing is an important component of reproducible research, but meaningful data sharing can be difficult. Here authors describe a new open source tool, AFQ-Browser, that builds an interactive website allowing visualization and exploratory data analysis of published diffusion MRI data.

    • Jason D. Yeatman
    • , Adam Richie-Halford
    •  & Ariel Rokem

  • Article
    | Open Access

    Current methods for prioritization of non-coding genetic risk variants are based on sequence and chromatin features. Here, Gao et al. develop ARVIN, which predicts causal regulatory variants using disease-relevant gene-regulatory networks, and validate this approach in reporter gene assays.

    • Long Gao
    • , Yasin Uzun
    •  & Kai Tan

  • Article
    | Open Access

    Some bacteria can use inorganic phosphite and hypophosphite as sources of inorganic phosphorus. Here, the authors report crystal structures of the periplasmic proteins that bind these reduced phosphorus species and show that a P-H…π interaction between the ligand and binding site determines their specificity.

    • Claudine Bisson
    • , Nathan B. P. Adams
    •  & Andrew Hitchcock

  • Article
    | Open Access

    A central problem in biodiversity estimation from genetic markers is the ability of algorithms to retain ‘true’ species while discarding artefacts. Here, the authors present a new post-clusturing curation algorithm using OTU co-occurrences to estimate plant biodiversity from soil samples.

    • Tobias Guldberg Frøslev
    • , Rasmus Kjøller
    •  & Anders Johannes Hansen

  • Article
    | Open Access

    Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.

    • Ming-Qi Liu
    • , Wen-Feng Zeng
    •  & Peng-Yuan Yang

  • Article
    | Open Access

    High-throughput time-series data is increasingly available, yet estimating time-derivatives from such data can remain a challenge. Here, the authors provide a non-parametric method for inferring the first and second time-derivatives from multiple replicates of time-series data and for estimating errors in this inference and in any summary statistics.

    • Peter S. Swain
    • , Keiran Stevenson
    •  & Teuta Pilizota

  • Article
    | Open Access

    Currently available methods for phenotype to genetic markers association need to account for population structure. Here, Klasen et al. devise a statistical method called Quantitative Trait Cluster Association Test (QTCAT) that overcomes the need for population structure correction.

    • Jonas R. Klasen
    • , Elke Barbez
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    The formation of chromatin loops is mainly mediated by DNA-binding proteins (DBPs) that bind to the interacting sites and form complexes in 3D space. Here, Zhang et al.present an algorithm integrating ChIP-seq and Hi-C data to systematically identify both the 1D- and 3D-cooperation between DBPs.

    • Kai Zhang
    • , Nan Li
    •  & Wei Wang

  • Article
    | Open Access

    Two-photon laser scanning microscopy allows functional calcium imaging of large neuronal populations in vivo, but the recorded signals typically suffer from low signal to noise. Here the authors develop an algorithm, MLspike, which estimates action potentials from noisy calcium signals, and benchmark it against existing methods.

    • Thomas Deneux
    • , Attila Kaszas
    •  & Ivo Vanzetta

  • Article
    | Open Access

    RNA editing rate detected from bulk RNA-seq data can vary widely. Here, by constructing a hierarchical Bayesian model, the authors report substantial variance in editing signatures detected by RNA-seq data from both single cells and a cognate bulk sample.

    • Dewi Harjanto
    • , Theodore Papamarkou
    •  & Anastasia Papavasiliou

  • Article
    | Open Access

    Analysis of cancer genome sequencing data has been used to predict genes associated with the pathogenesis of cancer. Here, the authors propose a new algorithm entitled RUBIC that predicts breaks in DNA as opposed to previously published methods that predict amplifications and deletions of DNA.

    • Ewald van Dyk
    • , Marlous Hoogstraat
    •  & Lodewyk F. A. Wessels

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