Computational biology and bioinformatics articles within Nature Communications

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  • Article
    | Open Access

    Mathematical approaches can be used to assess immune cell composition from the tumour's bulk expression data. Here the authors optimise the CYBERSORT-based deconvolution algorithm by including cell type-specific reference gene expression profiles generated from tumour-derived single-cell RNA sequencing data.

    • Max Schelker
    • , Sonia Feau
    •  & Andreas Raue

  • Article
    | Open Access

    There is a need to understand how mammary epithelial cells respond to changes at various developmental stages. Here, the authors use single-cell RNA sequencing of mammary epithelial cells at different adult developmental stages, identifying different cell types and charting their developmental trajectory.

    • Karsten Bach
    • , Sara Pensa
    •  & Walid T. Khaled

  • Article
    | Open Access

    Rising rates of peanut allergy pose a public health problem. Here, the authors profile blood transcriptomes during double-blind, placebo-controlled oral challenge in peanut-allergic children to identify gene and cell composition changes, and construct causal networks to detect key allergic reaction drivers.

    • C. T. Watson
    • , A. T. Cohain
    •  & S. Bunyavanich

  • Article
    | Open Access

    Reported associations between the human microbiome and disease are often inconsistent. Here, Duvallet et al. perform a meta-analysis of 28 gut microbiome studies spanning ten diseases, and find associations that are likely not disease-specific but potentially part of a shared response to disease.

    • Claire Duvallet
    • , Sean M. Gibbons
    •  & Eric J. Alm

  • Article
    | Open Access

    Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here Ichikawa et al perform de novo long-read genome assembly of three inbred medaka strains, and report long-range structure of centromeres and their methylation as well as correlation of structural variants with differential gene expression.

    • Kazuki Ichikawa
    • , Shingo Tomioka
    •  & Shinich Morishita

  • Article
    | Open Access

    Prioritizing genetic variants is a major challenge in genome-wide association studies. Here, the authors develop FUMA, a web-based bioinformatics tool that uses a combination of positional, eQTL and chromatin interaction mapping to prioritize likely causal variants and genes.

    • Kyoko Watanabe
    • , Erdogan Taskesen
    •  & Danielle Posthuma

  • Article
    | Open Access

    The authors use an integrative clustering approach to identify two laryngeal cancer clusters with distinct prognosis and show that mutations damaging the NSD1 and NSD2 methyltransferases segregate to the cluster with favorable prognosis, and independently predict longer survival in patients with laryngeal, but not other head and neck cancers.

    • Suraj Peri
    • , Evgeny Izumchenko
    •  & Erica A. Golemis

  • Article
    | Open Access

    Eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that exist at the kilo-megabase scale. Here Cattoni et al. combine super-resolution microscopy with DNA-labeling methods to quantify absolute frequencies of interactions within TADs.

    • Diego I. Cattoni
    • , Andrés M. Cardozo Gizzi
    •  & Marcelo Nollmann

  • Article
    | Open Access

    Single cell profiling yields high dimensional data of very large numbers of cells, posing challenges of visualization and analysis. Here the authors introduce a method for analysis of mass cytometry data that can handle very large datasets and allows their intuitive and hierarchical exploration.

    • Vincent van Unen
    • , Thomas Höllt
    •  & Boudewijn P. F. Lelieveldt

  • Article
    | Open Access

    Translation initiation sequencing (TI-seq) has revealed unexpected diversity in protein isoforms. Here, Zhang et al. present Ribo-TISH, a computational toolkit that can detect and compare TIs across conditions and improve open reading frame prediction from different types of ribosome profiling data.

    • Peng Zhang
    • , Dandan He
    •  & Yiwen Chen

  • Article
    | Open Access

    Tip-growing cells can find their growing path toward the source of attractive signals. Here, using experimental data and mathematical modeling, Luo et al. demonstrate that tip-localized exocytosis can integrate guidance cues with Rho GTPase signaling to control cell wall mechanics and direct tip growth in Arabidopsis pollen tubes.

    • Nan Luo
    • , An Yan
    •  & Zhenbiao Yang

  • Article
    | Open Access

    The NMR chemical shifts of a substance in urine strongly depend on the composition of the mixture itself, and this makes automatic assignment for quantification very difficult. Here the authors show the chemical shifts of signals and the concentration of NMR-invisible inorganic ions in urine, are predictable.

    • Panteleimon G. Takis
    • , Hartmut Schäfer
    •  & Claudio Luchinat

  • Article
    | Open Access

    The role of lncRNA is unclear with respect to epithelial-to-mesenchymal transition (EMT), which is linked to ovarian cancer metastasis. Here, the authors show lncRNA DNM3OS expression contributes to ovarian cancer EMT, cell migration/invasion, and correlates with worse overall patient survival.

    • Ramkrishna Mitra
    • , Xi Chen
    •  & Christine M. Eischen

  • Article
    | Open Access

    The NUDIX hydrolases are known to be involved in several cellular processes and diseases, such as cancer, but remain poorly characterized as a family. Here, the authors provide a comprehensive analysis of the structural, biochemical, and expression properties of 18 human NUDIX proteins, and begin to address their functional inter-relationships.

    • Jordi Carreras-Puigvert
    • , Marinka Zitnik
    •  & Thomas Helleday

  • Article
    | Open Access

    Matching fragment spectra to reference library spectra is an important procedure for annotating small molecules in untargeted mass spectrometry based metabolomics studies. Here, the authors develop strategies to estimate false discovery rates (FDR) by empirical Bayes and target-decoy based methods which enable a user to define the scoring criteria for spectral matching.

    • Kerstin Scheubert
    • , Franziska Hufsky
    •  & Sebastian Böcker

  • Article
    | Open Access

    IgG glycosylation is an important factor in immune function, yet the molecular details of protein glycosylation remain poorly understood. The data-driven approach presented here uses large-scale plasma IgG mass spectrometry measurements to infer new biochemical reactions in the glycosylation pathway.

    • Elisa Benedetti
    • , Maja Pučić-Baković
    •  & Jan Krumsiek

  • Article
    | Open Access

    The eukaryotic release factor eRF1 is able to recognize the three stop codons UAA, UAG and UGA with high accuracy, while discriminating against near-cognate codons. Here the authors use molecular dynamic simulation to provide insight into the molecular basis behind the remarkable codon specificity of eRF1.

    • Christoffer Lind
    • , Ana Oliveira
    •  & Johan Åqvist

  • Article
    | Open Access

    The globally-distributed Ranidae (true frogs) are the largest frog family. Here, Hammond et al. present a draft genome of the North American bullfrog, Rana (Lithobates) catesbeiana, as a foundation for future understanding of true frog genetics as amphibian species face difficult environmental challenges.

    • S. Austin Hammond
    • , René L. Warren
    •  & Inanc Birol

  • Article
    | Open Access

    Artemether lumefantrine is widely used for the treatment of uncomplicated malaria. The impact of imperfect patient adherence to the six-dose regimen is hard to assess. Using adherence data for unsupervised patients, the authors model how suboptimal adherence affects treatment outcomes.

    • Joseph D. Challenger
    • , Katia Bruxvoort
    •  & Lucy C. Okell

  • Article
    | Open Access

    Microbes live in communities and exchange metabolites, but the resulting dynamics are poorly understood. Here, the authors study the interplay between metabolite production strategies and population dynamics, and find that complex and unexpected dynamics emerge even in simple microbial economies.

    • Yoav Kallus
    • , John H. Miller
    •  & Eric Libby

  • Article
    | Open Access

    Tumorigenesis is a complex process driven by numerous risk factors. Here, genomic analysis of liver cancer reveals the evolution of mutational signatures during tumor development, highlighting mutational and structural signatures linked to environmental exposures and endogenous cellular processes.

    • Eric Letouzé
    • , Jayendra Shinde
    •  & Jessica Zucman-Rossi

  • Article
    | Open Access

    Haplotype information is important in investigating many biological phenomena. Here, Porubsky et al. combine Strand-seq with long-read or linked-read sequencing to obtain complete and genome-wide haplotypes of a single individual genome at manageable costs.

    • David Porubsky
    • , Shilpa Garg
    •  & Tobias Marschall

  • Article
    | Open Access

    RNA A-to-I editing introduces single nucleotide changes to RNA, but its role in cells remains unclear. Here, the authors analyse A-to-I editomes in human samples and find that A-to-I editing stabilizes RNA secondary structures and reduces the accessibility of AGO2-miRNA to target sites in mRNAs.

    • Anneke Brümmer
    • , Yun Yang
    •  & Xinshu Xiao

  • Article
    | Open Access

    Cancer is caused by accumulating genetic mutations. Here, the authors investigate the cooperative effect of these mutations in colorectal cancer patients and identify a giant cluster of mutation-propagating modules that undergoes percolation transition during tumorigenesis.

    • Dongkwan Shin
    • , Jonghoon Lee
    •  & Kwang-Hyun Cho

  • 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

    In eukaryotic cells, the ubiquitylation system regulates several cellular processes central to protein homoeostasis. Here the authors demonstrate the existence of an eukaryotic-like ubiquitylation cascade requiring E1, E2 and E3-like enzymes in the archaeon C. subterraneum, shedding light on the evolution of the ubiquitin-proteasome system.

    • Rory Hennell James
    • , Eva F. Caceres
    •  & Nicholas P. Robinson

  • Article
    | Open Access

    Altered mRNA splicing features in many cancers, but it has not been linked to drug response. Here, with their meta-analytic framework, the authors analyse pharmacogenomic data to identify isoform-based biomarkers predictive of in vitro drug response, and show them to frequently be strong predictors.

    • Zhaleh Safikhani
    • , Petr Smirnov
    •  & Benjamin Haibe-Kains

  • Article
    | Open Access

    Normal tissue adjacent to the tumour (NAT) is often used as a control in cancer studies. Here, the authors analyse across cancer types the transcriptomes of healthy, NAT, and tumour tissues, and find that NAT presents a unique state, potentially due to inflammatory response of the NAT to the tumour tissue.

    • Dvir Aran
    • , Roman Camarda
    •  & Atul J. Butte

  • Article
    | Open Access

    Existing transcriptional regulatory networks models fall short of deciphering the cooperation between multiple transcription factors on dynamic gene expression. Here the authors develop an integrative method that combines gene expression and transcription factor-DNA binding data to decode transcription regulatory logics.

    • Bin Yan
    • , Daogang Guan
    •  & Hailong Zhu

  • Article
    | Open Access

    Binding of viral envelope glycoproteins (Env) to the host cell CD4 receptor mediates HIV-1 entry. Here, the authors develop compounds that inhibit the CD4-induced conformational changes in Env and show that the gp120 β20-β21 element is a key regulator for Env transitions.

    • Alon Herschhorn
    • , Christopher Gu
    •  & Joseph G. Sodroski

  • Article
    | Open Access

    A map of the activities of all genomic regulatory elements across cell types and conditions would be a tremendous resource. The computational method introduced here predicts genome-wide accessible sites from gene expression data and allows the authors to build a database of regulatory element activities using publicly available transcriptome data.

    • Weiqiang Zhou
    • , Ben Sherwood
    •  & Hongkai Ji

  • Article
    | Open Access

    Tree branches follow allometric scalings between length, thickness and dry mass. Here, Eloy and colleagues develop a functional-structural model that shows how such allometries in tree architecture can emerge through evolution as a result of competition for light, wind biomechanics, and wind sensing.

    • Christophe Eloy
    • , Meriem Fournier
    •  & Bruno Moulia

  • Article
    | Open Access

    Inaccuracy of influenza forecasts based on dynamical models is partly due to nonlinear error growth. Here the authors address the error structure of a compartmental influenza model, and develop a new improved forecast approach combining dynamical error correction and statistical filtering techniques.

    • Sen Pei
    •  & Jeffrey Shaman

  • Article
    | Open Access

    Germline mutations in homologous recombination (HR) DNA repair genes are linked to breast and ovarian cancer. Here, the authors show that mutually exclusive bi-allelic inactivation of HR genes are present in other cancer types and associated with genomic features of HR deficiency, expanding the potential use of HR-directed therapies.

    • Nadeem Riaz
    • , Pedro Blecua
    •  & Jorge S. Reis-Filho

  • Article
    | Open Access

    Hepatocellular carcinoma is known to harbour numerous genomic and epigenomic aberrations, driving transcriptomic deregulation. Here, the authors integrate genomic, epigenomic, and expression data to reveal three prognostic subtypes, providing insight to the pathobiology of hepatocellular carcinoma.

    • Hyun Goo Woo
    • , Ji-Hye Choi
    •  & Yoon Jun Kim

  • Article
    | Open Access

    Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

    • Pedro H. Oliveira
    • , Marie Touchon
    •  & Eduardo P. C. Rocha

  • Article
    | Open Access

    Individual SNPs have small effects on anthropometric traits, yet the impact of CNVs has remained largely unknown. Here, Kutalik and co-workers perform a large-scale genome-wide meta-analysis of structural variation and find rare CNVs associated with height, weight and BMI with large effect sizes.

    • Aurélien Macé
    • , Marcus A. Tuke
    •  & Zoltán Kutalik

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