Systems analysis articles within Nature Communications

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  • Article
    | Open Access

    Fermentation parameters of industrial processes are often not the ideal growth conditions for industrial microbes. Here, the authors reveal that young genes are more responsive to environmental stress than ancient genes using a new gene age assignment method and provide targeted genes for metabolic engineering.

    • Tyler W. Doughty
    • , Iván Domenzain
    •  & John P. Morrissey

  • Article
    | Open Access

    The origin of the heterogeneity of metabolic and inflammatory profiles exhibited by white adipocytes is little understood. Here, using scRNA-seq and computational methods, the authors show that differentiating preadipocytes exhibit gene expression differences and suggest underlying regulators.

    • Alfred K. Ramirez
    • , Simon N. Dankel
    •  & Simon Kasif

  • Article
    | Open Access

    Cytokines critically control the differentiation and functions of activated naïve and memory T cells. Here the authors show, using multi-omics and single-cell analyses, that naïve and memory T cells exhibit distinct cytokine responses, in which an ‘effectorness gradient’ is depicted by a transcriptional continuum, which shapes the downstream genetic programs.

    • Eddie Cano-Gamez
    • , Blagoje Soskic
    •  & Gosia Trynka

  • Article
    | Open Access

    Aberrant tissue repair may result in heterotopic ossification (HO), but how this process is regulated by local inflammatory responses is still unclear. Here the authors show, using a mouse burn/trauma model, that TGFβ-producing monocytes/macrophages at the injury site contribute to HO induction, while CD47 activation helps antagonize this process.

    • Michael Sorkin
    • , Amanda K. Huber
    •  & Benjamin Levi

  • Article
    | Open Access

    Avian influenza A virus (IAV) strains replicate poorly in mammalian hosts, but mechanisms underlying species restriction are incompletely understood. Here, Bogdanow et al. show that avian and mammalian adapted IAV strains have evolved different RNA structure features for regulation of M segment RNA splicing.

    • Boris Bogdanow
    • , Xi Wang
    •  & Matthias Selbach

  • Article
    | Open Access

    Osteoarthritis results from the progressive destruction of cartilage matrix. Here, Kim et al. identify tankyrase as a regulator of cartilage matrix anabolism, and find that tankyrase inhibition, by preventing SOX9 PARylation, protects from cartilage destruction in a mouse model of osteoarthritis.

    • Sukyeong Kim
    • , Sangbin Han
    •  & Jin-Hong Kim

  • Article
    | Open Access

    Natural killer (NK) cells are important innate immune cells with diverse functions. Here the authors use single-cell RNA-sequencing of purified human bone marrow and peripheral blood NK cells to define five populations of NK cells with distinct transcriptomic profile to further our understanding of NK development and heterogeneity.

    • Chao Yang
    • , Jason R. Siebert
    •  & Subramaniam Malarkannan

  • Article
    | Open Access

    The white pulp of spleen is an important immune structure dynamically modulated during development and immune responses. Here the authors define, using multi-color lineage tracing and single-cell transcriptome analysis, the subset distribution and differentiation trajectory of fibroblastic reticular cells to serve structural insights for splenic white pulps.

    • Hung-Wei Cheng
    • , Lucas Onder
    •  & Burkhard Ludewig

  • Article
    | Open Access

    Computational protein-protein interaction (PPI) prediction has the potential to complement experimental efforts to map interactomes. Here, the authors show that proteins tend to interact if one is similar to the other’s partners and that PPI prediction based on this principle is highly accurate.

    • István A. Kovács
    • , Katja Luck
    •  & Albert-László Barabási

  • Article
    | Open Access

    Genome-reduced bacteria often show impaired growth under laboratory conditions. Here the authors use adaptive laboratory evolution to optimise growth performance and show transcriptome and translatome-wide remodeling of the organism.

    • Donghui Choe
    • , Jun Hyoung Lee
    •  & Byung-Kwan Cho

  • Article
    | Open Access

    Tissue-resident macrophages are highly specialized phagocytes that serve multiple functions. Here, using high-dimension analyses and fate-mapping experiments, the authors show that fetal liver-derived macrophages dominate the mammary gland in neonatal and adult, and display characteristic phenotypes and functions.

    • Norma Jäppinen
    • , Inês Félix
    •  & Marko Salmi

  • Article
    | Open Access

    Tumours of different tissues can show similarities in genomic alterations. Here, the authors combine tumour transcriptome and protein interaction data in a network-based analysis of 11 tumours types, and identify clusters of tumours with specific signatures for multi-tumour drug targeting and survival prognosis.

    • Ítalo Faria do Valle
    • , Giulia Menichetti
    •  & Daniel Remondini

  • Article
    | Open Access

    B-cell development is tightly regulated by transcription programs that are coordinated by transcription factors (TF) and locus accessibility. Here the authors show that, in mice and humans, the epigenetic reader BRWD1 inhibits and promotes the accessibility of enhancers for early and late B lymphopoiesis, respectively.

    • Malay Mandal
    • , Mark Maienschein-Cline
    •  & Marcus R. Clark

  • Article
    | Open Access

    Finding one’s way to a food source along a complex gradient is central to survival for many animals. Here, the authors report that in C. elegans, the distinct response dynamics of two sensory neurons to odor gradients can support a navigation model more efficient than the biased-random walk.

    • Eyal Itskovits
    • , Rotem Ruach
    •  & Alon Zaslaver

  • Article
    | Open Access

    Diatoms account for 40% of marine primary production and their sensitivity to ocean acidification could have ecosystem-wide consequences. Here, the authors developed and applied a stress test, demonstrating that resilience of diatoms increases significantly in ocean acidification conditions.

    • Jacob J. Valenzuela
    • , Adrián López García de Lomana
    •  & Nitin S. Baliga

  • Article
    | Open Access

    Nodes with high centrality in protein–protein interaction (PPI) networks are known to be essential in some organisms. Here, the authors in contrast find that in the interactome of A. thaliana central nodes are enriched in conditional and immune phenotypes and are preferred targets of pathogens.

    • Hadia Ahmed
    • , T. C. Howton
    •  & M. Shahid Mukhtar

  • Article
    | Open Access

    Single cell analysis provides insight into cell states and transitions, but to interpret the data, improved algorithms are needed. Here, the authors present CellRouter as a method to analyse single-cell trajectories from RNA-sequencing data, and provide insight into erythroid, myeloid and lymphoid differentiation.

    • Edroaldo Lummertz da Rocha
    • , R. Grant Rowe
    •  & George Q. Daley

  • 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

    Fast-growing bacteria produce many proteins in excess of what seems optimal for exponential growth. Here, the authors present a mathematical model and experimental evidence supporting that this overexpression serves as a strategic reserve to quickly meet demand upon sudden improvement in growth conditions.

    • Matteo Mori
    • , Severin Schink
    •  & Terence Hwa

  • Article
    | Open Access

    The contribution of metabolic pathways to protein secretion is largely unknown. Here, the authors find conserved metabolic patterns in yeast by examining genome-wide transcriptional responses in high protein secretion mutants and reveal critical factors that can be tuned for efficient protein secretion.

    • Mingtao Huang
    • , Jichen Bao
    •  & Jens Nielsen

  • Article
    | Open Access

    High-grade serous ovarian cancers (HGS-OvCa) frequently develop chemotherapy resistance. Here, the authors through a systematic analysis of proteomic and drug response data of 14 HGS-OvCa PDXs demonstrate that targeting apoptosis regulators can improve response of these tumors to inhibitors of the PI3K/mTOR pathway.

    • Ioannis K. Zervantonakis
    • , Claudia Iavarone
    •  & Joan S. Brugge

  • Article
    | Open Access

    Metabolites act as enzyme inhibitors, but their global impact on metabolism has scarcely been considered. Here, the authors generate a human genome-wide metabolite-enzyme inhibition network, and find that inhibition occurs largely due to limited structural diversity of metabolites, leading to a global constraint on metabolism which subcellular compartmentalization minimizes.

    • Mohammad Tauqeer Alam
    • , Viridiana Olin-Sandoval
    •  & Markus Ralser

  • Article
    | Open Access

    While we have abundant data for transcription factor (TF) binding sites and TF expression at the mRNA level, our knowledge of TFs at the protein level and their DNA-binding activities is sparser. Here, the authors address this by using the catTFRE approach to profile active TFs in 24 adult and 8 fetal mouse tissues, and presenting the TF networks in major mouse organs.

    • Quan Zhou
    • , Mingwei Liu
    •  & Jun Qin

  • Article
    | Open Access

    Crohn’s disease is associated with altered intestinal microbiota. Here, the authors show that the microbe Atopobium parvulumis associated with Crohn’s disease patients, triggers colitis in a mouse model, and that scavenging microbe-induced hydrogen sulfide improved symptoms in mice.

    • Walid Mottawea
    • , Cheng-Kang Chiang
    •  & Alain Stintzi

  • Article
    | Open Access

    Translating omics data sets into biological insight is one of the great challenges of our time. Here, the authors make headway by synchronising pairs of omics data types via invariants across conditions and by integrating datasets into a genome-scale model of E. coli metabolism and gene expression.

    • Ali Ebrahim
    • , Elizabeth Brunk
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    Many drugs are small molecule inhibitors of cell signalling. Through single cell analysis and mathematical modelling here the authors show that cell-to-cell variability diversifies inhibition response into digital and analogue, and that the two translate into distinct long-term functional responses.

    • Robert M. Vogel
    • , Amir Erez
    •  & Grégoire Altan-Bonnet

  • Article
    | Open Access

    High-grade serous ovarian cancer is the most common and aggressive ovarian cancer, with uncertain cell of origin. Here, the authors undertake a mass spectrometric analysis of 26 cancer cell lines and identify a protein signature that classifies ovarian cancer tissues into epithelial and mesenchymal groups.

    • F. Coscia
    • , K. M. Watters
    •  & M. Mann

  • Article
    | Open Access

    Analysis of network structure is usually based on knowledge of connections alone, ignoring additional information such as gender or age of individuals in social networks. Here the authors devise an approach that incorporates such metadata and uses it to improve the detection of network communities.

    • M. E. J. Newman
    •  & Aaron Clauset

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