Cellular signalling networks articles within Nature Communications

Featured

• Article
  21 March 2019 | Open Access

  A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae

  Whole-cell models hold great promise for fundamental and translational biology, but genome-scale modelling of signalling networks has been a challenge. Here, the authors present a genome-scale, mechanistic and executable model of the network controlling and executing the S. cerevisiae cell cycle.

  • Ulrike Münzner
  • , Edda Klipp
  •  & Marcus Krantz

• Article
  26 February 2019 | Open Access

  A network-centric approach to drugging TNF-induced NF-κB signaling

  Chemical perturbation of specific protein–protein interactions is notoriously difficult, yet necessary when complete inhibition of a signalling pathway is detrimental to the cell. Here, the authors use a systems approach and identify two first-in-class small molecules that specifically inhibit TNF-induced NF-κB activation.

  • Nicolas A. Pabon
  • , Qiuhong Zhang
  •  & Robin E. C. Lee

• Article
  16 January 2019 | Open Access

  Image-based modeling of kidney branching morphogenesis reveals GDNF-RET based Turing-type mechanism and pattern-modulating WNT11 feedback

  Many organs develop through branching morphogenesis, but whether the underlying mechanisms are shared is unknown. Here, the authors show that a ligand-receptor based Turing mechanisms, similar to that observed in lung development, likely underlies branching morphogenesis of the kidney.

  • Denis Menshykau
  • , Odyssé Michos
  •  & Dagmar Iber

• Article
  12 July 2018 | Open Access

  Network-based approach to prediction and population-based validation of in silico drug repurposing

  Repurposing approved drugs could accelerate treatment options for various diseases. Here, the authors use network proximity of disease gene products and drug targets in the human protein interactome to identify drug-disease associations for cardiovascular disease, and validate these using longitudinal healthcare data.

  • Feixiong Cheng
  • , Rishi J. Desai
  •  & Joseph Loscalzo

• Article
  05 February 2018 | Open Access

  Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways

  Innate immunity combines intra- and intercellular signalling to develop responses that limit pathogen spread. Here the authors analyse feedback and feedforward loops connecting IRF3, NF-κB and STAT pathways, and suggest they allow coordinating cell fate decisions in cellular populations in response to the virus-mimicking agent poly(I:C).

  • Maciej Czerkies
  • , Zbigniew Korwek
  •  & Tomasz Lipniacki

• Article
  05 December 2017 | Open Access

  Network dynamics-based cancer panel stratification for systemic prediction of anticancer drug response

  Genomic alterations underlie the variability of drug responses between cancers, but our mechanistic understanding is limited. Here the authors use the p53 network to study how rewiring of signalling networks by genomic alterations impact their dynamic response to pharmacological perturbation.

  • Minsoo Choi
  • , Jue Shi
  •  & Kwang-Hyun Cho

• Article
  16 November 2017 | Open Access

  A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

  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
  04 August 2017 | Open Access

  Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures

  Deregulation of E2F family transcription factors is associated with cancer progression and metastasis. Here, the authors construct a map of the regulatory network around the E2F family, and using gene expression profiles, identify tumour type-specific regulatory cores and receptor expression signatures associated with epithelial-mesenchymal transition in bladder and breast cancer.

  • Faiz M. Khan
  • , Stephan Marquardt
  •  & Brigitte M. Pützer

• Article
  01 June 2017 | Open Access

  Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome

  Robust quantification of the differentiation potential of single cells is a task of great importance. Here the authors integrate single-cell RNA-Seq profiles with a cellular interaction network to compute the signaling entropy, and show that it can identify normal and cancer stem-cell phenotypes.

  • Andrew E. Teschendorff
  •  & Tariq Enver

• Article
  21 November 2016 | Open Access

  A systems study reveals concurrent activation of AMPK and mTOR by amino acids

  mTORC1 is known to mediate the signalling activity of amino acids. Here, the authors combine modelling with experiments and find that amino acids acutely stimulate mTORC2, IRS/PI3K and AMPK, independently of mTORC1. AMPK activation through CaMKKβ sustains autophagy under non-starvation conditions.

  • Piero Dalle Pezze
  • , Stefanie Ruf
  •  & Kathrin Thedieck

• Article
  16 November 2016 | Open Access

  In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

  Pathway analysis aids interpretation of large-scale gene expression data, but existing algorithms fall short of providing robust pathway identification. The method introduced here includes coexpression analysis and gene importance estimation to robustly identify relevant pathways and biomarkers for patient stratification.

  • Ivan V. Ozerov
  • , Ksenia V. Lezhnina
  •  & Alex Zhavoronkov

• Article
  30 September 2016 | Open Access

  Dichotomy of cellular inhibition by small-molecule inhibitors revealed by single-cell analysis

  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
  22 July 2015 | Open Access

  A draft network of ligand–receptor-mediated multicellular signalling in human

  Cell-to-cell communication relies upon interactions between secreted ligands and cell surface receptors. Here, Ramilowski et al.present a draft cell-to-cell communication network based on expression of ligand-receptor pairs in 144 different human cell types.

  • Jordan A. Ramilowski
  • , Tatyana Goldberg
  •  & Alistair R. R. Forrest

• Article
  11 October 2011 | Open Access

  Travelling and splitting of a wave of hedgehog expression involved in spider-head segmentation

  During development, waves of gene expression are required for segmentation of the body axis. In this study, repeated splitting of a wave of hedgehog gene expression is shown during segmentation of the spiderAchaearanea tepidariorum.

  • Masaki Kanayama
  • , Yasuko Akiyama-Oda
  •  & Hiroki Oda