Bayesian inference articles within Nature Communications

Featured

• Article
  11 July 2023 | Open Access

  The role of vaccination and public awareness in forecasts of Mpox incidence in the United Kingdom

  An outbreak of Mpox in the UK began in May 2022 and peaked in July. In this modelling study, the authors show that the decline in cases was likely due to behavioural changes among high-risk populations, whilst vaccination could prevent a rebound.

  • Samuel P. C. Brand
  • , Massimo Cavallaro
  •  & Matt J. Keeling

• Article
  09 December 2022 | Open Access

  Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments

  Here the authors explore the distributional differences expected from distinct biophysical models of transcription and show how measurements from single-cell genomics experiments can shed light on the underlying biological processes.

  • Gennady Gorin
  • , John J. Vastola
  •  & Lior Pachter

• Article
  10 October 2022 | Open Access

  Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE

  Changes in protein subcellular localization can be determined using mass spectrometry. Here, the authors present a statistical approach to determine relocalising proteins from spatial proteomics experiments.

  • Oliver M. Crook
  • , Colin T. R. Davies
  •  & Kathryn S. Lilley

• Article
  19 August 2022 | Open Access

  Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era

  This mathematical modelling study projects the dynamics of SARS-CoV-2 in England until the end of 2022 assuming that the Omicron BA.2 sublineage remains dominant. They show that booster vaccination was highly effective in mitigating severe outcomes and that future dynamics will depend greatly on assumptions about waning immunity.

  • Rosanna C. Barnard
  • , Nicholas G. Davies
  •  & W. John Edmunds

• Article
  13 April 2022 | Open Access

  Data-driven learning how oncogenic gene expression locally alters heterocellular networks

  While mechanistic models play increasing roles in immuno-oncology, hand network curation is current practice. Here the authors use a Bayesian data-driven approach to infer how expression of a secreted oncogene alters the cellular landscape within the tumor.

  • David J. Klinke II
  • , Audry Fernandez
  •  & Anika C. Pirkey

• Article
  08 March 2022 | Open Access

  Fossil coleoid cephalopod from the Mississippian Bear Gulch Lagerstätte sheds light on early vampyropod evolution

  The authors describe a new cephalopod from the Carboniferous (Mississippian) Bear Gulch Lagerstätte of Montana, USA. This specimen extends the fossil record of vampyropods back by ~82 million years and changes our understanding of their evolution.

  • Christopher D. Whalen
  •  & Neil H. Landman

• Article
  08 December 2021 | Open Access

  Fish predators control outbreaks of Crown-of-Thorns Starfish

  Outbreaks of Crown-of-Thorn Starfish (CoTS) have caused coral cover declines across the Indo-Pacific. Here the authors analyse long-term CoTS, coral reef fish monitoring, and fisheries catch data from the Great Barrier Reef to demonstrate removal of predatory fish as a contributor to CoTS outbreaks.

  • Frederieke J. Kroon
  • , Diego R. Barneche
  •  & Michael J. Emslie

• Article
  15 March 2021 | Open Access

  Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji

  Dengue and Zika virus are closely related flaviviruses but can have contrasting transmission dynamics in the same populations. Here, the authors use a model combining serological, surveillance and viral sequence data to explain differences in transmission dynamics in Fiji.

  • Alasdair D. Henderson
  • , Mike Kama
  •  & Adam J. Kucharski

• Article
  08 January 2021 | Open Access

  Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

  While temperature impacts the function of all cellular components, it’s hard to rule out how the temperature dependence of cell phenotypes emerged from the dependence of individual components. Here, the authors develop a Bayesian genome scale modelling approach to identify thermal determinants of yeast metabolism.

  • Gang Li
  • , Yating Hu
  •  & Jens Nielsen

• Article
  25 September 2020 | Open Access

  A machine learning Automated Recommendation Tool for synthetic biology

  Synthetic Biology often lacks the predictive power needed for efficient bioengineering. Here the authors present ART, a machine learning and probabilistic predictive tool to guide synthetic biology design in a systematic fashion.

  • Tijana Radivojević
  • , Zak Costello
  •  & Hector Garcia Martin

• Article
  13 July 2020 | Open Access

  Gene regulatory network inference from sparsely sampled noisy data

  Gene regulatory network inference is a topical problem in systems biology. Here, the authors presents BINGO, a powerful method for network inference from time series data.

  • Atte Aalto
  • , Lauri Viitasaari
  •  & Jorge Gonçalves

• Article
  07 February 2019 | Open Access

  Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping

  High-throughput sequencing and analyzes of antibody repertoire provide important information on immune responses, but current methodologies are limited in sequence assembly precision and haplotype inference validity. Here the authors propose a new Bayesian haplotyping method, and attest its broad application with a large, multi-individual dataset.

  • Moriah Gidoni
  • , Omri Snir
  •  & Gur Yaari

• Article
  12 June 2018 | Open Access

  Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells

  During atherosclerosis, endothelial cells release purines in response to oxidized phospholipids. Here, Hitzel et al. show that oxidized phospholipids activate an MTHFD2-regulated gene network in endothelial cells which reprograms amino acid metabolism towards production of purines and thus compensates for their loss.

  • Juliane Hitzel
  • , Eunjee Lee
  •  & Ralf P. Brandes

• Article
  08 June 2018 | Open Access

  Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

  During the last Ebola virus outbreak in West Africa, a large amount of viral genomic data was obtained. Here, Dellicour et al. use phylodynamic approaches to assess effect of intervention strategies such as border closures.

  • Simon Dellicour
  • , Guy Baele
  •  & Philippe Lemey

• Article
  05 December 2017 | Open Access

  Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions

  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
  05 May 2017 | Open Access

  Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes

  Global patterns of gene transcription can be represented with reduced dimensionality. Here, the authors devise a method called Tradict that learns and uses 100 marker genes to predict transcriptome-wide pathway expression levels and patterns that reflect cell activity and state.

  • Surojit Biswas
  • , Konstantin Kerner
  •  & Philip A. Wigge

• Article
  02 November 2010 | Open Access

  Global distribution of the sickle cell gene and geographical confirmation of the malaria hypothesis

  Sixty years ago it was suggested that the sickle cell disease mutation survives because the heterozygous genotype confers resistance to malaria, resulting in correlation of the two geographical distributions. The authors use a new global assembly of sickle allele frequencies to support this hypothesis at the global scale.

  • Frédéric B. Piel
  • , Anand P. Patil
  •  & Simon I. Hay