Nature Search

Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists

Variation in responses to bacterial and viral stimuli between Batwa rainforest hunter-gatherers and Bakiga agriculturalists from Uganda suggests population-level divergence under natural selection, with hunter-gatherers disproportionately showing signatures of positive selection.

Genelle F. Harrison
Joaquin Sanz
Luis B. Barreiro
Research29 Jul 2019
Nature Ecology & Evolution

Volume: 3, P: 1253-1264
Author Correction: Evolution of immune genes is associated with the Black Death

Jennifer Klunk
Tauras P. Vilgalys
Luis B. Barreiro
Amendments and Corrections15 Jan 2025
Nature

Volume: 637, P: E30
Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines

The identification of T cell epitopes is a critical step in understanding the immune response to infection and in designing vaccine based approaches. Here the authors introduce a frame work of antigen discovery called MHCvalidator and Epitrack to identify new antigenic features for T-cell COVID-19 vaccines and characterise a novel non-canonical epitope from a truncated Spike variant and mutation of an immunodominant epitope in the BNT162b4 vaccine.

Kevin A. Kovalchik
David J. Hamelin
Etienne Caron
ResearchOpen Access28 Nov 2024
Nature Communications

Volume: 15, P: 1-22
Evolution of immune genes is associated with the Black Death

Klunk and colleagues identify signatures of natural selection imposed by Yersinia pestis and demonstrate their effect on genetic diversity and susceptibility to certain diseases in the present day.

Jennifer Klunk
Tauras P. Vilgalys
Luis B. Barreiro
Research19 Oct 2022
Nature

Volume: 611, P: 312-319
Reply to: Insufficient evidence for natural selection associated with the Black Death

Tauras P. Vilgalys
Jennifer Klunk
Luis B. Barreiro
Research19 Feb 2025
Nature

Volume: 638, P: E23-E29
Synchrony and idiosyncrasy in the gut microbiome of wild baboons

Analysing gut microbial time series from wild baboons, the authors show that microbiome dynamics are rarely synchronized across hosts in shared environments but are highly individualized even within the same social groups.

Johannes R. Björk
Mauna R. Dasari
Elizabeth A. Archie
Research02 Jun 2022
Nature Ecology & Evolution

Volume: 6, P: 955-964
IL-15, gluten and HLA-DQ8 drive tissue destruction in coeliac disease

An HLA- and gluten-dependent mouse model of coeliac disease with villous atrophy provides evidence for the cooperative role of IL-15 and gluten-specific CD4⁺ T cells in licensing the full activation of cytotoxic T cells that are necessary for inducing epithelial damage.

Valérie Abadie
Sangman M. Kim
Bana Jabri
Research12 Feb 2020
Nature

Volume: 578, P: 600-604
Multiscale PHATE identifies multimodal signatures of COVID-19

Disease signatures in high-dimensional biomedical data are detected with a visualization algorithm.

Manik Kuchroo
Jessie Huang
Smita Krishnaswamy
Research28 Feb 2022
Nature Biotechnology

Volume: 40, P: 681-691
Non-CG methylation and multiple histone profiles associate child abuse with immune and small GTPase dysregulation

Early-life adversity is thought to increase the risk of psychopathology through epigenetic mechanisms. Here, the authors profile 6 histone marks, chromatin states and DNA methylation in the lateral amygdala in subjects with a history of early-life adversity.

Pierre-Eric Lutz
Marc-Aurèle Chay
Gustavo Turecki
ResearchOpen Access18 Feb 2021
Nature Communications

Volume: 12, P: 1-16
Gene-by-environment interactions in urban populations modulate risk phenotypes

Individuals with different genotypes may respond differently to environmental variation. Here, Favé et al. find substantial impacts of different environment exposures on the transcriptome and clinical endophenotypes when controlling for genetic ancestry by analyzing data from ∼1000 individuals from a founder population in Quebec.

Marie-Julie Favé
Fabien C. Lamaze
Philip Awadalla
ResearchOpen Access06 Mar 2018
Nature Communications

Volume: 9, P: 1-12
Recombination affects accumulation of damaging and disease-associated mutations in human populations

Philip Awadalla and colleagues report an analysis of the relationship between recombination and deleterious variation using high-coverage sequence data from over 1,400 individuals. They find that the recombination rate modulates the distribution of putatively deleterious variants across the human genome.

Julie G Hussin
Alan Hodgkinson
Philip Awadalla
Research16 Feb 2015
Nature Genetics

Volume: 47, P: 400-404
At-admission prediction of mortality and pulmonary embolism in an international cohort of hospitalised patients with COVID-19 using statistical and machine learning methods

Munib Mesinovic
Xin Ci Wong
David Zucman
ResearchOpen Access16 Jul 2024
Scientific Reports

Volume: 14, P: 1-43
ISARIC-COVID-19 dataset: A Prospective, Standardized, Global Dataset of Patients Hospitalized with COVID-19

Ali Abbas
Sheryl Ann Abdukahil
Luis Felipe Reyes
ResearchOpen Access30 Jul 2022
Scientific Data

Volume: 9, P: 1-22

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