Nature Search

De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome

Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core and dispensable transcriptome, and reveal conservation and divergence of gene expression balance across homoeologous subgenomes.

Benjamen White
Thomas Lux
Anthony Hall
ResearchOpen Access06 Oct 2025
Nature Communications

Volume: 16, P: 1-15
Design and nonviral delivery of live attenuated vaccine to prevent chronic hepatitis C virus-like infection

Hepatitis C virus lacks an effective vaccine, partly due to the absence of suitable animal models for testing. Here, the authors develop a live-attenuated vaccine, using synonymous mutagenesis in rodent hepacivirus, and demonstrate induction of a protective T cell response and protection from chronic infection in rats.

Sheetal Trivedi
Piyush Dravid
Amit Kapoor
ResearchOpen Access15 Aug 2025
Nature Communications

Volume: 16, P: 1-13
Sequence data as evidence

Edward C. Holmes
Andrew J. Leigh Brown
Peter Simmonds
Research26 Aug 1993
Nature

Volume: 364, P: 766
Broad and strong memory CD4⁺ and CD8⁺ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

Questions have arisen as to whether patients with severe COVID-19 disease can generate a T cell response against SARS-CoV-2. Tao Dong and colleagues report that convalescent patients with COVID-19 harbor functional memory CD4⁺ and CD8⁺ T cells that recognize multiple epitopes that span the viral proteome. CD4⁺ T cells predominated the memory response in patients with severe disease, whereas higher proportions of CD8⁺ T cells were found in patients with mild disease.

Yanchun Peng
Alexander J. Mentzer
Tao Dong
Research04 Sept 2020
Nature Immunology

Volume: 21, P: 1336-1345
HIV-1 tropism and co-receptor use

Matthias T. Dittmar
Áine McKnight
Peter Simmonds
Research06 Feb 1997
Nature

Volume: 385, P: 495-496
Genomic investigations of unexplained acute hepatitis in children

An investigation using various methods reports an association between adeno-associated virus 2 and paediatric hepatitis of unknown aetiology.

Sofia Morfopoulou
Sarah Buddle
Judith Breuer
ResearchOpen Access30 Mar 2023
Nature

Volume: 617, P: 564-573
IPO plans sour on both sides of the pond

Biotech companies had to lower their pricing before floating on public markets.

Peter Mitchell
News27 Jul 2004
Nature Biotechnology

Volume: 22, P: 929-930
Alexander Lerner: a call for action

PETER ARCHER
DAVID SHEPPARD
A.H. VANDEN HEUVEL
Correspondence06 Dec 1979
Nature

Volume: 282, P: 554
From Czestochowa to Yale

Peter N. Campbell
Books & Arts05 Jan 1995
Nature

Volume: 373, P: 31-32
Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants

Paul R Burton
David G Clayton
Matthew A Brown
Research21 Oct 2007
Nature Genetics

Volume: 39, P: 1329-1337
Whaling: Don't trade the moratorium away

Mark Peter Simmonds
Sue Fisher
Correspondence15 Feb 2012
Nature

Volume: 482, P: 308
Hypoxanthine, Xanthine, and Uric Acid Concentrations in the Cerebrospinal Fluid, Plasma, and Urine of Hypoxemic Pigs

Jan Peter Poulsen
Stephanie Øyasæter
Ola Didrik Saugstad
Research01 Nov 1990
Pediatric Research

Volume: 28, P: 477-481
Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

Sofosbuvir is a common therapy in hepatitis C virus infection, which targets the NS5B polymerase. Here, Smith et al. analyze the association between whole genome HCV polymorphisms and sofosbuvir treatment failure and identify three common polymorphisms present in non-targeted NS2 and NS3 proteins associated with reduced treatment response.

David A. Smith
Carlota Fernandez-Antunez
M. Azim Ansari
ResearchOpen Access20 Oct 2021
Nature Communications

Volume: 12, P: 1-11
Seroepidemiology of enterovirus A71 infection in prospective cohort studies of children in southern China, 2013-2018

Hand, foot and mouth disease, caused by enterovirus A71 (EV-A71) infection, is common in children in China. Here, the authors estimate EV-A71 incidence and seroprevalence using data from two longitudinal cohorts and find that, despite high infection rates, a large proportion of children under 6 are susceptible.

Juan Yang
Qiaohong Liao
Hongjie Yu
ResearchOpen Access26 Nov 2022
Nature Communications

Volume: 13, P: 1-10
Influence of grazing

Peter D. Moore
News & Views01 Jul 1976
Nature

Volume: 262, P: 6-7
Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil

Emerging variants of SARS-CoV-2 raise concerns about vaccine efficiency. Here, the authors present a post-hoc analysis for the ChAdOx1 nCoV-19 (AZD1222) vaccine trial in Brazil and provide efficacy against symptomatic COVID-19 caused by the Zeta (P.2) and other variants.

Sue Ann Costa Clemens
Pedro M. Folegatti
Rafael Zimmer
ResearchOpen Access06 Oct 2021
Nature Communications

Volume: 12, P: 1-10
Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

Chris Spencer, Eleanor Barnes and colleagues use human genotyping arrays and whole-genome viral sequencing to perform a systematic genome-to-genome study of 542 individuals chronically infected with hepatitis C virus (HCV). They show that both HLA alleles and genes encoding factors of the innate immune system drive viral genome polymorphism and that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific polymorphism encoded in the HCV polyprotein.

M Azim Ansari
Vincent Pedergnana
Chris C A Spencer
Research10 Apr 2017
Nature Genetics

Volume: 49, P: 666-673
Prisoners of war — host adaptation and its constraints on virus evolution

Studies of ancient DNA and endogenous viral elements have revealed extraordinary conservation of virus genome sequences over thousands or millions of years. In this Opinion article, Simmonds, Aiewsakun and Katzourakis describe a niche-filling model that describes how viruses can rapidly evolve to adapt to new host environments while their longer-term evolution is increasingly driven by their hosts.

Peter Simmonds
Pakorn Aiewsakun
Aris Katzourakis
Reviews05 Dec 2018
Nature Reviews Microbiology

Volume: 17, P: 321-328
The circadian clock components BMAL1 and REV-ERBα regulate flavivirus replication

The circadian clock can affect pathogen replication, but underlying molecular mechanisms are unclear. Here the authors demonstrate that the circadian components BMAL1 and REV-ERBα affect entry of hepatitis C virus (HCV) into hepatocytes and genome replication of HCV and related flaviviruses dengue and zika.

Xiaodong Zhuang
Andrea Magri
Jane A. McKeating
ResearchOpen Access22 Jan 2019
Nature Communications

Volume: 10, P: 1-13
Rapid increase in ozone-depleting chloroform emissions from China

Atmospheric levels of chloroform increased after 2010, as a result of emissions in eastern China, according to analyses of measurements and inverse modelling.

Xuekun Fang
Sunyoung Park
Ronald G. Prinn
Research21 Dec 2018
Nature Geoscience

Volume: 12, P: 89-93
MAIT cells are activated during human viral infections

Mucosal Associated Invariant T cells have been implicated in response to bacterial pathogens. Here the authors show that in human viral infections, these cells are activated by IL-18 in cooperation with other pro-inflammatory cytokines, producing interferon gamma and granzyme B.

Bonnie van Wilgenburg
Iris Scherwitzl
Paul Klenerman
ResearchOpen Access23 Jun 2016
Nature Communications

Volume: 7, P: 1-11
Reply to ‘Evolutionary stasis of viruses?’

Peter Simmonds
Pakorn Aiewsakun
Aris Katzourakis
Correspondence27 Feb 2019
Nature Reviews Microbiology

Volume: 17, P: 329-330
Low European methyl chloroform emissions inferred from long-term atmospheric measurements

Stefan Reimann
Alistair J. Manning
Doris Folini
Research03 Feb 2005
Nature

Volume: 433, P: 506-508
ZINC-MEDIATED URATE BINDING TO HUMAN ALBUMIN: 63

James L Fleckenstein
Peter A Simkin
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 754
EFFECTS OF 4′-THIOADENOSINE ON HL-60 HUMAN PROMYELOCYTIC LEUKEMIA CELLS: 134

George A Miura
Richard K Gordon
Peter K Chiang
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 766
CHANGES OF PURINE METABOLISM DURING DIFFERENTIATION OF RAT HEART MYOBLASTS: 138

Mathias M Müller
Helmut Rumpold
Peter Zilla
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 766
CORRECTED CLEARANCE IDENTIFIES UNDEREXCRETION OF URIC ACID IN A GOUTY KINDRED: 64

James L Fleckenstein
Peter A Simkin
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 754
Antisoma–Roche deal—a new kind of buyout?

Peter Mitchell
News01 Jan 2003
Nature Biotechnology

Volume: 21, P: 3
Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Evelien M. Adriaenssens
Simon Roux
Bas E. Dutilh
Amendments and Corrections22 Aug 2023
Nature Biotechnology

Volume: 41, P: 1346
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

An exciting genome-wide association study in the British population for seven common diseases. This analysis confirms previously identified loci and provides strong evidence for many novel disease susceptibility loci.

Paul R. Burton
David G. Clayton
Jane Worthington
Research07 Jun 2007
Nature

Volume: 447, P: 661-678
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

Mohammed Sebaihia
Brendan W Wren
Julian Parkhill
Research25 Jun 2006
Nature Genetics

Volume: 38, P: 779-786
Virus taxonomy in the age of metagenomics

Although viral sequences are important in taxonomy, classification has typically also required biological properties, thus excluding viruses that were identified by metagenomics. The proposals in this Consensus Statement, which are supported by the International Committee on Taxonomy of Viruses (ICTV), enable viruses that are discovered by sequence alone to be incorporated into virus classification.

Peter Simmonds
Mike J. Adams
F. Murilo Zerbini
ReviewsOpen Access03 Jan 2017
Nature Reviews Microbiology

Volume: 15, P: 161-168
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Copy number variants (CNVs) account for a major proportion of human genetic diversity and may contribute to genetic susceptibility to disease. Here, a large, genome-wide study of association between common CNVs and eight common human diseases is presented. The study provides a wealth of technical insights that will inform future study design and analysis. The results also indicate that common CNVs that can be 'typed' on existing platforms are unlikely to contribute much to the genetic basis of common diseases.

Nick Craddock
Matthew E. Hurles
Peter Donnelly
Research01 Apr 2010
Nature

Volume: 464, P: 713-720
TRANSITIONAL URATE CRYSTALS: A FACTOR IN GOUTY ARTHRITIS?: 191

Peter A Simkin
Richard S Benedict
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 775
GENETIC EXPRESSION OF ADENOSINE DEAMINASE (ADA) IN HUMAN LYMPHOID MALIGNANCIES: 67

T Eng Gan
Peter Daddona
Beverly Mitchell
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 755
EVIDENCE FOR A MEMBRANE ADENOSINE RECEPTOR IN LEISHMANIA MEXICANA MEXICANA (WR224): 79

Brian D Hansen
J Perez-Arbelo
Peter K Chiang
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 757
A functional investigation of the suppression of CpG and UpA dinucleotide frequencies in plant RNA virus genomes

Ahmad Ibrahim
Jelke Fros
Peter Simmonds
ResearchOpen Access04 Dec 2019
Scientific Reports

Volume: 9, P: 1-14
Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Evelien M. Adriaenssens
Simon Roux
Bas E. Dutilh
Correspondence10 Jul 2023
Nature Biotechnology

Volume: 41, P: 898-902
Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

New methods and larger sample groups are used to precisely determine the alleles in the HLA complex which contribute susceptibility to type 1 diabetes.

Sergey Nejentsev
Joanna M. M. Howson
Jane Worthington
Research14 Nov 2007
Nature

Volume: 450, P: 887-892
Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza

Influenza can occasionally result in life-threatening sequelae. Openshaw and colleagues describe the functional and transcriptional response to natural infection with influenza virus and find that a transition to an ‘anti-bacterial response’ is associated with more-severe symptoms.

Jake Dunning
Simon Blankley
Mark J. Griffiths
Research18 May 2018
Nature Immunology

Volume: 19, P: 625-635
Divertor shaping with neutral baffling as a solution to the tokamak power exhaust challenge

Power exhaust is one of the biggest challenges stopping fusion energy. This article shows experimental evidence for strategically shaping the power exhaust region as a solution to this challenge, utilising physics understanding to strike a balance between engineering complexity and power exhaust benefits, consistent with reduced models and simulations.

Kevin Verhaegh
James Harrison
V. Zamkovska
ResearchOpen Access23 May 2025
Communications Physics

Volume: 8, P: 1-15
Author Correction: Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza

Jake Dunning
Simon Blankley
Peter J. M. Openshaw
Amendments and Corrections07 Feb 2019
Nature Immunology

Volume: 20, P: 373
Survival and disease characteristics of de novo versus recurrent metastatic breast cancer in a cohort of young patients

Hayley S. McKenzie
Tom Maishman
Ellen Copson
ResearchOpen Access31 Mar 2020
British Journal of Cancer

Volume: 122, P: 1618-1629
The evolution of SARS-CoV-2

In this Review, Markov, Katzourakis and colleagues explore the evolution of SARS-CoV-2 at different scales, the phases of the COVID-19 pandemic, factors that drive the evolution of the virus, theories for the emergence of epidemiologically important variants and potential future evolutionary scenarios and their likely health repercussions.

Peter V. Markov
Mahan Ghafari
Aris Katzourakis
Reviews05 Apr 2023
Nature Reviews Microbiology

Volume: 21, P: 361-379
Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.

Barbara Mühlemann
Terry C. Jones
Eske Willerslev
Research09 May 2018
Nature

Volume: 557, P: 418-423
Overview and experience of the YODA Project with clinical trial data sharing after 5 years

Joseph S. Ross
Joanne Waldstreicher
Harlan M. Krumholz
ResearchOpen Access27 Nov 2018
Scientific Data

Volume: 5, P: 1-14
Lion and spotted hyena distributions within a buffer area of the Serengeti-Mara ecosystem

Stanslaus B. Mwampeta
Clay M. Wilton
Jerrold L. Belant
ResearchOpen Access15 Nov 2021
Scientific Reports

Volume: 11, P: 1-8
ERYTHROCYTE GTP DEPLETION IN PNP DEFICIENCY PRESENTING WITH HAEMOLYTIC ANAEMIA AND HYPODRICAEMIA: 193

H Anne Simmonds
Lynette D Fairbanks
Peter Timms
Research01 Jul 1985
Pediatric Research

Volume: 19, P: 776
Chronic Olanzapine Treatment Causes Differential Expression of Genes in Frontal Cortex of Rats as Revealed by DNA Microarray Technique

S Hossein Fatemi
Teri J Reutiman
Mitsunori Fukuda
Research11 Jan 2006
Neuropsychopharmacology

Volume: 31, P: 1888-1899
Plasma Concentrations of Neuroactive Steroids before and after Electroconvulsive Therapy in Major Depression

Thomas C Baghai
Flavia di Michele
Rainer Rupprecht
Research09 Feb 2005
Neuropsychopharmacology

Volume: 30, P: 1181-1186

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