Nature Search

Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19

The immune response is key in determining disease severity of COVID19. Here Nouailles et al., apply bulk proteomics and scRNA-Seq of lung and blood samples of SARS-CoV-2 infected Syrian hamsters and provide a temporal atlas of the systemic and pulmonary cellular responses.

Geraldine Nouailles
Emanuel Wyler
Martin Witzenrath
ResearchOpen Access11 Aug 2021
Nature Communications

Volume: 12, P: 1-18
Augmentation of wastewater-based epidemiology with machine learning to support global health surveillance

Wastewater-based epidemiology has already proven to be a powerful tool to monitor the spread of a number of diseases. This Perspective discusses the integration with machine learning, highlighting its potential in a number of wastewater-based epidemiology applications.

Eva Aßmann
Timo Greiner
Christopher Irrgang
Reviews02 Jun 2025
Nature Water

P: 1-11
The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination

Maatz, Lindberg et al. identify molecular alterations and immune response changes in endomyocardial biopsies from patients with myocarditis after COVID-19 infection, after anti-COVID-19 vaccination or from non-COVID-related causes.

Henrike Maatz
Eric L. Lindberg
Carsten Tschöpe
ResearchOpen Access24 Feb 2025
Nature Cardiovascular Research

Volume: 4, P: 330-345
Publisher Correction: Herpesviruses mimic zygotic genome activation to promote viral replication

Eva Neugebauer
Stephanie Walter
Florian Full
Amendments and CorrectionsOpen Access05 Mar 2025
Nature Communications

Volume: 16, P: 1
Author Correction: Virus-induced senescence is a driver and therapeutic target in COVID-19

Soyoung Lee
Yong Yu
Clemens A. Schmitt
Amendments and Corrections04 Feb 2025
Nature

Volume: 638, P: E46
Herpesviruses mimic zygotic genome activation to promote viral replication

Neugebauer et al. show activation of the usually silenced embryonic factor DUX4 by herpesviruses in vitro and in patients, and demonstrate that depletion of DUX4 by nanobody degraders abrogates viral replication.

Eva Neugebauer
Stephanie Walter
Florian Full
ResearchOpen Access16 Jan 2025
Nature Communications

Volume: 16, P: 1-15
Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids

Modelling herpes simplex virus infection in brain organoids reveals that combined antiviral and anti-inflammatory treatment prevents neuronal damage caused by viral infection.

Agnieszka Rybak-Wolf
Emanuel Wyler
Nikolaus Rajewsky
ResearchOpen Access22 Jun 2023
Nature Microbiology

Volume: 8, P: 1252-1266
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters

Comparison of mucosal and systemic immunity after vaccination with the live-attenuated vaccine sCPD9, mRNA vaccine BNT162b2 or an adenovirus-vectored vaccine following SARS-CoV-2 challenge in hamsters.

Geraldine Nouailles
Julia M. Adler
Jakob Trimpert
ResearchOpen Access03 Apr 2023
Nature Microbiology

Volume: 8, P: 860-874
Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program

Herpes simplex virus 1 (HSV-1) induces major reprogramming of the host cell environment. Here, the authors profile the transcriptomes of individual HSV-1-infected human fibroblasts and provide evidence of an antiviral program mediated by the activation of the host transcription factor NRF2.

Emanuel Wyler
Vedran Franke
Markus Landthaler
ResearchOpen Access25 Oct 2019
Nature Communications

Volume: 10, P: 1-14
SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals

Viruses manipulate host cell pathways to support infection. Here the authors show that SARS-CoV-2 infection modulates cellular metabolism and limits autophagy, and identify druggable host pathways for virus inhibition.

Nils C. Gassen
Jan Papies
Marcel A. Müller
ResearchOpen Access21 Jun 2021
Nature Communications

Volume: 12, P: 1-15
Detecting actively translated open reading frames in ribosome profiling data

RiboTaper quantifies the three-nucleotide periodicity in Ribo-seq data to find translated open reading frames (ORFs). The de novo inferred set of ORFs comprehensively defines the cellular proteome across a wide expression range and comprises few additional translated noncoding regions.

Lorenzo Calviello
Neelanjan Mukherjee
Uwe Ohler
Research14 Dec 2015
Nature Methods

Volume: 13, P: 165-170
Proteomic and transcriptomic profiling of brainstem, cerebellum and olfactory tissues in early- and late-phase COVID-19

Radke et al. found an interferon response in the brainstem nuclei of acute COVID-19 that, in addition to the inflammatory reaction, spreads throughout the vascular unit altering glial cells and resolves in late disease states in the absence of brain infection.

Josefine Radke
Jenny Meinhardt
Helena Radbruch
Research16 Feb 2024
Nature Neuroscience

Volume: 27, P: 409-420
The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants

Multiple variants of SARS-CoV-2 are inhibited by a trispecific DARPin.

Sylvia Rothenberger
Daniel L. Hurdiss
Jakob Trimpert
ResearchOpen Access21 Jul 2022
Nature Biotechnology

Volume: 40, P: 1845-1854
Virus-induced senescence is a driver and therapeutic target in COVID-19

Virus-induced senescence is a central pathogenic feature in COVID-19, and senolytics, which promote apoptosis of senescent cells, can reduce disease severity in hamsters,mice, as well as humans infected with SARS-CoV-2.

Soyoung Lee
Yong Yu
Clemens A. Schmitt
Research13 Sept 2021
Nature

Volume: 599, P: 283-289
Integrative functional genomics decodes herpes simplex virus 1

Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.

Adam W. Whisnant
Christopher S. Jürges
Lars Dölken
ResearchOpen Access27 Apr 2020
Nature Communications

Volume: 11, P: 1-14
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway

The RNA-binding protein RC3H1/ROQUIN1 promotes the degradation of mRNA by binding to a consensus CDE present in the 3′UTR. Here the authors expand the set of consensus sequences through which RCH31 binds and regulates mRNA encoding members of the DNA damage response and IKK/NF-κB pathway.

Yasuhiro Murakawa
Michael Hinz
Markus Landthaler
ResearchOpen Access14 Jul 2015
Nature Communications

Volume: 6, P: 1-14
A biomathematical model of SARS-CoV-2 in Syrian hamsters

Sibylle Schirm
Geraldine Nouailles
Markus Scholz
ResearchOpen Access18 Dec 2024
Scientific Reports

Volume: 14, P: 1-18
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19

Morgan Essex
Belén Millet Pascual-Leone
Bastian Opitz
ResearchOpen Access01 Aug 2024
npj Biofilms and Microbiomes

Volume: 10, P: 1-15
Author Correction: Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses

Swetha Rajasekaran
Jalal Siddiqui
Wayne Miles
Amendments and CorrectionsOpen Access30 Sept 2021
Communications Biology

Volume: 4, P: 1
Human alveolar progenitors generate dual lineage bronchioalveolar organoids

The GSK3 inhibitor CHIR99021 is required to maintain the alveolar lineage in alveolar progenitors grown in airway media or AT2 cells become plastic, with the observed effects acting outside of its role as a GSK3B inhibitor.

Karen Hoffmann
Benedikt Obermayer
Mirjana Kessler
ResearchOpen Access25 Aug 2022
Communications Biology

Volume: 5, P: 1-17
Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses

Swetha Rajasekaran et al. integrate transcriptional, proteomic, and metabolomic data to explore how cells adapt to inactivation of RB1, a hallmark of cancer. Combined with their genetic analyses in a Drosophila model, the authors identify key metabolic pathways that may be involved in the growth of RB1-depleted cancer cells.

Swetha Rajasekaran
Jalal Siddiqui
Wayne Miles
ResearchOpen Access17 Aug 2021
Communications Biology

Volume: 4, P: 1-13

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