Nature Search

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins

Protein degradation in clinical samples is largely unexplored. Here, the authors analyze the transcriptome and proteome of clinical tissue samples and develop an algorithm to assess protein degradation, showing that protein degradation is negligible in most tissue samples and does not correlate with transcript degradation.

Wenguang Shao
Tiannan Guo
Ruedi Aebersold
ResearchOpen Access07 Jun 2019
Nature Communications

Volume: 10, P: 1-8
Erratum: ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics

Yanlei Ma
Jiping Yue
Xiaoyang Wu
Amendments and CorrectionsOpen Access11 Jul 2017
Nature Communications

Volume: 8, P: 1
Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency

The authors combine multi-layered omics with clinical and biochemical features from individuals affected with methylmalonic aciduria, a rare inherited disease affecting succinyl-CoA synthesis, revealing that anaplerotic rewiring is a targetable feature.

Patrick Forny
Ximena Bonilla
D. Sean Froese
ResearchOpen Access26 Jan 2023
Nature Metabolism

Volume: 5, P: 80-95
Histopathology-based protein multiplex generation using deep learning

HistoPlexer, a deep learning model, generates multiplexed protein expression maps from H&E images, capturing tumour–immune cell interactions. It outperforms baselines, enhances immune subtyping and survival prediction and offers a cost-effective tool for precision oncology.

Sonali Andani
Boqi Chen
Gunnar Rätsch
ResearchOpen Access04 Aug 2025
Nature Machine Intelligence

Volume: 7, P: 1292-1307
A computational framework for the inference of protein complex remodeling from whole-proteome measurements

AlteredPQR is a software tool, available as an R package, to infer remodeling of protein functional modules from whole-cell or tissue lysate proteomic measurements.

Marija Buljan
Amir Banaei-Esfahani
Ruedi Aebersold
ResearchOpen Access25 Sept 2023
Nature Methods

Volume: 20, P: 1523-1529
Lithium extraction with energy generation

Traditional techniques for lithium extraction require considerable energy consumption. A spontaneous process with net energy output driven by counterion gradients presents a promising solution for energetically efficient lithium extraction and enrichment from brine.

Wenguang Wang
Lu Shao
News & Views24 Oct 2024
Nature Water

Volume: 2, P: 1051-1052
Feasibility of multiomics tumor profiling for guiding treatment of melanoma

In the Tumor Profiler proof-of-concept observational study, a multiomics approach for profiling tumors from patients with melanoma was feasible, returning data within 4 weeks and informing treatment recommendations in 75% of cases.

Nicola Miglino
Nora C. Toussaint
Andreas Wicki
ResearchOpen Access27 May 2025
Nature Medicine

Volume: 31, P: 2430-2441
ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics

The cytoskeleton plays a key role in cell/cell junction formation, but how the coordinated behaviour of the cytoskeleton contributes is not known. Here the authors show that actin-microtubule crosslinker ACF7 plays a key role in tight junction stabilization and wound healing in intestinal epithelium.

Yanlei Ma
Jiping Yue
Xiaoyang Wu
ResearchOpen Access25 May 2017
Nature Communications

Volume: 8, P: 1-16
A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation

Wenguang Shao
Min Zhang
Stanley C. K. Lau
ResearchOpen Access23 Sept 2015
Scientific Reports

Volume: 5, P: 1-12
Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma

Nicola Miglino
Nora C. Toussaint
Andreas Wicki
Amendments and CorrectionsOpen Access01 Aug 2025
Nature Medicine

Volume: 31, P: 2817-2818
The chromatin guardian ATRX is a strong prognostic biomarker in melanoma

Céline Arlette Frei
Cassandra Litchfield
Gregor Zuend
ResearchOpen Access18 Dec 2025
Scientific Reports

Volume: 16, P: 1-12
Comparative cost analysis of a diagnostic multi-omics platform for decision support in advanced cancer – results from the Tumor Profiler Melanoma project

Tarun Mehra
Dominik Menges
Andreas Wicki
ResearchOpen Access17 Dec 2025
npj Precision Oncology

Volume: 10, P: 1-9
Identifying sources of tick blood meals using unidentified tandem mass spectral libraries

The identification of hosts of blood-sucking insects is important for studying ecological factors that affect pathogen distribution. Önder et al. report a proteomics-based methodology for the analysis of blood remnants in ticks that identifies the host species from which the tick has fed up to 6 months earlier.

Özlem Önder
Wenguang Shao
Dustin Brisson
Research23 Apr 2013
Nature Communications

Volume: 4, P: 1-10
In vivo epidermal migration requires focal adhesion targeting of ACF7

The spectraplakin protein ACF7 binds to actin at focal adhesions and targets microtubule plus ends to focal adhesions, promoting their disassembly. Here the authors reveal that ACF7 is phosphorylated by Src/FAK, and this regulates actin binding and focal adhesion dynamics in vitro and in vivo.

Jiping Yue
Yao Zhang
Xiaoyang Wu
ResearchOpen Access24 May 2016
Nature Communications

Volume: 7, P: 1-15
Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia

The molecular mechanisms underlying drug resistance in relapsed or refractory (rr) acute myeloid leukemia (AML) remain to be explored. Here, the use of bulk and single cell multi-omics and ex vivo drug profiling for 21 rrAML patients reveals mechanisms of resistance to the Bcl-2 inhibitor venetoclax and treatment vulnerabilities.

Rebekka Wegmann
Ximena Bonilla
Alexandre P. A. Theocharides
ResearchOpen Access30 Oct 2024
Nature Communications

Volume: 15, P: 1-18
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

Trisomy 21 (T21) is a major cause of Down syndrome but little is known about its impact on the cellular proteome. Here, the authors define the proteome of T21 fibroblasts and its turnover and also map proteomic differences in monozygotic T21-discordant twins, revealing extensive, organelle-specific changes caused by T21.

Yansheng Liu
Christelle Borel
Ruedi Aebersold
ResearchOpen Access31 Oct 2017
Nature Communications

Volume: 8, P: 1-15
Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer

Long-read single-cell RNA sequencing is capable of detecting isoform-level gene expression and genomic alterations such as mutations and gene fusions, thereby providing cell-specific genotype-phenotype information. Here, the authors use long-read scRNA-seq on metastatic ovarian cancer samples and detect cell-type specific isoforms and gene fusions that may otherwise be misclassified in short-read data.

Arthur Dondi
Ulrike Lischetti
Niko Beerenwinkel
ResearchOpen Access27 Nov 2023
Nature Communications

Volume: 14, P: 1-19
Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo

Zhaoyong Zhang
Eric Zeng
Jincun Zhao
ResearchOpen Access12 Aug 2021
Cell Discovery

Volume: 7, P: 1-15
Regulation of BMP2K in AP2M1-mediated EGFR internalization during the development of gallbladder cancer

Xiaoling Song
Maolan Li
Yingbin Liu
ResearchOpen Access13 Aug 2020
Signal Transduction and Targeted Therapy

Volume: 5, P: 1-3
A tissue-based draft map of the murine MHC class I immunopeptidome

Heiko Schuster
Wenguang Shao
Etienne Caron
ResearchOpen Access07 Aug 2018
Scientific Data

Volume: 5, P: 1-11
Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries

Özlem Önder
Wenguang Shao
Dustin Brisson
Protocols13 Mar 2014
Nature Protocols

Volume: 9, P: 842-850

Search

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins

Erratum: ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics

Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency

Histopathology-based protein multiplex generation using deep learning

A computational framework for the inference of protein complex remodeling from whole-proteome measurements

Lithium extraction with energy generation

Feasibility of multiomics tumor profiling for guiding treatment of melanoma

ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics

A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation

Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma

The chromatin guardian ATRX is a strong prognostic biomarker in melanoma

Comparative cost analysis of a diagnostic multi-omics platform for decision support in advanced cancer – results from the Tumor Profiler Melanoma project

Identifying sources of tick blood meals using unidentified tandem mass spectral libraries

In vivo epidermal migration requires focal adhesion targeting of ACF7

Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer

Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo

Regulation of BMP2K in AP2M1-mediated EGFR internalization during the development of gallbladder cancer

A tissue-based draft map of the murine MHC class I immunopeptidome

Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries

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