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Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning

Imputation in mass spectrometry-based proteomics is a recurrent step of importance for downstream analysis. Here, the authors offer an extensive comparison workflow of 27 established with three new scalable, fast and performant methods from deep learning for large and high-dimensional data.

Henry Webel
Lili Niu
Simon Rasmussen
ResearchOpen Access26 Jun 2024
Nature Communications

Volume: 15, P: 1-15
Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models

Clinical multi-omics data are integrated and analyzed using a generative deep-learning model.

Rosa Lundbye Allesøe
Agnete Troen Lundgaard
Moustafa Abdalla
ResearchOpen Access02 Jan 2023
Nature Biotechnology

Volume: 41, P: 399-408
Mass spectrometry-based proteomics data from thousands of HeLa control samples

Henry Webel
Yasset Perez-Riverol
Simon Rasmussen
ResearchOpen Access23 Jan 2024
Scientific Data

Volume: 11, P: 1-7
Noninvasive proteomic biomarkers for alcohol-related liver disease

Interogation of mass-spectrometry-based proteomics of liver and plasma from a cohort of patients with alcohol-related liver disease identifies noninvasive biomarkers associated with early stages of disease progression, including significant fibrosis, inflammation and steatosis.

Lili Niu
Maja Thiele
Matthias Mann
ResearchOpen Access02 Jun 2022
Nature Medicine

Volume: 28, P: 1277-1287
A decentralized delivery program for rheumatic heart disease treatment and prevention in Uganda

Doreen Nakagaayi
Jafesi Pulle
David Watkins
Correspondence02 Jan 2024
Nature Medicine

Volume: 30, P: 12-13
Author Correction: Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models

Rosa Lundbye Allesøe
Agnete Troen Lundgaard
Moustafa Abdalla
Amendments and CorrectionsOpen Access02 May 2023
Nature Biotechnology

Volume: 41, P: 1026
Markers of inflammation predict survival in newly diagnosed cirrhosis: a prospective registry study

Thit Mynster Kronborg
Henry Webel
Nina Kimer
ResearchOpen Access16 Nov 2023
Scientific Reports

Volume: 13, P: 1-11
A proteomics sample metadata representation for multiomics integration and big data analysis

The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and integrate them into ProteomeXchange repositories.

Chengxin Dai
Anja Füllgrabe
Yasset Perez-Riverol
ReviewsOpen Access06 Oct 2021
Nature Communications

Volume: 12, P: 1-8
Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering

A metagenomic analysis of 757 sewage samples from 101 countries suggests that global differences in some species might be caused by regional environmental selection.

Marie Louise Jespersen
Patrick Munk
Frank M. Aarestrup
ResearchOpen Access08 Jul 2023
Communications Biology

Volume: 6, P: 1-9

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