Understudied proteins: opportunities and challenges for functional proteomics

G Kustatscher, T Collins, AC Gingras, T Guo… - Nature …, 2022 - nature.com
Most research aiming at understanding the molecular foundations of life and disease has
focused on a limited set of increasingly well-known proteins while the biological functions of …

mRNAs, proteins and the emerging principles of gene expression control

C Buccitelli, M Selbach - Nature Reviews Genetics, 2020 - nature.com
Gene expression involves transcription, translation and the turnover of mRNAs and proteins.
The degree to which protein abundances scale with mRNA levels and the implications in …

The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest

D Szklarczyk, R Kirsch, M Koutrouli… - Nucleic acids …, 2023 - academic.oup.com
Much of the complexity within cells arises from functional and regulatory interactions among
proteins. The core of these interactions is increasingly known, but novel interactions …

The ProteomeXchange consortium at 10 years: 2023 update

EW Deutsch, N Bandeira, Y Perez-Riverol… - Nucleic acids …, 2023 - academic.oup.com
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput
proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www …

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Y Perez-Riverol, J Bai, C Bandla… - Nucleic acids …, 2022 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www. ebi. ac. uk/pride/) is
the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is …

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

D Szklarczyk, AL Gable, KC Nastou, D Lyon… - Nucleic acids …, 2021 - academic.oup.com
Cellular life depends on a complex web of functional associations between biomolecules.
Among these associations, protein–protein interactions are particularly important due to their …

[HTML][HTML] Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context

M Morgenstern, CD Peikert, P Lübbert, I Suppanz… - Cell metabolism, 2021 - cell.com
Mitochondria are key organelles for cellular energetics, metabolism, signaling, and quality
control and have been linked to various diseases. Different views exist on the composition of …

The PRIDE database at 20 years: 2025 update

Y Perez-Riverol, C Bandla, DJ Kundu… - Nucleic Acids …, 2024 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www. ebi. ac. uk/pride/) is
the world's leading mass spectrometry (MS)-based proteomics data repository and one of …

Visualization of very large high-dimensional data sets as minimum spanning trees

D Probst, JL Reymond - Journal of Cheminformatics, 2020 - Springer
The chemical sciences are producing an unprecedented amount of large, high-dimensional
data sets containing chemical structures and associated properties. However, there are …

Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target

S Lechner, MIP Malgapo, C Grätz… - Nature chemical …, 2022 - nature.com
Drugs that target histone deacetylase (HDAC) entered the pharmacopoeia in the 2000s.
However, some enigmatic phenotypes suggest off-target engagement. Here, we developed …