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 …

Multi-omics approaches to define calcific aortic valve disease pathogenesis

MC Blaser, S Kraler, TF Lüscher, E Aikawa - Circulation research, 2021 - Am Heart Assoc
Calcific aortic valve disease sits at the confluence of multiple world-wide epidemics of aging,
obesity, diabetes, and renal dysfunction, and its prevalence is expected to nearly triple over …

Mass-spectrometry-based draft of the Arabidopsis proteome

J Mergner, M Frejno, M List, M Papacek, X Chen… - Nature, 2020 - nature.com
Plants are essential for life and are extremely diverse organisms with unique molecular
capabilities. Here we present a quantitative atlas of the transcriptomes, proteomes and …

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

D Wang, B Eraslan, T Wieland, B Hallström… - Molecular systems …, 2019 - embopress.org
Abstract Genome‐, transcriptome‐and proteome‐wide measurements provide insights into
how biological systems are regulated. However, fundamental aspects relating to which …

Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers

A Karollus, T Mauermeier, J Gagneur - Genome biology, 2023 - Springer
Background The largest sequence-based models of transcription control to date are
obtained by predicting genome-wide gene regulatory assays across the human genome …

Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics

R Lou, Y Cao, S Li, X Lang, Y Li, Y Zhang… - Nature …, 2023 - nature.com
A plethora of software suites and multiple classes of spectral libraries have been developed
to enhance the depth and robustness of data-independent acquisition (DIA) data …

Mass spectrometry-based draft of the mouse proteome

P Giansanti, P Samaras, Y Bian, C Meng, A Coluccio… - Nature …, 2022 - nature.com
The laboratory mouse ranks among the most important experimental systems for biomedical
research and molecular reference maps of such models are essential informational tools …

Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine

ST Li, Y Ke, Y Zhu, TY Zhu, H Huang, L Li, Z Hou… - Nature Plants, 2024 - nature.com
Rice is one of the most important staple food and model species in plant biology, yet its
quantitative proteomes are largely uncharacterized. Here we quantify the relative protein …

Uncovering the impacts of alternative splicing on the proteome with current omics techniques

M Reixachs‐Solé, E Eyras - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
The high‐throughput sequencing of cellular RNAs has underscored a broad effect of isoform
diversification through alternative splicing on the transcriptome. Moreover, the differential …

Instrumentation at the leading edge of proteomics

TM Peters-Clarke, JJ Coon, NM Riley - Analytical Chemistry, 2024 - ACS Publications
The proteome, or collection of proteoforms expressed in a biological system, is dynamic and
heterogeneous. As our appreciation for the complexity of the proteome has evolved, so have …