LLPS of FXR1 drives spermiogenesis by activating translation of stored mRNAs

JY Kang, Z Wen, D Pan, Y Zhang, Q Li, A Zhong, X Yu… - Science, 2022 - science.org
Postmeiotic spermatids use a unique strategy to coordinate gene expression with
morphological transformation, in which transcription and translation take place at separate …

Utility of proteomics in emerging and re-emerging infectious diseases caused by RNA viruses

M Sperk, R Van Domselaar, JE Rodriguez… - Journal of Proteome …, 2020 - ACS Publications
Emerging and re-emerging infectious diseases due to RNA viruses cause major negative
consequences for the quality of life, public health, and overall economic development. Most …

Regulation of translation by site-specific ribosomal RNA methylation

MD Jansson, SJ Häfner, K Altinel, D Tehler… - Nature structural & …, 2021 - nature.com
Ribosomes are complex ribozymes that interpret genetic information by translating
messenger RNA (mRNA) into proteins. Natural variation in ribosome composition has been …

Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis

E Hartman, AM Scott, C Karlsson, T Mohanty… - Nature …, 2023 - nature.com
The incorporation of machine learning methods into proteomics workflows improves the
identification of disease-relevant biomarkers and biological pathways. However, machine …

MSstats Version 4.0: statistical analyses of quantitative mass spectrometry-based proteomic experiments with chromatography-based quantification at scale

D Kohler, M Staniak, TH Tsai, T Huang… - Journal of Proteome …, 2023 - ACS Publications
The MSstats R-Bioconductor family of packages is widely used for statistical analyses of
quantitative bottom-up mass spectrometry-based proteomic experiments to detect …

Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms

J Lehtiö, T Arslan, I Siavelis, Y Pan, F Socciarelli… - Nature cancer, 2021 - nature.com
Despite major advancements in lung cancer treatment, long-term survival is still rare and a
deeper understanding of molecular phenotypes would allow the identification of specific …

Reprogrammed transsulfuration promotes basal-like breast tumor progression via realigning cellular cysteine persulfidation

K Erdélyi, T Ditrói, HJ Johansson… - Proceedings of the …, 2021 - National Acad Sciences
Basal-like breast cancer (BLBC) is the most aggressive subtype of breast tumors with poor
prognosis and limited molecular-targeted therapy options. We show that BLBC cells have a …

Molecular mechanisms of nanomaterial-bacterial interactions revealed by omics—the role of nanomaterial effect level

M Mortimer, Y Wang, PA Holden - Frontiers in Bioengineering and …, 2021 - frontiersin.org
Nanotechnology is employed across a wide range of antibacterial applications in clinical
settings, food, pharmaceutical and textile industries, water treatment and consumer goods …

MS-DAP platform for downstream data analysis of label-free proteomics uncovers optimal workflows in benchmark data sets and increased sensitivity in analysis of …

F Koopmans, KW Li, RV Klaassen… - Journal of Proteome …, 2022 - ACS Publications
In the rapidly moving proteomics field, a diverse patchwork of data analysis pipelines and
algorithms for data normalization and differential expression analysis is used by the …

Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma

JT Topham, ES Tsang, JM Karasinska… - Nature …, 2022 - nature.com
Oncogenic KRAS mutations are absent in approximately 10% of patients with metastatic
pancreatic ductal adenocarcinoma (mPDAC) and may represent a subgroup of mPDAC with …