AIMC Topic: Proteomics

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Meltome Atlas of Arabidopsis thaliana proteome: a melting temperature-based identification of heat and cold resistant proteins using in-silico approach.

BMC genomics
BACKGROUND: Plants are always exposed to a variety of stressful environments, including heat and drought stress, which severely impact the growth, development, and productivity of the plants. To overcome such challenges, plants have evolved diverse a...

SpecQuality: A Tool for Reliable Spectral Quality Assessment in Proteomics and Proteogenomics.

Journal of the American Society for Mass Spectrometry
Proteogenomics integrates genomics and mass spectrometry (MS) data to understand complex biological systems, disease mechanisms, and potential biomarkers. However, the high volume and noise in MS data present computational and interpretational challe...

Integrated transcriptomics and proteomics reveal ferroptosis induced by B[a]P and BPDE in mouse hippocampal neurons.

Scientific reports
The environmental pollutant Benzo[a]pyrene (B[a]P) and its ultimate metabolite B[a]P-7,8-diol-9,10-epoxide (BPDE) exhibit neurotoxic effects, yet the underlying molecular mechanisms remain enigmatic. Recently, ferroptosis has emerged as a potential p...

Multi-omics strategies for biomarker discovery and application in personalized oncology.

Molecular biomedicine
Multi-omics strategies, integrating genomics, transcriptomics, proteomics, and metabolomics, have revolutionized biomarker discovery and enabled novel applications in personalized oncology. Despite rapid technological developments, a comprehensive sy...

AI-driven multi-omics integration in precision oncology: bridging the data deluge to clinical decisions.

Clinical and experimental medicine
Cancer's staggering molecular heterogeneity demands innovative approaches beyond traditional single-omics methods. The integration of multi-omics data, spanning genomics, transcriptomics, proteomics, metabolomics and radiomics, can improve diagnostic...

Distinct immune-metabolic phenotypes underlie poor coronary collateral circulation.

Cardiovascular diabetology
BACKGROUND: Coronary collateral circulation (CCC) significantly impacts myocardial perfusion and clinical outcomes in coronary artery disease patients, yet the underlying molecular heterogeneity remains inadequately characterized.

Recent Advances in Integrating Machine Learning with Omics Approaches in Food Science and Nutrition Research.

Journal of agricultural and food chemistry
Omics technologies are revolutionizing food and nutrition research by enabling high-throughput analysis of food components and microorganisms and revealing the intricate relationships between food and human health. Machine learning (ML) methods are p...

OmniCLIC: A Unified Omics Contrastive Learning Framework for Effective Integration and Classification of Multiomics Data.

Journal of chemical information and modeling
Integrating multiomics data for cancer subtype classification remains a critical yet challenging task due to the high dimensionality, heterogeneity, and limited interpretability of omics features. To address these limitations, we propose OmniCLIC, a ...

Multi-omics-based decoding of circulating biomarkers in amyotrophic lateral sclerosis and risks in environmental toxins.

BMC pharmacology & toxicology
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the interplay of genetic and environmental factors, and currently, there there is a lack of effective diagnostic or therapeutic strategies available...

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.

Nature communications
Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico g...