Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation

ES Nakayasu, M Gritsenko, PD Piehowski, Y Gao… - Nature …, 2021 - nature.com
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new
disease biomarkers. However, certain critical steps of study design such as cohort selection …

Identification of bioactive metabolites using activity metabolomics

MM Rinschen, J Ivanisevic, M Giera… - Nature reviews Molecular …, 2019 - nature.com
The metabolome, the collection of small-molecule chemical entities involved in metabolism,
has traditionally been studied with the aim of identifying biomarkers in the diagnosis and …

Opportunities and obstacles for deep learning in biology and medicine

T Ching, DS Himmelstein… - Journal of the …, 2018 - royalsocietypublishing.org
Deep learning describes a class of machine learning algorithms that are capable of
combining raw inputs into layers of intermediate features. These algorithms have recently …

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

R Argelaguet, B Velten, D Arnol, S Dietrich… - Molecular systems …, 2018 - embopress.org
Multi‐omics studies promise the improved characterization of biological processes across
molecular layers. However, methods for the unsupervised integration of the resulting …

Integrated omics: tools, advances and future approaches

BB Misra, C Langefeld, M Olivier… - Journal of molecular …, 2019 - jme.bioscientifica.com
With the rapid adoption of high-throughput omic approaches to analyze biological samples
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …

Integrating artificial intelligence and nanotechnology for precision cancer medicine

O Adir, M Poley, G Chen, S Froim, N Krinsky… - Advanced …, 2020 - Wiley Online Library
Artificial intelligence (AI) and nanotechnology are two fields that are instrumental in realizing
the goal of precision medicine—tailoring the best treatment for each cancer patient. Recent …

Machine learning applications for mass spectrometry-based metabolomics

UW Liebal, ANT Phan, M Sudhakar, K Raman… - Metabolites, 2020 - mdpi.com
The metabolome of an organism depends on environmental factors and intracellular
regulation and provides information about the physiological conditions. Metabolomics helps …

Machine learning and integrative analysis of biomedical big data

B Mirza, W Wang, J Wang, H Choi, NC Chung, P Ping - Genes, 2019 - mdpi.com
Recent developments in high-throughput technologies have accelerated the accumulation
of massive amounts of omics data from multiple sources: genome, epigenome …

Perspective of artificial intelligence in healthcare data management: A journey towards precision medicine

NS Gupta, P Kumar - Computers in Biology and Medicine, 2023 - Elsevier
Mounting evidence has highlighted the implementation of big data handling and
management in the healthcare industry to improve the clinical services. Various private and …

Machine and deep learning meet genome-scale metabolic modeling

G Zampieri, S Vijayakumar, E Yaneske… - PLoS computational …, 2019 - journals.plos.org
Omic data analysis is steadily growing as a driver of basic and applied molecular biology
research. Core to the interpretation of complex and heterogeneous biological phenotypes …