scholarly journals A Customizable Analysis Flow in Integrative Multi-Omics

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1606
Author(s):  
Samuel M. Lancaster ◽  
Akshay Sanghi ◽  
Si Wu ◽  
Michael P. Snyder
Keyword(s):  
Machine Learning ◽  
Mass Spectrometry ◽  
Systems Biology ◽  
Nucleic Acid ◽  
Best Practices ◽  
Data Integration ◽  
Study Design ◽  
Molecular Interactions ◽  
Analysis Workflow ◽  
Integration Techniques

The number of researchers using multi-omics is growing. Though still expensive, every year it is cheaper to perform multi-omic studies, often exponentially so. In addition to its increasing accessibility, multi-omics reveals a view of systems biology to an unprecedented depth. Thus, multi-omics can be used to answer a broad range of biological questions in finer resolution than previous methods. We used six omic measurements—four nucleic acid (i.e., genomic, epigenomic, transcriptomics, and metagenomic) and two mass spectrometry (proteomics and metabolomics) based—to highlight an analysis workflow on this type of data, which is often vast. This workflow is not exhaustive of all the omic measurements or analysis methods, but it will provide an experienced or even a novice multi-omic researcher with the tools necessary to analyze their data. This review begins with analyzing a single ome and study design, and then synthesizes best practices in data integration techniques that include machine learning. Furthermore, we delineate methods to validate findings from multi-omic integration. Ultimately, multi-omic integration offers a window into the complexity of molecular interactions and a comprehensive view of systems biology.

Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning

2021 ◽  
Author(s):  
Raghothama Chaerkady ◽  
Yebin Zhou ◽  
Jared A. Delmar ◽  
Shao Huan Samuel Weng ◽  
Junmin Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Mass Spectrometry ◽  
Mast Cells

scholarly journals Frontispiz: In Vivo Subcellular Mass Spectrometry Enables Proteo‐Metabolomic Single‐Cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole ( X. laevis )

2021 ◽  
Vol 133 (23) ◽  
Author(s):  
Camille Lombard‐Banek ◽  
Jie Li ◽  
Erika P. Portero ◽  
Rosemary M. Onjiko ◽  
Chase D. Singer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Systems Biology ◽  
Single Cell ◽  
Cell Systems

scholarly journals Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexandre Maciel-Guerra ◽  
Necati Esener ◽  
Katharina Giebel ◽  
Daniel Lea ◽  
Martin J. Green ◽  
...  
Keyword(s):  
Machine Learning ◽  
Mass Spectrometry ◽  
Treatment Success ◽  
Clinical Mastitis ◽  
Supervised Machine Learning ◽  
Structural Protein ◽  
Cohen’S Kappa ◽  
Maldi Tof ◽  
Streptococcus Uberis ◽  
Cohen's Kappa

AbstractStreptococcus uberis is one of the leading pathogens causing mastitis worldwide. Identification of S. uberis strains that fail to respond to treatment with antibiotics is essential for better decision making and treatment selection. We demonstrate that the combination of supervised machine learning and matrix-assisted laser desorption ionization/time of flight (MALDI-TOF) mass spectrometry can discriminate strains of S. uberis causing clinical mastitis that are likely to be responsive or unresponsive to treatment. Diagnostics prediction systems trained on 90 individuals from 26 different farms achieved up to 86.2% and 71.5% in terms of accuracy and Cohen’s kappa. The performance was further increased by adding metadata (parity, somatic cell count of previous lactation and count of positive mastitis cases) to encoded MALDI-TOF spectra, which increased accuracy and Cohen’s kappa to 92.2% and 84.1% respectively. A computational framework integrating protein–protein networks and structural protein information to the machine learning results unveiled the molecular determinants underlying the responsive and unresponsive phenotypes.

scholarly journals Best practices in machine learning for chemistry

2021 ◽  
Vol 13 (6) ◽  
pp. 505-508
Author(s):  
Nongnuch Artrith ◽  
Keith T. Butler ◽  
François-Xavier Coudert ◽  
Seungwu Han ◽  
Olexandr Isayev ◽  
...  
Keyword(s):  
Machine Learning ◽  
Best Practices

scholarly journals A data integration methodology for systems biology

2005 ◽  
Vol 102 (48) ◽  
pp. 17296-17301 ◽  
Author(s):  
D. Hwang ◽  
A. G. Rust ◽  
S. Ramsey ◽  
J. J. Smith ◽  
D. M. Leslie ◽  
...  
Keyword(s):  
Systems Biology ◽  
Data Integration

Interpretable machine learning model to detect chemically adulterated urine samples analyzed by high resolution mass spectrometry

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Gabriel L. Streun ◽  
Andrea E. Steuer ◽  
Lars C. Ebert ◽  
Akos Dobay ◽  
Thomas Kraemer
Keyword(s):  
Machine Learning ◽  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
High Resolution ◽  
Retention Time ◽  
Drug Testing ◽  
High Resolution Mass Spectrometry ◽  
Urine Samples ◽  
Machine Learning Model ◽  
Resolution Mass

Abstract Objectives Urine sample manipulation including substitution, dilution, and chemical adulteration is a continuing challenge for workplace drug testing, abstinence control, and doping control laboratories. The simultaneous detection of sample manipulation and prohibited drugs within one single analytical measurement would be highly advantageous. Machine learning algorithms are able to learn from existing datasets and predict outcomes of new data, which are unknown to the model. Methods Authentic human urine samples were treated with pyridinium chlorochromate, potassium nitrite, hydrogen peroxide, iodine, sodium hypochlorite, and water as control. In total, 702 samples, measured with liquid chromatography coupled to quadrupole time-of-flight mass spectrometry, were used. After retention time alignment within Progenesis QI, an artificial neural network was trained with 500 samples, each featuring 33,448 values. The feature importance was analyzed with the local interpretable model-agnostic explanations approach. Results Following 10-fold cross-validation, the mean sensitivity, specificity, positive predictive value, and negative predictive value was 88.9, 92.0, 91.9, and 89.2%, respectively. A diverse test set (n=202) containing treated and untreated urine samples could be correctly classified with an accuracy of 95.4%. In addition, 14 important features and four potential biomarkers were extracted. Conclusions With interpretable retention time aligned liquid chromatography high-resolution mass spectrometry data, a reliable machine learning model could be established that rapidly uncovers chemical urine manipulation. The incorporation of our model into routine clinical or forensic analysis allows simultaneous LC-MS analysis and sample integrity testing in one run, thus revolutionizing this field of drug testing.

scholarly journals Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma

2020 ◽  
Vol 20 (1) ◽  
pp. 841-857
Author(s):  
Malena Manzi ◽  
Martín Palazzo ◽  
María Elena Knott ◽  
Pierre Beauseroy ◽  
Patricio Yankilevich ◽  
...  
Keyword(s):  
Machine Learning ◽  
Mass Spectrometry ◽  
Renal Cell Carcinoma ◽  
Early Detection ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Learning Approach ◽  
Cell Renal Cell Carcinoma ◽  
Machine Learning Approach
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