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Selection of microbial biomarkers with genetic algorithm and principal component analysis

Ping Zhang, Nicholas P. West, Pin-Yen Chen, Mike W. C. Thang, Gareth Price, Allan W. Cripps, Amanda J. Cox
2019 BMC Bioinformatics  
This study aimed to develop a prediction model that combines PCA and a genetic algorithm (GA) for identifying sets of bacterial species associated with obesity and metabolic syndrome (Mets).  ...  The advantages of combining PCA with GA were demonstrated. The proposed algorithm overcomes the limitation of PCA for data analysis.  ...  The microbial compositional profiling data used was generated as part of projects funded by the Australian Institute of Sport and the Gold Coast Hospital Foundation.  ... 
doi:10.1186/s12859-019-3001-4 pmid:31823717 pmcid:PMC6904994 fatcat:5amw3fqedvhepa6o7mirpkglqe

Combination of Principal Component Analysis and Genetic Algorithm for Microbial Biomarker Identification in Obesity

Ping Zhang, Nicholas West, Pin-Yen Chen, Allan Cripps, Amanda Cox
2018 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
Results: GA has selected the subsets of the principal components (PCs) produced by PCA.  ...  Genetic algorithms (GA) can be useful and efficient for searching the best combination of variables to build a prediction model.  ...  The microbial compositional profiling data used was generated as part of projects funded by the Australian Institute of Sport and the Gold Coast Hospital Foundation.  ... 
doi:10.1109/bibm.2018.8621413 dblp:conf/bibm/ZhangWCCC18 fatcat:ql5qsyggw5hdvjspvgpxnxqnly

Identification of Pathogens by Mass Spectrometry

Y.-P. Ho, P. M. Reddy
2010 Clinical Chemistry  
MS coupled with various chromatography- and affinity-based techniques simplifies the complexity of the signals of the microbial biomarkers and provides more accurate results.  ...  Direct analysis of whole pathogenic microbial cells using MS without sample fractionation reveals specific biomarkers for taxonomy and provides rapid and high-throughput capabilities.  ...  Acknowledgments: We thank the National Science Council of the Republic of China for financially supporting part of the work mentioned in this review.  ... 
doi:10.1373/clinchem.2009.138867 pmid:20167691 pmcid:PMC7108202 fatcat:5hw35pmp2fc5nlswlxuofj7gpu

Impact of No-Tillage and Conventional Tillage Systems on Soil Microbial Communities

Reji P. Mathew, Yucheng Feng, Leonard Githinji, Ramble Ankumah, Kipling S. Balkcom
2012 Applied and Environmental Soil Science  
Results of principal components analysis based on soil physicochemical and enzyme variables were in agreement with those based on PLFA and ARISA profiles.  ...  Soil organic carbon was positively correlated with most of the PLFA biomarkers.  ...  Zhanjiang (John) Liu for the use of LI-COR 4300 sequencer in the Fish Molecular Genetics and Biotechnology Laboratory at Auburn University and Dr.  ... 
doi:10.1155/2012/548620 fatcat:smhvnoswmnc6bggjico2li7ony

Sparse-Low Rank Matrix Decomposition Framework For Identifying Potential Biomarkers For Inflammatory Bowel Disease

Ahmad Al Kawam, Erchin Serpedin, Mustafa Shawaqfeh
2018 Zenodo  
Publication in the conference proceedings of EUSIPCO, Kos island, Greece, 2017  ...  Feature transformation methods are divided into two types: supervised algorithms such as principal component analysis (PCA) and unsupervised approaches such as linear discriminant analysis-(LDA) and partial  ...  Robust Principal Component Analysis RPCA modifies the standard PCA to accounts for grossly corrupted observations.  ... 
doi:10.5281/zenodo.1159331 fatcat:k5hl43c4obcbzk4gh3ji3zqta4

Differentiation of Cystic Fibrosis-Related Pathogens by Volatile Organic Compound Analysis with Secondary Electrospray Ionization Mass Spectrometry

Jérôme Kaeslin, Srdjan Micic, Ronja Weber, Simona Müller, Nathan Perkins, Christoph Berger, Renato Zenobi, Tobias Bruderer, Alexander Moeller
2021 Metabolites  
From 180 headspace samples, the six pathogens are distinguishable in the first three principal components and predictive analysis with a support vector machine algorithm using leave-one-out cross-validation  ...  Secondary electrospray ionization high-resolution mass spectrometry (SESI-HRMS) is an ideal technique for VOC-biomarker discovery because of its speed, sensitivity towards polar molecules and compound  ...  Principal component scores plots of the 6 pathogen groups generated by the selected 31 m/z-representants. (A) PC scores plot of the first two principal components (58.49%).  ... 
doi:10.3390/metabo11110773 pmid:34822431 pmcid:PMC8617967 fatcat:v2xhwksbqzas5ec7yo3b4t4rhq

Inflammatory Bowel Disease Biomarkers of Human Gut Microbiota Selected via Ensemble Feature Selection Methods [article]

Hilal Hacilar, O.Ufuk Nalbantoglu, Oya Aran, Burcu Bakir-Gungor
2020 arXiv   pre-print
To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy  ...  , ii) to discover IBD associated biomarkers, iii) to find subgroups of IBD patients using k means and hierarchical clustering.  ...  Figure 9 . 9 Principal component analysis of (a, c) all IBD-associated metagenomics dataset, (b, d) reduced dataset that includes features for top scoring 24 species.  ... 
arXiv:2001.03019v1 fatcat:rytcsqinevarjhmciwzlr6aj74

Predictive Modeling of Type 1 Diabetes Stages Using Disparate Data Sources

Brigitte I. Frohnert, Bobbie-Jo Webb-Robertson, Lisa M. Bramer, Sara M. Reehl, Kathy Waugh, Andrea K. Steck, Jill M. Norris, Marian Rewers
2019 Diabetes  
Predictors of IA and progression to diabetes were identified across disparate sources using an integrative machine learning algorithm and optimization-based feature selection.  ...  This study aims to model genetic, immunologic, metabolomics, and proteomic biomarkers for development of islet autoimmunity (IA) and progression to type 1 diabetes in a prospective high-risk cohort.  ...  The biomarker panels identified in this analysis represent an individualized prediction algorithm based on a set of disparate features (e.g., metabolites, proteins in combination with genetics, and standard  ... 
doi:10.2337/db18-1263 pmid:31740441 pmcid:PMC6971485 fatcat:tgxinolxlzdqzodgwueewhasom

Associations of the intestinal microbiome with the complement system in neovascular age-related macular degeneration

Denise C. Zysset-Burri, Irene Keller, Lieselotte E. Berger, Carlo R. Largiadèr, Matthias Wittwer, Sebastian Wolf, Martin S. Zinkernagel
2020 npj Genomic Medicine  
To investigate this issue, a shotgun metagenomics analysis of 57 neovascular AMD and 58 healthy controls as well as of 16 complement C3-deficient mice and 16 wildtypes was performed.  ...  Using a classification model, Negativicutes was identified as a potential biomarker for AMD and furthermore, it positively correlated with CFH.  ...  Relative abundances of microbiota at phyla level in all study subjects (a) and averaged for study groups (b). c Principal component analysis of microbial species abundance grouped patients and controls  ... 
doi:10.1038/s41525-020-00141-0 pmid:32922859 pmcid:PMC7463023 fatcat:gjy74mnpn5br5ikgvgjc2krxyy

Gut Microbiome Reveals Specific Dysbiosis in Primary Osteoporosis

Zhiming Xu, Zheng Xie, Jianguang Sun, Shilei Huang, Yangyang Chen, Chengxiang Li, Xing Sun, Bicheng Xia, Lingyang Tian, Caijuan Guo, Feng Li, Guofu Pi
2020 Frontiers in Cellular and Infection Microbiology  
The classification model is constructed by random forest algorithm so as to screen the key biomarkers.  ...  The purpose of this study was to characterize the gut microbiome of patients with PO and its possible role in the occurrence and development of the disease.  ...  ., Ltd (Beijing, China) for 16srRNA sequencing and data analysis.  ... 
doi:10.3389/fcimb.2020.00160 pmid:32373553 pmcid:PMC7186314 fatcat:fiqwxw7nwvatjed6q5nuoc7tte

Diagnostic Models for Atopic Dermatitis Based on Serum Microbial Extracellular Vesicle Metagenomic Analysis: A Pilot Study

Jinho Yang, Andrea McDowell, Hochan Seo, Sungwon Kim, Taek Ki Min, Young-Koo Jee, Youngwoo Choi, Hae-Sim Park, Bok Yang Pyun, Yoon-Keun Kim
2020 Allergy Asthma and Immunology Research  
AD diagnostic models developed using biomarkers selected on the basis of linear discriminant analysis effect size from the class to genus levels all yielded area under the receiver operating characteristic  ...  Furthermore, metagenomic analysis of microbe-derived extracellular vesicles (EVs) has revealed the importance and relevance of microbial EVs in human health.  ...  In this study, only serum samples were used, and biomarkers were selected based on the metagenomic analysis of microbial EVs derived from serum.  ... 
doi:10.4168/aair.2020.12.5.792 pmid:32638560 pmcid:PMC7346989 fatcat:azgherqmdfg5ffgiuxpjxdjwby

Validation of a Salivary RNA Test for Childhood Autism Spectrum Disorder

Steven D Hicks, Alexander T Rajan, Kayla E Wagner, Sarah Barns, Randall L Carpenter, Frank A Middleton
2018 Frontiers in Genetics  
Prior to analysis, the sample was randomly divided into a training set (82% of subjects) and an independent validation test set (18% of subjects).  ...  Comprehensive human and microbial RNA abundance was measured in the saliva of all participants using unbiased next generation sequencing.  ...  ACKNOWLEDGMENTS The authors thank Jessica Bieler, MPH (Penn State), Richard Uhlig and Cynthia Dowd Greene (Quadrant Biosciences Inc.) for assistance with study design.  ... 
doi:10.3389/fgene.2018.00534 pmid:30473705 pmcid:PMC6237842 fatcat:hxwiqb6iwvdpteruz36z6swhlm

Integrated biomedical data analysis utilizing various types of data for biomarkers identification

Ping Zhang, Amanda Cox, Allan Cripps, Nicholas West
2017 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
The set of functions included in the analysis template were used for finding the biomarkers and their combinatorial effect associated with obesity.  ...  Realising the nature of the data in biomedical research and translational biomedicine, we developed a data analysis pipeline with a set of computational functions and an integrated method that can serve  ...  Principal component analysis (PCA) and hierarchical clustering analysis were developed as functions for exploratory analysis on selected data sets.  ... 
doi:10.1109/bibm.2017.8217879 dblp:conf/bibm/ZhangCCW17 fatcat:rtzgdrttyvcyrmjsbjt4qacgmm

Colorectal cancer diagnostic model utilizing metagenomic and metabolomic data of stool microbial extracellular vesicles

Da Jung Kim, Jinho Yang, Hochan Seo, Won Hee Lee, Dong Ho Lee, Sungmin Kym, Young Soo Park, Jae Gyu Kim, In-Jin Jang, Yoon-Keun Kim, Joo-Youn Cho
2020 Scientific Reports  
A total of 40 healthy volunteers and 32 patients with CRC were enrolled in this study. Metagenomic profiling by sequencing 16 S rDNA was performed for assessing microbial codiversity.  ...  Metagenomic profiling demonstrated that bacterial phyla, particularly of Firmicutes and Proteobacteria, were significantly altered in patients with colorectal cancer.  ...  (A) Score plot of the three-dimensional principal component analysis (PCA) shows metabolic patterns of stool EV samples.  ... 
doi:10.1038/s41598-020-59529-8 pmid:32071370 fatcat:vrki4mypyvea3mzbeprcu67nbi

Nestlé's research on nutrition and the human gut microbiome

Enea Rezzonico, Annick Mercenier, Ed Baetge, Scott Parkinson, Thomas Beck, Johannes le Coutre, Harald Brüssow
2015 Scientific American  
We also reviewed the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our knowledge of unclassified and poorly understood gut microbes that are undocumented  ...  Abstract The human gut microbiome has received great attention because many studies have revealed that it is associated with a variety of diseases.  ...  Visualization is typically performed by constructing graphs using inter-class analysis, principal component analysis, or principal coordinates analysis.  ... 
doi:10.1038/scientificamerican0315-79 fatcat:rikav6kvzffi3ggxayig4d32ie
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