436 results on '"Yang, Pengyi"'
Search Results
152. Hybrid Methods to Select Informative Gene Sets in Microarray Data Classification
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Yang, Pengyi, primary and Zhang, Zili, additional
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153. ISL1 Regulates Peroxisome Proliferator-Activated Receptor γ Activation and Early Adipogenesis via Bone Morphogenetic Protein 4-Dependent and -Independent Mechanisms
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Ma, Xiuquan, primary, Yang, Pengyi, additional, Kaplan, Warren H., additional, Lee, Bon Hyang, additional, Wu, Lindsay E., additional, Yang, Jean Yee-Hwa, additional, Yasunaga, Mayu, additional, Sato, Kenzo, additional, Chisholm, Donald J., additional, and James, David E., additional
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- 2014
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154. Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors
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Oldfield, Andrew J., primary, Yang, Pengyi, additional, Conway, Amanda E., additional, Cinghu, Senthilkumar, additional, Freudenberg, Johannes M., additional, Yellaboina, Sailu, additional, and Jothi, Raja, additional
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- 2014
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155. Stability of Feature Selection Algorithms and Ensemble Feature Selection Methods in Bioinformatics
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Yang, Pengyi, primary, Zhou, Bing B., additional, Yang, Jean Yee‐Hwa, additional, and Zomaya, Albert Y., additional
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- 2013
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156. Mapping the insulin signalling network
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James, David, primary, Humphrey, Sean J., additional, Yang, Guang, additional, Yang, Pengyi, additional, Fazakerley, Daniel, additional, Stoeckli, Jacqueline, additional, and Yang, Jean, additional
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- 2013
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157. A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data
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Yang, Pengyi, Zhou, Bing B., Zhang, Zili, Zomaya, Albert Y., Yang, Pengyi, Zhou, Bing B., Zhang, Zili, and Zomaya, Albert Y.
- Abstract
Background: Feature selection techniques are critical to the analysis of high dimensional datasets. This is especially true in gene selection from microarray data which are commonly with extremely high feature-to-sample ratio. In addition to the essential objectives such as to reduce data noise, to reduce data redundancy, to improve sample classification accuracy, and to improve model generalization property, feature selection also helps biologists to focus on the selected genes to further validate their biological hypotheses. Results: In this paper we describe an improved hybrid system for gene selection. It is based on a recently proposed genetic ensemble (GE) system. To enhance the generalization property of the selected genes or gene subsets and to overcome the overfitting problem of the GE system, we devised a mapping strategy to fuse the goodness information of each gene provided by multiple filtering algorithms. This information is then used for initialization and mutation operation of the genetic ensemble system. Conclusion: We used four benchmark microarray datasets (including both binary-class and multi-class classification problems) for concept proving and model evaluation. The experimental results indicate that the proposed multi-filter enhanced genetic ensemble (MF-GE) system is able to improve sample classification accuracy, generate more compact gene subset, and converge to the selection results more quickly. The MF-GE system is very flexible as various combinations of multiple filters and classifiers can be incorporated based on the data characteristics and the user preferences.
- Published
- 2010
158. An embedded two-layer feature selection approach for microarray data analysis
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Yang, Pengyi, Zhang, Zili, Yang, Pengyi, and Zhang, Zili
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Feature selection is an important technique in dealing with application problems with large number of variables and limited training samples, such as image processing, combinatorial chemistry, and microarray analysis. Commonly employed feature selection strategies can be divided into filter and wrapper. In this study, we propose an embedded two-layer feature selection approach to combining the advantages of filter and wrapper algorithms while avoiding their drawbacks. The hybrid algorithm, called GAEF (Genetic Algorithm with embedded filter), divides the feature selection process into two stages. In the first stage, Genetic Algorithm (GA) is employed to pre-select features while in the second stage a filter selector is used to further identify a small feature subset for accurate sample classification. Three benchmark microarray datasets are used to evaluate the proposed algorithm. The experimental results suggest that this embedded two-layer feature selection strategy is able to improve the stability of the selection results as well as the sample classification accuracy.
- Published
- 2009
159. An agent-based hybrid system for microarray data analysis
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Zhang, Zili, Yang, Pengyi, Wu, Xindong, Zhang, Chengqi, Zhang, Zili, Yang, Pengyi, Wu, Xindong, and Zhang, Chengqi
- Abstract
This article reports our experience in agent-based hybrid construction for microarray data analysis. The contributions are twofold: We demonstrate that agent-based approaches are suitable for building hybrid systems in general, and that a genetic ensemble system is appropriate for microarray data analysis in particular. Created using an agent-based framework, this genetic ensemble system for microarray data analysis excels in both sample classification accuracy and gene selection reproducibility.
- Published
- 2009
160. A particle swarm based hybrid system for imbalances medical data sampling
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Yang, Pengyi, Xu, Liang, Zhou, Bing B., Zhang, Zili, Zomaya, Albert Y., Yang, Pengyi, Xu, Liang, Zhou, Bing B., Zhang, Zili, and Zomaya, Albert Y.
- Abstract
Background Medical and biological data are commonly with small sample size, missing values, and most importantly, imbalanced class distribution. In this study we propose a particle swarm based hybrid system for remedying the class imbalance problem in medical and biological data mining. This hybrid system combines the particle swarm optimization (PSO) algorithm with multiple classifiers and evaluation metrics for evaluation fusion. Samples from the majority class are ranked using multiple objectives according to their merit in compensating the class imbalance, and then combined with the minority class to form a balanced dataset. Results One important finding of this study is that different classifiers and metrics often provide different evaluation results. Nevertheless, the proposed hybrid system demonstrates consistent improvements over several alternative methods with three different metrics. The sampling results also demonstrate good generalization on different types of classification algorithms, indicating the advantage of information fusion applied in the hybrid system. Conclusion The experimental results demonstrate that unlike many currently available methods which often perform unevenly with different datasets the proposed hybrid system has a better generalization property which alleviates the method-data dependency problem. From the biological perspective, the system provides indication for further investigation of the highly ranked samples, which may result in the discovery of new conditions or disease subtypes.
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- 2009
161. A hybrid approach to selecting susceptible single nucleotide polymorphisms for complex disease analysis
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Peng, Yonghong, Zhang, Yufeng, Yang, Pengyi, Zhang, Zili, Peng, Yonghong, Zhang, Yufeng, Yang, Pengyi, and Zhang, Zili
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An increasingly popular and promising way for complex disease diagnosis is to employ artificial neural networks (ANN). Single nucleotide polymorphisms (SNP) data from individuals is used as the inputs of ANN to find out specific SNP patterns related to certain disease. Due to the large number of SNPs, it is crucial to select optimal SNP subset and their combinations so that the inputs of ANN can be reduced. With this observation in mind, a hybrid approach - a combination of genetic algorithms (GA) and ANN (called GANN) is used to automatically determine optimal SNP set and optimize the structure of ANN. The proposed GANN algorithm is evaluated by using both a synthetic dataset and a real SNP dataset of a complex disease.
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- 2008
162. An ensemble of classifiers with genetic algorithmBased Feature Selection
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Zhang, Zili, Yang, Pengyi, Zhang, Zili, and Yang, Pengyi
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Different data classification algorithms have been developed and applied in various areas to analyze and extract valuable information and patterns from large datasets with noise and missing values. However, none of them could consistently perform well over all datasets. To this end, ensemble methods have been suggested as the promising measures. This paper proposes a novel hybrid algorithm, which is the combination of a multi-objective Genetic Algorithm (GA) and an ensemble classifier. While the ensemble classifier, which consists of a decision tree classifier, an Artificial Neural Network (ANN) classifier, and a Support Vector Machine (SVM) classifier, is used as the classification committee, the multi-objective Genetic Algorithm is employed as the feature selector to facilitate the ensemble classifier to improve the overall sample classification accuracy while also identifying the most important features in the dataset of interest. The proposed GA-Ensemble method is tested on three benchmark datasets, and compared with each individual classifier as well as the methods based on mutual information theory, bagging and boosting. The results suggest that this GA-Ensemble method outperform other algorithms in comparison, and be a useful method for classification and feature selection problems.
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- 2008
163. Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway
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Yang, Pengyi, primary, Patrick, Ellis, additional, Tan, Shi-Xiong, additional, Fazakerley, Daniel J., additional, Burchfield, James, additional, Gribben, Christopher, additional, Prior, Matthew J., additional, James, David E., additional, and Hwa Yang, Yee, additional
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- 2013
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164. Re-Fraction: A Machine Learning Approach for Deterministic Identification of Protein Homologues and Splice Variants in Large-scale MS-based Proteomics
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Yang, Pengyi, primary, Humphrey, Sean J., additional, Fazakerley, Daniel J., additional, Prior, Matthew J., additional, Yang, Guang, additional, James, David E., additional, and Yang, Jean Yee-Hwa, additional
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- 2012
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165. Gene-gene interaction filtering with ensemble of filters
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Yang, Pengyi, primary, Ho, Joshua WK, additional, Yang, Yee Hwa, additional, and Zhou, Bing B, additional
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- 2011
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166. A Review of Ensemble Methods in Bioinformatics
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Yang, Pengyi, primary, Hwa Yang, Yee, additional, B. Zhou, Bing, additional, and Y. Zomaya, Albert, additional
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- 2010
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167. A genetic ensemble approach for gene-gene interaction identification
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Yang, Pengyi, primary, Ho, Joshua WK, additional, Zomaya, Albert Y, additional, and Zhou, Bing B, additional
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- 2010
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168. Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles
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Yoo, Paul D, primary, Shwen Ho, Yung, additional, Ng, Jason, additional, Charleston, Michael, additional, Saksena, Nitin K, additional, Yang, Pengyi, additional, and Zomaya, Albert Y, additional
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- 2010
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169. A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data
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Yang, Pengyi, primary, Zhou, Bing B, additional, Zhang, Zili, additional, and Zomaya, Albert Y, additional
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- 2010
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170. An Agent-Based Hybrid System for Microarray Data Analysis
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Zhang, Zili, primary, Yang, Pengyi, additional, Wu, Xindong, additional, and Zhang, Chengqi, additional
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- 2009
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171. A particle swarm based hybrid system for imbalanced medical data sampling
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Yang, Pengyi, primary, Xu, Liang, additional, Zhou, Bing B, additional, Zhang, Zili, additional, and Zomaya, Albert Y, additional
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- 2009
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172. A Hybrid Approach to Selecting Susceptible Single Nucleotide Polymorphisms for Complex Disease Analysis
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Yang, Pengyi, primary and Zhang, Zili, additional
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- 2008
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173. Ensemble-Based Wrapper Methods for Feature Selection and Class Imbalance Learning.
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Yang, Pengyi, Liu, Wei, Zhou, Bing B., Chawla, Sanjay, and Zomaya, Albert Y.
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- 2013
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174. Genetic Algorithm-Based Multi-objective Optimisation for QoS-Aware Web Services Composition.
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Li, Li, Yang, Pengyi, Ou, Ling, Zhang, Zili, and Cheng, Peng
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Finding an optimal solution for QoS-aware Web service composition with various restrictions on qualities is a multi-objective optimisation problem. A popular multi-objective genetic algorithm, NSGA-II, is studied in order to provide a set of optimal solutions for QoS-based service composition. Experiments with different numbers of abstract and concrete services confirm the expected behaviour of the algorithm. [ABSTRACT FROM AUTHOR]
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- 2010
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175. Multiagent Framework for Bio-data Mining.
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Yang, Pengyi, Tao, Li, Xu, Liang, and Zhang, Zili
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This paper proposes to apply multiagent based data mining technologies to biological data analysis. The rationale is justified from multiple perspectives with an emphasis on biological context. Followed by that, an initial multiagent based bio-data mining framework is presented. Based on the framework, we developed a prototype system to demonstrate how it helps the biologists to perform a comprehensive mining task for answering biological questions. The system offers a new way to reuse biological datasets and available data mining algorithms with ease. [ABSTRACT FROM AUTHOR]
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- 2009
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176. A Clustering Based Hybrid System for Mass Spectrometry Data Analysis.
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Yang, Pengyi and Zhang, Zili
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Recently, much attention has been given to the mass spectrometry (MS) technology based disease classification, diagnosis, and protein-based biomarker identification. Similar to microarray based investigation, proteomic data generated by such kind of high-throughput experiments are often with high feature-to-sample ratio. Moreover, biological information and pattern are compounded with data noise, redundancy and outliers. Thus, the development of algorithms and procedures for the analysis and interpretation of such kind of data is of paramount importance. In this paper, we propose a hybrid system for analyzing such high dimensional data. The proposed method uses the k-mean clustering algorithm based feature extraction and selection procedure to bridge the filter selection and wrapper selection methods. The potential informative mass/charge (m/z) markers selected by filters are subject to the k-mean clustering algorithm for correlation and redundancy reduction, and a multi-objective Genetic Algorithm selector is then employed to identify discriminative m/z markers generated by k-mean clustering algorithm. Experimental results obtained by using the proposed method indicate that it is suitable for m/z biomarker selection and MS based sample classification. [ABSTRACT FROM AUTHOR]
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- 2008
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177. Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data
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Yu, Lijia, Cao, Yue, Yang, Jean Y. H., and Yang, Pengyi
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Background: A key task in single-cell RNA-seq (scRNA-seq) data analysis is to accurately detect the number of cell types in the sample, which can be critical for downstream analyses such as cell type identification. Various scRNA-seq data clustering algorithms have been specifically designed to automatically estimate the number of cell types through optimising the number of clusters in a dataset. The lack of benchmark studies, however, complicates the choice of the methods. Results: We systematically benchmark a range of popular clustering algorithms on estimating the number of cell types in a variety of settings by sampling from the Tabula Muris data to create scRNA-seq datasets with a varying number of cell types, varying number of cells in each cell type, and different cell type proportions. The large number of datasets enables us to assess the performance of the algorithms, covering four broad categories of approaches, from various aspects using a panel of criteria. We further cross-compared the performance on datasets with high cell numbers using Tabula Muris and Tabula Sapiens data. Conclusions: We identify the strengths and weaknesses of each method on multiple criteria including the deviation of estimation from the true number of cell types, variability of estimation, clustering concordance of cells to their predefined cell types, and running time and peak memory usage. We then summarise these results into a multi-aspect recommendation to the users. The proposed stability-based approach for estimating the number of cell types is implemented in an R package and is freely available from (
https://github.com/PYangLab/scCCESS ).- Published
- 2022
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178. Hybrid Methods to Select Informative Gene Sets in Microarray Data Classification.
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Carbonell, Jaime G., Siekmann, Jörg, Orgun, Mehmet A., Thornton, John, Yang, Pengyi, and Zhang, Zili
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One of the key applications of microarray studies is to select and classify gene expression profiles of cancer and normal subjects. In this study, two hybrid approaches-genetic algorithm with decision tree (GADT) and genetic algorithm with neural network (GANN)-are utilized to select optimal gene sets which contribute to the highest classification accuracy. Two benchmark microarray datasets were tested, and the most significant disease related genes have been identified. Furthermore, the selected gene sets achieved comparably high sample classification accuracy (96.79% and 94.92% in colon cancer dataset, 98.67% and 98.05% in leukemia dataset) compared with those obtained by mRMR algorithm. The study results indicate that these two hybrid methods are able to select disease related genes and improve classification accuracy. [ABSTRACT FROM AUTHOR]
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- 2007
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179. Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data.
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Cao, Yue, Ghazanfar, Shila, Yang, Pengyi, and Yang, Jean
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RNA sequencing , *COVID-19 , *MACHINE learning , *LEARNING strategies , *PREDICTION models , *DEEP learning - Abstract
The advances of single-cell transcriptomic technologies have led to increasing use of single-cell RNA sequencing (scRNA-seq) data in large-scale patient cohort studies. The resulting high-dimensional data can be summarized and incorporated into patient outcome prediction models in several ways; however, there is a pressing need to understand the impact of analytical decisions on such model quality. In this study, we evaluate the impact of analytical choices on model choices, ensemble learning strategies and integrate approaches on patient outcome prediction using five scRNA-seq COVID-19 datasets. First, we examine the difference in performance between using single-view feature space versus multi-view feature space. Next, we survey multiple learning platforms from classical machine learning to modern deep learning methods. Lastly, we compare different integration approaches when combining datasets is necessary. Through benchmarking such analytical combinations, our study highlights the power of ensemble learning, consistency among different learning methods and robustness to dataset normalization when using multiple datasets as the model input. [ABSTRACT FROM AUTHOR]
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- 2023
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180. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal.
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Lackford, Brad, Yao, Chengguo, Charles, Georgette M, Weng, Lingjie, Zheng, Xiaofeng, Choi, Eun‐A, Xie, Xiaohui, Wan, Ji, Xing, Yi, Freudenberg, Johannes M, Yang, Pengyi, Jothi, Raja, Hu, Guang, and Shi, Yongsheng
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MESSENGER RNA ,GENETIC regulation ,ADENYLATION (Biochemistry) ,STEM cells ,SOMATIC cells ,GENE expression - Abstract
mRNA alternative polyadenylation (APA) plays a critical role in post-transcriptional gene control and is highly regulated during development and disease. However, the regulatory mechanisms and functional consequences of APA remain poorly understood. Here, we show that an mRNA 3′ processing factor, Fip1, is essential for embryonic stem cell ( ESC) self-renewal and somatic cell reprogramming. Fip1 promotes stem cell maintenance, in part, by activating the ESC-specific APA profiles to ensure the optimal expression of a specific set of genes, including critical self-renewal factors. Fip1 expression and the Fip1-dependent APA program change during ESC differentiation and are restored to an ESC-like state during somatic reprogramming. Mechanistically, we provide evidence that the specificity of Fip1-mediated APA regulation depends on multiple factors, including Fip1- RNA interactions and the distance between APA sites. Together, our data highlight the role for post-transcriptional control in stem cell self-renewal, provide mechanistic insight on APA regulation in development, and establish an important function for APA in cell fate specification. [ABSTRACT FROM AUTHOR]
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- 2014
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181. Sample Subset Optimization Techniques for Imbalanced and Ensemble Learning Problems in Bioinformatics Applications.
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Yang, Pengyi, Yoo, Paul D., Fernando, Juanita, Zhou, Bing B., Zhang, Zili, and Zomaya, Albert Y.
- Abstract
Data sampling is a widely used technique in a broad range of machine learning problems. Traditional sampling approaches generally rely on random resampling from a given dataset. However, these approaches do not take into consideration additional information, such as sample quality and usefulness. We recently proposed a data sampling technique, called sample subset optimization (SSO). The SSO technique relies on a cross-validation procedure for identifying and selecting the most useful samples as subsets. In this paper, we describe the application of SSO techniques to imbalanced and ensemble learning problems, respectively. For imbalanced learning, the SSO technique is employed as an under-sampling technique for identifying a subset of highly discriminative samples in the majority class. In ensemble learning, the SSO technique is utilized as a generic ensemble technique where multiple optimized subsets of samples from each class are selected for building an ensemble classifier. We demonstrate the utilities and advantages of the proposed techniques on a variety of bioinformatics applications where class imbalance, small sample size, and noisy data are prevalent. [ABSTRACT FROM PUBLISHER]
- Published
- 2014
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182. Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2.
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Humphrey, Sean J., Yang, Guang, Yang, Pengyi, Fazakerley, Daniel J., Stöckli, Jacqueline, Yang, Jean Y., and James, David E.
- Abstract
Summary: A major challenge of the post-genomics era is to define the connectivity of protein phosphorylation networks. Here, we quantitatively delineate the insulin signaling network in adipocytes by high-resolution mass spectrometry-based proteomics. These data reveal the complexity of intracellular protein phosphorylation. We identified 37,248 phosphorylation sites on 5,705 proteins in this single-cell type, with approximately 15% responding to insulin. We integrated these large-scale phosphoproteomics data using a machine learning approach to predict physiological substrates of several diverse insulin-regulated kinases. This led to the identification of an Akt substrate, SIN1, a core component of the mTORC2 complex. The phosphorylation of SIN1 by Akt was found to regulate mTORC2 activity in response to growth factors, revealing topological insights into the Akt/mTOR signaling network. The dynamic phosphoproteome described here contains numerous phosphorylation sites on proteins involved in diverse molecular functions and should serve as a useful functional resource for cell biologists. [Copyright &y& Elsevier]
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- 2013
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183. Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator.
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Yang, Pengyi, Ma, Jie, Wang, Penghao, Zhu, Yunping, Zhou, Bing B., and Yang, Yee Hwa (Jean)
- Abstract
A critical component in mass spectrometry (MS)-based proteomics is an accurate protein identification procedure. Database search algorithms commonly generate a list of peptide-spectrum matches (PSMs). The validity of these PSMs is critical for downstream analysis since proteins that are present in the sample are inferred from those PSMs. A variety of postprocessing algorithms have been proposed to validate and filter PSMs. Among them, the most popular ones include a semi-supervised learning (SSL) approach known as Percolator and an empirical modeling approach known as PeptideProphet. However, they are predominantly designed for commercial database search algorithms, i.e., SEQUEST and MASCOT. Therefore, it is highly desirable to extend and optimize those PSM postprocessing algorithms for open source database search algorithms such as X!Tandem. In this paper, we propose a Self-boosted Percolator for postprocessing X!Tandem search results. We find that the SSL algorithm utilized by Percolator depends heavily on the initial ranking of PSMs. Starting with a poor PSM ranking list may cause Percolator to perform suboptimally. By implementing Percolator in a cascade learning manner, we can progressively improve the performance through multiple boost runs, enabling many more PSM identifications without sacrificing false discovery rate (FDR). [ABSTRACT FROM PUBLISHER]
- Published
- 2012
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184. Global redox proteome and phosphoproteome analysis reveals redox switch in Akt.
- Author
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Su, Zhiduan, Burchfield, James G., Yang, Pengyi, Humphrey, Sean J., Yang, Guang, Francis, Deanne, Yasmin, Sabina, Shin, Sung-Young, Norris, Dougall M., Kearney, Alison L., Astore, Miro A., Scavuzzo, Jonathan, Fisher-Wellman, Kelsey H., Wang, Qiao-Ping, Parker, Benjamin L., Neely, G. Gregory, Vafaee, Fatemeh, Chiu, Joyce, Yeo, Reichelle, and Hogg, Philip J.
- Subjects
PROTEOMICS ,OXIDATION-reduction reaction ,FAT cells ,OXIDATIVE stress ,MTOR protein - Abstract
Protein oxidation sits at the intersection of multiple signalling pathways, yet the magnitude and extent of crosstalk between oxidation and other post-translational modifications remains unclear. Here, we delineate global changes in adipocyte signalling networks following acute oxidative stress and reveal considerable crosstalk between cysteine oxidation and phosphorylation-based signalling. Oxidation of key regulatory kinases, including Akt, mTOR and AMPK influences the fidelity rather than their absolute activation state, highlighting an unappreciated interplay between these modifications. Mechanistic analysis of the redox regulation of Akt identified two cysteine residues in the pleckstrin homology domain (C60 and C77) to be reversibly oxidized. Oxidation at these sites affected Akt recruitment to the plasma membrane by stabilizing the PIP
3 binding pocket. Our data provide insights into the interplay between oxidative stress-derived redox signalling and protein phosphorylation networks and serve as a resource for understanding the contribution of cellular oxidation to a range of diseases. Crosstalk between protein oxidation and other post-translational modifications remains unexplored. Here, the authors map the phosphoproteome, cysteine redox proteome and total proteome of adipocytes under acute oxidative stress and reveal crosstalk between cysteine oxidation and phosphorylation-based signalling. [ABSTRACT FROM AUTHOR]- Published
- 2019
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185. Interpretable deep learning in single-cell omics.
- Author
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Wagle, Manoj M, Long, Siqu, Chen, Carissa, Liu, Chunlei, and Yang, Pengyi
- Subjects
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DEEP learning , *MACHINE learning , *DATA analysis - Abstract
Motivation Single-cell omics technologies have enabled the quantification of molecular profiles in individual cells at an unparalleled resolution. Deep learning, a rapidly evolving sub-field of machine learning, has instilled a significant interest in single-cell omics research due to its remarkable success in analysing heterogeneous high-dimensional single-cell omics data. Nevertheless, the inherent multi-layer nonlinear architecture of deep learning models often makes them 'black boxes' as the reasoning behind predictions is often unknown and not transparent to the user. This has stimulated an increasing body of research for addressing the lack of interpretability in deep learning models, especially in single-cell omics data analyses, where the identification and understanding of molecular regulators are crucial for interpreting model predictions and directing downstream experimental validations. Results In this work, we introduce the basics of single-cell omics technologies and the concept of interpretable deep learning. This is followed by a review of the recent interpretable deep learning models applied to various single-cell omics research. Lastly, we highlight the current limitations and discuss potential future directions. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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186. Data Independent Acquisition Proteomic Analysis Can Discriminate between Actinic Keratosis, Bowen’s Disease, and Cutaneous Squamous Cell Carcinoma
- Author
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Azimi, Ali, Yang, Pengyi, Ali, Marina, Howard, Vicki, Mann, Graham J., Kaufman, Kimberley L., and Fernandez-Penas, Pablo
- Abstract
Actinic keratosis, Bowen’s disease and cutaneous squamous cell carcinoma (cSCC) are heterogeneous keratinocytic skin lesions. Biomarkers that can accurately stratify these lesion types are needed to support a new paradigm of personalized and precise management of skin neoplasia. In this paper, we used a data independent acquisition proteomics workflow, sequential window acquisition of all theoretical mass spectra, to analyze formalin-fixed paraffin-embedded samples of normal skin and keratinocytic skin lesions, including well-differentiated, moderately differentiated and poorly differentiated cSCC lesions. We quantified 3,574 proteins across the 93 samples studied. Differential abundance analysis identified 19, 5, and 6 protein markers exclusive to actinic keratosis, Bowen’s disease and cSCC lesions, respectively. Among cSCC lesions of various levels of tumor differentiation, 118, 230, and 17 proteins showed a potential as biomarkers of well-differentiated, moderately differentiated and poorly differentiated cSCC lesions, respectively. Bioinformatics analysis revealed that actinic keratosis and cSCC lesions were associated with decreased apoptosis, and Bowen’s disease lesions with over-representation of the DNA damage repair pathway. Differential expression of alternatively spliced FGFR2, Rho guanosine triphosphatase signaling, and RNA metabolism proteins were associated with the level of cSCC tumor differentiation. Proteome profiles also separated keratinocytic skin lesion subtypes on principal components analysis. Overall, protein markers have excellent potential to discriminate keratinocytic skin lesion subtypes and facilitate new diagnostic and therapeutic strategies.
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- 2020
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187. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region.
- Author
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Oldfield, Andrew J., Henriques, Telmo, Kumar, Dhirendra, Burkholder, Adam B., Cinghu, Senthilkumar, Paulet, Damien, Bennett, Brian D., Yang, Pengyi, Scruggs, Benjamin S., Lavender, Christopher A., Rivals, Eric, Adelman, Karen, and Jothi, Raja
- Abstract
Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results suggest NF-Y is a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation. The mechanisms underlying specific TSS selection in mammals remain unclear. Here the authors show that the ubiquitously expressed transcription factor NF-Y regulate fidelity of transcription initiation at gene promoters, maintaining the region upstream of TSSs in a nucleosome-depleted state, while protecting this region from ectopic transcription initiation. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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188. Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance
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Fazakerley, Daniel J, Chaudhuri, Rima, Yang, Pengyi, Maghzal, Ghassan J, Thomas, Kristen C, Krycer, James R, Humphrey, Sean J, Parker, Benjamin L, Fisher-Wellman, Kelsey H, Meoli, Christopher C, Hoffman, Nolan J, Diskin, Ciana, Burchfield, James G, Cowley, Mark J, Kaplan, Warren, Modrusan, Zora, Kolumam, Ganesh, Yang, Jean Yh, Chen, Daniel L, Samocha-Bonet, Dorit, Greenfield, Jerry R, Hoehn, Kyle L, Stocker, Roland, and James, David E
- Subjects
medicine ,Mitochondrial Diseases ,Muscle Weakness ,Ubiquinone ,Muscles ,food and beverages ,human biology ,Coenzyme Q ,Insulin resistance ,Oxidants ,Sensitivity and Specificity ,3. Good health ,Mitochondria ,Mice ,Adipose Tissue ,cell biology ,Adipocytes ,Insulin ,Animals ,Humans ,Ataxia ,human ,mouse - Abstract
Insulin resistance in muscle, adipocytes and liver is a gateway to a number of metabolic diseases. Here, we show a selective deficiency in mitochondrial coenzyme Q (CoQ) in insulin-resistant adipose and muscle tissue. This defect was observed in a range of in vitro insulin resistance models and adipose tissue from insulin-resistant humans and was concomitant with lower expression of mevalonate/CoQ biosynthesis pathway proteins in most models. Pharmacologic or genetic manipulations that decreased mitochondrial CoQ triggered mitochondrial oxidants and insulin resistance while CoQ supplementation in either insulin-resistant cell models or mice restored normal insulin sensitivity. Specifically, lowering of mitochondrial CoQ caused insulin resistance in adipocytes as a result of increased superoxide/hydrogen peroxide production via complex II. These data suggest that mitochondrial CoQ is a proximal driver of mitochondrial oxidants and insulin resistance, and that mechanisms that restore mitochondrial CoQ may be effective therapeutic targets for treating insulin resistance.
189. Highlights from the 11th ISCB Student Council Symposium 2015
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Wilkins, Katie, Hassan, Mehedi, Francescatto, Margherita, Jespersen, Jakob, Parra, R. Gonzalo, Cuypers, Bart, DeBlasio, Dan, Junge, Alexander, Jigisha, Anupama, Rahman, Farzana, Laenen, Griet, Willems, Sander, Thorrez, Lieven, Moreau, Yves, Raju, Nagarajan, Chothani, Sonia Pankaj, Ramakrishnan, C., Sekijima, Masakazu, Gromiha, M. Michael, Slator, Paddy J, Burroughs, Nigel J, Szałaj, Przemysław, Tang, Zhonghui, Michalski, Paul, Luo, Oskar, Li, Xingwang, Ruan, Yijun, Plewczynski, Dariusz, Fiscon, Giulia, Weitschek, Emanuel, Ciccozzi, Massimo, Bertolazzi, Paola, Felici, Giovanni, Meysman, Pieter, Vanaerschot, Manu, Berg, Maya, Imamura, Hideo, Dujardin, Jean-Claude, Laukens, Kris, Domanova, Westa, Krycer, James R., Chaudhuri, Rima, Yang, Pengyi, Vafaee, Fatemeh, Fazakerley, Daniel J., Humphrey, Sean J., James, David E., and Kuncic, Zdenka
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Biochemistry ,Molecular Biology ,Computer Science Applications - Full Text
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190. Temporal ordering of omics and multiomic events inferred from time-series data.
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Kaur, Sandeep, Peters, Timothy J., Yang, Pengyi, Luu, Laurence Don Wai, Vuong, Jenny, Krycer, James R., and O'Donoghue, Seán I.
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STREAMLINES (Fluids) , *ENVIRONMENTAL sciences , *ACQUISITION of data , *PATHLINES (Fluid dynamics) , *VISUALIZATION - Abstract
Temporal changes in omics events can now be routinely measured; however, current analysis methods are often inadequate, especially for multiomics experiments. We report a novel analysis method that can infer event ordering at better temporal resolution than the experiment, and integrates omic events into two concise visualizations (event maps and sparklines). Testing our method gave results well-correlated with prior knowledge and indicated it streamlines analysis of time-series data. [ABSTRACT FROM AUTHOR]
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- 2020
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191. Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data.
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Kim, Daniel, Tran, Andy, Kim, Hani Jieun, Lin, Yingxin, Yang, Jean Yee Hwa, and Yang, Pengyi
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GENE regulatory networks , *REGULATOR genes , *MULTIOMICS - Abstract
Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims to unravel the complex relationships between genes and their regulators. Deciphering these networks plays a critical role in understanding the underlying regulatory crosstalk that drives many cellular processes and diseases. Recent advances in sequencing technology have led to the development of state-of-the-art GRN inference methods that exploit matched single-cell multi-omic data. By employing diverse mathematical and statistical methodologies, these methods aim to reconstruct more comprehensive and precise gene regulatory networks. In this review, we give a brief overview on the statistical and methodological foundations commonly used in GRN inference methods. We then compare and contrast the latest state-of-the-art GRN inference methods for single-cell matched multi-omics data, and discuss their assumptions, limitations and opportunities. Finally, we discuss the challenges and future directions that hold promise for further advancements in this rapidly developing field. [ABSTRACT FROM AUTHOR]
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- 2023
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192. Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates.
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Hoffman, Nolan J., Parker, Benjamin L., Chaudhuri, Rima, Fisher-Wellman, Kelsey H., Kleinert, Maximilian, Humphrey, Sean J., Yang, Pengyi, Holliday, Mira, Trefely, Sophie, Fazakerley, Daniel J., Stöckli, Jacqueline, Burchfield, James G., Jensen, Thomas E., Jothi, Raja, Kiens, Bente, Wojtaszewski, Jørgen F.P., Richter, Erik A., and James, David E.
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- 2015
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193. Ensemble deep learning of embeddings for clustering multimodal single-cell omics data.
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Yu, Lijia, Liu, Chunlei, Yang, Jean Yee Hwa, and Yang, Pengyi
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DEEP learning , *PYTHON programming language , *GENE expression - Abstract
Motivation Recent advances in multimodal single-cell omics technologies enable multiple modalities of molecular attributes, such as gene expression, chromatin accessibility, and protein abundance, to be profiled simultaneously at a global level in individual cells. While the increasing availability of multiple data modalities is expected to provide a more accurate clustering and characterization of cells, the development of computational methods that are capable of extracting information embedded across data modalities is still in its infancy. Results We propose SnapCCESS for clustering cells by integrating data modalities in multimodal single-cell omics data using an unsupervised ensemble deep learning framework. By creating snapshots of embeddings of multimodality using variational autoencoders, SnapCCESS can be coupled with various clustering algorithms for generating consensus clustering of cells. We applied SnapCCESS with several clustering algorithms to various datasets generated from popular multimodal single-cell omics technologies. Our results demonstrate that SnapCCESS is effective and more efficient than conventional ensemble deep learning-based clustering methods and outperforms other state-of-the-art multimodal embedding generation methods in integrating data modalities for clustering cells. The improved clustering of cells from SnapCCESS will pave the way for more accurate characterization of cell identity and types, an essential step for various downstream analyses of multimodal single-cell omics data. Availability and implementation SnapCCESS is implemented as a Python package and is freely available from https://github.com/PYangLab/SnapCCESS under the open-source license of GPL-3. The data used in this study are publicly available (see section 'Data availability'). [ABSTRACT FROM AUTHOR]
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- 2023
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194. scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction.
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Cao, Yue, Lin, Yingxin, Patrick, Ellis, Yang, Pengyi, and Yang, Jean Yee Hwa
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DATA structures , *GENE regulatory networks , *FORECASTING , *BIOINFORMATICS , *MOTIVATION (Psychology) - Abstract
Motivation With the recent surge of large-cohort scale single cell research, it is of critical importance that analytical methods can fully utilize the comprehensive characterization of cellular systems that single cell technologies produce to provide insights into samples from individuals. Currently, there is little consensus on the best ways to compress information from the complex data structures of these technologies to summary statistics that represent each sample (e.g. individuals). Results Here, we present scFeatures, an approach that creates interpretable cellular and molecular representations of single-cell and spatial data at the sample level. We demonstrate that summarizing a broad collection of features at the sample level is both important for understanding underlying disease mechanisms in different experimental studies and for accurately classifying disease status of individuals. Availability and implementation scFeatures is publicly available as an R package at https://github.com/SydneyBioX/scFeatures. All data used in this study are publicly available with accession ID reported in the Section 2. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
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- 2022
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195. Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm.
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Wu, Zhixuan, Shen, Sophie, Mizikovsky, Dalia, Cao, Yuanzhao, Naval-Sanchez, Marina, Tan, Siew Zhuan, Alvarez, Yanina D., Sun, Yuliangzi, Chen, Xiaoli, Zhao, Qiongyi, Kim, Daniel, Yang, Pengyi, Hill, Timothy A., Jones, Alun, Fairlie, David P., Pébay, Alice, Hewitt, Alex W., Tam, Patrick P.L., White, Melanie D., and Nefzger, Christian M.
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MESODERM , *WNT signal transduction , *GENE expression profiling , *CELL differentiation , *RNA sequencing , *CELLULAR control mechanisms - Abstract
Wnt signaling is a critical determinant of cell lineage development. This study used Wnt dose-dependent induction programs to gain insights into molecular regulation of stem cell differentiation. We performed single-cell RNA sequencing of hiPSCs responding to a dose escalation protocol with Wnt agonist CHIR-99021 during the exit from pluripotency to identify cell types and genetic activity driven by Wnt stimulation. Results of activated gene sets and cell types were used to build a multiple regression model that predicts the efficiency of cardiomyocyte differentiation. Cross-referencing Wnt-associated gene expression profiles to the Connectivity Map database, we identified the small-molecule drug, tranilast. We found that tranilast synergistically activates Wnt signaling to promote cardiac lineage differentiation, which we validate by in vitro analysis of hiPSC differentiation and in vivo analysis of developing quail embryos. Our study provides an integrated workflow that links experimental datasets, prediction models, and small-molecule databases to identify drug-like compounds that control cell differentiation. [Display omitted] • Wnt dose controls differentiation of mesendoderm gene programs and cell types • Multiple regression model predicts cardiac differentiation efficiency • Tranilast enhances differentiation by promoting mesoderm and suppressing endoderm • Tranilast synergistically promotes cardiac differentiation in vivo and in vitro Wu et al. use scRNA-seq to evaluate how Wnt signaling dose affects derivation of cell types from pluripotency. They build a computational model to identify a gene set predictive of cardiomyocyte differentiation and identify a small-molecule Wnt regulator, tranilast, that promotes cardiac differentiation both in vivo and in vitro. [ABSTRACT FROM AUTHOR]
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- 2024
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196. scDC: single cell differential composition analysis.
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Cao, Yue, Lin, Yingxin, Ormerod, John T., Yang, Pengyi, Yang, Jean Y.H., and Lo, Kitty K.
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STATISTICAL hypothesis testing , *CONFIDENCE intervals , *CELLS , *DATA analysis , *SCIENTIFIC community - Abstract
Background: Differences in cell-type composition across subjects and conditions often carry biological significance. Recent advancements in single cell sequencing technologies enable cell-types to be identified at the single cell level, and as a result, cell-type composition of tissues can now be studied in exquisite detail. However, a number of challenges remain with cell-type composition analysis – none of the existing methods can identify cell-type perfectly and variability related to cell sampling exists in any single cell experiment. This necessitates the development of method for estimating uncertainty in cell-type composition. Results: We developed a novel single cell differential composition (scDC) analysis method that performs differential cell-type composition analysis via bootstrap resampling. scDC captures the uncertainty associated with cell-type proportions of each subject via bias-corrected and accelerated bootstrap confidence intervals. We assessed the performance of our method using a number of simulated datasets and synthetic datasets curated from publicly available single cell datasets. In simulated datasets, scDC correctly recovered the true cell-type proportions. In synthetic datasets, the cell-type compositions returned by scDC were highly concordant with reference cell-type compositions from the original data. Since the majority of datasets tested in this study have only 2 to 5 subjects per condition, the addition of confidence intervals enabled better comparisons of compositional differences between subjects and across conditions. Conclusions: scDC is a novel statistical method for performing differential cell-type composition analysis for scRNA-seq data. It uses bootstrap resampling to estimate the standard errors associated with cell-type proportion estimates and performs significance testing through GLM and GLMM models. We have made this method available to the scientific community as part of the scdney package (Single Cell Data Integrative Analysis) R package, available from https://github.com/SydneyBioX/scdney. [ABSTRACT FROM AUTHOR]
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- 2019
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197. scReClassify: post hoc cell type classification of single-cell rNA-seq data.
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Kim, Taiyun, Lo, Kitty, Geddes, Thomas A., Kim, Hani Jieun, Yang, Jean Yee Hwa, and Yang, Pengyi
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BIOLOGICAL systems , *TISSUES , *CELLS , *TECHNOLOGICAL innovations , *CLASSIFICATION , *DEVELOPMENTAL biology - Abstract
Background: Single-cell RNA-sequencing (scRNA-seq) is a fast emerging technology allowing global transcriptome profiling on the single cell level. Cell type identification from scRNA-seq data is a critical task in a variety of research such as developmental biology, cell reprogramming, and cancers. Typically, cell type identification relies on human inspection using a combination of prior biological knowledge (e.g. marker genes and morphology) and computational techniques (e.g. PCA and clustering). Due to the incompleteness of our current knowledge and the subjectivity involved in this process, a small amount of cells may be subject to mislabelling. Results: Here, we propose a semi-supervised learning framework, named scReClassify, for 'post hoc' cell type identification from scRNA-seq datasets. Starting from an initial cell type annotation with potentially mislabelled cells, scReClassify first performs dimension reduction using PCA and next applies a semi-supervised learning method to learn and subsequently reclassify cells that are likely mislabelled initially to the most probable cell types. By using both simulated and real-world experimental datasets that profiled various tissues and biological systems, we demonstrate that scReClassify is able to accurately identify and reclassify misclassified cells to their correct cell types. Conclusions: scReClassify can be used for scRNA-seq data as a post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure. It is implemented as an R package and is freely available from https://github.com/SydneyBioX/scReClassify [ABSTRACT FROM AUTHOR]
- Published
- 2019
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198. NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity.
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Lu, Chang, Wang, Jun, Zhang, Zili, Yang, Pengyi, and Yu, Guoxian
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GENE ontology , *QUALITY assurance , *PREDICTION models , *COMPUTATIONAL biology , *CYTOLOGY - Abstract
Gene Ontology (GO) provides GO annotations (GOA) that associate gene products with GO terms that summarize their cellular, molecular and functional aspects in the context of biological pathways. GO Consortium (GOC) resorts to various quality assurances to ensure the correctness of annotations. Due to resources limitations, only a small portion of annotations are manually added/checked by GO curators, and a large portion of available annotations are computationally inferred. While computationally inferred annotations provide greater coverage of known genes, they may also introduce annotation errors (noise) that could mislead the interpretation of the gene functions and their roles in cellular and biological processes. In this paper, we investigate how to identify noisy annotations, a rarely addressed problem, and propose a novel approach called NoisyGOA. NoisyGOA first measures taxonomic similarity between ontological terms using the GO hierarchy and semantic similarity between genes. Next, it leverages the taxonomic similarity and semantic similarity to predict noisy annotations. We compare NoisyGOA with other alternative methods on identifying noisy annotations under different simulated cases of noisy annotations, and on archived GO annotations. NoisyGOA achieved higher accuracy than other alternative methods in comparison. These results demonstrated both taxonomic similarity and semantic similarity contribute to the identification of noisy annotations. Our study shows that annotation errors are predictable and removing noisy annotations improves the performance of gene function prediction. This study can prompt the community to study methods for removing inaccurate annotations, a critical step for annotating gene and pathway functions. [ABSTRACT FROM AUTHOR]
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- 2016
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199. Selective photodegradation of 1-methylimidazole-2-thiol by the magnetic and dual conductive imprinted photocatalysts based on TiO2/Fe3O4/MWCNTs.
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Luo, Yingying, Lu, Ziyang, Jiang, Yinhua, Wang, Dandan, Yang, Lili, Huo, Pengwei, Da, Zulin, Bai, Xuliang, Xie, Xulan, and Yang, Pengyi
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PHOTODEGRADATION , *1-Methylimidazole , *THIOLS , *MAGNETIC materials , *PHOTOCATALYSTS , *TITANIUM dioxide , *IRON oxides , *MULTIWALLED carbon nanotubes - Abstract
Highlights: [•] Magnetic and dual conductive imprinted photocatalysts (MCIPs) were prepared. [•] The MCIPs were used to treat 1-methylimidazole-2-thiol. [•] The MCIPs exhibited high photocatalytic activity and selectivity. [•] The photodegradation processes obeyed the pseudo-first-order kinetic reaction. [•] The mechanism of photodegradation were carefully discussed. [ABSTRACT FROM AUTHOR]
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- 2014
- Full Text
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200. Global redox proteome and phosphoproteome analysis reveals redox switch in Akt
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Reichelle X. Yeo, Philip J. Hogg, Deanne Francis, Sean J. Humphrey, Joyce Chiu, Miro A. Astore, Benjamin L. Parker, Dougall M. Norris, James G. Burchfield, Jonathan Scavuzzo, Sabina Yasmin, Sung-Young Shin, Zhiduan Su, Guang Yang, G. Gregory Neely, Daniel J. Fazakerley, Pengyi Yang, Lan K. Nguyen, David E. James, Fatemeh Vafaee, Kelsey H. Fisher-Wellman, Alison L Kearney, Qiao-Ping Wang, Serdar Kuyucak, Burchfield, James G [0000-0002-6609-6151], Yang, Pengyi [0000-0003-1098-3138], Humphrey, Sean J [0000-0002-2666-9744], Vafaee, Fatemeh [0000-0002-7521-2417], Hogg, Philip J [0000-0001-6486-2863], Fazakerley, Daniel J [0000-0001-8241-2903], and Apollo - University of Cambridge Repository
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Proteomics ,0301 basic medicine ,Proteome ,Proto-Oncogene Proteins c-akt ,Science ,General Physics and Astronomy ,Protein oxidation ,Article ,General Biochemistry, Genetics and Molecular Biology ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Protein Domains ,Adipocytes ,Animals ,Humans ,Protein phosphorylation ,Cysteine ,Phosphorylation ,lcsh:Science ,Protein kinase B ,PI3K/AKT/mTOR pathway ,Multidisciplinary ,Chemistry ,TOR Serine-Threonine Kinases ,Insulin signalling ,General Chemistry ,Phosphoproteins ,Cell biology ,Pleckstrin homology domain ,Oxidative Stress ,Crosstalk (biology) ,030104 developmental biology ,lcsh:Q ,Oxidation-Reduction ,030217 neurology & neurosurgery ,Post-translational modifications ,Signal Transduction - Abstract
Protein oxidation sits at the intersection of multiple signalling pathways, yet the magnitude and extent of crosstalk between oxidation and other post-translational modifications remains unclear. Here, we delineate global changes in adipocyte signalling networks following acute oxidative stress and reveal considerable crosstalk between cysteine oxidation and phosphorylation-based signalling. Oxidation of key regulatory kinases, including Akt, mTOR and AMPK influences the fidelity rather than their absolute activation state, highlighting an unappreciated interplay between these modifications. Mechanistic analysis of the redox regulation of Akt identified two cysteine residues in the pleckstrin homology domain (C60 and C77) to be reversibly oxidized. Oxidation at these sites affected Akt recruitment to the plasma membrane by stabilizing the PIP3 binding pocket. Our data provide insights into the interplay between oxidative stress-derived redox signalling and protein phosphorylation networks and serve as a resource for understanding the contribution of cellular oxidation to a range of diseases., Crosstalk between protein oxidation and other post-translational modifications remains unexplored. Here, the authors map the phosphoproteome, cysteine redox proteome and total proteome of adipocytes under acute oxidative stress and reveal crosstalk between cysteine oxidation and phosphorylation-based signalling.
- Published
- 2019
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