Bmc Genomics, Jack Y Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng
Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes
Comparison of feature selection and classification for MALDI-MS data (2009)
Liu, Qingzhong, Sung, Andrew H, Qiao, Mengyu, Chen, Zhongxue, Yang, Jack Y, Yang, Mary, ...
Abstract Introduction In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better...
Reconstruct gene regulatory network using slice pattern model (2009)
Wang, Yadong, Wang, Guohua, Yang, Bo, Tao, Haijun, Yang, Jack Y, Deng, Youping, ...
Abstract Background Gene expression time series array data has become a useful resource for investigating gene functions and the interactions between genes. However, the gene expression arrays are...
Prediction of DNA-binding residues from protein sequence information using random forests (2009)
Wang, Liangjiang, Yang, Mary, Yang, Jack Y
Abstract Background Protein-DNA interactions are involved in many biological processes essential for cellular function. To understand the molecular mechanism of protein-DNA recognition, it is...
Yang, Mary, Athey, Brian D, Arabnia, Hamid R, Sung, Andrew H, Liu, Qingzhong, Yang, Jack Y, ...
Abstract The advent of high-throughput next generation sequencing technologies have fostered enormous potential applications of supercomputing techniques in genome sequencing, epi-genetics,...
Partial Least Squares Based Dimension Reduction with Gene Selection for Tumor Classification (2008)
Guo-zheng Li, Xue-qiang Zeng, Jack Y. Yang
Abstract Analyzing gene expression data from DNA microarrays by commonly used classifiers is a hard task, be-cause there are only a few observations but with thou-sands of measured genes in the data...
Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes (2008)
Yang, Jack Y, Niemierko, Andrzej, Yang, Mary, Deng, Youping
Abstract Background Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that...
Predicting protein disorder by analyzing amino acid sequence (2008)
Abstract Background Many protein regions and some entire proteins have no definite tertiary structure, presenting instead as dynamic, disorder ensembles under different physiochemical circumstances....
Yuan, Jiazheng, Zhu, Mengxia, Lightfoot, David A, Iqbal, M Javed, Yang, Jack Y, Meksem, Khalid
Abstract Background Sudden death syndrome (SDS) of soybean ( Glycine max L. Merr.) is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines ,...
Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis (2008)
Li, Guo-Zheng, Bu, Hua-Long, Yang, Mary, Zeng, Xue-Qiang, Yang, Jack Y
Abstract Background Dimension reduction is a critical issue in the analysis of microarray data, because the high dimensionality of gene expression microarray data set hurts generalization performance...
Wang, Guohua, Wang, Yadong, Feng, Weixing, Wang, Xin, Yang, Jack Y, Zhao, Yuming, ...
Abstract Background Prostate cancer is one of the leading causes of cancer death in men. Androgen ablation, the most commonly-used therapy for progressive prostate cancer, is ineffective once the...
ILOOP – a web application for two-channel microarray interwoven loop design (2008)
Pirooznia, Mehdi, Gong, Ping, Yang, Jack Y, Yang, Mary, Perkins, Edward J, Deng, Youping
Abstract Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data...
The unfoldomics decade: an update on intrinsically disordered proteins (2008)
Dunker, A Keith, Oldfield, Christopher J, Meng, Jingwei, Romero, Pedro, Yang, Jack Y, Chen, Jessica, ...
Abstract Background Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z,...
Yang, Jack Y, Yang, Mary, Arabnia, Hamid R, Deng, Youping
Abstract Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and...
Asymmetric bagging and feature selection for activities prediction of drug molecules (2008)
Li, Guo-Zheng, Meng, Hao-Hua, Lu, Wen-Cong, Yang, Jack Y, Yang, Mary
Abstract Background Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by...
Dimension reduction with redundant gene elimination for tumor classification (2008)
Zeng, Xue-Qiang, Li, Guo-Zheng, Yang, Jack Y, Yang, Mary, Wu, Geng-Feng
Abstract Background Analysis of gene expression data for tumor classification is an important application of bioinformatics methods. But it is hard to analyse gene expression data from DNA microarray...
Guo-zheng Li, Hao-hua Meng, Mary Qu Yang, Youping Deng, Jack Y. Yang, Jack Y. Yang
Background: Since the high dimensionality of gene expression microarray data set hurts generalization performance of classifiers, feature selection has been widely used in the bioinformatics field,...
Abstract – Determining membrane protein structures is consistently challenging today’s experiments, although such proteins account for significant portions of proteins in genomes and play crucial...
Guo-zheng Li, Jack Y. Yang, Wen-cong Lu, Dan Li, Mary Qu
Molecular activities are critical for drug design, they can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle...
Guo-zheng Li, Hao-hua Meng, Wen-cong Lu, Jack Y. Yang, Mary Qu Yang, Mary Qu Yang
bagging and feature selection for activities prediction
Protein disorder prediction at multiple levels of sensitivity and specificity (2008)
Hecker, Joshua, Yang, Jack Y, Cheng, Jianlin
Abstract Background Many protein regions and some entire proteins have no definite tertiary structure, existing instead as dynamic, disorder ensembles under different physiochemical circumstances....
Investigation of transmembrane proteins using a computational approach (2008)
Yang, Jack Y, Yang, Mary, Dunker, A Keith, Deng, Youping, Huang, Xudong
Abstract Background An important subfamily of membrane proteins are the transmembrane α-helical proteins, in which the membrane-spanning regions are made up of α-helices. Given the obvious...
Yang, Jack Y, Li, Guo-Zheng, Meng, Hao-Hua, Yang, Mary, Deng, Youping
Abstract Background Since the high dimensionality of gene expression microarray data sets degrades the generalization performance of classifiers, feature selection, which selects relevant features...
Yang, Jack Y, Yang, Mary Qu, Luo, Zuojie, Ma, Yan, Li, Jianling, Deng, Youping, ...
Abstract Background The prognosis for many cancers could be improved dramatically if they could be detected while still at the microscopic disease stage. It follows from a comprehensive statistical...
Wang, Guohua, Wang, Xin, Wang, Yadong, Yang, Jack Y, Li, Lang, Nephew, Kenneth P, ...
Abstract This is a first report, using our MotifModeler informatics program, to simultaneously identify transcription factor (TF) and microRNA (miRNA) binding sites from gene expression microarray...
Habib, Tanwir, Zhang, Chaoyang, Yang, Jack Y, Yang, Mary Qu, Deng, Youping
Abstract Background Occurrence of protein in the cell is an important step in understanding its function. It is highly desirable to predict a protein's subcellular locations automatically from its...
A comparative study of different machine learning methods on microarray gene expression data (2008)
Pirooznia, Mehdi, Yang, Jack Y, Yang, Mary Qu, Deng, Youping
Abstract Background Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as...
Oldfield, Christopher J, Meng, Jingwei, Yang, Jack Y, Yang, Mary Qu, Uversky, Vladimir N, Dunker, A Keith
Abstract Background Proteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins,...
Promoting synergistic research and education in genomics and bioinformatics (2008)
Yang, Jack Y, Yang, Mary Qu, Zhu, Mengxia (Michelle), Arabnia, Hamid R, Deng, Youping
Abstract Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health,...
Yang, Jack Y., Yang, Mary Qu, Arabnia, Hamid R., Deng, Youping
Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International...
Research Predicting protein disorder by analyzing amino acid sequence (2008)
Bmc Genomics, Jack Y Yang, Mary Qu Yang
This is an open access article distributed under the terms of the Creative Commons Attribution License
Predicting Protein Structure and Function Using Machine Learning Methods (2005)
Yang, Mary Q., Yang, Jack Y., Ersoy, Okay K.
Many of the central questions in bioinformatics relate to protein structure and function. We are mainly be concerned with three problems: identifying transmembrane segments in proteins,...
Since the discoveries of Overhauser effects and DNA double helix structure, many protein structures have been determined experimentally, especially by utilizing the Overhauser effects. Biologists are...
Combined Supervised and Unsupervised Learning in Genomic Data Mining (2003)
Since the discoveries of Overhauser effects and DNA double helix structure, many protein structures have been determined experimentally, especially by utilizing the Overhauser effects. Biologists are...
Transcriptome profiling of Saccharomyces cerevisiae mutants lacking C2H2 zinc finger proteins
Mao, Jinghe, Habib, Tanwir, Shenwu, Ming, Kang, Baobin, Allen, Wilbur, Robertson, LaShonda, ...
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners
Oldfield, Christopher J, Meng, Jingwei, Yang, Jack Y, Yang, Mary Qu, Uversky, Vladimir N, Dunker, A Keith
A comparative study of different machine learning methods on microarray gene expression data
Pirooznia, Mehdi, Yang, Jack Y, Yang, Mary Qu, Deng, Youping
Wang, Guohua, Wang, Xin, Wang, Yadong, Yang, Jack Y, Li, Lang, Nephew, Kenneth P, ...
This is a first report, using our MotifModeler informatics program, to simultaneously identify transcription factor (TF) and microRNA (miRNA) binding sites from gene expression microarray data. Based...
Investigation of transmembrane proteins using a computational approach
Yang, Jack Y, Yang, Mary Qu, Dunker, A Keith, Deng, Youping, Huang, Xudong
Dimension reduction with redundant gene elimination for tumor classification
Zeng, Xue-Qiang, Li, Guo-Zheng, Yang, Jack Y, Yang, Mary Qu, Wu, Geng-Feng
Asymmetric bagging and feature selection for activities prediction of drug molecules
Li, Guo-Zheng, Meng, Hao-Hua, Lu, Wen-Cong, Yang, Jack Y, Yang, Mary Qu
The unfoldomics decade: an update on intrinsically disordered proteins
Dunker, A Keith, Oldfield, Christopher J, Meng, Jingwei, Romero, Pedro, Yang, Jack Y, Chen, Jessica Walton, ...
ILOOP – a web application for two-channel microarray interwoven loop design
Pirooznia, Mehdi, Gong, Ping, Yang, Jack Y, Yang, Mary Qu, Perkins, Edward J, Deng, Youping
Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust...
Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis
Li, Guo-Zheng, Bu, Hua-Long, Yang, Mary Qu, Zeng, Xue-Qiang, Yang, Jack Y
Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes
Yang, Jack Y, Niemierko, Andrzej, Yang, Mary Qu, Deng, Youping
Yang, Mary Qu, Athey, Brian D, Arabnia, Hamid R, Sung, Andrew H, Liu, Qingzhong, Yang, Jack Y, ...
The advent of high-throughput next generation sequencing technologies have fostered enormous potential applications of supercomputing techniques in genome sequencing, epi-genetics, metagenomics,...