Bmc Genomics, Jack Y Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng
Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes
Ruan, Jianhua, Deng, Youping, Perkins, Edward J, Zhang, Weixiong
Abstract Background One of the most challenging tasks in the post-genomic era is to reconstruct the transcriptional regulatory networks. The goal is to reveal, for each gene that responds to a...
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...
Chen, Zhongxue, McGee, Monnie, Liu, Qingzhong, Kong, Megan, Deng, Youping, Scheuermann, Richard H
Abstract Introduction Affymetrix GeneChip ® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the...
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,...
Gust, Kurt A., Pirooznia, Mehdi, Quinn, Michael J., Johnson, Mark S., Escalon, Lynn, Indest, Karl J., ...
Munitions constituents (MCs) including hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), 2,4,6-trinitrotoluene (TNT), and TNT derivatives are recognized to elicit aberrant neuromuscular responses in...
Bmc Bioinformatics, Mehdi Pirooznia, Youping Deng
SVM Classifier – a comprehensive java interface for support vector machine classification of microarray 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...
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...
Batch Blast Extractor: an automated blastx parser application (2008)
Pirooznia, Mehdi, Perkins, Edward J, Deng, Youping
Abstract Motivation BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output...
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...
Rawat, Arun, Seifert, Georg J, Deng, Youping
Abstract Background Most existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek...
Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J. Brown
biology for gene expression data analysis. With the help of clustering algorithms such as Kmeans, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between...
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,...
Bmc Bioinformatics, Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, ...
Background: Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every...
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...
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...
Gong, Ping, Guan, Xin, Inouye, Laura S, Deng, Youping, Pirooznia, Mehdi, Perkins, Edward J
Abstract Background Explosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on...
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...
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...
GOfetcher: a database with complex searching facility for gene ontology (2008)
Pirooznia, Mehdi, Habib, Tanwir, Perkins, Edward J., Deng, Youping
Motivation: An important contribution to the Gene Ontology (GO) project is to develop tools that facilitate the creation, maintenance and use of ontologies. Several tools have been created for...
Li, Peng, Zhang, Chaoyang, Perkins, Edward J, Gong, Ping, Deng, Youping
Abstract Background The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In...
Pirooznia, Mehdi, Gong, Ping, Guan, Xin, Inouye, Laura S, Yang, Kuan, Perkins, Edward J, ...
Abstract Background Eisenia fetida , commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has...
GeneVenn - A web application for comparing gene lists using (2007)
Mehdi Pirooznia, Vijayaraj Nagarajan, Youping Deng
Numerous methods are available to compare results of multiple microarray studies. One of the simplest but most effective of these procedures is to examine the overlap of resulting gene lists in a...
Comparison of probabilistic Boolean network and dynamic (2007)
Peng Li, Chaoyang Zhang, Edward J Perkins, Ping Gong, Youping Deng, Ping Gong, ...
Proceedings
Deng, Youping, Ni, Jun, Zhang, Chaoyang
Abstract The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21–22, 2006. Twenty-six peer-reviewed papers were selected for publication...
Zhang, Chaoyang, Li, Peng, Rajendran, Arun, Deng, Youping, Chen, Dequan
Abstract Background Multicategory Support Vector Machines (MC-SVM) are powerful classification systems with excellent performance in a variety of data classification problems. Since the process of...
Identification of new members of hydrophobin family using primary structure analysis (2006)
Yang, Kuan, Deng, Youping, Zhang, Chaoyang, Elasri, Mohamed
Abstract Background Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are...
Pirooznia, Mehdi, Deng, Youping
Abstract Motivation Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very...
Deng, Youping, Dong, Yinghua, Thodima, Venkata, Clem, Rollie J, Passarelli, A Lorena
Abstract Background Little is known about the genome sequences of lepidopteran insects, although this group of insects has been studied extensively in the fields of endocrinology, development,...
A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity (2006)
Nagarajan, Vijayaraj, Kaushik, Navodit, Murali, Beddhu, Zhang, Chaoyang, Lakhera, Sanyogita, Elasri, Mohamed O, ...
Abstract Background Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of...
RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers (2006)
Thodima, Venkata, Pirooznia, Mehdi, Deng, Youping
Abstract Background Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial...
Elena V. Boyko, C. Michael Smith, Vankatappa K. Thara, Jon M. Bruno, Youping Deng, Sharon R. Starkey, ...
Bmc Bioinformatics, Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng, Dequan Chen, ...
Parallelization of multicategory support vector machines
BMC Bioinformatics Proceedings RiboaptDB: A Comprehensive Database of Ribozymes and (2006)
Background: Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach...
Bioinformatics and Bioscience (SCBB06) (2006)
Youping Deng, Jun Ni, Chaoyang Zhang, Open Access
its application: review of the Symposium of Computations in
Bmc Genomics, Youping Deng, Yinghua Dong, Venkata Thodima, Rollie J Clem, Lorena Passarelli, ...
Research article Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperda
Bmc Bioinformatics, Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed Elasri, Open Access, ...
Identification of new members of hydrophobin family using primary structure analysis
Incremental genetic K-means algorithm and its application in gene expression data analysis (2004)
Lu, Yi, Lu, Shiyong, Fotouhi, Farshad, Deng, Youping, Brown, Susan J
Abstract Background In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as...
Jiang, Hongying, Deng, Youping, Chen, Huann-Sheng, Tao, Lin, Sha, Qiuying, Chen, Jun, ...
Abstract Background Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common...
Zhu, Qingsong, Deng, Youping, Vanka, Phaneendra, Brown, Susan J., Muthukrishnan, Subbaratnam, Kramer, Karl J.
Motivation: Multiple chitinases as well as lectins closely related to them have been characterized previously from many insect species and the corresponding genes/cDNAs have been cloned. However, the...
BMC Bioinformatics BioMed Central Methodology article (2004)
Hongying Jiang, Youping Deng, Huann-sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, ...
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes
Crystallographically-oriented CoCrTa thin-film media for high areal density recording / (1993)
Thesis (Ph. D.)--Carnegie Mellon University, 1993.
Wang, Jian, Dai, Heping, Yousaf, Nasim, Moussaif, Mustapha, Deng, Youping, Boufelliga, Amale, ...
Grb10 has been described as a cellular partner of several receptor tyrosine kinases, including the insulin receptor (IR) and the insulin-like growth factor I (IGF-I) receptor (IGF-IR). Its cellular...
Incremental genetic K-means algorithm and its application in gene expression data analysis
Lu, Yi, Lu, Shiyong, Fotouhi, Farshad, Deng, Youping, Brown, Susan J
A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity
Nagarajan, Vijayaraj, Kaushik, Navodit, Murali, Beddhu, Zhang, Chaoyang, Lakhera, Sanyogita, Elasri, Mohamed O, ...
Wang, Jian, Dai, Heping, Yousaf, Nasim, Moussaif, Mustapha, Deng, Youping, Boufelliga, Amale, ...
Grb10 has been described as a cellular partner of several receptor tyrosine kinases, including the insulin receptor (IR) and the insulin-like growth factor I (IGF-I) receptor (IGF-IR). Its cellular...
Incremental genetic K-means algorithm and its application in gene expression data analysis
Lu, Yi, Lu, Shiyong, Fotouhi, Farshad, Deng, Youping, Brown, Susan J
A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity
Nagarajan, Vijayaraj, Kaushik, Navodit, Murali, Beddhu, Zhang, Chaoyang, Lakhera, Sanyogita, Elasri, Mohamed O, ...
Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data
Zhang, Chaoyang, Li, Peng, Rajendran, Arun, Deng, Youping, Chen, Dequan
Deng, Youping, Ni, Jun, Zhang, Chaoyang
The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21–22, 2006. Twenty-six peer-reviewed papers were selected for publication in this...
GeneVenn - A web application for comparing gene lists using Venn diagrams
Pirooznia, Mehdi, Nagarajan, Vijayaraj, Deng, Youping
Numerous methods are available to compare results of multiple microarray studies. One of the simplest but most effective of these procedures is to examine the overlap of resulting gene lists in a...
Transcriptome profiling of Saccharomyces cerevisiae mutants lacking C2H2 zinc finger proteins
Mao, Jinghe, Habib, Tanwir, Shenwu, Ming, Kang, Baobin, Allen, Wilbur, Robertson, LaShonda, ...
Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida
Gong, Ping, Guan, Xin, Inouye, Laura S, Deng, Youping, Pirooznia, Mehdi, Perkins, Edward J
A comparative study of different machine learning methods on microarray gene expression data
Pirooznia, Mehdi, Yang, Jack Y, Yang, Mary Qu, Deng, Youping
Investigation of transmembrane proteins using a computational approach
Yang, Jack Y, Yang, Mary Qu, Dunker, A Keith, Deng, Youping, Huang, Xudong
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...
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,...
A distribution-free convolution model for background correction of oligonucleotide microarray data
Chen, Zhongxue, McGee, Monnie, Liu, Qingzhong, Kong, Megan, Deng, Youping, Scheuermann, Richard H
Reconstruct gene regulatory network using slice pattern model
Wang, Yadong, Wang, Guohua, Yang, Bo, Tao, Haijun, Yang, Jack Y, Deng, Youping, ...