Youping Deng

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 12

Top Topics

Saccharomyces Cerevisiae

Gene Regulatory Networks

Top Venues

Int. J. Comput. Biol. Drug Des.

BMC Syst. Biol.

Publications

Zhuokun Feng, Yuanyuan Fu, Youping Deng
Enhancing visibility and inclusivity of queer scientists to advance equality in academia. Patterns 5 (6) (2024)
Joshua G. Burkhart, Guanming Wu, Xubo Song, Francesco Raimondi, Shannon K. McWeeney, Melissa H. Wong, Youping Deng
Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. Patterns 4 (7) (2023)
Rosa Alcazar, Maria Alvarez, Rachel Arnold, Mentewab Ayalew, Lyle G. Best, Michael C. Campbell, Kamal Chowdhury, Katherine E. L. Cox, Christina Daulton, Youping Deng, Carla Easter, Karla Fuller, Shazia Tabassum Hakim, Ava M. Hoffman, Natalie Kucher, Andrew Lee, Joslynn Lee, Jeffrey T. Leek, Robert Meller, Loyda B. Méndez, Miguel P. Méndez-González, Stephen Mosher, Michele Nishiguchi, Siddharth Pratap, Tiffany Rolle, Sourav Roy, Rachel Saidi, Michael C. Schatz, Shurjo Sen, James Sniezek, Edu Suarez Martinez, Frederick Tan, Jennifer Vessio, Karriem Watson, Wendy Westbroek, Joseph Wilcox, Xianfa Xie
Diversifying the Genomic Data Science Research Community. CoRR (2022)
Yuanyuan Fu, Zhougui Ling, Hamid R. Arabnia, Youping Deng
Current trend and development in bioinformatics research. BMC Bioinform. (9) (2020)
Bjarne Bartlett, Yong Zhu, Mark Menor, Vedbar S. Khadka, Jicai Zhang, Jie Zheng, Bin Jiang, Youping Deng
Development of a RNA-Seq based prognostic signature for colon cancer. Int. J. Comput. Biol. Drug Des. 13 (5/6) (2020)
Zongtao Yu, Yuanyuan Fu, Junmei Ai, Jicai Zhang, Gang Huang, Youping Deng
Development of predicitve models to distinguish metals from non-metal toxicants, and individual metal from one another. BMC Bioinform. (9) (2020)
Xiaoli Chen, Yong Zhu, Mayumi Jijiwa, Masaki Nasu, Junmei Ai, Shengming Dai, Bin Jiang, Jicai Zhang, Gang Huang, Youping Deng
Identification of plasma lipid species as promising diagnostic markers for prostate cancer. BMC Medical Informatics Decis. Mak. (9) (2020)
Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez, Youping Deng
Tissue-associated microbial detection in cancer using human sequencing data. BMC Bioinform. (9) (2020)
Ling Hu, Rong Zhang, Qiong Yuan, Yinping Gao, Mary Qu Yang, Chunxiang Zhang, Jiankun Huang, Yufei Sun, William Yang, Jack Y. Yang, Zhen-li Min, Jing Cheng, Youping Deng, Xiamin Hu
The emerging role of microRNA-4487/6845-3p in Alzheimer's disease pathologies is induced by Aβ25-35 triggered in SH-SY5Y cell. BMC Syst. Biol. 12 (7) (2018)
Mengjie Guo, Sicheng Lu, Hongming Huang, Yaohui Wang, Mary Qu Yang, Ye Yang, Zhimin Fan, Bin Jiang, Youping Deng
Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer. BMC Syst. Biol. 12 (7) (2018)
Jeffrey Mitchel, Laszlo Prokai, Youping Deng, Fan Zhang, Robert Barber
Risk-associated and pathway-based method to detect association with Alzheimer's disease. Int. J. Comput. Biol. Drug Des. 11 (1/2) (2018)
Naureen Aslam Khattak, Sheikh Arslan Sehgal, Yongsheng Bai, Youping Deng
Structure Modeling and Molecular Docking Studies of Schizophrenia Candidate Genes, Synapsins 2 (SYN2) and Trace Amino Acid Receptor (TAAR6). ISBRA (2017)
William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Y. Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen, Liangjiang Wang, Dong Xu, Hamid R. Arabnia, Weida Tong, Mary Qu Yang
Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinform. 15 (S-17) (2014)
Jack Y. Yang, A. Keith Dunker, Jun S. Liu, Xiang Qin, Hamid R. Arabnia, William Yang, Andrzej Niemierko, Zhongxue Chen, Zuojie Luo, Liangjiang Wang, Yunlong Liu, Dong Xu, Youping Deng, Weida Tong, Mary Qu Yang
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinform. 15 (S-17) (2014)
Daogang Guan, Jiaofang Shao, Youping Deng, Panwen Wang, Zhongying Zhao, Yan Liang, Junwen Wang, Bin Yan
CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. Bioinform. 30 (8) (2014)
Chang Liu, Lili Lu, Quan Kong, Yan Li, Haihua Wu, William Yang, Shandan Xu, Xinyu Yang, Xiaolei Song, Jack Y. Yang, Mary Qu Yang, Youping Deng
Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2. BMC Bioinform. 15 (S-17) (2014)
Daogang Guan, Jiaofang Shao, Zhongying Zhao, Panwen Wang, Jing Qin, Youping Deng, Kenneth R. Boheler, Junwen Wang, Bin Yan
PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
J. David Schaffer, Jin-Woo Park, Erin Barnes, Qiyi Lu, Xingye Qiao, Youping Deng, Yan Li, Walker H. Land Jr.
GRNN Ensemble Classifier for Lung Cancer Prognosis Using Only Demographic and TNM features. Complex Adaptive Systems (2012)
Chao-Yang Pang, Gang Jiang, Shipeng Wang, Ben-Qiong Hu, Qingzhong Liu, Youping Deng, Xudong Huang
Gene order computation using Alzheimer's DNA microarray gene expression data and the ant colony optimisation algorithm. Int. J. Data Min. Bioinform. 6 (6) (2012)
William S. Ford, Jin-Woo Park, Aaron S. Campbell, Youping Deng, Yan Li, Walker H. Land Jr.
Classifying Lung Cancer Recurrence Time Using Novel Ensemble Method with Gene Network based Input Models. Complex Adaptive Systems (2012)
Walker H. Land Jr., Xingye Qiao, Daniel Margolis, William S. Ford, Christopher T. Paquette, Joseph F. Perez-Rogers, Jeffrey A. Borgia, Jack Y. Yang, Youping Deng
Kernelized partial least squares for feature reduction and classification of gene microarray data. BMC Syst. Biol. 5 (S-3) (2011)
Xi Wu, Peng Li, Nan Wang, Ping Gong, Edward J. Perkins, Youping Deng, Chaoyang Zhang
State Space Model with hidden variables for reconstruction of gene regulatory networks. BMC Syst. Biol. 5 (S-3) (2011)
Feng Xu, Chen Zhao, Yuhua Li, Jiang Li, Youping Deng, Tieliu Shi
Exploring virus relationships based on virus-host protein-protein interaction network. BMC Syst. Biol. 5 (S-3) (2011)
Jigang Wang, Xiaojie Qiu, Yuhua Li, Youping Deng, Tieliu Shi
A transcriptional dynamic network during Arabidopsis thaliana pollen development. BMC Syst. Biol. 5 (S-3) (2011)
Zhongxue Chen, Jianzhong Liu, Hon Ng, Saralees Nadarajah, Howard L. Kaufman, Jack Y. Yang, Youping Deng
Statistical methods on detecting differentially expressed genes for RNA-seq data. BMC Syst. Biol. 5 (S-3) (2011)
Ke Zhang, Yunlong Liu, Jack Y. Yang, Hamid R. Arabnia, Andrzej Niemierko, Arif Ghafoor, Weizhong Li, Youping Deng
From genes to networks: in systematic points of view. BMC Syst. Biol. 5 (S-3) (2011)
Ke Zhang, Haiyan Wang, Arne C. Bathke, Solomon W. Harrar, Hans-Peter Piepho, Youping Deng
Gene set analysis for longitudinal gene expression data. BMC Bioinform. 12 (2011)
Jun Liu, Jianxun Chen, Xiaoming Liu, Lei Chun, Jinshan Tang, Youping Deng
Mass segmentation using a combined method for cancer detection. BMC Syst. Biol. 5 (S-3) (2011)
Youping Deng, David R. Johnson, Xin Guan, Choo-Yaw Ang, Junmei Ai, Edward J. Perkins
In vitro gene regulatory networks predict in vivo function of liver. BMC Syst. Biol. 4 (2010)
Zhengjun Fan, Yuan Gao, Zehao Jia, Youping Deng, Dequan Chen
Effects of cooling cornea by Low-Temperature Saline Washing on postoperative pain in Photorefractive Keratectomy. Int. J. Funct. Informatics Pers. Medicine 3 (3) (2010)
Xiaolong Zhang, Ting Wang, Huiping Luo, Jack Y. Yang, Youping Deng, Jinshan Tang, Mary Qu Yang
3D Protein structure prediction with genetic tabu search algorithm. BMC Syst. Biol. 4 (S-1) (2010)
Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang
A novel gene network inference algorithm using predictive minimum description length approach. BMC Syst. Biol. 4 (S-1) (2010)
Alexander Pozhikov, Mehdi Pirooznia, Rachel Ryan, Chaoyang Zhang, Ping Gong, Edward J. Perkins, Youping Deng, Marius Brouwer
Generation and Analysis of Expressed Sequence Tags from the Sheepshead Minnow (Cyprinodon Variegatus). BIOCOMP (2009)
Jinghe Mao, Ming Shenwu, Marketta Blue, Manuel Ong, Mary Roth, Ruth Welti, Youping Deng
Plasma Lipidomic Profiling Reveals the Potential Biomarkers in Type 2 Diabetic Patients. BIOCOMP (2009)
Vijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng
Gene Regulatory Network Inference Using Predictive Minimum Description Length Principle and Conditional Mutual Information. IJCBS (2009)
Mehdi Pirooznia, Douglas Crawford, Jeffrey Vanwye, Russell Gibson, Chaoyang Zhang, Youping Deng, Timothy McLean
Genomic Resources for Karenia brevis. BIOCOMP (2009)
Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng
Inferring Gene Regulatory Network of Yeast Cell-Cycle using Dynamic Bayesian Network. BIOCOMP (2008)
Ping Gong, Mehdi Pirooznia, Xin Guan, J. Cristobal Vera, Chun Liang, Youping Deng, Chaoyang Zhang, Edward J. Perkins
A Strategy for High Throughput Microarray Oligo Probe Design Using 454 and Sanger Sequencing Data of Eisenia fetida Expressed Sequence Tags. BIOCOMP (2008)
Arun Rawat, Georg J. Seifert, Youping Deng
Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data. BMC Bioinform. 9 (S-9) (2008)
Mehdi Pirooznia, Tanwir Habib, Edward J. Perkins, Youping Deng
GOfetcher: a database with complex searching facility for gene ontology. Bioinform. 24 (21) (2008)
Mehdi Pirooznia, Ping Gong, Chaoyang Zhang, Edward J. Perkins, Youping Deng
Creating a Workflow for Expressed Sequence Tags Analysis. BIOCOMP (2008)
Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng
. BMC Bioinform. 8 (S-7) (2007)
Jack Y. Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng
Non-Monotonic Radio-Sensitivity over Tumor Volumes on Adjuvant Radio Therapy A New Insight on Cell Killing and Modeling. BIBE (2007)
Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks. BMC Bioinform. 8 (S-7) (2007)
Arun Rajendran, Peng Li, Chaoyang Zhang, Youping Deng
Parallel Training of Multi-class Support Vector Machines Using Sequential Minimal Optimization. MLMTA (2007)
Mehdi Pirooznia, Youping Deng
Efficiency of Hybrid Normalization of Microarray Gene Expression: A Simulation Study. AINA Workshops (1) (2007)
Chaoyang Zhang, Surender Dargan, Hong Lan, Youping Deng
Web-Based Information Retrieval with Local and Global Link Analyis. IKE (2007)
Mehdi Pirooznia, Arun Rawat, Jack Y. Yang, Mary Qu Yang, Ping Gong, Edward J. Perkins, Youping Deng
An Effective Interwoven Loop Design Application for Two-Channel Microarray Experiments. BIBE (2007)
Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng, Dequan Chen
Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data. BMC Bioinform. 7 (S-4) (2006)
Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng
Parallel Multicategory Support Vector Machines (PMC-SVM) for Classifying Microcarray Data. IMSCCS (1) (2006)
Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed O. Elasri
Identification of New Members of Hydrophobin Family Using Primary Structure Analysis. IMSCCS (1) (2006)
Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed O. Elasri
Identification of new members of hydrophobin family using primary structure analysis. BMC Bioinform. 7 (S-4) (2006)
Youping Deng, Jun Ni, Chaoyang Zhang
Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06). BMC Bioinform. 7 (S-4) (2006)
Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng
A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity. BMC Bioinform. 7 (S-2) (2006)
Youping Deng, Yinghua Dong, Susan J. Brown, Chaoyang Zhang
An Integrated Web-Based Model for Management, Analysis and Retrieval of EST Biological Information. APWeb Workshops (2006)
Venkata Thodima, Mehdi Pirooznia, Youping Deng
RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers. BMC Bioinform. 7 (S-2) (2006)
Mehdi Pirooznia, Youping Deng
SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data. BMC Bioinform. 7 (S-4) (2006)
Navodit Kaushik, Chaoyang Zhang, Beddhu Murali, Vijayaraj Nagarajan, Sanyogita Lakhera, Youping Deng
Parallel Virtual Screening for Prediction of Antimicrobial Activity Using Fourier Transforms. PDPTA (2005)
Judong Shen, Shing I. Chang, E. Stanley Lee, Youping Deng, Susan J. Brown
Determination of cluster number in clustering microarray data. Appl. Math. Comput. 169 (2) (2005)
Youping Deng, Venkatachalam Chokalingam, Chaoyang Zhang
Markov Chain Correlation Based Clustering of Gene Expression Data. ITCC (2) (2005)
Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J. Brown
Incremental genetic K-means algorithm and its application in gene expression data analysis. BMC Bioinform. 5 (2004)
Hongying Jiang, Youping Deng, Huann-Sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, Chung-Jui Tsai, Shuanglin Zhang
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinform. 5 (2004)
Qingsong Zhu, Youping Deng, Phaneendra Vanka, Susan J. Brown, Subbaratnam Muthukrishnan, Karl J. Kramer
Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome. Bioinform. 20 (2) (2004)
Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J. Brown
FGKA: a Fast Genetic K-means Clustering Algorithm. SAC (2004)