FGKA: a Fast Genetic K-means Clustering Algorithm. - Yi Lu 015; Shiyong Lu; Farshad Fotouhi; Youping Deng; Susan J. Brown (SAC, 2004)

Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome. - Qingsong Zhu; Youping Deng; Phaneendra Vanka; Susan J. Brown; Subbaratnam Muthukrishnan; Karl J. Kramer (Bioinform., 2004)

Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. - Hongying Jiang; Youping Deng; Huann-Sheng Chen; Lin Tao; Qiuying Sha; Jun Chen; Chung-Jui Tsai; Shuanglin Zhang (BMC Bioinform., 2004)

Incremental genetic K-means algorithm and its application in gene expression data analysis. - Yi Lu 015; Shiyong Lu; Farshad Fotouhi; Youping Deng; Susan J. Brown (BMC Bioinform., 2004)

Markov Chain Correlation Based Clustering of Gene Expression Data. - Youping Deng; Venkatachalam Chokalingam; Chaoyang Zhang (ITCC (2), 2005)

Parallel Virtual Screening for Prediction of Antimicrobial Activity Using Fourier Transforms. - Navodit Kaushik; Chaoyang Zhang; Beddhu Murali; Vijayaraj Nagarajan; Sanyogita Lakhera; Youping Deng (PDPTA, 2005)

Determination of cluster number in clustering microarray data. - Judong Shen; Shing I. Chang; E. Stanley Lee; Youping Deng; Susan J. Brown (Appl. Math. Comput., 2005)

An Integrated Web-Based Model for Management, Analysis and Retrieval of EST Biological Information. - Youping Deng; Yinghua Dong; Susan J. Brown; Chaoyang Zhang (APWeb Workshops, 2006)

Parallel Multicategory Support Vector Machines (PMC-SVM) for Classifying Microcarray Data. - Chaoyang Zhang; Peng Li; Arun Rajendran; Youping Deng (IMSCCS (1), 2006)

Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06). - Youping Deng; Jun Ni 001; Chaoyang Zhang (BMC Bioinform., 2006)

A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity. - Vijayaraj Nagarajan; Navodit Kaushik; Beddhu Murali; Chaoyang Zhang; Sanyogita Lakhera; Mohamed O. Elasri; Youping Deng (BMC Bioinform., 2006)

SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data. - Mehdi Pirooznia; Youping Deng (BMC Bioinform., 2006)

RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers. - Venkata Thodima; Mehdi Pirooznia; Youping Deng (BMC Bioinform., 2006)

Identification of new members of hydrophobin family using primary structure analysis. - Kuan Yang; Youping Deng; Chaoyang Zhang; Mohamed O. Elasri (BMC Bioinform., 2006)

Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data. - Chaoyang Zhang; Peng Li; Arun Rajendran; Youping Deng; Dequan Chen (BMC Bioinform., 2006)

Efficiency of Hybrid Normalization of Microarray Gene Expression: A Simulation Study. - Mehdi Pirooznia; Youping Deng (AINA Workshops (1), 2007)

An Effective Interwoven Loop Design Application for Two-Channel Microarray Experiments. - Mehdi Pirooznia; Arun Rawat; Jack Y. Yang; Mary Qu Yang; Ping Gong 001; Edward J. Perkins; Youping Deng (BIBE, 2007)

Non-Monotonic Radio-Sensitivity over Tumor Volumes on Adjuvant Radio Therapy A New Insight on Cell Killing and Modeling. - Jack Y. Yang; Andrzej Niemierko; Mary Qu Yang; Youping Deng (BIBE, 2007)

Web-Based Information Retrieval with Local and Global Link Analyis. - Chaoyang Zhang; Surender Dargan; Hong Lan; Youping Deng (IKE, 2007)

Parallel Training of Multi-class Support Vector Machines Using Sequential Minimal Optimization. - Arun Rajendran; Peng Li; Chaoyang Zhang; Youping Deng (MLMTA, 2007)

Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks. - Peng Li; Chaoyang Zhang; Edward J. Perkins; Ping Gong 001; Youping Deng (BMC Bioinform., 2007)

Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. - Mehdi Pirooznia; Ping Gong 001; Xin Guan; Laura S. Inouye; Kuan Yang; Edward J. Perkins; Youping Deng (BMC Bioinform., 2007)

A Strategy for High Throughput Microarray Oligo Probe Design Using 454 and Sanger Sequencing Data of Eisenia fetida Expressed Sequence Tags. - Ping Gong 001; Mehdi Pirooznia; Xin Guan; J. Cristobal Vera; Chun Liang; Youping Deng; Chaoyang Zhang; Edward J. Perkins (BIOCOMP, 2008)

Inferring Gene Regulatory Network of Yeast Cell-Cycle using Dynamic Bayesian Network. - Peng Li; Chaoyang Zhang; Edward J. Perkins; Ping Gong 001; Youping Deng (BIOCOMP, 2008)

Creating a Workflow for Expressed Sequence Tags Analysis. - Mehdi Pirooznia; Ping Gong 001; Chaoyang Zhang; Edward J. Perkins; Youping Deng (BIOCOMP, 2008)

GOfetcher: a database with complex searching facility for gene ontology. - Mehdi Pirooznia; Tanwir Habib; Edward J. Perkins; Youping Deng (Bioinform., 2008)

Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data. - Arun Rawat; Georg J. Seifert; Youping Deng (BMC Bioinform., 2008)

Plasma Lipidomic Profiling Reveals the Potential Biomarkers in Type 2 Diabetic Patients. - Jinghe Mao; Ming Shenwu; Marketta Blue; Manuel Ong; Mary Roth; Ruth Welti; Youping Deng (BIOCOMP, 2009)

Genomic Resources for Karenia brevis. - Mehdi Pirooznia; Douglas Crawford; Jeffrey Vanwye; Russell Gibson; Chaoyang Zhang; Youping Deng; Timothy McLean (BIOCOMP, 2009)

Generation and Analysis of Expressed Sequence Tags from the Sheepshead Minnow (Cyprinodon Variegatus). - Alexander Pozhikov; Mehdi Pirooznia; Rachel Ryan; Chaoyang Zhang; Ping Gong 001; Edward J. Perkins; Youping Deng; Marius Brouwer (BIOCOMP, 2009)

Gene Regulatory Network Inference Using Predictive Minimum Description Length Principle and Conditional Mutual Information. - Vijender Chaitankar; Chaoyang Zhang; Preetam Ghosh; Edward J. Perkins; Ping Gong 001; Youping Deng (IJCBS, 2009)

A novel gene network inference algorithm using predictive minimum description length approach. - Vijender Chaitankar; Preetam Ghosh; Edward J. Perkins; Ping Gong 001; Youping Deng; Chaoyang Zhang (BMC Syst. Biol., 2010)

In vitro gene regulatory networks predict in vivo function of liver. - Youping Deng; David R. Johnson; Xin Guan; Choo-Yaw Ang; Junmei Ai; Edward J. Perkins (BMC Syst. Biol., 2010)

3D Protein structure prediction with genetic tabu search algorithm. - Xiaolong Zhang 002; Ting Wang; Huiping Luo; Jack Y. Yang; Youping Deng; Jinshan Tang; Mary Qu Yang (BMC Syst. Biol., 2010)

Effects of cooling cornea by Low-Temperature Saline Washing on postoperative pain in Photorefractive Keratectomy. - Zhengjun Fan; Yuan Gao; Zehao Jia; Youping Deng; Dequan Chen (Int. J. Funct. Informatics Pers. Medicine, 2010)

Gene set analysis for longitudinal gene expression data. - Ke Zhang; Haiyan Wang 008; Arne C. Bathke; Solomon W. Harrar; Hans-Peter Piepho; Youping Deng (BMC Bioinform., 2011)

Statistical methods on detecting differentially expressed genes for RNA-seq data. - Zhongxue Chen; Jianzhong Liu; Hon Ng; Saralees Nadarajah; Howard L. Kaufman; Jack Y. Yang; Youping Deng (BMC Syst. Biol., 2011)

Kernelized partial least squares for feature reduction and classification of gene microarray data. - 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 (BMC Syst. Biol., 2011)

Mass segmentation using a combined method for cancer detection. - Jun Liu 011; Jianxun Chen; Xiaoming Liu 004; Lei Chun; Jinshan Tang; Youping Deng (BMC Syst. Biol., 2011)

A transcriptional dynamic network during Arabidopsis thaliana pollen development. - Jigang Wang; Xiaojie Qiu; Yuhua Li; Youping Deng; Tieliu Shi (BMC Syst. Biol., 2011)

State Space Model with hidden variables for reconstruction of gene regulatory networks. - Xi Wu 007; Peng Li; Nan Wang 002; Ping Gong 001; Edward J. Perkins; Youping Deng; Chaoyang Zhang (BMC Syst. Biol., 2011)

Exploring virus relationships based on virus-host protein-protein interaction network. - Feng Xu; Chen Zhao; Yuhua Li; Jiang Li; Youping Deng; Tieliu Shi (BMC Syst. Biol., 2011)

From genes to networks: in systematic points of view. - Ke Zhang; Yunlong Liu; Jack Y. Yang; Hamid R. Arabnia; Andrzej Niemierko; Arif Ghafoor; Weizhong Li; Youping Deng (BMC Syst. Biol., 2011)

Gene order computation using Alzheimer's DNA microarray gene expression data and the ant colony optimisation algorithm. - Chao-Yang Pang; Gang Jiang; Shipeng Wang; Ben-Qiong Hu; Qingzhong Liu; Youping Deng; Xudong Huang (Int. J. Data Min. Bioinform., 2012)

Classifying Lung Cancer Recurrence Time Using Novel Ensemble Method with Gene Network based Input Models. - William S. Ford; Jin-Woo Park; Aaron S. Campbell; Youping Deng; Yan Li; Walker H. Land Jr. (Complex Adaptive Systems, 2012)

GRNN Ensemble Classifier for Lung Cancer Prognosis Using Only Demographic and TNM features. - J. David Schaffer; Jin-Woo Park; Erin Barnes; Qiyi Lu; Xingye Qiao; Youping Deng; Yan Li; Walker H. Land Jr. (Complex Adaptive Systems, 2012)

CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. - Daogang Guan; Jiaofang Shao; Youping Deng; Panwen Wang; Zhongying Zhao 002; Yan Liang; Junwen Wang; Bin Yan (Bioinform., 2014)

Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2. - 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 (BMC Bioinform., 2014)

Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. - 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; et al. (BMC Bioinform., 2014)

Identification of genes and pathways involved in kidney renal clear cell carcinoma. - 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; et al. (BMC Bioinform., 2014)

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. - Daogang Guan; Jiaofang Shao; Zhongying Zhao 002; Panwen Wang; Jing Qin 004; Youping Deng; Kenneth R. Boheler; Junwen Wang; Bin Yan (Nucleic Acids Res., 2014)

Structure Modeling and Molecular Docking Studies of Schizophrenia Candidate Genes, Synapsins 2 (SYN2) and Trace Amino Acid Receptor (TAAR6). - Naureen Aslam Khattak; Sheikh Arslan Sehgal; Yongsheng Bai; Youping Deng (ISBRA, 2017)

Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer. - Mengjie Guo; Sicheng Lu; Hongming Huang; Yaohui Wang; Mary Qu Yang; Ye Yang; Zhimin Fan; Bin Jiang; Youping Deng (BMC Syst. Biol., 2018)

The emerging role of microRNA-4487/6845-3p in Alzheimer's disease pathologies is induced by Aβ25-35 triggered in SH-SY5Y cell. - 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; et al. (BMC Syst. Biol., 2018)

Risk-associated and pathway-based method to detect association with Alzheimer's disease. - Jeffrey Mitchel; Laszlo Prokai; Youping Deng; Fan Zhang; Robert Barber (Int. J. Comput. Biol. Drug Des., 2018)

Current trend and development in bioinformatics research. - Yuanyuan Fu; Zhougui Ling; Hamid R. Arabnia; Youping Deng (BMC Bioinform., 2020)

Tissue-associated microbial detection in cancer using human sequencing data. - Rebecca M. Rodriguez; Vedbar S. Khadka; Mark Menor; Brenda Y. Hernandez; Youping Deng (BMC Bioinform., 2020)

Development of predicitve models to distinguish metals from non-metal toxicants, and individual metal from one another. - Zongtao Yu; Yuanyuan Fu; Junmei Ai; Jicai Zhang; Gang Huang 002; Youping Deng (BMC Bioinform., 2020)

Development of a RNA-Seq based prognostic signature for colon cancer. - Bjarne Bartlett; Yong Zhu; Mark Menor; Vedbar S. Khadka; Jicai Zhang; Jie Zheng; Bin Jiang; Youping Deng (Int. J. Comput. Biol. Drug Des., 2020)

Identification of plasma lipid species as promising diagnostic markers for prostate cancer. - Xiaoli Chen; Yong Zhu; Mayumi Jijiwa; Masaki Nasu; Junmei Ai; Shengming Dai; Bin Jiang; Jicai Zhang; Gang Huang 002; Youping Deng (BMC Medical Informatics Decis. Mak., 2020)

Diversifying the Genomic Data Science Research Community. - 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; et al. (CoRR, 2022)

Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. - Joshua G. Burkhart; Guanming Wu; Xubo Song; Francesco Raimondi 001; Shannon K. McWeeney; Melissa H. Wong; Youping Deng (Patterns, 2023)

sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data. - Ken Nakatsu; Mayumi Jijiwa; Vedbar Khadka; Masaki Nasu; Youping Deng (Briefings Bioinform., 2024)

Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform. - Yujia Qin; Angela Maggio; Dale Hawkins; Laura Beaudry; Allen Kim; Daniel Pan; Ting Gong; Yuanyuan Fu; Hua Yang; Youping Deng (Briefings Bioinform., 2024)

Enhancing visibility and inclusivity of queer scientists to advance equality in academia. - Zhuokun Feng; Yuanyuan Fu; Youping Deng (Patterns, 2024)

Highlighting the achievements and impact of women in data science. - Lauren Higa; Youping Deng (Patterns, 2025)