Youping Deng

68 papers C 2Misc 3Journal 47Unranked 16
YearRankTypeTitle / Venue / Authors
2025 J jnl
Highlighting the achievements and impact of women in data science.
Patterns
Lauren Higa, Youping Deng
2025 J jnl
Is AI overhyped?
Patterns
Jason H. Moore, Anand K. Gavai, Yingji Xia, Mohammadamin Mahmanzar, Youping Deng
2024 J jnl
Enhancing visibility and inclusivity of queer scientists to advance equality in academia.
Patterns
Zhuokun Feng, Yuanyuan Fu, Youping Deng
2024 J jnl
Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform.
Briefings Bioinform.
Yujia Qin, Angela Maggio, Dale Hawkins, Laura Beaudry, Allen Kim, Daniel Pan, Ting Gong, Yuanyuan Fu, Hua Yang, Youping Deng
2024 J jnl
sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data.
Briefings Bioinform.
Ken Nakatsu, Mayumi Jijiwa, Vedbar Khadka, Masaki Nasu, Youping Deng
2023 J jnl
Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease.
Patterns
Joshua G. Burkhart, Guanming Wu, Xubo Song, Francesco Raimondi, Shannon K. McWeeney, Melissa H. Wong, Youping Deng
2022 J jnl
Diversifying the Genomic Data Science Research Community.
CoRR
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
2020 J jnl
Current trend and development in bioinformatics research.
BMC Bioinform.
Yuanyuan Fu, Zhougui Ling, Hamid R. Arabnia, Youping Deng
2020 J jnl
Development of a RNA-Seq based prognostic signature for colon cancer.
Int. J. Comput. Biol. Drug Des.
Bjarne Bartlett, Yong Zhu, Mark Menor, Vedbar S. Khadka, Jicai Zhang, Jie Zheng, Bin Jiang, Youping Deng
2020 J jnl
Development of predicitve models to distinguish metals from non-metal toxicants, and individual metal from one another.
BMC Bioinform.
Zongtao Yu, Yuanyuan Fu, Junmei Ai, Jicai Zhang, Gang Huang, Youping Deng
2020 J jnl
Identification of plasma lipid species as promising diagnostic markers for prostate cancer.
BMC Medical Informatics Decis. Mak.
Xiaoli Chen, Yong Zhu, Mayumi Jijiwa, Masaki Nasu, Junmei Ai, Shengming Dai, Bin Jiang, Jicai Zhang, Gang Huang, Youping Deng
2020 J jnl
Tissue-associated microbial detection in cancer using human sequencing data.
BMC Bioinform.
Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez, Youping Deng
2018 J jnl
Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer.
BMC Syst. Biol.
Mengjie Guo, Sicheng Lu, Hongming Huang, Yaohui Wang, Mary Qu Yang, Ye Yang, Zhimin Fan, Bin Jiang, Youping Deng
2018 J jnl
Risk-associated and pathway-based method to detect association with Alzheimer's disease.
Int. J. Comput. Biol. Drug Des.
Jeffrey Mitchel, Laszlo Prokai, Youping Deng, Fan Zhang, Robert Barber
2018 J jnl
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.
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
2017 — conf
Structure Modeling and Molecular Docking Studies of Schizophrenia Candidate Genes, Synapsins 2 (SYN2) and Trace Amino Acid Receptor (TAAR6).
ISBRA
Naureen Aslam Khattak, Sheikh Arslan Sehgal, Yongsheng Bai, Youping Deng
2014 J jnl
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms.
BMC Bioinform.
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
2014 J jnl
CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data.
Bioinform.
Daogang Guan, Jiaofang Shao, Youping Deng, Panwen Wang, Zhongying Zhao, Yan Liang, Junwen Wang, Bin Yan
2014 J jnl
Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2.
BMC Bioinform.
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
2014 J jnl
Identification of genes and pathways involved in kidney renal clear cell carcinoma.
BMC Bioinform.
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
2014 J jnl
PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data.
Nucleic Acids Res.
Daogang Guan, Jiaofang Shao, Zhongying Zhao, Panwen Wang, Jing Qin, Youping Deng, Kenneth R. Boheler, Junwen Wang, Bin Yan
2012 — conf
Classifying Lung Cancer Recurrence Time Using Novel Ensemble Method with Gene Network based Input Models.
Complex Adaptive Systems
William S. Ford, Jin-Woo Park, Aaron S. Campbell, Youping Deng, Yan Li, Walker H. Land Jr.
2012 — conf
GRNN Ensemble Classifier for Lung Cancer Prognosis Using Only Demographic and TNM features.
Complex Adaptive Systems
J. David Schaffer, Jin-Woo Park, Erin Barnes, Qiyi Lu, Xingye Qiao, Youping Deng, Yan Li, Walker H. Land Jr.
2012 J jnl
Gene order computation using Alzheimer's DNA microarray gene expression data and the ant colony optimisation algorithm.
Int. J. Data Min. Bioinform.
Chao-Yang Pang, Gang Jiang, Shipeng Wang, Ben-Qiong Hu, Qingzhong Liu, Youping Deng, Xudong Huang
2011 J jnl
A transcriptional dynamic network during Arabidopsis thaliana pollen development.
BMC Syst. Biol.
Jigang Wang, Xiaojie Qiu, Yuhua Li, Youping Deng, Tieliu Shi
2011 J jnl
Exploring virus relationships based on virus-host protein-protein interaction network.
BMC Syst. Biol.
Feng Xu, Chen Zhao, Yuhua Li, Jiang Li, Youping Deng, Tieliu Shi
2011 J jnl
From genes to networks: in systematic points of view.
BMC Syst. Biol.
Ke Zhang, Yunlong Liu, Jack Y. Yang, Hamid R. Arabnia, Andrzej Niemierko, Arif Ghafoor, Weizhong Li, Youping Deng
2011 J jnl
Gene set analysis for longitudinal gene expression data.
BMC Bioinform.
Ke Zhang, Haiyan Wang, Arne C. Bathke, Solomon W. Harrar, Hans-Peter Piepho, Youping Deng
2011 J jnl
Kernelized partial least squares for feature reduction and classification of gene microarray data.
BMC Syst. Biol.
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
2011 J jnl
Mass segmentation using a combined method for cancer detection.
BMC Syst. Biol.
Jun Liu, Jianxun Chen, Xiaoming Liu, Lei Chun, Jinshan Tang, Youping Deng
2011 J jnl
State Space Model with hidden variables for reconstruction of gene regulatory networks.
BMC Syst. Biol.
Xi Wu, Peng Li, Nan Wang, Ping Gong, Edward J. Perkins, Youping Deng, Chaoyang Zhang
2011 J jnl
Statistical methods on detecting differentially expressed genes for RNA-seq data.
BMC Syst. Biol.
Zhongxue Chen, Jianzhong Liu, Hon Ng, Saralees Nadarajah, Howard L. Kaufman, Jack Y. Yang, Youping Deng
2010 J jnl
3D Protein structure prediction with genetic tabu search algorithm.
BMC Syst. Biol.
Xiaolong Zhang, Ting Wang, Huiping Luo, Jack Y. Yang, Youping Deng, Jinshan Tang, Mary Qu Yang
2010 J jnl
A novel gene network inference algorithm using predictive minimum description length approach.
BMC Syst. Biol.
Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang
2010 J jnl
Effects of cooling cornea by Low-Temperature Saline Washing on postoperative pain in Photorefractive Keratectomy.
Int. J. Funct. Informatics Pers. Medicine
Zhengjun Fan, Yuan Gao, Zehao Jia, Youping Deng, Dequan Chen
2010 J jnl
In vitro gene regulatory networks predict in vivo function of liver.
BMC Syst. Biol.
Youping Deng, David R. Johnson, Xin Guan, Choo-Yaw Ang, Junmei Ai, Edward J. Perkins
2009 — conf
Gene Regulatory Network Inference Using Predictive Minimum Description Length Principle and Conditional Mutual Information.
IJCBS
Vijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng
2009 — conf
Generation and Analysis of Expressed Sequence Tags from the Sheepshead Minnow (Cyprinodon Variegatus).
BIOCOMP
Alexander Pozhikov, Mehdi Pirooznia, Rachel Ryan, Chaoyang Zhang, Ping Gong, Edward J. Perkins, Youping Deng, Marius Brouwer
2009 — conf
Genomic Resources for Karenia brevis.
BIOCOMP
Mehdi Pirooznia, Douglas Crawford, Jeffrey Vanwye, Russell Gibson, Chaoyang Zhang, Youping Deng, Timothy McLean
2009 — conf
Plasma Lipidomic Profiling Reveals the Potential Biomarkers in Type 2 Diabetic Patients.
BIOCOMP
Jinghe Mao, Ming Shenwu, Marketta Blue, Manuel Ong, Mary Roth, Ruth Welti, Youping Deng
2008 — conf
A Strategy for High Throughput Microarray Oligo Probe Design Using 454 and Sanger Sequencing Data of Eisenia fetida Expressed Sequence Tags.
BIOCOMP
Ping Gong, Mehdi Pirooznia, Xin Guan, J. Cristobal Vera, Chun Liang, Youping Deng, Chaoyang Zhang, Edward J. Perkins
2008 — conf
Creating a Workflow for Expressed Sequence Tags Analysis.
BIOCOMP
Mehdi Pirooznia, Ping Gong, Chaoyang Zhang, Edward J. Perkins, Youping Deng
2008 J jnl
GOfetcher: a database with complex searching facility for gene ontology.
Bioinform.
Mehdi Pirooznia, Tanwir Habib, Edward J. Perkins, Youping Deng
2008 — conf
Inferring Gene Regulatory Network of Yeast Cell-Cycle using Dynamic Bayesian Network.
BIOCOMP
Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng
2008 J jnl
Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data.
BMC Bioinform.
Arun Rawat, Georg J. Seifert, Youping Deng
2007 C conf
An Effective Interwoven Loop Design Application for Two-Channel Microarray Experiments.
BIBE
Mehdi Pirooznia, Arun Rawat, Jack Y. Yang, Mary Qu Yang, Ping Gong, Edward J. Perkins, Youping Deng
2007 J jnl
Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm
BMC Bioinform.
Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng
2007 J jnl
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks.
BMC Bioinform.
Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng
2007 — conf
Efficiency of Hybrid Normalization of Microarray Gene Expression: A Simulation Study.
AINA Workshops (1)
Mehdi Pirooznia, Youping Deng
2007 C conf
Non-Monotonic Radio-Sensitivity over Tumor Volumes on Adjuvant Radio Therapy A New Insight on Cell Killing and Modeling.
BIBE
Jack Y. Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng
2007 — conf
Parallel Training of Multi-class Support Vector Machines Using Sequential Minimal Optimization.
MLMTA
Arun Rajendran, Peng Li, Chaoyang Zhang, Youping Deng
2007 Misc conf
Web-Based Information Retrieval with Local and Global Link Analyis.
IKE
Chaoyang Zhang, Surender Dargan, Hong Lan, Youping Deng
2006 J jnl
A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity.
BMC Bioinform.
Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng
2006 — conf
An Integrated Web-Based Model for Management, Analysis and Retrieval of EST Biological Information.
APWeb Workshops
Youping Deng, Yinghua Dong, Susan J. Brown, Chaoyang Zhang
2006 J jnl
Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06).
BMC Bioinform.
Youping Deng, Jun Ni, Chaoyang Zhang
2006 — conf
Identification of New Members of Hydrophobin Family Using Primary Structure Analysis.
IMSCCS (1)
Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed O. Elasri
2006 J jnl
Identification of new members of hydrophobin family using primary structure analysis.
BMC Bioinform.
Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed O. Elasri
2006 — conf
Parallel Multicategory Support Vector Machines (PMC-SVM) for Classifying Microcarray Data.
IMSCCS (1)
Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng
2006 J jnl
Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data.
BMC Bioinform.
Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng, Dequan Chen
2006 J jnl
RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers.
BMC Bioinform.
Venkata Thodima, Mehdi Pirooznia, Youping Deng
2006 J jnl
SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data.
BMC Bioinform.
Mehdi Pirooznia, Youping Deng
2005 J jnl
Determination of cluster number in clustering microarray data.
Appl. Math. Comput.
Judong Shen, Shing I. Chang, E. Stanley Lee, Youping Deng, Susan J. Brown
2005 — conf
Markov Chain Correlation Based Clustering of Gene Expression Data.
ITCC (2)
Youping Deng, Venkatachalam Chokalingam, Chaoyang Zhang
2005 Misc conf
Parallel Virtual Screening for Prediction of Antimicrobial Activity Using Fourier Transforms.
PDPTA
Navodit Kaushik, Chaoyang Zhang, Beddhu Murali, Vijayaraj Nagarajan, Sanyogita Lakhera, Youping Deng
2004 J jnl
Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome.
Bioinform.
Qingsong Zhu, Youping Deng, Phaneendra Vanka, Susan J. Brown, Subbaratnam Muthukrishnan, Karl J. Kramer
2004 Misc conf
FGKA: a Fast Genetic K-means Clustering Algorithm.
SAC
Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J. Brown
2004 J jnl
Incremental genetic K-means algorithm and its application in gene expression data analysis.
BMC Bioinform.
Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J. Brown
2004 J jnl
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes.
BMC Bioinform.
Hongying Jiang, Youping Deng, Huann-Sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, Chung-Jui Tsai, Shuanglin Zhang