Comparison of Gene Expression Effects in Liver Tissue and Primary Hepatocyte Cell Cultures After Exposure to Hexahydro-1, 3, 5Trinitro-1, 3, 5-Triazine. - Edward J. Perkins; Wenjun Bao; Xin Guan; Choo-Yaw Ang; Russell D. Wolfinger; Tzu-Ming Chu; Ping Gong 001; Sharon A. Meyer; Laura S. Inouye (IMSCCS (1), 2006)

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)

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)

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)

Discovery of Biomarker Genes from Earthworm Microarray Data by Discriminant Analysis and Clustering. - Ying Li; Nan Wang 002; Edward J. Perkins; Ping Gong 001 (IJCBS, 2009)

Effects of cDNA microarray time-series data size on gene regulatory network inference accuracy. - Vijender Chaitankar; Preetam Ghosh; Chaoyang Zhang; Ping Gong 001; Edward J. Perkins (BCB, 2010)

In silico identification of microRNAs from expressed sequence tags of three earthworm species. - Ping Gong 001; Fuliang Xie; Baohong Zhang; Edward J. Perkins (BCB, 2010)

Performance evaluation of the time-delayed dynamic Bayesian network approach to inferring gene regulatory networks from time series microarray data. - Haoni Li; Peng Li; Chaoyang Zhang; Nan Wang 002; Ping Gong 001; Edward J. Perkins (BCB, 2010)

Gene selection using 1-norm regularization for multi-class microarray data. - Xiaofei Nan; Nan Wang 002; Ping Gong 001; Chaoyang Zhang; Yixin Chen 002; Dawn Wilkins (BIBM, 2010)

Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks. - Vijender Chaitankar; Preetam Ghosh; Edward J. Perkins; Ping Gong 001; Chaoyang Zhang (BMC Bioinform., 2010)

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 silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. - Ping Gong 001; Fuliang Xie; Baohong Zhang; Edward J. Perkins (Comput. Biol. Chem., 2010)

Reconstruction of gene regulatory networks using state space model. - Xi Wu 007; Nan Wang 002; Chaoyang Zhang; Ping Gong 001 (BIBM Workshops, 2011)

RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. - Ying Li; Ping Gong 001; Edward J. Perkins; Chaoyang Zhang; Nan Wang 002 (BMC Bioinform., 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)

Biomarker discovery using 1-norm regularization for multiclass earthworm microarray gene expression data. - Xiaofei Nan; Nan Wang 002; Ping Gong 001; Chaoyang Zhang; Yixin Chen 002; Dawn Wilkins (Neurocomputing, 2012)

Deciphering chemically-induced reversible neurotoxicity by reconstructing perturbed pathways from time series microarray gene expression data. - Yi Yang; Si Li; Andrew S. Maxwell; Natalie D. Barker; Yan Peng; Ying Li; Haoni Li; Xi Wu 007; Peng Li; Tao Huang; Chenhua Zhang; Nan Wang 002; et al. (GENSiPS, 2013)

Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment. - Yi Yang; Andrew S. Maxwell; Xiaowei Zhang 005; Nan Wang 002; Edward J. Perkins; Chaoyang Zhang; Ping Gong 001 (BMC Bioinform., 2013)

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data. - Yan Peng; Andrew S. Maxwell; Natalie D. Barker; Jennifer G. Laird; Alan J. Kennedy; Nan Wang 002; Chaoyang Zhang; Ping Gong 001 (BMC Bioinform., 2014)

Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network. - Peng Li; Ping Gong 001; Haoni Li; Edward J. Perkins; Nan Wang 002; Chaoyang Zhang (EURASIP J. Bioinform. Syst. Biol., 2014)

Factorial analysis of error correction performance using simulated next-generation sequencing data. - Isaac Akogwu; Nan Wang 002; Chaoyang Zhang; Hwanseok Choi; Huixiao Hong; Ping Gong 001 (BIBM, 2016)

Deep learning architectures for multi-label classification of intelligent health risk prediction. - Andrew S. Maxwell; Runzhi Li; Bei Yang; Heng Weng; Aihua Ou; Huixiao Hong; Zhaoxian Zhou; Ping Gong 001; Chaoyang Zhang (BMC Bioinform., 2017)

Comparative toxicogenomics of three insensitive munitions constituents 2, 4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans. - Ping Gong 001; Keri B. Donohue; Anne M. Mayo; Yuping Wang; Huixiao Hong; Mitchell S. Wilbanks; Natalie D. Barker; Xin Guan; Kurt A. Gust (BMC Syst. Biol., 2018)

MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data. - Bei Yang; Yaohui Xu; Andrew S. Maxwell; Wonryull Koh; Ping Gong 001; Chaoyang Zhang (BMC Syst. Biol., 2018)

Similarities and differences between variants called with human reference genome HG19 or HG38. - Bohu Pan; Rebecca Kusko; Wenming Xiao; Yuanting Zheng; Zhichao Liu; Chunlin Xiao; Sugunadevi Sakkiah; Wenjing Guo; Ping Gong 001; Chaoyang Zhang; Weigong Ge; Leming Shi; et al. (BMC Bioinform., 2019)

Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38. - Bohu Pan; Rebecca Kusko; Wenming Xiao; Yuanting Zheng; Zhichao Liu; Chunlin Xiao; Sugunadevi Sakkiah; Wenjing Guo; Ping Gong 001; Chaoyang Zhang; Weigong Ge; Leming Shi; et al. (BMC Bioinform., 2019)

Structure-activity relationship-based chemical classification of highly imbalanced Tox21 datasets. - Gabriel Idakwo; Sundar Thangapandian; Joseph Luttrell IV; Yan Li; Nan Wang 002; Zhaoxian Zhou; Huixiao Hong; Bei Yang; Chaoyang Zhang; Ping Gong 001 (J. Cheminformatics, 2020)

An autoencoder-based deep learning method for genotype imputation. - Meng Song; Jonathan Greenbaum; Joseph Luttrell IV; Weihua Zhou; Chong Wu; Zhe Luo; Chuan Qiu; Lan Juan Zhao; Kuan-Jui Su; Qing Tian 004; Hui Shen 007; Huixiao Hong; et al. (Frontiers Artif. Intell., 2022)