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)

Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine. - Edward J. Perkins; Wenjun Bao; Xin Guan; Choo-Yaw Ang; Russell D. Wolfinger; Tzu-Ming Chu; Sharon A. Meyer; Laura S. Inouye (BMC Bioinform., 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)

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

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)

Quail Genomics: a knowledgebase for Northern bobwhite. - Arun Rawat; Kurt A. Gust; Mohamed O. Elasri; Edward J. Perkins (BMC Bioinform., 2010)

Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. - Jonathan D. Wren; Doris M. Kupfer; Edward J. Perkins; Susan Bridges; Daniel Berleant (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 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)

Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. - Jason E. Shoemaker; Kalyan Gayen; Natàlia Garcia-Reyero; Edward J. Perkins; Daniel L. Villeneuve; Li Liu 035; Francis J. Doyle (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)

Downstream Exploration of DNA-Bound Searching Proteins: A Diffusion-Reaction Model. - Michael L. Mayo; Edward J. Perkins; Preetam Ghosh (BIBE, 2011)

A Scalable Information Theory Based Gene Regulatory Network Inference Method from Time Series and Knock-Out Data. - Vijender Chaitankar; Preetam Ghosh; Mohamed O. Elasri; Edward J. Perkins (BICoB, 2011)

Poster: Gene regulatory network inference using time lagged context likelihood of relatedness. - Vijender Chaitankar; Preetam Ghosh; Mohamed O. Elasri; Edward J. Perkins (ICCABS, 2011)

sREVEAL: Scalable extensions of REVEAL towards regulatory network inference. - Vijender Chaitankar; Preetam Ghosh; Mohamed O. Elasri; Edward J. Perkins (ISDA, 2011)

Principles of genomic robustness inspire fault-tolerant WSN topologies: A network science based case study. - Preetam Ghosh; Michael L. Mayo; Vijender Chaitankar; Tanwir Habib; Edward J. Perkins; Sajal K. Das 001 (PerCom 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)

First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA. - Michael L. Mayo; Edward J. Perkins; Preetam Ghosh (BMC Bioinform., 2011)

Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. - Jonathan D. Wren; Doris M. Kupfer; Edward J. Perkins; Susan Bridges; Stephen Winters-Hilt; Mikhail G. Dozmorov; Ulisses M. Braga-Neto (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)

Genome scale inference of transcriptional regulatory networks using mutual information on complex interactions. - Vijender Chaitankar; Preetam Ghosh; Mohamed O. Elasri; Kurt A. Gust; Edward J. Perkins (BCB, 2012)

sCoIn: A scoring algorithm based on complex interactions for reverse engineering regulatory networks. - Vijender Chaitankar; Preetam Ghosh; Mohamed O. Elasri; Kurt A. Gust; Edward J. Perkins (BIBE, 2012)

Performance of wireless sensor topologies inspired by E. coli genetic networks. - Bhanu K. Kamapantula; Ahmed Abdelzaher 001; Preetam Ghosh; Michael L. Mayo; Edward J. Perkins; Sajal K. Das 001 (PerCom Workshops, 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)

Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. - Jonathan D. Wren; Mikhail G. Dozmorov; Dennis Burian; Rakesh Kaundal; Andy D. Perkins; Edward J. Perkins; Doris M. Kupfer; Gordon K. Springer (BMC Bioinform., 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)

Correlating In silico Feed-forward Loop Knockout Experiments with the Topological Features of Transcriptional Regulatory Networks. - Ahmed Abdelzaher 001; Michael L. Mayo; Preetam Ghosh; Edward J. Perkins (BICT, 2014)

Feature ranking in transcriptional networks: Packet receipt as a dynamical metric. - Bhanu K. Kamapantula; Michael L. Mayo; Edward J. Perkins; Ahmed Abdelzaher 001; Preetam Ghosh (BICT, 2014)

Dynamical impacts from structural redundancy of transcriptional motifs in gene-regulatory networks. - Bhanu K. Kamapantula; Michael L. Mayo; Edward J. Perkins; Preetam Ghosh (BICT, 2014)

Networks of interactions between feed-forward loop transcriptional motifs in gene-regulatory networks. - Michael L. Mayo; Ahmed Abdelzaher 001; Bhanu K. Kamapantula; Edward J. Perkins; Preetam Ghosh (BICT, 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)

Leveraging the robustness of genetic networks: a case study on bio-inspired wireless sensor network topologies. - Bhanu K. Kamapantula; Ahmed Abdelzaher 001; Preetam Ghosh; Michael L. Mayo; Edward J. Perkins; Sajal K. Das 001 (J. Ambient Intell. Humaniz. Comput., 2014)

Contribution of canonical feed-forward loop motifs on the fault-tolerance and information transport efficiency of transcriptional regulatory networks. - Ahmed Abdelzaher 001; Michael L. Mayo; Edward J. Perkins; Preetam Ghosh (Nano Commun. Networks, 2015)

Capacity estimates of additive inverse Gaussian molecular channels with relay characteristics. - Pratip Rana; Preetam Ghosh; Kevin Pilkiewicz; Edward J. Perkins; Chris Warner; Michael L. Mayo (EAI Endorsed Trans. Wirel. Spectr., 2016)

Novel enhanced applications of QSPR models: Temperature dependence of aqueous solubility. - Kyrylo Klimenko; Victor Kuzmin; Liudmila Ognichenko; Leonid Gorb; Manoj Shukla; Natalia Vinas; Edward J. Perkins; Pavel G. Polishchuk; Anatoly G. Artemenko; Jerzy Leszczynski (J. Comput. Chem., 2016)

Abundance of connected motifs in transcriptional networks, a case study using random forests regression. - Khajamoinuddin Syed; Bhanu K. Kamapantula; Michael L. Mayo; Edward J. Perkins; Preetam Ghosh (EAI Endorsed Trans. Mob. Commun. Appl., 2016)

The Structural Role of Feed-Forward Loop Motif in Transcriptional Regulatory Networks. - Bhanu K. Kamapantula; Michael L. Mayo; Edward J. Perkins; Preetam Ghosh (Mob. Networks Appl., 2016)

Physiological fidelity or model parsimony? The relative performance of reverse-toxicokinetic modeling approaches. - Michael A. Rowland; Edward J. Perkins; Michael L. Mayo (BMC Syst. Biol., 2017)

Low SWaP, In-Situ Data Logger for Strain Measurement of Paddlefish Rostrums in Motion. - Clayton R. Thurmer; Jason D. Ray; Jordan D. Klein; Steven L. Bunkley; Anton Netchaev; Reena R. Patel; Guillermo A. Riveros; Edward J. Perkins; Jan Jeffery Hoover (UEMCON, 2018)

Keanu: a novel visualization tool to explore biodiversity in metagenomes. - Adam Thrash; Mark Arick II; Robyn A. Barbato; Robert M. Jones; Thomas A. Douglas; Julie Esdale; Edward J. Perkins; Natàlia Garcia-Reyero (BMC Bioinform., 2019)

Adverse Outcome Pathways for Engineered Systems. - R. Cody Salter; Natàlia Garcia-Reyero; Alicia Ruvinsky; Maria Seale; Edward J. Perkins (SysCon, 2023)

Air Filter Loading Characteristics for an Epigenetic Modeling Approach to Adaptive Prognostics. - Maria A. Seale; Gentry Berry; Richard C. Salter; Alicia I. Ruvinsky; Edward J. Perkins; Natàlia Garcia-Reyero (IEEE DataPort, 2024)