Edward J. Perkins

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 11

Top Topics

Computational Biology

Feature Ranking

Gene Expression

Top Venues

EAI Endorsed Trans. Wirel. Spectr.

EURASIP J. Bioinform. Syst. Biol.

Publications

R. Cody Salter, Natàlia Garcia-Reyero, Alicia Ruvinsky, Maria Seale, Edward J. Perkins
Adverse Outcome Pathways for Engineered Systems. SysCon (2023)
Adam Thrash, Mark Arick II, Robyn A. Barbato, Robert M. Jones, Thomas A. Douglas, Julie Esdale, Edward J. Perkins, Natàlia Garcia-Reyero
Keanu: a novel visualization tool to explore biodiversity in metagenomes. BMC Bioinform. (2) (2019)
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
Low SWaP, In-Situ Data Logger for Strain Measurement of Paddlefish Rostrums in Motion. UEMCON (2018)
Michael A. Rowland, Edward J. Perkins, Michael L. Mayo
Physiological fidelity or model parsimony? The relative performance of reverse-toxicokinetic modeling approaches. BMC Syst. Biol. 11 (1) (2017)
Pratip Rana, Preetam Ghosh, Kevin Pilkiewicz, Edward J. Perkins, Chris Warner, Michael L. Mayo
Capacity estimates of additive inverse Gaussian molecular channels with relay characteristics. EAI Endorsed Trans. Wirel. Spectr. 2 (9) (2016)
Bhanu K. Kamapantula, Michael L. Mayo, Edward J. Perkins, Preetam Ghosh
The Structural Role of Feed-Forward Loop Motif in Transcriptional Regulatory Networks. Mob. Networks Appl. 21 (1) (2016)
Khajamoinuddin Syed, Bhanu K. Kamapantula, Michael L. Mayo, Edward J. Perkins, Preetam Ghosh
Abundance of connected motifs in transcriptional networks, a case study using random forests regression. EAI Endorsed Trans. Mob. Commun. Appl. 2 (10) (2016)
Kyrylo Klimenko, Victor Kuzmin, Liudmila Ognichenko, Leonid Gorb, Manoj Shukla, Natalia Vinas, Edward J. Perkins, Pavel G. Polishchuk, Anatoly G. Artemenko, Jerzy Leszczynski
Novel enhanced applications of QSPR models: Temperature dependence of aqueous solubility. J. Comput. Chem. 37 (22) (2016)
Khajamoinuddin Syed, Bhanu K. Kamapantula, Michael L. Mayo, Edward J. Perkins, Preetam Ghosh
Abundance of connected motifs in transcriptional networks, a case study using random forests regression. BICT (2015)
Ahmed Abdelzaher, Michael L. Mayo, Edward J. Perkins, Preetam Ghosh
Contribution of canonical feed-forward loop motifs on the fault-tolerance and information transport efficiency of transcriptional regulatory networks. Nano Commun. Networks 6 (3) (2015)
Pratip Rana, Preetam Ghosh, Kevin Pilkiewicz, Edward J. Perkins, Chris Warner, Michael L. Mayo
Capacity estimates of additive inverse Gaussian molecular channels with relay characteristics. BICT (2015)
Bhanu K. Kamapantula, Michael L. Mayo, Edward J. Perkins, Ahmed Abdelzaher, Preetam Ghosh
Feature ranking in transcriptional networks: Packet receipt as a dynamical metric. BICT (2014)
Bhanu K. Kamapantula, Michael L. Mayo, Edward J. Perkins, Preetam Ghosh
Dynamical impacts from structural redundancy of transcriptional motifs in gene-regulatory networks. BICT (2014)
Bhanu K. Kamapantula, Ahmed Abdelzaher, Preetam Ghosh, Michael L. Mayo, Edward J. Perkins, Sajal K. Das
Leveraging the robustness of genetic networks: a case study on bio-inspired wireless sensor network topologies. J. Ambient Intell. Humaniz. Comput. 5 (3) (2014)
Peng Li, Ping Gong, Haoni Li, Edward J. Perkins, Nan Wang, Chaoyang Zhang
Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network. EURASIP J. Bioinform. Syst. Biol. 2014 (2014)
Michael L. Mayo, Ahmed Abdelzaher, Bhanu K. Kamapantula, Edward J. Perkins, Preetam Ghosh
Networks of interactions between feed-forward loop transcriptional motifs in gene-regulatory networks. BICT (2014)
Ahmed Abdelzaher, Michael L. Mayo, Preetam Ghosh, Edward J. Perkins
Correlating In silico Feed-forward Loop Knockout Experiments with the Topological Features of Transcriptional Regulatory Networks. BICT (2014)
Yi Yang, Si Li, Andrew S. Maxwell, Natalie D. Barker, Yan Peng, Ying Li, Haoni Li, Xi Wu, Peng Li, Tao Huang, Chenhua Zhang, Nan Wang, Edward J. Perkins, Chaoyang Zhang, Ping Gong
Deciphering chemically-induced reversible neurotoxicity by reconstructing perturbed pathways from time series microarray gene expression data. GENSiPS (2013)
Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Andy D. Perkins, Edward J. Perkins, Doris M. Kupfer, Gordon K. Springer
Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 14 (S-14) (2013)
Yi Yang, Andrew S. Maxwell, Xiaowei Zhang, Nan Wang, Edward J. Perkins, Chaoyang Zhang, Ping Gong
Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment. BMC Bioinform. 14 (S-14) (2013)
Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Kurt A. Gust, Edward J. Perkins
Genome scale inference of transcriptional regulatory networks using mutual information on complex interactions. BCB (2012)
Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Kurt A. Gust, Edward J. Perkins
sCoIn: A scoring algorithm based on complex interactions for reverse engineering regulatory networks. BIBE (2012)
Bhanu K. Kamapantula, Ahmed Abdelzaher, Preetam Ghosh, Michael L. Mayo, Edward J. Perkins, Sajal K. Das
Performance of wireless sensor topologies inspired by E. coli genetic networks. PerCom Workshops (2012)
Ying Li, Ping Gong, Edward J. Perkins, Chaoyang Zhang, Nan Wang
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. BMC Bioinform. 12 (S-10) (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)
Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Stephen Winters-Hilt, Mikhail G. Dozmorov, Ulisses M. Braga-Neto
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 12 (S-10) (2011)
Michael L. Mayo, Edward J. Perkins, Preetam Ghosh
Downstream Exploration of DNA-Bound Searching Proteins: A Diffusion-Reaction Model. BIBE (2011)
Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Edward J. Perkins
A Scalable Information Theory Based Gene Regulatory Network Inference Method from Time Series and Knock-Out Data. BICoB (2011)
Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Edward J. Perkins
sREVEAL: Scalable extensions of REVEAL towards regulatory network inference. ISDA (2011)
Michael L. Mayo, Edward J. Perkins, Preetam Ghosh
First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA. BMC Bioinform. 12 (S-10) (2011)
Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Edward J. Perkins
Poster: Gene regulatory network inference using time lagged context likelihood of relatedness. ICCABS (2011)
Preetam Ghosh, Michael L. Mayo, Vijender Chaitankar, Tanwir Habib, Edward J. Perkins, Sajal K. Das
Principles of genomic robustness inspire fault-tolerant WSN topologies: A network science based case study. PerCom Workshops (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)
Arun Rawat, Kurt A. Gust, Mohamed O. Elasri, Edward J. Perkins
Quail Genomics: a knowledgebase for Northern bobwhite. BMC Bioinform. 11 (S-6) (2010)
Ping Gong, Fuliang Xie, Baohong Zhang, Edward J. Perkins
In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. Comput. Biol. Chem. 34 (5-6) (2010)
Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Daniel Berleant
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinform. 11 (S-6) (2010)
Haoni Li, Peng Li, Chaoyang Zhang, Nan Wang, Ping Gong, Edward J. Perkins
Performance evaluation of the time-delayed dynamic Bayesian network approach to inferring gene regulatory networks from time series microarray data. BCB (2010)
Jason E. Shoemaker, Kalyan Gayen, Natàlia Garcia-Reyero, Edward J. Perkins, Daniel L. Villeneuve, Li Liu, Francis J. Doyle
Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. BMC Syst. Biol. 4 (2010)
Vijender Chaitankar, Preetam Ghosh, Chaoyang Zhang, Ping Gong, Edward J. Perkins
Effects of cDNA microarray time-series data size on gene regulatory network inference accuracy. BCB (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)
Ping Gong, Fuliang Xie, Baohong Zhang, Edward J. Perkins
In silico identification of microRNAs from expressed sequence tags of three earthworm species. BCB (2010)
Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Chaoyang Zhang
Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks. BMC Bioinform. 11 (S-6) (2010)
Ying Li, Nan Wang, Edward J. Perkins, Ping Gong
Discovery of Biomarker Genes from Earthworm Microarray Data by Discriminant Analysis and Clustering. IJCBS (2009)
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)
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)
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)
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)
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)
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)
Edward J. Perkins, Wenjun Bao, Xin Guan, Choo-Yaw Ang, Russell D. Wolfinger, Tzu-Ming Chu, Sharon A. Meyer, Laura S. Inouye
Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine. BMC Bioinform. 7 (S-4) (2006)
Edward J. Perkins, Wenjun Bao, Xin Guan, Choo-Yaw Ang, Russell D. Wolfinger, Tzu-Ming Chu, Ping Gong, Sharon A. Meyer, Laura S. Inouye
Comparison of Gene Expression Effects in Liver Tissue and Primary Hepatocyte Cell Cultures After Exposure to Hexahydro-1, 3, 5Trinitro-1, 3, 5-Triazine. IMSCCS (1) (2006)