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ORCIDEdward J. Perkins
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- affiliation: US Army Engineer Research and Development Center, Vicksburg, MS, USA
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Journal Articles
- 2019
[j26]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. 20-S(2): 141-149 (2019)- 2017
- [j25]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): 35:1-35:11 (2017) - 2016
- [j24]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): e3 (2016) - [j23]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): 2045-2051 (2016) - [j22]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): e3 (2016) - [j21]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): 191-205 (2016) - 2015
- [j20]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): 133-144 (2015) - 2014
- [j19]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: 12 (2014) - [j18]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): 323-339 (2014) - 2013
- [j17]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): S1 (2013) - [j16]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): S3 (2013) - 2011
- [j15]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): S1 (2011) - [j14]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): S18 (2011) - [j13]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): S20 (2011) - [j12]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): S3 (2011) - 2010
- [j11]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): S1 (2010) - [j10]Arun Rawat, Kurt A. Gust, Mohamed O. Elasri, Edward J. Perkins:
Quail Genomics: a knowledgebase for Northern bobwhite. BMC Bioinform. 11(S-6): S13 (2010) - [j9]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): S19 (2010) - [j8]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: 89 (2010) - [j7]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: 153 (2010) - [j6]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): S7 (2010) - [j5]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): 313-319 (2010) - 2008
- [j4]Mehdi Pirooznia, Tanwir Habib, Edward J. Perkins, Youping Deng:
GOfetcher: a database with complex searching facility for gene ontology. Bioinform. 24(21): 2561-2563 (2008) - 2007
- [j3]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) - [j2]Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng:
Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. BMC Bioinform. 8(S-7) (2007) - 2006
- [j1]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)
Conference and Workshop Papers
- 2023
- [c28]R. Cody Salter, Natàlia Garcia-Reyero, Alicia Ruvinsky, Maria Seale, Edward J. Perkins:
Adverse Outcome Pathways for Engineered Systems. SysCon 2023: 1-8 - 2018
- [c27]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: 424-428 - 2015
- [c26]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: 108-115 - [c25]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: 237-240 - 2014
- [c24]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 - [c23]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 - [c22]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 - [c21]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 - 2013
- [c20]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: 45-48 - 2012
- [c19]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: 643-648 - [c18]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: 572-577 - [c17]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: 302-307 - 2011
- [c16]Michael L. Mayo, Edward J. Perkins, Preetam Ghosh:
Downstream Exploration of DNA-Bound Searching Proteins: A Diffusion-Reaction Model. BIBE 2011: 21-26 - [c15]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: 74-79 - [c14]Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Edward J. Perkins:
Poster: Gene regulatory network inference using time lagged context likelihood of relatedness. ICCABS 2011: 236 - [c13]Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Edward J. Perkins:
sREVEAL: Scalable extensions of REVEAL towards regulatory network inference. ISDA 2011: 1365-1370 - [c12]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: 160-165 - 2010
- [c11]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: 410-413 - [c10]Ping Gong, Fuliang Xie, Baohong Zhang, Edward J. Perkins:
In silico identification of microRNAs from expressed sequence tags of three earthworm species. BCB 2010: 430-434 - [c9]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: 466-468 - 2009
- [c8]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: 174-180 - [c7]Ying Li, Nan Wang, Edward J. Perkins, Ping Gong:
Discovery of Biomarker Genes from Earthworm Microarray Data by Discriminant Analysis and Clustering. IJCBS 2009: 23-29 - [c6]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: 487-490 - 2008
- [c5]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: 801-805 - [c4]Mehdi Pirooznia, Ping Gong, Chaoyang Zhang, Edward J. Perkins, Youping Deng:
Creating a Workflow for Expressed Sequence Tags Analysis. BIOCOMP 2008: 806-808 - [c3]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: 1040-1043 - 2007
- [c2]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: 187-191 - 2006
- [c1]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: 164-170
Data and Artifacts
- 2024
- [d1]Maria A. Seale, Gentry Berry, Richard C. Salter, Alicia I. Ruvinsky, Edward J. Perkins, Natàlia Garcia-Reyero:
Air Filter Loading Characteristics for an Epigenetic Modeling Approach to Adaptive Prognostics. IEEE DataPort, 2024
Coauthor Index
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