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For: Li Z, Li P, Krishnan A, Liu J. Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis. ACTA ACUST UNITED AC 2011;27:2686-91. [PMID: 21816876 DOI: 10.1093/bioinformatics/btr454] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Zhang J, Hu C, Zhang Q. Gene regulatory network inference based on a nonhomogeneous dynamic Bayesian network model with an improved Markov Monte Carlo sampling. BMC Bioinformatics 2023;24:264. [PMID: 37355560 DOI: 10.1186/s12859-023-05381-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023]  Open
2
Song Q, Ruffalo M, Bar-Joseph Z. Using single cell atlas data to reconstruct regulatory networks. Nucleic Acids Res 2023;51:e38. [PMID: 36762475 PMCID: PMC10123116 DOI: 10.1093/nar/gkad053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023]  Open
3
Imani M, Ghoreishi SF. Graph-Based Bayesian Optimization for Large-Scale Objective-Based Experimental Design. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022;33:5913-5925. [PMID: 33877989 DOI: 10.1109/tnnls.2021.3071958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
4
Ajmal HB, Madden MG. Dynamic Bayesian Network Learning to Infer Sparse Models From Time Series Gene Expression Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2794-2805. [PMID: 34181549 DOI: 10.1109/tcbb.2021.3092879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
5
Dirmeier S, Beerenwinkel N. Structured hierarchical models for probabilistic inference from perturbation screening data. Ann Appl Stat 2022. [DOI: 10.1214/21-aoas1580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
6
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. Methods Mol Biol 2021. [PMID: 34270057 DOI: 10.1007/978-1-0716-1625-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
7
Mahmoodi SH, Aghdam R, Eslahchi C. An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests. Sci Rep 2021;11:7605. [PMID: 33828122 PMCID: PMC8027014 DOI: 10.1038/s41598-021-87074-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/24/2021] [Indexed: 10/31/2022]  Open
8
Ajmal HB, Madden MG. Inferring dynamic gene regulatory networks with low-order conditional independencies – an evaluation of the method. Stat Appl Genet Mol Biol 2020. [DOI: 10.1515/sagmb-2020-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
9
Nasrin S, Drobitch J, Shukla P, Tulabandhula T, Bandyopadhyay S, Trivedi AR. Bayesian reasoning machine on a magneto-tunneling junction network. NANOTECHNOLOGY 2020;31:484001. [PMID: 32936787 DOI: 10.1088/1361-6528/abae97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
10
Liu W, Sun X, Peng L, Zhou L, Lin H, Jiang Y. RWRNET: A Gene Regulatory Network Inference Algorithm Using Random Walk With Restart. Front Genet 2020;11:591461. [PMID: 33101398 PMCID: PMC7545090 DOI: 10.3389/fgene.2020.591461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 11/30/2022]  Open
11
Che D, Guo S, Jiang Q, Chen L. PFBNet: a priori-fused boosting method for gene regulatory network inference. BMC Bioinformatics 2020;21:308. [PMID: 32664870 PMCID: PMC7362553 DOI: 10.1186/s12859-020-03639-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 07/02/2020] [Indexed: 02/08/2023]  Open
12
Bakhteh S, Ghaffari-Hadigheh A, Chaparzadeh N. Identification of Minimum Set of Master Regulatory Genes in Gene Regulatory Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:999-1009. [PMID: 30334767 DOI: 10.1109/tcbb.2018.2875692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
13
Fan A, Wang H, Xiang H, Zou X. Inferring Large-Scale Gene Regulatory Networks Using a Randomized Algorithm Based on Singular Value Decomposition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:1997-2008. [PMID: 29993839 DOI: 10.1109/tcbb.2018.2825446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
14
Muldoon JJ, Yu JS, Fassia MK, Bagheri N. Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants. Bioinformatics 2019;35:3421-3432. [PMID: 30932143 PMCID: PMC6748731 DOI: 10.1093/bioinformatics/btz105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/24/2019] [Accepted: 02/11/2019] [Indexed: 12/21/2022]  Open
15
Kizhakkethil Youseph AS, Chetty M, Karmakar G. Reverse engineering genetic networks using nonlinear saturation kinetics. Biosystems 2019;182:30-41. [PMID: 31185246 DOI: 10.1016/j.biosystems.2019.103977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/25/2019] [Accepted: 05/27/2019] [Indexed: 01/01/2023]
16
Maeda K. Gene grouping strategy for network modeling from a small time-series dataset: An illustrative analysis of human organogenesis. Biosystems 2019;179:24-29. [PMID: 30797967 DOI: 10.1016/j.biosystems.2019.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
17
Wu L, Qiu X, Yuan YX, Wu H. Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach. J Am Stat Assoc 2019;114:657-667. [PMID: 34385718 DOI: 10.1080/01621459.2017.1423074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
18
Wang Z, Gudibanda A, Ugwuowo U, Trail F, Townsend JP. Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
19
Xing L, Guo M, Liu X, Wang C, Zhang L. Gene Regulatory Networks Reconstruction Using the Flooding-Pruning Hill-Climbing Algorithm. Genes (Basel) 2018;9:E342. [PMID: 29986472 PMCID: PMC6071145 DOI: 10.3390/genes9070342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 11/17/2022]  Open
20
Nedungadi P, Iyer A, Gutjahr G, Bhaskar J, Pillai AB. Data-Driven Methods for Advancing Precision Oncology. CURRENT PHARMACOLOGY REPORTS 2018;4:145-156. [PMID: 33520605 PMCID: PMC7845924 DOI: 10.1007/s40495-018-0127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
21
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes. Sci Rep 2017;7:17244. [PMID: 29222512 PMCID: PMC5722905 DOI: 10.1038/s41598-017-17143-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022]  Open
22
Inferring Gene Regulatory Networks Based on a Hybrid Parallel Genetic Algorithm and the Threshold Restriction Method. Interdiscip Sci 2017;10:221-232. [DOI: 10.1007/s12539-017-0269-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 09/24/2017] [Accepted: 10/19/2017] [Indexed: 12/14/2022]
23
Xing L, Guo M, Liu X, Wang C, Wang L, Zhang Y. An improved Bayesian network method for reconstructing gene regulatory network based on candidate auto selection. BMC Genomics 2017;18:844. [PMID: 29219084 PMCID: PMC5773867 DOI: 10.1186/s12864-017-4228-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
24
Yu B, Xu JM, Li S, Chen C, Chen RX, Wang L, Zhang Y, Wang MH. Inference of time-delayed gene regulatory networks based on dynamic Bayesian network hybrid learning method. Oncotarget 2017;8:80373-80392. [PMID: 29113310 PMCID: PMC5655205 DOI: 10.18632/oncotarget.21268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/27/2017] [Indexed: 01/31/2023]  Open
25
Ko S, Lim H, Kim DW. Reverse engineering for causal discovery based on monotonic characteristic of causal structure. Pattern Recognit Lett 2017. [DOI: 10.1016/j.patrec.2017.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
26
Khanteymoori AR, Olyaee MH, Abbaszadeh O, Valian M. A novel method for Bayesian networks structure learning based on Breeding Swarm algorithm. Soft comput 2017. [DOI: 10.1007/s00500-017-2557-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
27
Liu W, Zhu W, Liao B, Chen H, Ren S, Cai L. Improving gene regulatory network structure using redundancy reduction in the MRNET algorithm. RSC Adv 2017. [DOI: 10.1039/c7ra01557g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
28
Young WC, Raftery AE, Yeung KY. A posterior probability approach for gene regulatory network inference in genetic perturbation data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2016;13:1241-1251. [PMID: 27775378 DOI: 10.3934/mbe.2016041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
29
BGRMI: A method for inferring gene regulatory networks from time-course gene expression data and its application in breast cancer research. Sci Rep 2016;6:37140. [PMID: 27876826 PMCID: PMC5120305 DOI: 10.1038/srep37140] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/24/2016] [Indexed: 02/06/2023]  Open
30
Li Y, Chen H, Zheng J, Ngom A. The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016;13:792-803. [PMID: 26336144 DOI: 10.1109/tcbb.2015.2474409] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
31
Effective gene expression data generation framework based on multi-model approach. Artif Intell Med 2016;70:41-61. [PMID: 27431036 DOI: 10.1016/j.artmed.2016.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/27/2016] [Indexed: 11/20/2022]
32
Pikovsky A. Reconstruction of a neural network from a time series of firing rates. Phys Rev E 2016;93:062313. [PMID: 27415286 DOI: 10.1103/physreve.93.062313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Indexed: 06/06/2023]
33
Lo LY, Wong ML, Lee KH, Leung KS. High-order dynamic Bayesian Network learning with hidden common causes for causal gene regulatory network. BMC Bioinformatics 2015;16:395. [PMID: 26608050 PMCID: PMC4659244 DOI: 10.1186/s12859-015-0823-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 11/11/2015] [Indexed: 12/18/2022]  Open
34
Isewon I, Oyelade J, Brors B, Adebiyi E. In Silico Gene Regulatory Network of the Maurer's Cleft Pathway in Plasmodium falciparum. Evol Bioinform Online 2015;11:231-8. [PMID: 26526876 PMCID: PMC4620995 DOI: 10.4137/ebo.s25585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 07/28/2015] [Accepted: 08/03/2015] [Indexed: 11/15/2022]  Open
35
Time-Delayed Models of Gene Regulatory Networks. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015;2015:347273. [PMID: 26576197 PMCID: PMC4632181 DOI: 10.1155/2015/347273] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/31/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022]
36
Lo LY, Wong ML, Lee KH, Leung KS. Time Delayed Causal Gene Regulatory Network Inference with Hidden Common Causes. PLoS One 2015;10:e0138596. [PMID: 26394325 PMCID: PMC4578777 DOI: 10.1371/journal.pone.0138596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 09/01/2015] [Indexed: 01/07/2023]  Open
37
Lo LY, Leung KS, Lee KH. Inferring Time-Delayed Causal Gene Network Using Time-Series Expression Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:1169-1182. [PMID: 26451828 DOI: 10.1109/tcbb.2015.2394442] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
38
Kim JR, Choo SM, Choi HS, Cho KH. Identification of Gene Networks with Time Delayed Regulation Based on Temporal Expression Profiles. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:1161-1168. [PMID: 26451827 DOI: 10.1109/tcbb.2015.2394312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
39
Chen C, Yao Y, Zhang L, Xu M, Jiang J, Dou T, Lin W, Zhao G, Huang M, Zhou Y. A Comprehensive Analysis of the Transcriptomes of Marssonina brunnea and Infected Poplar Leaves to Capture Vital Events in Host-Pathogen Interactions. PLoS One 2015. [PMID: 26222429 PMCID: PMC4519268 DOI: 10.1371/journal.pone.0134246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
40
Zhang W, Zhou T. A Sparse Reconstruction Approach for Identifying Gene Regulatory Networks Using Steady-State Experiment Data. PLoS One 2015. [PMID: 26207991 PMCID: PMC4514654 DOI: 10.1371/journal.pone.0130979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
41
Inferring Broad Regulatory Biology from Time Course Data: Have We Reached an Upper Bound under Constraints Typical of In Vivo Studies? PLoS One 2015;10:e0127364. [PMID: 25984725 PMCID: PMC4435750 DOI: 10.1371/journal.pone.0127364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 04/13/2015] [Indexed: 12/21/2022]  Open
42
Zhang X, Zhao J, Hao JK, Zhao XM, Chen L. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Res 2015;43:e31. [PMID: 25539927 PMCID: PMC4357691 DOI: 10.1093/nar/gku1315] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 11/13/2022]  Open
43
Yang C, Wei H. Designing microarray and RNA-Seq experiments for greater systems biology discovery in modern plant genomics. MOLECULAR PLANT 2015;8:196-206. [PMID: 25680773 DOI: 10.1016/j.molp.2014.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 05/07/2023]
44
Computational phosphorylation network reconstruction: methods and resources. Methods Mol Biol 2015;1306:177-94. [PMID: 25930703 DOI: 10.1007/978-1-4939-2648-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
45
Astola L, Molenaar J. A New Modified Histogram Matching Normalization for Time Series Microarray Analysis. MICROARRAYS 2014;3:203-11. [PMID: 27600344 PMCID: PMC4996360 DOI: 10.3390/microarrays3030203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 11/16/2022]
46
Young WC, Raftery AE, Yeung KY. Fast Bayesian inference for gene regulatory networks using ScanBMA. BMC SYSTEMS BIOLOGY 2014;8:47. [PMID: 24742092 PMCID: PMC4006459 DOI: 10.1186/1752-0509-8-47] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/04/2014] [Indexed: 11/22/2022]
47
Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KWY, Nie Q. Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC SYSTEMS BIOLOGY 2014;8:3. [PMID: 24397936 PMCID: PMC3896677 DOI: 10.1186/1752-0509-8-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 12/19/2013] [Indexed: 11/10/2022]
48
Extrapolating In Vitro Results to Predict Human Toxicity. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-4939-0521-8_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Using gene expression programming to infer gene regulatory networks from time-series data. Comput Biol Chem 2013;47:198-206. [DOI: 10.1016/j.compbiolchem.2013.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 09/19/2013] [Accepted: 09/21/2013] [Indexed: 11/22/2022]
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Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH. Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics 2013;14 Suppl 6:S1. [PMID: 23734902 PMCID: PMC3633009 DOI: 10.1186/1471-2105-14-s6-s1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
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