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For: Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003;301:102-5. [PMID: 12843395 DOI: 10.1126/science.1081900] [Citation(s) in RCA: 880] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
201
An algebra-based method for inferring gene regulatory networks. BMC SYSTEMS BIOLOGY 2014;8:37. [PMID: 24669835 PMCID: PMC4022379 DOI: 10.1186/1752-0509-8-37] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 03/06/2014] [Indexed: 11/10/2022]
202
Meister A, Du C, Li YH, Wong WH. Modeling stochastic noise in gene regulatory systems. QUANTITATIVE BIOLOGY 2014;2:1-29. [PMID: 25632368 DOI: 10.1007/s40484-014-0025-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
203
Qabaja A, Jarada T, Elsheikh A, Alhajj R. Prediction of gene-based drug indications using compendia of public gene expression data and PubMed abstracts. J Bioinform Comput Biol 2014;12:1450007. [PMID: 24969745 DOI: 10.1142/s0219720014500073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
204
Zhou X, Liu J. Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer. PLoS One 2014;9:e92023. [PMID: 24637666 PMCID: PMC3956890 DOI: 10.1371/journal.pone.0092023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/19/2014] [Indexed: 12/19/2022]  Open
205
CaSPIAN: a causal compressive sensing algorithm for discovering directed interactions in gene networks. PLoS One 2014;9:e90781. [PMID: 24622336 PMCID: PMC3951243 DOI: 10.1371/journal.pone.0090781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 02/05/2014] [Indexed: 11/21/2022]  Open
206
Dimitrakopoulou K, Dimitrakopoulos GN, Wilk E, Tsimpouris C, Sgarbas KN, Schughart K, Bezerianos A. Influenza A immunomics and public health omics: the dynamic pathway interplay in host response to H1N1 infection. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014;18:167-83. [PMID: 24512282 DOI: 10.1089/omi.2013.0062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
207
Jang IS, Margolin A, Califano A. hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. Interface Focus 2014;3:20130011. [PMID: 24511376 PMCID: PMC3915831 DOI: 10.1098/rsfs.2013.0011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
208
Su RQ, Lai YC, Wang X, Do Y. Uncovering hidden nodes in complex networks in the presence of noise. Sci Rep 2014;4:3944. [PMID: 24487720 PMCID: PMC3909906 DOI: 10.1038/srep03944] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/13/2014] [Indexed: 11/10/2022]  Open
209
Christadore LM, Pham L, Kolaczyk ED, Schaus SE. Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets. BMC SYSTEMS BIOLOGY 2014;8:7. [PMID: 24444313 PMCID: PMC3911882 DOI: 10.1186/1752-0509-8-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/21/2013] [Indexed: 11/10/2022]
210
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]
211
Qabaja A, Alshalalfa M, Alanazi E, Alhajj R. Prediction of novel drug indications using network driven biological data prioritization and integration. J Cheminform 2014;6:1. [PMID: 24397863 PMCID: PMC3896815 DOI: 10.1186/1758-2946-6-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 11/28/2013] [Indexed: 11/23/2022]  Open
212
Inference of Vohradský's models of genetic networks by solving two-dimensional function optimization problems. PLoS One 2014;8:e83308. [PMID: 24386175 PMCID: PMC3875442 DOI: 10.1371/journal.pone.0083308] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/01/2013] [Indexed: 11/21/2022]  Open
213
Melendez J, Patel M, Oakes BL, Xu P, Morton P, McClean MN. Real-time optogenetic control of intracellular protein concentration in microbial cell cultures. Integr Biol (Camb) 2014;6:366-72. [DOI: 10.1039/c3ib40102b] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
214
Laubenbacher R, Hinkelmann F, Murrugarra D, Veliz-Cuba A. Algebraic Models and Their Use in Systems Biology. DISCRETE AND TOPOLOGICAL MODELS IN MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-40193-0_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
215
Wang Z, Wang Y, Wang N, Wang J, Wang Z, Vallejos CE, Wu R. Towards a comprehensive picture of the genetic landscape of complex traits. Brief Bioinform 2014;15:30-42. [PMID: 22930650 PMCID: PMC3896925 DOI: 10.1093/bib/bbs049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/09/2012] [Indexed: 12/11/2022]  Open
216
Braun R. Systems analysis of high-throughput data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014;844:153-87. [PMID: 25480641 PMCID: PMC4426208 DOI: 10.1007/978-1-4939-2095-2_8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
217
Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, Pratilas CA, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander C. Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol 2013;9:e1003290. [PMID: 24367245 PMCID: PMC3868523 DOI: 10.1371/journal.pcbi.1003290] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 08/26/2013] [Indexed: 12/16/2022]  Open
218
Ye G, Tang M, Cai JF, Nie Q, Xie X. Low-rank regularization for learning gene expression programs. PLoS One 2013;8:e82146. [PMID: 24358148 PMCID: PMC3866120 DOI: 10.1371/journal.pone.0082146] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 10/30/2013] [Indexed: 12/25/2022]  Open
219
Iorio F, Saez-Rodriguez J, Bernardo DD. Network based elucidation of drug response: from modulators to targets. BMC SYSTEMS BIOLOGY 2013;7:139. [PMID: 24330611 PMCID: PMC3878740 DOI: 10.1186/1752-0509-7-139] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 07/19/2013] [Indexed: 11/20/2022]
220
Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol 2013;9:e1003388. [PMID: 24348232 PMCID: PMC3861043 DOI: 10.1371/journal.pcbi.1003388] [Citation(s) in RCA: 382] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/27/2013] [Indexed: 01/19/2023]  Open
221
Nagarajan R, Scutari M. Impact of noise on molecular network inference. PLoS One 2013;8:e80735. [PMID: 24339879 PMCID: PMC3855153 DOI: 10.1371/journal.pone.0080735] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/07/2013] [Indexed: 11/19/2022]  Open
222
Reconstructing biological gene regulatory networks: where optimization meets big data. EVOLUTIONARY INTELLIGENCE 2013. [DOI: 10.1007/s12065-013-0098-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
223
Simcha DM, Younes L, Aryee MJ, Geman D. Identification of direction in gene networks from expression and methylation. BMC SYSTEMS BIOLOGY 2013;7:118. [PMID: 24182195 PMCID: PMC4228359 DOI: 10.1186/1752-0509-7-118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 10/17/2013] [Indexed: 01/27/2023]
224
Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J. Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster. PLoS Comput Biol 2013;9:e1003281. [PMID: 24204230 PMCID: PMC3814631 DOI: 10.1371/journal.pcbi.1003281] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/02/2013] [Indexed: 12/19/2022]  Open
225
Michailidis G, d'Alché-Buc F. Autoregressive models for gene regulatory network inference: sparsity, stability and causality issues. Math Biosci 2013;246:326-34. [PMID: 24176667 DOI: 10.1016/j.mbs.2013.10.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 10/09/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
226
Sławek J, Arodź T. ENNET: inferring large gene regulatory networks from expression data using gradient boosting. BMC SYSTEMS BIOLOGY 2013;7:106. [PMID: 24148309 PMCID: PMC4015806 DOI: 10.1186/1752-0509-7-106] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/17/2013] [Indexed: 01/19/2023]
227
Puniyani K, Xing EP. GINI: from ISH images to gene interaction networks. PLoS Comput Biol 2013;9:e1003227. [PMID: 24130465 PMCID: PMC3794902 DOI: 10.1371/journal.pcbi.1003227] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 07/30/2013] [Indexed: 12/22/2022]  Open
228
Zhang X, Shao B, Wu Y, Qi O. A reverse engineering approach to optimize experiments for the construction of biological regulatory networks. PLoS One 2013;8:e75931. [PMID: 24069453 PMCID: PMC3777925 DOI: 10.1371/journal.pone.0075931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 08/22/2013] [Indexed: 01/15/2023]  Open
229
Shin GW, Na J, Seo M, Chung B, Nam HG, Lee SJ, Jung GY. Precise Expression Profiling by Stuffer-Free Multiplex Ligation-Dependent Probe Amplification. Anal Chem 2013;85:9383-9. [DOI: 10.1021/ac402314h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
230
Brouard C, Vrain C, Dubois J, Castel D, Debily MA, d'Alché-Buc F. Learning a Markov Logic network for supervised gene regulatory network inference. BMC Bioinformatics 2013;14:273. [PMID: 24028533 PMCID: PMC3849013 DOI: 10.1186/1471-2105-14-273] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/03/2013] [Indexed: 11/23/2022]  Open
231
Meister A, Li YH, Choi B, Wong WH. Learning a nonlinear dynamical system model of gene regulation: A perturbed steady-state approach. Ann Appl Stat 2013. [DOI: 10.1214/13-aoas645] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
232
Wang YK, Hurley DG, Schnell S, Print CG, Crampin EJ. Integration of steady-state and temporal gene expression data for the inference of gene regulatory networks. PLoS One 2013;8:e72103. [PMID: 23967277 PMCID: PMC3743784 DOI: 10.1371/journal.pone.0072103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 07/05/2013] [Indexed: 01/02/2023]  Open
233
Chowdhury AR, Chetty M, Vinh NX. Evaluating influence of microRNA in reconstructing gene regulatory networks. Cogn Neurodyn 2013;8:251-9. [PMID: 24808933 DOI: 10.1007/s11571-013-9265-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 12/11/2022]  Open
234
Santra T, Kolch W, Kholodenko BN. Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology. BMC SYSTEMS BIOLOGY 2013;7:57. [PMID: 23829771 PMCID: PMC3726398 DOI: 10.1186/1752-0509-7-57] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 06/28/2013] [Indexed: 12/31/2022]
235
Wang Y, Wang N, Wang J, Wang Z, Wu R. Delivering systems pharmacogenomics towards precision medicine through mathematics. Adv Drug Deliv Rev 2013;65:905-11. [PMID: 23523629 PMCID: PMC3988791 DOI: 10.1016/j.addr.2013.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 02/13/2013] [Accepted: 03/13/2013] [Indexed: 12/13/2022]
236
Petri G, Scolamiero M, Donato I, Vaccarino F. Topological Strata of Weighted Complex Networks. PLoS One 2013;8:e66506. [PMID: 23805226 PMCID: PMC3689815 DOI: 10.1371/journal.pone.0066506] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 05/07/2013] [Indexed: 11/18/2022]  Open
237
Chowdhury AR, Chetty M, Vinh NX. Incorporating time-delays in S-System model for reverse engineering genetic networks. BMC Bioinformatics 2013;14:196. [PMID: 23777625 PMCID: PMC3839642 DOI: 10.1186/1471-2105-14-196] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 06/07/2013] [Indexed: 11/10/2022]  Open
238
Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013;138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 522] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
239
Cai X, Bazerque JA, Giannakis GB. Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations. PLoS Comput Biol 2013;9:e1003068. [PMID: 23717196 PMCID: PMC3662697 DOI: 10.1371/journal.pcbi.1003068] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 03/28/2013] [Indexed: 12/22/2022]  Open
240
McCormick MA, Kennedy BK. Genome-scale studies of aging: challenges and opportunities. Curr Genomics 2013;13:500-7. [PMID: 23633910 PMCID: PMC3468883 DOI: 10.2174/138920212803251454] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Revised: 06/08/2012] [Accepted: 07/25/2012] [Indexed: 12/21/2022]  Open
241
Tjärnberg A, Nordling TE, Studham M, Sonnhammer EL. Optimal Sparsity Criteria for Network Inference. J Comput Biol 2013;20:398-408. [DOI: 10.1089/cmb.2012.0268] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
242
McLean TI. "Eco-omics": a review of the application of genomics, transcriptomics, and proteomics for the study of the ecology of harmful algae. MICROBIAL ECOLOGY 2013;65:901-915. [PMID: 23553002 DOI: 10.1007/s00248-013-0220-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/14/2013] [Indexed: 06/02/2023]
243
Chen BS, Li CW. Analysing microarray data in drug discovery using systems biology. Expert Opin Drug Discov 2013;2:755-68. [PMID: 23488963 DOI: 10.1517/17460441.2.5.755] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
244
Li S, Hsu L, Peng J, Wang P. BOOTSTRAP INFERENCE FOR NETWORK CONSTRUCTION WITH AN APPLICATION TO A BREAST CANCER MICROARRAY STUDY. Ann Appl Stat 2013;7:391-417. [PMID: 24563684 DOI: 10.1214/12-aoas589] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
245
Qi H, Blanchard A, Lu T. Engineered genetic information processing circuits. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013;5:273-87. [DOI: 10.1002/wsbm.1216] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
246
Bo W, Fu G, Wang Z, Xu F, Shen Y, Xu J, Huang Z, Gai J, Vallejos CE, Wu R. Systems mapping: how to map genes for biomass allocation toward an ideotype. Brief Bioinform 2013;15:660-9. [PMID: 23428353 DOI: 10.1093/bib/bbs089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
247
Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS. Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Brief Bioinform 2013;15:592-611. [DOI: 10.1093/bib/bbs071] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
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Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS. Mol Syst Biol 2013;8:601. [PMID: 22864383 PMCID: PMC3421447 DOI: 10.1038/msb.2012.32] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/29/2012] [Indexed: 01/20/2023]  Open
249
Balabanov S, Wilhelm T, Venz S, Keller G, Scharf C, Pospisil H, Braig M, Barett C, Bokemeyer C, Walther R, Brümmendorf TH, Schuppert A. Combination of a proteomics approach and reengineering of meso scale network models for prediction of mode-of-action for tyrosine kinase inhibitors. PLoS One 2013;8:e53668. [PMID: 23326482 PMCID: PMC3541187 DOI: 10.1371/journal.pone.0053668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 12/03/2012] [Indexed: 12/19/2022]  Open
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Fatumo S, Adebiyi M, Adebiyi E. In silico models for drug resistance. Methods Mol Biol 2013;993:39-65. [PMID: 23568463 DOI: 10.1007/978-1-62703-342-8_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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