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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)
151
Inferring causal networks using fuzzy cognitive maps and evolutionary algorithms with application to gene regulatory network reconstruction. Appl Soft Comput 2015. [DOI: 10.1016/j.asoc.2015.08.039] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
152
Guner U, Jang H, Realff MJ, Lee JH. An Extended Constrained Total Least-Squares Method for the Identification of Genetic Networks from Noisy Measurements. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
153
Takenaka Y, Seno S, Matsuda H. Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution. J Bioinform Comput Biol 2015;13:1543002. [PMID: 26508425 DOI: 10.1142/s0219720015430027] [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] [Indexed: 11/18/2022]
154
Liu LZ, Wu FX, Zhang WJ. Properties of sparse penalties on inferring gene regulatory networks from time-course gene expression data. IET Syst Biol 2015;9:16-24. [PMID: 25569860 DOI: 10.1049/iet-syb.2013.0060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
155
Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A. Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Cell 2015;162:441-451. [PMID: 26186195 DOI: 10.1016/j.cell.2015.05.056] [Citation(s) in RCA: 273] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/17/2015] [Accepted: 05/28/2015] [Indexed: 01/01/2023]
156
Discriminating direct and indirect connectivities in biological networks. Proc Natl Acad Sci U S A 2015;112:12893-8. [PMID: 26420864 DOI: 10.1073/pnas.1507168112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
157
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]
158
Farine DR, Whitehead H. Constructing, conducting and interpreting animal social network analysis. J Anim Ecol 2015;84:1144-63. [PMID: 26172345 PMCID: PMC4973823 DOI: 10.1111/1365-2656.12418] [Citation(s) in RCA: 500] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/25/2015] [Indexed: 11/27/2022]
159
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
160
Nair A, Chetty M, Wangikar PP. Improving gene regulatory network inference using network topology information. MOLECULAR BIOSYSTEMS 2015;11:2449-63. [PMID: 26126758 DOI: 10.1039/c5mb00122f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
161
Lin W, Wang Y, Ying H, Lai YC, Wang X. Consistency between functional and structural networks of coupled nonlinear oscillators. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015;92:012912. [PMID: 26274252 DOI: 10.1103/physreve.92.012912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Indexed: 06/04/2023]
162
Shao B, Liu X, Zhang D, Wu J, Ouyang Q. From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits. PLoS One 2015;10:e0128630. [PMID: 26061094 PMCID: PMC4464762 DOI: 10.1371/journal.pone.0128630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/29/2015] [Indexed: 11/19/2022]  Open
163
Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration. PLoS Comput Biol 2015;11:e1004295. [PMID: 26042810 PMCID: PMC4456145 DOI: 10.1371/journal.pcbi.1004295] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 04/21/2015] [Indexed: 01/18/2023]  Open
164
Matos MRA, Knapp B, Kaderali L. lpNet: a linear programming approach to reconstruct signal transduction networks. Bioinformatics 2015;31:3231-3. [PMID: 26026168 DOI: 10.1093/bioinformatics/btv327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 05/19/2015] [Indexed: 11/14/2022]  Open
165
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
166
Shao B, Wu J, Tian B, Ouyang Q. Minimum network constraint on reverse engineering to develop biological regulatory networks. J Theor Biol 2015;380:9-15. [PMID: 25981630 DOI: 10.1016/j.jtbi.2015.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 04/23/2015] [Accepted: 05/04/2015] [Indexed: 12/20/2022]
167
Grabow C, Grosskinsky S, Kurths J, Timme M. Collective relaxation dynamics of small-world networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015;91:052815. [PMID: 26066220 DOI: 10.1103/physreve.91.052815] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Indexed: 06/04/2023]
168
Albert R, Thakar J. Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015;6:353-69. [PMID: 25269159 DOI: 10.1002/wsbm.1273] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
169
Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN. Silence on the relevant literature and errors in implementation. Nat Biotechnol 2015;33:336-9. [PMID: 25850052 DOI: 10.1038/nbt.3185] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
170
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
171
Gong W, Koyano-Nakagawa N, Li T, Garry DJ. Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data. BMC Bioinformatics 2015;16:74. [PMID: 25887857 PMCID: PMC4359553 DOI: 10.1186/s12859-015-0460-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/12/2015] [Indexed: 02/07/2023]  Open
172
Linde J, Schulze S, Henkel SG, Guthke R. Data- and knowledge-based modeling of gene regulatory networks: an update. EXCLI JOURNAL 2015;14:346-78. [PMID: 27047314 PMCID: PMC4817425 DOI: 10.17179/excli2015-168] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/10/2015] [Indexed: 02/01/2023]
173
Le Novère N. Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet 2015;16:146-58. [PMID: 25645874 PMCID: PMC4604653 DOI: 10.1038/nrg3885] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
174
Prabakaran S, Gunawardena J, Sontag E. Paradoxical results in perturbation-based signaling network reconstruction. Biophys J 2015;106:2720-8. [PMID: 24940789 DOI: 10.1016/j.bpj.2014.04.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/18/2014] [Accepted: 04/23/2014] [Indexed: 11/29/2022]  Open
175
Aghdam R, Ganjali M, Zhang X, Eslahchi C. CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test. MOLECULAR BIOSYSTEMS 2015;11:942-9. [PMID: 25607659 DOI: 10.1039/c4mb00413b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
176
Liu LZ, Wu FX, Zhang WJ. Properties of sparse penalties on inferring gene regulatory networks from time-course gene expression data. IET Syst Biol 2015. [PMID: 25569860 DOI: 10.1049/iet‐syb.2013.0060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
177
Tjärnberg A, Nordling TEM, Studham M, Nelander S, Sonnhammer ELL. Avoiding pitfalls in L1-regularised inference of gene networks. MOLECULAR BIOSYSTEMS 2015;11:287-96. [DOI: 10.1039/c4mb00419a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
178
Chan SC, Zhang L, Wu HC, Tsui KM. A Maximum A Posteriori Probability and Time-Varying Approach for Inferring Gene Regulatory Networks from Time Course Gene Microarray Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:123-135. [PMID: 26357083 DOI: 10.1109/tcbb.2014.2343951] [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]
179
Zhang Z, Zheng Z, Niu H, Mi Y, Wu S, Hu G. Solving the inverse problem of noise-driven dynamic networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015;91:012814. [PMID: 25679664 DOI: 10.1103/physreve.91.012814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Indexed: 06/04/2023]
180
Controlling networks of nonlinearly-coupled nodes using response surfaces. Sci Rep 2014;4:7574. [PMID: 25524558 PMCID: PMC4271252 DOI: 10.1038/srep07574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/02/2014] [Indexed: 11/08/2022]  Open
181
Chang YH, Gray JW, Tomlin CJ. Exact reconstruction of gene regulatory networks using compressive sensing. BMC Bioinformatics 2014;15:400. [PMID: 25495633 PMCID: PMC4308013 DOI: 10.1186/s12859-014-0400-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 11/27/2014] [Indexed: 02/04/2023]  Open
182
Sontag ED. A technique for determining the signs of sensitivities of steady states in chemical reaction networks. IET Syst Biol 2014;8:251-67. [PMID: 25478700 DOI: 10.1049/iet-syb.2014.0025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
183
Bag S, Anbarasu A. Revealing the Strong Functional Association of adipor2 and cdh13 with adipoq: A Gene Network Study. Cell Biochem Biophys 2014;71:1445-56. [PMID: 25388841 DOI: 10.1007/s12013-014-0367-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
184
Bouffier AM, Arnold J, Schüttler HB. A MINE alternative to D-optimal designs for the linear model. PLoS One 2014;9:e110234. [PMID: 25356931 PMCID: PMC4214713 DOI: 10.1371/journal.pone.0110234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/16/2014] [Indexed: 12/04/2022]  Open
185
Ghasemi O, Ma Y, Lindsey ML, Jin YF. Using systems biology approaches to understand cardiac inflammation and extracellular matrix remodeling in the setting of myocardial infarction. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014;6:77-91. [PMID: 24741709 DOI: 10.1002/wsbm.1248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
186
Cai C, Chen L, Jiang X, Lu X. Modeling signal transduction from protein phosphorylation to gene expression. Cancer Inform 2014;13:59-67. [PMID: 25392684 PMCID: PMC4216050 DOI: 10.4137/cin.s13883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/04/2014] [Accepted: 05/04/2014] [Indexed: 11/24/2022]  Open
187
Studham ME, Tjärnberg A, Nordling TEM, Nelander S, Sonnhammer ELL. Functional association networks as priors for gene regulatory network inference. ACTA ACUST UNITED AC 2014;30:i130-8. [PMID: 24931976 PMCID: PMC4058914 DOI: 10.1093/bioinformatics/btu285] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
188
Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C. Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. THE JOURNAL OF IMMUNOLOGY 2014;193:4485-96. [PMID: 25267973 DOI: 10.4049/jimmunol.1401280] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
189
Ravindranath AC, Perualila-Tan N, Kasim A, Drakakis G, Liggi S, Brewerton SC, Mason D, Bodkin MJ, Evans DA, Bhagwat A, Talloen W, Göhlmann HWH, Shkedy Z, Bender A. Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis. MOLECULAR BIOSYSTEMS 2014;11:86-96. [PMID: 25254964 DOI: 10.1039/c4mb00328d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
190
Oates CJ, Dondelinger F, Bayani N, Korkola J, Gray JW, Mukherjee S. Causal network inference using biochemical kinetics. Bioinformatics 2014;30:i468-74. [PMID: 25161235 PMCID: PMC4147905 DOI: 10.1093/bioinformatics/btu452] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
191
Adabor ES, Acquaah-Mensah GK, Oduro FT. SAGA: a hybrid search algorithm for Bayesian Network structure learning of transcriptional regulatory networks. J Biomed Inform 2014;53:27-35. [PMID: 25181467 DOI: 10.1016/j.jbi.2014.08.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 08/17/2014] [Accepted: 08/22/2014] [Indexed: 11/16/2022]
192
Reconstructing propagation networks with natural diversity and identifying hidden sources. Nat Commun 2014;5:4323. [PMID: 25014310 PMCID: PMC4104449 DOI: 10.1038/ncomms5323] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 06/06/2014] [Indexed: 11/26/2022]  Open
193
Zhu F, Guan Y. Predicting dynamic signaling network response under unseen perturbations. ACTA ACUST UNITED AC 2014;30:2772-8. [PMID: 24919880 DOI: 10.1093/bioinformatics/btu382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
194
Santra T. A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. Front Bioeng Biotechnol 2014;2:13. [PMID: 25152886 PMCID: PMC4126456 DOI: 10.3389/fbioe.2014.00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/28/2014] [Indexed: 11/29/2022]  Open
195
Li X, Wu L, Liu W, Jin Y, Chen Q, Wang L, Fan X, Li Z, Cheng Y. A network pharmacology study of Chinese medicine QiShenYiQi to reveal its underlying multi-compound, multi-target, multi-pathway mode of action. PLoS One 2014;9:e95004. [PMID: 24817581 PMCID: PMC4015902 DOI: 10.1371/journal.pone.0095004] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 03/21/2014] [Indexed: 01/04/2023]  Open
196
Wu S, Liu ZP, Qiu X, Wu H. Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations. PLoS One 2014;9:e95276. [PMID: 24802016 PMCID: PMC4011728 DOI: 10.1371/journal.pone.0095276] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 03/26/2014] [Indexed: 12/20/2022]  Open
197
Lee J, Tiwari A, Shum V, Mills GB, Mancini MA, Igoshin OA, Balázsi G. Unraveling the regulatory connections between two controllers of breast cancer cell fate. Nucleic Acids Res 2014;42:6839-49. [PMID: 24792166 PMCID: PMC4066784 DOI: 10.1093/nar/gku360] [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] [Indexed: 02/07/2023]  Open
198
Idowu MA. Cyclin-Dependent Kinases as Drug Targets for Cell Growth and Proliferation Disorders. A Role for Systems Biology Approach in Drug Development. Part II—CDKs as Drug Targets in Hypertrophic Cell Growth. Modelling of Drugs Targeting CDKs. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]  Open
199
Wang YXR, Huang H. Review on statistical methods for gene network reconstruction using expression data. J Theor Biol 2014;362:53-61. [PMID: 24726980 DOI: 10.1016/j.jtbi.2014.03.040] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 12/16/2022]
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Jia B, Wang X. Regularized EM algorithm for sparse parameter estimation in nonlinear dynamic systems with application to gene regulatory network inference. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2014;2014:5. [PMID: 24708632 PMCID: PMC3998071 DOI: 10.1186/1687-4153-2014-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 02/26/2014] [Indexed: 11/10/2022]
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