Page 82 - GPD-1-2

Gene & Protein in Disease Recent advances and challenges of network biology

elucidate molecular networks that cause disease. Nature, https://doi.org/10.1038/s41477-020-0743-y
452(7186): 429–435.
152. Bodein A, Scott-Boyer MP0, Perin O, et al., 2022,
https://doi.org/10.1038/nature06757 Interpretation of network-based integration from multi-
omics longitudinal data. Nucl Acids Res, 50(5): e27.
142. Valle I, Roweth HG, Malloy MW, et al., 2021, Network
medicine framework shows that proximity of polyphenol https://doi.org/10.1093/nar/gkab1200
targets and disease proteins predicts therapeutic effects of 153. Taylor KJ, Sims AH, Liang L, et al., 2010, Dynamic changes in
polyphenols. Nature Food, 2: 143–155.
gene expression in vivo predict prognosis of tamoxifen-treated
https://doi.org/10.1038/s43016-021-00243-7 patients with breast cancer. Breast Cancer Res, 12(3): R39.
143. Erler JT, Linding R, 2012, Network medicine strikes a blow https://doi.org/10.1186/bcr2593
against breast cancer. Cell, 149(4): 731–733.
154. Alcalá-Corona SA, Sandoval-Motta S, Espinal-Enríquez J,
https://doi.org/10.1016/j.cell.2012.04.014 et al., 2021, Modularity in biological networks. Front Genet,
12: 1708–1708.
144. Lee MJ, Ye AS, Gardino AK, et al., 2012, Sequential
application of anticancer drugs enhances cell death by https://doi.org/10.3389/fgene.2021.701331
rewiring apoptotic signaling networks. Cell, 149(4): 780–794.
155. Mucha PJ, Richardson T, Macon K, et al., 2010, Community
https://doi.org/10.1016/j.cell.2012.03.031 structure in time-dependent, multiscale, and multiplex
145. Cheng F, Desai RJ, Handy DE, et al., 2018, Network-based networks. Science, 328(5980): 876–878.
approach to prediction and population-based validation of https://doi.10.1126/science.1184819
in silico drug repurposing. Nat Commun, 9: 2691.
156. Agostino GD, Scala A, 2014, Networks of Networks: The
https://doi.org/10.1038/s41467-018-05116-5 Last Frontier of Complexity. Berlin: Springer.
146. Cheng F, István A, Barabási AL, 2019, Network-based https://doi.org/10.1007/978-3-319-03518-5
prediction of drug combinations. Nat Commun, 10: 1197.
157. Bianconi G, 2018, Multilayer Networks: Structure and
https://doi.org/10.1038/s41467-019-09186-x Function. Oxford: Oxford University Press.
147. Zhou Y, Hou Y, Shen J, et al., 2020, Network-based drug https://doi.org/10.1093/oso/9780198753919.001.0001
repurposing for novel coronavirus 2019-nCoV/SARS-
CoV-2. Cell Discov, 6: 14. 158. Pilosof S, Porter MA, Pascual M, et al., 2017, The multilayer
nature of ecological networks. Nat Ecol Evol, 1(4): 0101.
https://doi.org/10.1038/s41421-020-0153-3
https://doi.org/10.1038/s41559-017-0101
148. Gysi DM, Valle TD, Zitnik M, et al., 2021, Network
medicine framework for identifying drug-repurposing 159. Liu XM, Maiorino E, Halu A, et al., 2020, Robustness and
opportunities for COVID-19. Proc Natl Acad Sci. U S A, lethality in multilayer biological molecular networks. Nat
118(19): e2025581118. Commun, 11(1): 6043.
https://doi.org/10.1038/s41467-020-19841-3
https://doi.org/10.1073/pnas.2025581118
160. Shang HX, Liu ZP, 2021, Prioritizing Type 2 diabetes genes
149. Stumpf MP, Wiuf C, May RM, 2005, Subnets of scale-
free networks are not scale-free: Sampling properties of by weighted PageRank on bilayer heterogeneous networks.
networks. Proc Natl Acad Sci U S A, 102(12): 4221–4224. IEEE/ACM Trans Comput Biol Bioinform, 18(1): 336–346.
https://doi.org/10.1109/TCBB.2019.2917190
https://doi.org/10.1073/pnas.0501179102
161. Shang HX, Liu ZP, 2020, Network-based prioritization of
150. Sathyanarayanan A, Gupta R, Thompson EW, et al., 2020,
A comparative study of multi-omics integration tools for cancer genes by integrative ranks from multi-omics data.
cancer driver gene identification and tumour subtyping. Comput Biol Med, 119: 103692.
Brief Bioinform, 21(6): 1920–1936. https://doi.org/10.1016/j.compbiomed.2020.103692
https://doi.org/10.1093/bib/bbz121 162. Li J, Zhao PX, 2016, Mining functional modules in
heterogeneous biological networks using multiplex
151. Zander M, Lewsey MG, Clark NM, et al., 2020, Publisher
correction: Integrated multi-omics framework of the plant PageRank approach. Front Plant Sci, 7: 903.
response to jasmonic acid. Nat Plants, 6(8): 1065–1065. https://doi.org/10.3389/fpls.2016.00903

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