Allen, S. P., Hall, B., Castelli, L. M., Francis, L., Woof, R., Siskos, A. P., Kouloura, E., Gray, E., Thompson, A. G., Talbot, K., Higginbottom, A., Myszczynska, M., Allen, C. F., Stopford, M. J., Hemingway, J., Bauer, C. S., Webster, C. P., De Vos, K. J., Turner, M. R., Keun, H. C., & Shaw, P. J. (2019). Astrocyte adenosine deaminase loss increases motor neuron toxicity in amyotrophic lateral sclerosis. Brain: A Journal of Neurology, 142(3), 586–605. https://doi.org/10.1093/brain/awy353

Bader, G. D., & Hogue, C. W. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4, 2. https://doi.org/10.1186/1471-2105-4-2

Article  PubMed  PubMed Central  Google Scholar 

Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Holko, M., Yefanov, A., Lee, H., Zhang, N., Robertson, C. L., Serova, N., Davis, S., & Soboleva, A. (2013). NCBI GEO: Archive for functional genomics data sets--update. Nucleic Acids Research, 41(Database issue), D991–D995. https://doi.org/10.1093/nar/gks1193

Bernardini, C., Censi, F., Lattanzi, W., Barba, M., Calcagnini, G., Giuliani, A., Tasca, G., Sabatelli, M., Ricci, E., & Michetti, F. (2013). Mitochondrial network genes in the skeletal muscle of amyotrophic lateral sclerosis patients. PLOS ONE, 8(2), e57739. https://doi.org/10.1371/journal.pone.0057739

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolstad, B. M., Irizarry, R. A., Astrand, M., & Speed, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (Oxford, England), 19(2), 185–193. https://doi.org/10.1093/bioinformatics/19.2.185

Article  CAS  PubMed  Google Scholar 

Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., & de Hoon, M. J. L. (2009). Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423. https://doi.org/10.1093/bioinformatics/btp163

Article  CAS  PubMed  PubMed Central  Google Scholar 

Collins, M. A., An, J., Hood, B. L., Conrads, T. P., & Bowser, R. P. (2015). Label-free LC–MS/MS proteomic analysis of cerebrospinal fluid identifies protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis. Journal of Proteome Research, 14(11), 4486–4501. https://doi.org/10.1021/acs.jproteome.5b00804

Article  CAS  PubMed  PubMed Central  Google Scholar 

Comte, B., Baumbach, J., Benis, A., Basílio, J., Debeljak, N., Flobak, Å., Franken, C., Harel, N., He, F., Kuiper, M., Méndez Pérez, J. A., Pujos-Guillot, E., Režen, T., Rozman, D., Schmid, J. A., Scerri, J., Tieri, P., Van Steen, K., Vasudevan, S., & Schmidt, H. H. H. W. (2020). Network and systems medicine: Position paper of the european collaboration on science and technology action on open multiscale systems medicine. Network and Systems Medicine, 3(1), 67–90. https://doi.org/10.1089/nsm.2020.0004

Article  PubMed  PubMed Central  Google Scholar 

Cortes, C., & Vapnik, V. (1995). Support-vector networks. Machine Learning, 20(3), 273–297. https://doi.org/10.1007/BF00994018

Article  Google Scholar 

Cox, L. E., Ferraiuolo, L., Goodall, E. F., Heath, P. R., Higginbottom, A., Mortiboys, H., Hollinger, H. C., Hartley, J. A., Brockington, A., Burness, C. E., Morrison, K. E., Wharton, S. B., Grierson, A. J., Ince, P. G., Kirby, J., & Shaw, P. J. (2010). Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS). PLoS ONE, 5(3), e9872. https://doi.org/10.1371/journal.pone.0009872

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dupuis, L., Pradat, P. F., Ludolph, A. C., & Loeffler, J. P. (2011). Energy metabolism in amyotrophic lateral sclerosis. The Lancet. Neurology, 10(1), 75–82. https://doi.org/10.1016/S1474-4422(10)70224-6

Article  CAS  PubMed  Google Scholar 

Fabregat, A., Jupe, S., Matthews, L., Sidiropoulos, K., Gillespie, M., Garapati, P., Haw, R., Jassal, B., Korninger, F., May, B., Milacic, M., Roca, C. D., Rothfels, K., Sevilla, C., Shamovsky, V., Shorser, S., Varusai, T., Viteri, G., Weiser, J., & D’Eustachio, P. (2018). The reactome pathway knowledgebase. Nucleic Acids Research, 46(D1), D649–D655. https://doi.org/10.1093/nar/gkx1132

Article  CAS  PubMed  Google Scholar 

Fiscon, G., Conte, F., Farina, L., & Paci, P. (2018). Network-based approaches to explore complex biological systems towards network medicine. Genes. https://doi.org/10.3390/genes9090437

Article  PubMed  PubMed Central  Google Scholar 

Friedman, J. H. (2001). Greedy function approximation: A gradient boosting machine. The Annals of Statistics, 29(5), 1189–1232. https://doi.org/10.1214/aos/1013203451

Article  Google Scholar 

Gao, X. K., Sheng, Z. K., Lu, Y. H., Sun, Y. T., Rao, X. S., Shi, L. J., Cong, X. X., Chen, X., Wu, H. B., Huang, M., Zheng, Q., Guo, J., Jiang, L. J., Zheng, L. L., & Zhou, Y. T. (2023). VAPB-mediated ER-targeting stabilizes IRS-1 signalosomes to regulate insulin/IGF signaling. Cell Discovery, 9(1), 1–18. https://doi.org/10.1038/s41421-023-00576-6

Article  CAS  Google Scholar 

Gov, E., & Arga, K. Y. (2017). Differential co-expression analysis reveals a novel prognostic gene module in ovarian cancer. Scientific Reports, 7(1), 4996. https://doi.org/10.1038/s41598-017-05298-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grima, N., Liu, S., Southwood, D., Henden, L., Smith, A., Lee, A., Rowe, D. B., D’Silva, S., Blair, I. P., & Williams, K. L. (2023). RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: Considerations for biomarker discovery. Neuropathology and Applied Neurobiology, 49(6), e12943. https://doi.org/10.1111/nan.12943

Article  CAS  PubMed  PubMed Central  Google Scholar 

Halbgebauer, S., Abu-Rumeileh, S., Oeckl, P., Steinacker, P., Roselli, F., Wiesner, D., Mammana, A., Beekes, M., Kortazar-Zubizarreta, I., Perez de Nanclares, G., Capellari, S., Giese, A., Castilla, J., Ludolph, A. C., Žáková, D., Parchi, P., & Otto, M. (2022). Blood β-synuclein and neurofilament light chain during the course of prion disease. Neurology, 98(14), e1434–e1445. https://doi.org/10.1212/WNL.0000000000200002

Article  CAS  PubMed  Google Scholar 

Hua, Y., Dai, X., Xu, Y., Xing, G., Liu, H., Lu, T., Chen, Y., & Zhang, Y. (2022). Drug repositioning: Progress and challenges in drug discovery for various diseases. European Journal of Medicinal Chemistry, 234, 114239. https://doi.org/10.1016/j.ejmech.2022.114239

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huber, W., Carey, V. J., Gentleman, R., Anders, S., Carlson, M., Carvalho, B. S., Bravo, H. C., Davis, S., Gatto, L., Girke, T., Gottardo, R., Hahne, F., Hansen, K. D., Irizarry, R. A., Lawrence, M., Love, M. I., MacDonald, J., Obenchain, V., Oleś, A. K., & Morgan, M. (2015). Orchestrating high-throughput genomic analysis with bioconductor. Nature Methods, 12(2), 115–121. https://doi.org/10.1038/nmeth.3252

Article  CAS  PubMed  PubMed Central  Google Scholar 

Imamura, K., Izumi, Y., Watanabe, A., Tsukita, K., Woltjen, K., Yamamoto, T., Hotta, A., Kondo, T., Kitaoka, S., Ohta, A., Tanaka, A., Watanabe, D., Morita, M., Takuma, H., Tamaoka, A., Kunath, T., Wray, S., Furuya, H., Era, T., … Inoue, H. (2017). The Src/c-Abl pathway is a potential therapeutic target in amyotrophic lateral sclerosis. Science Translational Medicine, 9(391), eaaf3962. https://doi.org/10.1126/scitranslmed.aaf3962

Article  PubMed  Google Scholar 

Jiang, J., Wang, Y., & Deng, M. (2022). New developments and opportunities in drugs being trialed for amyotrophic lateral sclerosis from 2020 to 2022. Frontiers in Pharmacology, 13, 1054006.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kalghatgi, S., Spina, C. S., Costello, J. C., Liesa, M., Morones-Ramirez, J. R., Slomovic, S., Molina, A., Shirihai, O. S., & Collins, J. J. (2013). Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in Mammalian cells. Science Translational Medicine, 5(192), 192ra85. https://doi.org/10.1126/scitranslmed.3006055

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kamburov, A., Wierling, C., Lehrach, H., & Herwig, R. (2009). ConsensusPathDB—A database for integrating human functional interaction networks. Nucleic Acids Research, 37, D623-628. https://doi.org/10.1093/nar/gkn698

Article  CAS  PubMed  Google Scholar 

Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1), 27–30. https://doi.org/10.1093/nar/28.1.27

Article  CAS  PubMed  PubMed Central  Google Scholar 

Katzeff, J. S., Bright, F., Lo, K., Kril, J. J., Connolly, A., Crossett, B., Ittner, L. M., Kassiou, M., Loy, C. T., Hodges, J. R., Piguet, O., Kiernan, M. C., Halliday, G. M., & Kim, W. S. (2020). Altered serum protein levels in frontotemporal dementia and amyotrophic lateral sclerosis indicate calcium and immunity dysregulation. Scientific Reports, 10(1), 13741. https://doi.org/10.1038/s41598-020-70687-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kodavati, M., Wang, H., & Hegde, M. L. (2020). Altered mitochondrial dynamics in motor neuron disease: An emerging perspective. Cells