460. Starosta, A.; Konieczny, P. Therapeutic aspects of cell signaling and communication in Duchenne muscular dystrophy. *Cell. Mol. Life Sci.* **2021**, *78*, 4867–4891. [CrossRef]

461. Mund, A.; Coscia, F.; Kriston, A.; Hollandi, R.; Kovács, F.; Brunner, A.D.; Migh, E.; Schweizer, L.; Santos, A.; Bzorek, M.; et al. Deep Visual Proteomics defines single-cell identity and heterogeneity. *Nat. Biotechnol.* **2022**, *40*, 1231–1240. [CrossRef]

462. Rosenberger, F.A.; Thielert, M.; Strauss, M.T.; Schweizer, L.; Ammar, C.; Mädler, S.C.; Metousis, A.; Skowronek, P.; Wahle, M.; Madden, K.; et al. Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome. *Nat. Methods* **2023**, *20*, 1530–1536. [CrossRef] [PubMed]

463. Kelsey, G.; Stegle, O.; Reik, W. Single-cell epigenomics: Recording the past and predicting the future. *Science* **2017**, *358*, 69–75. [CrossRef] [PubMed]

464. Wang, K.C.; Chang, H.Y. Epigenomics: Technologies and Applications. *Circ. Res.* **2018**, *122*, 1191–1199. [CrossRef] [PubMed]

465. Pinheiro, I.; Torres-Padilla, M.E.; Almouzni, G. Epigenomics in the single cell era, an important read out for genome function and cell identity. *Epigenomics* **2021**, *13*, 981–984. [CrossRef]

466. Li, Y. Modern epigenetics methods in biological research. *Methods* **2021**, *187*, 104–113. [CrossRef]

467. Robinson, D.C.L.; Dilworth, F.J. Epigenetic Regulation of Adult Myogenesis. *Curr. Top. Dev. Biol.* **2018**, *126*, 235–284. [CrossRef]

468. Plaza-Diaz, J.; Izquierdo, D.; Torres-Martos, A.; Baig, A.T.; Aguilera, C.M.; Ruiz-Ojeda, F.J. Impact of Physical Activity and Exercise on the Epigenome in Skeletal Muscle and Effects on Systemic Metabolism. *Biomedicines* **2022**, *10*, 126. [CrossRef]

469. Massenet, J.; Gardner, E.; Chazaud, B.; Dilworth, F.J. Epigenetic regulation of satellite cell fate during skeletal muscle regeneration. *Skelet. Muscle* **2021**, *11*, 4. [CrossRef]

470. Consalvi, S.; Saccone, V.; Mozzetta, C. Histone deacetylase inhibitors: A potential epigenetic treatment for Duchenne muscular dystrophy. *Epigenomics* **2014**, *6*, 547–560. [CrossRef]

471. Schreyer, L.; Reilly, J.; McConkey, H.; Kerkhof, J.; Levy, M.A.; Hu, J.; Hnaini, M.; Sadikovic, B.; Campbell, C. The discovery of the DNA methylation episignature for Duchenne muscular dystrophy. *Neuromuscul. Disord.* **2023**, *33*, 5–14. [CrossRef]

472. Sandonà, M.; Cavioli, G.; Renzini, A.; Cedola, A.; Gigli, G.; Coletti, D.; McKinsey, T.A.; Moresi, V.; Saccone, V. Histone Deacetylases: Molecular Mechanisms and Therapeutic Implications for Muscular Dystrophies. *Int. J. Mol. Sci.* **2023**, *24*, 4306. [CrossRef]

473. Chen, C.; Wang, J.; Pan, D.; Wang, X.; Xu, Y.; Yan, J.; Wang, L.; Yang, X.; Yang, M.; Liu, G.P. Applications of multi-omics analysis in human diseases. *MedComm* **2023**, *4*, e315. [CrossRef] [PubMed]

474. Tavassoly, I.; Goldfarb, J.; Iyengar, R. Systems biology primer: The basic methods and approaches. *Essays Biochem.* **2018**, *62*, 487–500. [CrossRef] [PubMed]

475. Greising, S.M.; Gransee, H.M.; Mantilla, C.B.; Sieck, G.C. Systems biology of skeletal muscle: Fiber type as an organizing principle. *Wiley Interdiscip. Rev. Syst. Biol. Med.* **2012**, *4*, 457–473. [CrossRef] [PubMed]

476. Heier, C.R.; Zhang, A.; Nguyen, N.Y.; Tully, C.B.; Panigrahi, A.; Gordish-Dressman, H.; Pandey, S.N.; Guglieri, M.; Ryan, M.M.; Clemens, P.R.; et al. Multi-Omics Identifies Circulating miRNA and Protein Biomarkers for Facioscapulohumeral Dystrophy. *J. Pers. Med.* **2020**, *10*, 236. [CrossRef]

477. Liu, J.C.; Dong, S.S.; Shen, H.; Yang, D.Y.; Chen, B.B.; Ma, X.Y.; Peng, Y.R.; Xiao, H.M.; Deng, H.W. Multi-omics research in sarcopenia: Current progress and future prospects. *Ageing Res. Rev.* **2022**, *76*, 101576. [CrossRef] [PubMed]

478. McCourt, J.L.; Stearns-Reider, K.M.; Mamsa, H.; Kannan, P.; Afsharinia, M.H.; Shu, C.; Gibbs, E.M.; Shin, K.M.; Kurmangaliyev, Y.Z.; Schmitt, L.R.; et al. Multi-omics analysis of sarcospan overexpression in mdx skeletal muscle reveals compensatory remodeling of cytoskeleton-matrix interactions that promote mechanotransduction pathways. *Skelet. Muscle* **2023**, *13*, 1. [CrossRef]

479. Bornstein, B.; Heinemann-Yerushalmi, L.; Krief, S.; Adler, R.; Dassa, B.; Leshkowitz, D.; Kim, M.; Bewick, G.; Banks, R.W.; Zelzer, E. Molecular characterization of the intact mouse muscle spindle using a multi-omics approach. *eLife* **2023**, *12*, e81843. [CrossRef]

480. Van Pelt, D.W.; Kharaz, Y.A.; Sarver, D.C.; Eckhardt, L.R.; Dzierzawski, J.T.; Disser, N.P.; Piacentini, A.N.; Comerford, E.; McDonagh, B.; Mendias, C.L. Multiomics analysis of the mdx/mTR mouse model of Duchenne muscular dystrophy. *Connect. Tissue Res.* **2021**, *62*, 24–39. [CrossRef]

481. Elasbali, A.M.; Al-Soud, W.A.; Adnan, M.; Alhassan, H.H.; Mohammad, T.; Hassan, M.I. Discovering Promising Biomarkers and Therapeutic Targets for Duchenne Muscular Dystrophy: A Multiomics Meta-Analysis Approach. *Mol. Neurobiol.* **2024**. [CrossRef]

482. Signorelli, M.; Tsonaka, R.; Aartsma-Rus, A.; Spitali, P. Multiomic characterization of disease progression in mice lacking dystrophin. *PLoS ONE* **2023**, *18*, e0283869. [CrossRef] [PubMed]

483. Wu, X.; Dong, N.; Yu, L.; Liu, M.; Jiang, J.; Tang, T.; Zhao, H.; Fang, Q. Identification of immune-related features involved in Duchenne muscular dystrophy: A bidirectional transcriptome and proteome-driven analysis. *Front. Immunol.* **2022**, *13*, 1017423. [CrossRef] [PubMed]

484. Mournetas, V.; Massouridès, E.; Dupont, J.B.; Kornobis, E.; Polvèche, H.; Jarrige, M.; Dorval, A.R.L.; Gosselin, M.R.F.; Manousopoulou, A.; Garbis, S.D.; et al. Myogenesis modelled by human pluripotent stem cells: A multi-omic study of Duchenne myopathy early onset. *J. Cachexia Sarcopenia Muscle* **2021**, *12*, 209–232. [CrossRef]

485. Wijekoon, N.; Gonawala, L.; Ratnayake, P.; Dissanayaka, P.; Gunarathne, I.; Amaratunga, D.; Liyanage, R.; Senanayaka, S.; Wijesekara, S.; Gunasekara, H.H.; et al. Integrated genomic, proteomic and cognitive assessment in Duchenne Muscular Dystrophy suggest astrocyte centric pathology. *Heliyon* **2023**, *9*, e18530. [CrossRef] [PubMed]

486. Rajczewski, A.T.; Jagtap, P.D.; Griffin, T.J. An overview of technologies for MS-based proteomics-centric multi-omics. *Expert Rev. Proteom.* **2022**, *19*, 165–181. [CrossRef] [PubMed]
487. Argelaguet, R.; Velten, B.; Arnol, D.; Dietrich, S.; Zenz, T.; Marioni, J.C.; Buettner, F.; Huber, W.; Stegle, O. Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. *Mol. Syst. Biol.* **2018**, *14*, e8124. [CrossRef]

488. Mann, M.; Kumar, C.; Zeng, W.F.; Strauss, M.T. Artificial intelligence for proteomics and biomarker discovery. *Cell Syst.* **2021**, *12*, 759–770. [CrossRef]

489. Vera, C.D.; Zhang, A.; Pang, P.D.; Wu, J.C. Treating Duchenne Muscular Dystrophy: The Promise of Stem Cells, Artificial Intelligence, and Multi-Omics. *Front Cardiovasc. Med.* **2022**, *9*, 851491. [CrossRef]

490. Torun, F.M.; Virreira Winter, S.; Doll, S.; Riese, F.M.; Vorobeyev, A.; Mueller-Reif, J.B.; Geyer, P.E.; Strauss, M.T. Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data. *J. Proteome Res.* **2023**, *22*, 359–367. [CrossRef]

491. Procopio, A.; Cesarelli, G.; Donisi, L.; Merola, A.; Amato, F.; Cosentino, C. Combined mechanistic modeling and machine-learning approaches in systems biology—A systematic literature review. *Comput. Methods Programs Biomed.* **2023**, *240*, 107681. [CrossRef]

492. Fortunato, F.; Tonelli, L.; Farnè, M.; Selvatici, R.; Ferlini, A. DMD deletions underlining mild dystrophinopathies: Literature review highlights phenotype-related mutation clusters and provides insights about genetic mechanisms and prognosis. *Front. Neurol.* **2024**, *14*, 1288721. [CrossRef]

493. Marques, M.J.; Ferretti, R.; Vomero, V.U.; Minatel, E.; Neto, H.S. Intrinsic laryngeal muscles are spared from myonecrosis in the mdx mouse model of Duchenne muscular dystrophy. *Muscle Nerve* **2007**, *35*, 349–353. [CrossRef] [PubMed]

494. Lorena, M.D.S.V.; Santos, E.K.D.; Ferretti, R.; Nagana Gowda, G.A.; Odom, G.L.; Chamberlain, J.S.; Matsumura, C.Y. Biomarkers for Duchenne muscular dystrophy progression: Impact of age in the mdx tongue spared muscle. *Skelet. Muscle* **2023**, *13*, 16. [CrossRef] [PubMed]

**Disclaimer/Publisher's Note:** The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
487. Argelaguet, R.; Velten, B.; Arnol, D.; Dietrich, S.; Zenz, T.; Marioni, J.C.; Buettner, F.; Huber, W.; Stegle, O. Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. *Mol. Syst. Biol.* **2018**, *14*, e8124. [CrossRef]

488. Mann, M.; Kumar, C.; Zeng, W.F.; Strauss, M.T. Artificial intelligence for proteomics and biomarker discovery. *Cell Syst.* **2021**, *12*, 759–770. [CrossRef]

489. Vera, C.D.; Zhang, A.; Pang, P.D.; Wu, J.C. Treating Duchenne Muscular Dystrophy: The Promise of Stem Cells, Artificial Intelligence, and Multi-Omics. *Front Cardiovasc. Med.* **2022**, *9*, 851491. [CrossRef]

490. Torun, F.M.; Virreira Winter, S.; Doll, S.; Riese, F.M.; Vorobeyev, A.; Mueller-Reif, J.B.; Geyer, P.E.; Strauss, M.T. Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data. *J. Proteome Res.* **2023**, *22*, 359–367. [CrossRef]

491. Procopio, A.; Cesarelli, G.; Donisi, L.; Merola, A.; Amato, F.; Cosentino, C. Combined mechanistic modeling and machine-learning approaches in systems biology—A systematic literature review. *Comput. Methods Programs Biomed.* **2023**, *240*, 107681. [CrossRef]

492. Fortunato, F.; Tonelli, L.; Farnè, M.; Selvatici, R.; Ferlini, A. DMD deletions underlining mild dystrophinopathies: Literature review highlights phenotype-related mutation clusters and provides insights about genetic mechanisms and prognosis. *Front. Neurol.* **2024**, *14*, 1288721. [CrossRef]

493. Marques, M.J.; Ferretti, R.; Vomero, V.U.; Minatel, E.; Neto, H.S. Intrinsic laryngeal muscles are spared from myonecrosis in the mdx mouse model of Duchenne muscular dystrophy. *Muscle Nerve* **2007**, *35*, 349–353. [CrossRef] [PubMed]

494. Lorena, M.D.S.V.; Santos, E.K.D.; Ferretti, R.; Nagana Gowda, G.A.; Odom, G.L.; Chamberlain, J.S.; Matsumura, C.Y. Biomarkers for Duchenne muscular dystrophy progression: Impact of age in the mdx tongue spared muscle. *Skelet. Muscle* **2023**, *13*, 16. [CrossRef] [PubMed]

**Disclaimer/Publisher's Note:** The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.