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Research paper

An exploratory text analysis of the autophagy research field

ORCID Icon, ORCID Icon & ORCID Icon
Pages 1648-1661 | Received 04 Mar 2021, Accepted 14 Oct 2021, Published online: 23 Nov 2021

References

  • Klionsky DJ. Autophagy revisited: a conversation with Christian de Duve. Autophagy. 2008;4:740–743.
  • Nakatogawa H. Mechanisms governing autophagosome biogenesis. Nat Rev Mol Cell Biol. 2020;21:439–458.
  • Nishimura T, Tooze SA. Emerging roles of ATG proteins and membrane lipids in autophagosome formation. Cell Discov. 2020;6:32.
  • Schuck S. Microautophagy - distinct molecular mechanisms handle cargoes of many sizes. J Cell Sci. 2020;133:jcs246322.
  • Kaushik S, Cuervo AM. The coming of age of chaperone-mediated autophagy. Nat Rev Mol Cell Biol. 2018;19:365–381.
  • Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993;333:169–174.
  • Thumm M, Egner R, Koch B, et al. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett. 1994;349(2):275–280.
  • Harding TM, Morano KA, Scott SV, et al. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol. 1995;131:591–602.
  • Ohsumi Y. Historical landmarks of autophagy research. Cell Res. 2014;24:9–23.
  • Mizushima N. A brief history of autophagy from cell biology to physiology and disease. Nat Cell Biol. 2018;20:521–527.
  • Mizushima N, Levine B. Autophagy in human diseases. N Engl J Med. 2020;383:1564–1576.
  • Rebholz-Schuhmann D, Oellrich A, Hoehndorf R. Text-mining solutions for biomedical research: enabling integrative biology. Nat Rev Genet. 2012;13:829–839.
  • Fleuren WW, Alkema W. Application of text mining in the biomedical domain. Methods. 2015;74:97–106.
  • Extance A. How AI technology can tame the scientific literature. Nature. 2018;561:273–274.
  • Yang Y, Ma B, Jin Y, et al. Bioinformatic mining of kinase inhibitors that regulate autophagy through kinase signaling pathways. Mol Med Rep. 2014;10:3348–3356.
  • Jacomin AC, Samavedam S, Promponas V, et al. iLIR database: a web resource for LIR motif-containing proteins in eukaryotes. Autophagy. 2016;12:1945–1953.
  • Wang W, Zhang P, and Li L, et al. ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases. Database (Oxford). 2018;bay093.
  • Chen K, Yang D, and Zhao F, et al. Autophagy and tumor database: ATdb, a novel database connecting autophagy and tumor. Database (Oxford). 2020;baaa052.
  • Wang S, Liu C, Ouyang W, et al. Common genes involved in autophagy, cellular senescence and the inflammatory response in AMD and drug discovery identified via biomedical databases. Transl Vis Sci Technol. 2021;10:14.
  • Perera N, Dehmer M, Emmert-Streib F. Named entity recognition and relation detection for biomedical information extraction. Front Cell Dev Biol. 2020;8:673.
  • Golder SA, Macy MW. Diurnal and seasonal mood vary with work, sleep, and daylength across diverse cultures. Science. 2011;333:1878–1881.
  • Jordan SE, Hovet SE, Fung IC-H, et al. Using Twitter for public health surveillance from monitoring and prediction to public response. Data. 2019;4:6.
  • Khadjeh Nassirtoussi A, Aghabozorgi S, Ying Wah T, et al. Text mining of news-headlines for FOREX market prediction: a multi-layer dimension reduction Algorithm with semantics and sentiment. Exp Sys with Appl. 2015;42:306–324.
  • Brainard J. New tools aim to tame pandemic paper tsunami. Science. 2020;368:924–925.
  • Dunn WA Jr. Studies on the mechanisms of autophagy: formation of the autophagic vacuole. J Cell Biol. 1990;10:1923–1933.
  • Takeshige K, Baba M, Tsuboi S, et al. Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction. J Cell Biol. 1992;119:301–311.
  • Nitatori T, Sato N, Waguri S, et al. Delayed neuronal death in the CA1 pyramidal cell layer of the gerbil hippocampus following transient ischemia is apoptosis. J Neurosci. 1995;15:1001–1011.
  • Anglade P, Vyas S, Javoy-Agid F, et al. Apoptosis and autophagy in nigral neurons of patients with Parkinson’s disease. Histol Histopathol. 1997;12:25–31.
  • Seglen PO, Gordon PB. 3-Methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes. Proc Natl Acad Sci USA. 1982;79:1889–1892.
  • Blommaart EF, Krause U, Schellens JP, et al. The phosphatidylinositol 3-kinase inhibitors wortmannin and LY294002 inhibit autophagy in isolated rat hepatocytes. Eur J Biochem. 1997;243:240–246.
  • Liu RL. Identification of conclusive association entities in biomedical articles. J Biomed Semantics. 2019;10:1.
  • Yang L, Wang H, Shen Q, et al. Long non-coding RNAs involved in autophagy regulation. Cell Death Dis. 2017;8:e3073.
  • Klionsky DJ, Cregg JM, Dunn WA Jr., et al. A unified nomenclature for yeast autophagy-related genes. Dev Cell. 2003;5:539–545.
  • Vega-Rubin-de-Celis S. The role of beclin 1-Dependent autophagy in cancer. Biology (Basel). 2019;9:4.
  • Noda NN, Wang Z, and Zhang H. Liquid-liquid phase separation in autophagy. J Cell Biol. 2020;219:e202004062.
  • Hernandez-Caceres MP, Munoz L, Pradenas JM, et al. Mechanobiology of autophagy: the unexplored side of cancer. Front Oncol. 2021;11:632956.
  • Sou YS, Tanida I, Komatsu M, et al. Phosphatidylserine in addition to phosphatidylethanolamine is an in vitro target of the mammalian Atg8 modifiers, LC3, GABARAP, and GATE-16. J Biol Chem. 2006;281:3017–3024.
  • Durgan J, Lystad AH, Sloan K, et al. Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine. Mol Cell. 2021;81:2031–40 e8.
  • Johansen T, Lamark T. Selective autophagy: ATG8 family proteins, LIR motifs and cargo receptors. J Mol Biol. 2020;432:80–103.
  • Kirkin V. History of the selective autophagy research: how did it begin and where does it stand today? J Mol Biol. 2020;432:3–27.
  • Pankiv S, Clausen TH, Lamark T, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem. 2007;282:24131–24145.
  • Killackey SA, Philpott DJ, and Girardin SE. Mitophagy pathways in health and disease. J Cell Biol. 2020;219:e202004029.
  • Gatica D, Lahiri V, Klionsky DJ. Cargo recognition and degradation by selective autophagy. Nat Cell Biol. 2018;20:233–242.
  • Kirkin V, Rogov VV. A diversity of selective autophagy receptors determines the specificity of the autophagy pathway. Mol Cell. 2019;76:268–285.
  • Conway O, Akpinar HA, Rogov VV, et al. Selective autophagy receptors in neuronal health and disease. J Mol Biol. 2020;432:2483–2509.
  • Djajadikerta A, Keshri S, Pavel M, et al. Autophagy induction as a therapeutic strategy for neurodegenerative diseases. J Mol Biol. 2020;432:2799–2821.
  • Neumann M, King D, and Beltagy I, et al. ScispaCy: fast and robust models for biomedical natural language processing. ArXiv. 2019;abs/1902.07669.
  • Tang D, Kang R, Berghe TV, et al. The molecular machinery of regulated cell death. Cell Res. 2019;29:347–364.
  • Kist M, and Vucic D. Cell death pathways: intricate connections and disease implications. EMBO J. 2021;40:e106700.
  • Blei D, Ng A, and Jordan M. Latent Dirichlet Allocation. Journal of machine learning research. 2003;3:993–1022.
  • Asmussen CB, Møller C. Smart literature review: a practical topic modelling approach to exploratory literature review. J Big Data. 2019;6:93.
  • Griffiths TL, Steyvers M. Finding scientific topics. Proc Natl Acad Sci U S A. 2004;101(Suppl 1):5228–5235.
  • Cao J, Xia T, Li J, et al. A density-based method for adaptive LDA model selection. Neurocomputing. 2009;72:1775–1781.
  • Arun R, Suresh V, Veni Madhavan CE, et al. On finding the natural number of topics with latent dirichlet allocation: some observations. In: Zaki MJ, Yu JX, Ravindran B, et al., editors. Advances in knowledge discovery and data mining. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010. p. 391–402.
  • Deveaud R, Sanjuan E, and Bellot P. Accurate and effective latent concept modeling for Ad Hoc information retrieval. Document numérique. 2014;17:61–84.
  • Novikoff AB, Beaufay H, De Duve C. Electron microscopy of lysosomerich fractions from rat liver. J Biophys Biochem Cytol. 1956;2:179–184.
  • Clark SL Jr. Cellular differentiation in the kidneys of newborn mice studies with the electron microscope. J Biophys Biochem Cytol. 1957;3:349–362.
  • Eskelinen EL, Reggiori F, Baba M, et al. Seeing is believing: the impact of electron microscopy on autophagy research. Autophagy. 2011;7:935–956.
  • Arstila AU, Trump BF. Studies on cellular autophagocytosis. The formation of autophagic vacuoles in the liver after glucagon administration. Am J Pathol. 1968;53:687–733.
  • Amherdt M, Harris V, Renold AE, et al. Hepatic autography in uncontrolled experimental diabetes and its relationships to insulin and glucagon. J Clin Invest. 1974;54:188–193.
  • Lahiri V, Hawkins WD, Klionsky DJ. Watch what you (Self-) eat: autophagic mechanisms that modulate metabolism. Cell Metab. 2019;29:803–826.
  • Madeo F, Zimmermann A, Maiuri MC, et al. Essential role for autophagy in life span extension. J Clin Invest. 2015;125:85–93.
  • King JS. Autophagy across the eukaryotes: is S. cerevisiae the odd one out? Autophagy. 2012;8:1159–1162.
  • Till A, Saito R, Merkurjev D, et al. Evolutionary trends and functional anatomy of the human expanded autophagy network. Autophagy. 2015;11:1652–1667.
  • Zhang S, Hama Y, and Mizushima N. The evolution of autophagy proteins - diversification in eukaryotes and potential ancestors in prokaryotes. J Cell Sci. 2021; 134:jcs233742.
  • Hipp MS, Kasturi P, Hartl FU. The proteostasis network and its decline in ageing. Nat Rev Mol Cell Biol. 2019;20:421–435.
  • Klaips CL, Jayaraj GG, Hartl FU. Pathways of cellular proteostasis in aging and disease. J Cell Biol. 2018;217:51–63.
  • Yang Y, Klionsky DJ. Autophagy and disease: unanswered questions. Cell Death Differ. 2020;27:858–871.
  • Mulcahy Levy JM, Thorburn A. Autophagy in cancer: moving from understanding mechanism to improving therapy responses in patients. Cell Death Differ. 2020;27:843–857.
  • Stephani M, Dagdas Y. Plant selective autophagy-still an uncharted territory with a lot of hidden gems. J Mol Biol. 2020;432:63–79.
  • de la Ballina LR, Munson MJ, Simonsen A. Lipids and lipid-binding proteins in selective autophagy. J Mol Biol. 2020;432:135–159.
  • Galluzzi L, Green DR. Autophagy-independent functions of the autophagy machinery. Cell. 2019;177:1682–1699.
  • Duszenko M, Ginger ML, Brennand A, et al. Autophagy in protists. Autophagy. 2011;7:127–158.
  • Team RC. A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. 2020.
  • Galluzzi L, Baehrecke EH, Ballabio A, et al. Molecular definitions of autophagy and related processes. EMBO J. 2017;36:1811–1836.
  • Grün B, and Hornik K. topicmodels: an R package for fitting topic models Journal of Statistical Software. 2011;40:1–13.

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