The global evolution and impact of systems biology and artificial intelligence in stem cell research and therapeutics development: a scoping review

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Silva-Sousa, Thayna ; Usuda, Julia Nakanishi ; Al-Arawe, Nada ; Frias, Francisca ; Hinterseher, Irene ; Catar, Rusan ; Luecht, Christian ; Riesner, Katarina ; Hackel, Alexander ; Schimke, Lena F. ; Dias, Haroldo Dutra ; Filgueiras, Igor Salerno ; Nakaya, Helder, I ; Camara, Niels Olsen Saraiva ; Fischer, Stefan ; Riemekasten, Gabriela ; Ringden, Olle ; Penack, Olaf ; Winkler, Tobias ; Duda, Georg ; Fonseca, Dennyson Leandro M. ; Cabral-Marques, Otavio ; Moll, Guido

• Document type: Journal article
• Source: Stem Cells; v. 42, n. 11, p. 16-pg., 2024-10-13.

Abstract

Advanced bioinformatics analysis, such as systems biology (SysBio) and artificial intelligence (AI) approaches, including machine learning (ML) and deep learning (DL), is increasingly present in stem cell (SC) research. An approximate timeline on these developments and their global impact is still lacking. We conducted a scoping review on the contribution of SysBio and AI analysis to SC research and therapy development based on literature published in PubMed between 2000 and 2024. We identified an 8 to 10-fold increase in research output related to all 3 search terms between 2000 and 2021, with a 10-fold increase in AI-related production since 2010. Use of SysBio and AI still predominates in preclinical basic research with increasing use in clinically oriented translational medicine since 2010. SysBio- and AI-related research was found all over the globe, with SysBio output led by the (US, n = 1487), (UK, n = 1094), Germany (n = 355), The Netherlands (n = 339), Russia (n = 215), and France (n = 149), while for AI-related research the US (n = 853) and UK (n = 258) take a strong lead, followed by Switzerland (n = 69), The Netherlands (n = 37), and Germany (n = 19). The US and UK are most active in SCs publications related to AI/ML and AI/DL. The prominent use of SysBio in ESC research was recently overtaken by prominent use of AI in iPSC and MSC research. This study reveals the global evolution and growing intersection among AI, SysBio, and SC research over the past 2 decades, with substantial growth in all 3 fields and exponential increases in AI-related research in the past decade. Top: Depicting the observational period 2000-2024 to study the publishing trends considering the interrelationship between the search terms: stem cell research, systems biology, and artificial intelligence. Bottom: Representation of an adjunct AI-generated image constructed based on the article title and key words with Dall-E AI quoting: An image depicting a futuristic laboratory where advanced AI systems are analyzing stem cells for therapeutic development. The scene is filled with high-tech equipment, holographic displays, and scientists working alongside robots, showcasing the integration of AI in biological research.." (AU)

• FAPESP's process: 20/16246-2 - Holistic characterization of T cell exhaustion in patients with Zika
• Grantee: Dennyson Leandro Mathias da Fonseca
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 20/07069-0 - Systemic and integrative analysis of T lymphocyte exhaustion mechanisms in patients with COVID-19
• Grantee: Otávio Cabral Marques
• Support Opportunities: Regular Research Grants
• FAPESP's process: 23/07806-2 - Integrative systems bioinformatics analysis of antiviral immune responses.
• Grantee: Igor Salerno Filgueiras
• Support Opportunities: Scholarships in Brazil - Technical Training Program - Technical Training
• FAPESP's process: 20/01688-0 - Systemic and integrative analysis of the immune response to Zika and Dengue viral infections
• Grantee: Otávio Cabral Marques
• Support Opportunities: Scholarships in Brazil - Young Researchers
• FAPESP's process: 18/18886-9 - Systemic and integrative analysis of the immune response to Zika and Dengue viral infections
• Grantee: Otávio Cabral Marques
• Support Opportunities: Research Grants - Young Investigators Grants