{"title":"Artificial intelligence and machine learning heuristics for discovery of ncRNAs.","authors":"Alfredo Benso, Gianfranco Politano","doi":"10.1016/bs.pmbts.2025.01.002","DOIUrl":"10.1016/bs.pmbts.2025.01.002","url":null,"abstract":"<p><p>Artificial intelligence (AI) has emerged as a powerful tool in molecular biology, significantly advancing the study of long non-coding RNAs (lncRNAs). This chapter examines the application of AI techniques, including machine learning (ML) and deep learning (DL), in predicting lncRNA functions, identifying disease associations, and annotating protein interactions. The discussion covers key methodologies such as supervised and unsupervised ML algorithms, recurrent neural networks (RNNs), convolutional neural networks (CNNs), and transformer-based models. A detailed description of a deep learning pipeline for functional annotation of lncRNA-binding proteins (lncRBPs) is provided, highlighting challenges in dataset preparation, model design, and usability. Integrating experimental validation with computational predictions is emphasized as a pathway to bridge AI-driven insights with biological understanding.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"214 ","pages":"145-162"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bilal Ahmed Abbasi, Renuka Suravajhala, V S Sundararajan, Jayaraman Valadi, Prashanth Suravajhala
{"title":"Non-coding RNAs and their integrated biological networks.","authors":"Bilal Ahmed Abbasi, Renuka Suravajhala, V S Sundararajan, Jayaraman Valadi, Prashanth Suravajhala","doi":"10.1016/bs.pmbts.2025.05.014","DOIUrl":"10.1016/bs.pmbts.2025.05.014","url":null,"abstract":"<p><p>Non-coding RNAs (ncRNAs) regulate gene expression by acting as transcriptional modulators, either via binding to specific stretches of DNA sequences/proteins, or by interacting with transcription factors. Previous genome scans often dismissed ncRNAs as transcriptional noise; recent studies have established them as critical regulators in cellular function, epigenetic alterations, and RNA stability, far exceeding beyond their originally perceived passive roles. In this chapter, we explore the regulatory functions of ncRNAs, the complex interplay between coding and non-coding gene networks, and review available in silico tools/methods for ncRNA identification, annotation and analysis. Moreover, we highlight key studies and case examples demonstrating how ncRNAs contribute to disease pathophysiology particularly focusing on cancer, and neurological disorders illustrating their functional and clinical significance.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"214 ","pages":"179-194"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Wearable biosensors for autoimmune disorders.","authors":"Jyot Thesia, Alok Pandya","doi":"10.1016/bs.pmbts.2025.05.008","DOIUrl":"10.1016/bs.pmbts.2025.05.008","url":null,"abstract":"<p><p>Millions of people are affected worldwide by autoimmune disorders, including rheumatoid arthritis, lupus, multiple sclerosis and others, whose immune attacks also do not occur in a straightforward or stable manner. Dynamic changes of disease progression and treatment efficacy are not regularly monitored or diagnosed using conventional diagnostic and monitoring techniques. Wearable biosensors (WBS) provide a transformational solution for continuous, minimally invasive biomarker monitoring including cytokines, autoantibodies and acute phase proteins. This paper reviews the pathophysiology underlying WBS in autoimmune disease management, the relevant biomarkers, and the recent advances in biosensor technology. Sensitivity, specificity, stability and biocompatibility issues have also been addressed. Towards the future, our vision includes future prospects in big data analytics and artificial intelligence for predictive modeling, material science advancements for improving sensor performance, noninvasive monitoring technologies, and omics integration for a complete health status of the patient. These innovations have the ability to affect patients suffering from autoimmune disease in a personalized, data driven, and real time manner.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"215 ","pages":"405-418"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Targeting MYC with protein drugs.","authors":"Jumi A Shin","doi":"10.1016/bs.pmbts.2024.07.001","DOIUrl":"10.1016/bs.pmbts.2024.07.001","url":null,"abstract":"<p><p>After cardiovascular disease, cancer is our biggest killer. The \"war on cancer\" officially launched in 1971; despite decades of research and development, our arsenal of drugs against cancer still comprises mainly small molecules. Protein drugs, however, are poised to become the foundation for next-generation drugs that target MYC, a proto-oncogene that encodes the MYC transcription factor involved in the majority of human cancers. Such protein drugs work inside the cell in the nucleus, where they interact directly with the genome or can partner with MYC to blunt its detrimental activities. No small-molecule drug has been successful against MYC, but protein drug Omomyc has successfully inhibited solid tumors in human trials. Although MYC is a key regulator of normal cellular processes, we need to develop new tactics to contain MYC when it goes rogue.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"212 ","pages":"1-23"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143693187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Climate change, health, and wearable biosensors: Harnessing emerging technologies to bridge environmental exposures and physiological responses.","authors":"Nour Kassem, Perla Boutros, Sandra Barteit","doi":"10.1016/bs.pmbts.2025.06.010","DOIUrl":"10.1016/bs.pmbts.2025.06.010","url":null,"abstract":"<p><p>Climate change poses a growing threat to human health, increasing exposure to extreme environmental conditions. Wearable biosensors provide real-time monitoring of physiological responses to heat stress, including cardiovascular strain, thermoregulatory disruptions, sleep disturbances, and biomarkers of heat-related illnesses. These devices also assess behavioural adaptations, such as reduced physical activity, offering insights into physiological resilience and susceptibility. Wearable biosensors have broad applications in occupational health, enabling non-invasive detection of heat-related illnesses and the monitoring of air pollution impacts on respiratory and cardiovascular function. Validation studies emphasise the importance of sensor placement and multimodal analytics to enhance measurement accuracy under extreme conditions. By synchronising environmental and biometric data, these technologies support ecological momentary assessment, informing evidence-based policymaking and personalised health interventions. Despite their potential, challenges remain in ensuring equitable deployment, particularly in resource-limited settings. Issues such as affordability, data privacy, and validation across diverse populations must be addressed to enable widespread adoption. As climate change intensifies, integrating wearable biosensors into public health frameworks and adaptation policies will be essential for mitigating health risks and enhancing resilience in vulnerable populations.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"216 ","pages":"109-137"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Epigenetic and experimental approaches influencing non-coding RNAs.","authors":"Urvashi Vijay, Ashmeet Kaur, Sunil Polipalli","doi":"10.1016/bs.pmbts.2025.05.001","DOIUrl":"10.1016/bs.pmbts.2025.05.001","url":null,"abstract":"<p><p>Epigenetics having sundry ambiences which are robustly linked to non-coding RNAs, precisely small RNAs that are generally imputated in gene expression regulation and helps in directing cytosine methylation and histone modifications of complex organisms. A pivotal peculiarity of epigenetics is that the same genome shows unwonted phenotypes which are situated in different epigenetics states. In last decade, the majority tangled epigenetic phenomena studied encompasses transposon activity and silencing which are directly or indirectly associated in RNA component and are currently epitomize by piRNAs (piwi-interacting RNAs), position effect variegation, X-chromosome inactivation, parental imprinting, and paramutation. Envisagly, there are certain non - coding RNAs are players in epigenetics gene regulation but their mechanism is still underlying. In yeast, plants, and mice, ncRNAs facilitate the inheritance of epigenetic states, effectively transmitting information across generations. This transgenerational epigenetic inheritance underscores the potential of ncRNAs to act as carriers of heritable information, bridging the gap between environmental cues and genetic responses. In conclusion, ncRNAs play a central role in epigenetic regulation and the transfer of genetic information, highlighting their importance in the evolution and complexity of higher organisms. In this review article, ongoing research continues to uncover the multifaceted functions of these molecules, offering deeper insights into the regulatory architectures that underpin life.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"214 ","pages":"65-79"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nilesh Wagh, Pranav Amane, Rahul Kshirsagar, Sayanti Mandal, P B Kavi Kishor, Penna Suprasanna
{"title":"Exploring the critical role of non-coding RNAs in plant development and stress adaptation-current status and insights.","authors":"Nilesh Wagh, Pranav Amane, Rahul Kshirsagar, Sayanti Mandal, P B Kavi Kishor, Penna Suprasanna","doi":"10.1016/bs.pmbts.2025.01.003","DOIUrl":"10.1016/bs.pmbts.2025.01.003","url":null,"abstract":"<p><p>Non-coding RNAs (ncRNAs), a major fraction of the genome earlier considered as transcriptomic noise has now been uncovered as functional regulators over the past decade. NcRNAs are recognized for their structural and regulatory role in intricate network of plant development and stress response, offering novel insights into molecular mechanisms underlying plant resilience. Advanced sequencing technologies have facilitated the identification and characterization of ncRNAs, highlighting their significance in plant growth, development, and stress responses. This review comprehensively addresses the varied roles of ncRNAs in orchestrating stress perception and response with a brief introduction of various classes of ncRNAs. Further, mode of action and mechanistic role of ncRNAs in modulating genetic regulation of stress response are discussed, along with the role of various ncRNA involved in regulating plant architectural changes. The ncRNA are currently exploited for developing stress-resilient crop varieties with improved yield, especially in the context of global climate change and food security. By integrating molecular perspectives with practical implications, this review offers a thorough understanding of how ncRNAs contribute to plant stress responses, paving the way for innovative strategies in crop improvement and sustainable agriculture.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"214 ","pages":"19-64"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Peptide-based inhibitors of epigenetic proteins.","authors":"Jordi C J Hintzen, Jasmin Mecinović","doi":"10.1016/bs.pmbts.2024.04.004","DOIUrl":"10.1016/bs.pmbts.2024.04.004","url":null,"abstract":"<p><p>Epigenetic drug discovery has become an integral part of medicinal chemistry in the past two decades. Targeting epigenetic proteins-enzymes that modify histone proteins and DNA (writers and erasers) and proteins that recognize such modifications (readers)-has been firmly established as a medicinal strategy for treatment of many human diseases, including cancer and neurological disorders. In this chapter, we systematically describe peptide-based inhibitors of structurally and functionally diverse classes of epigenetic proteins. We show that epigenetic writers, such as DNA methyltransferases, histone methyltransferases and histone acetyltransferases, can be efficiently inhibited by peptides possessing nonproteinogenic amino acids. Moreover, the activity of epigenetic erasers, including TET enzymes, histone demethylases, and histone deacetylases, can be selectively modulated by diverse linear and cyclic peptides. Furthermore, we discuss chromatin-binding epigenetic reader proteins that can be inhibited by histone-mimicking peptides. Overall, this chapter highlights that peptides provide an important molecular platform for epigenetic drug discovery programmes in academia and industry.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"212 ","pages":"25-65"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143693155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Wearable sensors for animal health and wellness monitoring.","authors":"M R Krishnendu, Sanjay Singh","doi":"10.1016/bs.pmbts.2025.06.008","DOIUrl":"10.1016/bs.pmbts.2025.06.008","url":null,"abstract":"<p><p>Biosensors are rapidly emerging as a key tool in animal health management, therefore, gaining a significant recognition in the global market. Wearable sensors, integrated with advanced biosensing technologies, provide highly specialized devices for measuring both individual and multiple physiological parameters of animals, as well as monitoring their environment. These sensors are not only precise and sensitive but also reliable, user-friendly, and capable of accelerating the monitoring process. In livestock management, novel biosensors offer significant benefits in various areas, including disease detection, health monitoring, detection of reproductive cycles, and assessment of the overall physiological well-being of animals through environmental analysis. A wide range of advanced technologies are being applied in the development of wearable sensors, including microfluidics, fluorescence resonance energy transfer, surface plasmon resonance, image detection techniques, electrochemical sensing, cantilever-based sensing, and many others. The data generated from these integrated monitoring systems provides crucial insights into the biochemical, emotional, and physiological functions of farm animals. This not only helps identify the most productive animals but also enables farmers to predict which animals may be more resilient to common diseases. This chapter explores the various technological advancements used in wearable sensor development, digital animal health, and the different types of wearable sensors and their applications in livestock management.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"216 ","pages":"139-183"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}