This mini-review discusses the importance of microorganisms in various biological processes and the paradigm shift in researchers' perception of microorganisms' biology and genetics. Microorganisms are now understood to interact with their associated microorganisms, and advanced sequencing technology is used to study these interactions. The article highlights the importance of careful study design to efficiently generate and integrate data derived from meta-omics approaches such as (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics to fully explore the extent of interactions between host organisms and their associated microbiota. The article also discusses the usefulness of metabarcoding and metagenomics in studying coral holobiont diversity and composition. While metabarcoding can comprehensively explore the genetic diversity of various biological taxa, it has limitations in classifying prokaryotes based on 16S rRNA amplicons. On the other hand, metagenomics generates vast amounts of short reads sequencing data that can be used to examine microbial diversity with greater precision and predict the possible functions of the gene set that is presented in the sample. However, the ability to link species to their functional capabilities is challenging, especially for microbes with uncertain evolutionary relationships, hidden microbes, and microeukaryotes. Finally, the article highlights the potential usefulness of these approaches in conservation biology and molecular and environmental science.

Advanced genomics, transcriptomics and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids, and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research, the principles of genomics, transcriptomics and epigenomics, alongside their most advanced technologies (like single cell omics and spatial omics), which allows to investigate the molecular events that occur at single cell resolution retaining the spatial information.

The literature was scoped to help place mass spectrometric (MS) platforms in the spotlight of the life sciences, as a tool of OMICS and OMICS 2.0 technologies. Moreover, today’s appliances are so handy, that they literally place a whole lab on a single chip. Methods of OMICS (and the most recently developed term OMICS 2.0) are tackled, having in mind their aptness for educational purposes, as well as their feasibility. This same topic was highlighted in many reviews that have been periodically published. The author’s initial interest was the forensic application of MS, but since these interests changed, terms such as “biosensors” were also examined, so the review included means of discovery of efficient biomarkers and clinical therapeutic targets. Aside from simply reviewing the research status and the future perspectives, this article tackles terms such as Society 5.0 and OMICS 2.0. However, within the framework of this review, physical chemistry, bioinformatics, or specific software solutions were not specifically studied. Since the topic of generating permanent collections of digital content for retrospective analysis was also reviewed, the need for loads of data – cloud storage was discussed in the context of MS. These large quantities of data are easier to operate with if generated by MS, rather than by any other commercially available assay. In this manner, the review has strengthened an in-depth understanding of the applications of MS.

Background: Fold change is widely used in biomedical research to quantify the magnitude of group differences in omics variables. However, the exact calculation method is often not reported, leading to inconsistent results. This study re-evaluates different fold-change calculation methods and provides a clear preference. Methods: Data scenarios with different distributions of treatment/test and reference data were created to challenge the assumption of interchangeable calculation methods. The main difference lies in the definition of the expected values of the groups used to calculate the log ratio, which is the basis of the fold change calculation. In addition, a multi-omics biomedical dataset was analyzed. Results: Using the arithmetic mean as the expected value for the treatment and reference groups resulted in incorrect fold change values more frequently than other methods, especially when the standard deviations between subgroups differed widely. Conclusions: The inferior arithmetic mean method is often perceived as the standard, although mathematically different equations are possible that differ mainly in the estimation of the expected value. Alternatives that define expectation by median, geometric mean, or paired fold change combinations are less susceptible to violations of equal variances or similar treatment/reference distributions.

The integration of omics technologies, including genomics, metabolomics, proteomics, and microbiomics, has transformed sports science, particularly in soccer, where these advancements have the potential to enhance player performance, injury prevention, and recovery. This review examines the role of single nucleotide polymorphisms (SNPs) across key genes influencing various physiological traits crucial for elite soccer players. Genes related to the cardiovascular system (ACE, AGT, NOS3, VEGF), muscle structure and function (ACTN3, CKM, MLCK), neurotransmission (ADRA2A, ADRB2, BDNF, DRD1, DBH), connective tissue integrity (COL1A1, COL2A1, COL5A1, ELN, EMILIN1, TNC), energy metabolism (AMPD1, MCT1, UCP1/2/3), oxidative stress response (GSTM1, GSTP, GSTT), hormonal regulation (CYP2D6, HSD17B14), and growth factors (GDF-8, IGF2, HGF) are all highlighted for their roles in influencing soccer-specific traits like endurance, speed, and injury risk. Furthermore, the incorporation of omics data allows for personalized strategies in training, nutrition, and recovery, tailoring interventions to each player's genetic and biochemical profile. For example, genomic markers such as ACE I/D and ACTN3 R577X are linked to key athletic traits like endurance and muscle injury susceptibility, while proteomics sheds light on muscle repair mechanisms, and metabolomics provides real-time insights into energy metabolism and fatigue markers. Microbiomics explores the role of gut health in recovery and overall performance, revealing correlations between microbial diversity and enhanced athletic outcomes. This comprehensive approach, referred to as Socceromics, offers a more holistic understanding of an athlete’s health and performance capabilities. Integrating these findings into real-world applications is essential for optimizing training regimens and reducing injury risk, ultimately pushing the boundaries of what athletes can achieve on the field. Future research should focus on expanding the scope of omics integration and improving the generalizability of findings across diverse populations and genders, thus advancing the field of precision sports medicine.

In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, and genomic selection. In the recent past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and metabolomics, have been developed rapidly, providing powerful tools for the precision genetic breeding of forest plants. Genomics lays a solid foundation for understanding complex biological regulatory networks, while other omics technologies provide different perspectives at different levels. Multi-omics integration has combined the different omics technologies, becoming a powerful tool for genome-wide functional element identification in forest plant breeding. This review summarizes the recent progress of omics technologies and their applications in the genetic studies of forest plants. It will provide forest plant breeders with an elementary knowledge of multi-omics techniques for future breeding programs.

Maize (Zea mays L.) stands as one of the most extensively cultivated crops globally, offering significant contributions to food, animal feed, and biofuel production. Maize yield is significantly impacted by diverse climate and soil variables, yet its productivity faces hindrances due to abiotic stresses, including drought, salinity, extreme temperatures, and cold conditions. In confronting these hurdles, the field of crop breeding has undergone a transformation thanks to high-throughput sequencing technologies (HSTs). These advancements have streamlined the identification of beneficial quantitative trait loci (QTL), associations between markers and traits (MTAs), as well as genes and alleles that contribute to crop improvement. Presently, well-established omics techniques such as genomics, transcriptomics, proteomics, and metabolomics are being amalgamated into maize breeding studies. These approaches have unveiled new biological markers that are being employed to bolster maize's capacity to withstand an array of challenges. In this chapter, we explore the current knowledge regarding the morpho-physiological and molecular mechanisms that underlie the resistance and tolerance of maize to biotic and abiotic stresses. The focus is on utilizing omics techniques to augment maize's ability to withstand these challenges. Moreover, it emphasizes the significant potential of integrating various omics techniques to tackle the challenges presented by biotic and abiotic stress in maize productivity, contrasting with singular approaches.

For a significant period, conventional breeding and genetic modification were the key techniques that were effective in managing biotic and abiotic stresses in crops and adding desirable traits. However, the recent appearance of novel diseases and unexpected climatic changes that have substantial implications for agriculture worldwide have urged scientists to look for alternative methods to quickly manage seasonal crises. The primary emphasis of this chapter is on the obstacles and diverse biotechnological methods employed to enhance crop resilience against a range of biotic and abiotic stressors in plants. Furthermore, we consider gene transformation, omics techniques, genome editing, and other sophisticated biotechnological tools that utilize transcriptomic, proteomic, metabolomic, phenomics, RNA interference, and epigenome modifications for enhancing plant resilience. Lastly, we examine the potential of merging these eco-friendly and innovative methods with conventional breeding to promote modern agriculture and aid in enhancing tolerance to different biotic, abiotic stresses and growth promotion.

Identifying groups that share common features among datasets through clustering analysis is a typical problem in many fields of science, particularly in post-omics and systems biology research. In respect of this, quantifying how a measure can cluster or organize intrinsic groups is important since currently there is no statistical evaluation of how ordered is, or how much noise is embedded in the resulting clustered vector. Many of the literature focuses on how well the clustering algorithm orders the data, with several measures regarding external and internal statistical measures; but none measure has been developed to statistically quantify the noise in an arranged vector posterior a clustering algorithm, i.e., how much of the clustering is due to randomness. Here, we present a quantitative methodology, based on autocorrelation, to assess this problem.

Background: The pathophysiology of functional dyspepsia (FD) remains insufficiently understood, and the pain and economic constraints associated with endoscopic examinations hinder the precise definition and treatment of this disorder. Exploring the potential of multi-omics biomarkers for FD could yield promising targets for effectively diagnosing and treating this condition. Methods: We recruited 54 FD patients and 29 healthy volunteers and characterized their gut microbiota by shotgun metagenomic sequencing and their serum and urine metabolites by liquid chromatography-mass spectrometry (LC-MS). Results: We identified the changes in circulating metabolites associated with FD and linked to the gut microbial alterations. Among the differential circulating metabolites, we particularly highlighted the strong association of L-glutamate deficiency with the severity of FD symptoms and its strong predictive value for FD. Although no significant changes were noted in the gut microbial community structure of the FD samples, this might be attributed to symptom overlap between epigastric pain syndrome (EPS) and postprandial distress syndrome (PDS). However, significant alterations in the abundance of certain species were observed, including a substantial increase in the abundance of Streptococcus in the digestive tract of patients with FD. Finally, a cross-omics correlation network integrating metabolomic data with microbial community abundance was established, uncovering potential host-microbe-metabolite interactions. Conclusions: This work provides the first comprehensive description of the disrupted state of blood and urine metabolite composition and gut microbiota in patients with FD. These findings potentially offer promising targets for the diagnosis and treatment of this condition through a multi-omics approach, with particular emphasis on serum metabolomics.

Jujube (Ziziphus jujuba Mill.) stands as a pivotal fruit tree with significant economic, ecological, and social value. Recent years have witnessed remarkable strides in multi-omics-based biological re-search on jujube. This review began by summarizing advancements in jujube genomics. Subse-quently, we provided a comprehensive overview of the integrated application of genomics, tran-scriptomics, and metabolomics to explore pivotal genes governing jujube domestication traits, quality attributes (including sugar synthesis, terpenoids, and flavonoids), and responses to abiotic stress, and discussed the transcriptional regulatory mechanisms underlying these traits. Further-more, challenges in multi-omics research on jujube biological traits were outlined, and we pro-posed the integration of resources such as pan-genomics and sRNAome to unearth key molecules and regulatory networks influencing diverse biological traits. Incorporating these molecules into practical breeding strategies, including gene editing, transgenic approaches, and progressive breeding, holds the potential for achieving molecular-design breeding and efficient genetic en-hancement of jujube.

In this review, we will cover a general overview of the current panorama on lncRNAs with an actual or potential role as biological markers in cancer. We will discuss examples of multi-omics approaches that integrates information on somatic aberrations, gene expression and epigenomics, with the scope of providing a more comprehensive view of the functional impact of lncRNA profiles and how these paradigm can be exploited for the discovery and selection of lncRNAs with a functional role and their use as variables informing on progression and prognostic and help guiding the selection of therapeutic strategies for cancers. Finally, we propose a perspective for future evolution of the study of lncRNAs and the discovery of their functional and harnessing their potential to assist in clinical management of malignancies.

Omics technologies, viz., genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal breeding program because they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in cereal-omics promise—in combination with time efficiency—the cost benefits. In this review, we provide a comprehensive overview of the established cereal-omics methods in five major cereals, viz., rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants, (2) high-density transcriptomics data to study gene expression patterns, (3) global and targeted proteome profiling to study protein structure and interaction, (4) metabolomic profiling to quantify organ level small-density metabolites and their composition, and (5) high-resolution high-throughput image-based phenomics approaches are surveyed in this review.

Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical layer that reflects information expressed by the genome, the transcriptome and the proteome, but also as the closest layer to the phenome. The combination of metabolomics data with the information available from genomics, transcriptomics, and proteomics offers unprecedented possibilities to enhance current understanding of biological functions, elucidate their underlying mechanisms and uncover hidden associations between omics variables. As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics. Here, we review and propose five criteria – hypothesis, data types, strategies, study design and study focus – to classify statistical multi-omics data integration approaches into state-of-the-art classes under which all existing statistical methods fall. The purpose of this review is to look at various aspects that lead the choice of the statistical integrative analysis pipeline in terms of the different classes. We will draw a particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.

Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence, and heavy metals. The effective management at molecular level is mandatory for thorough understanding of plant response to abiotic stress. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in wheat. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in wheat. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in wheat. This review also provides a comprehensive catalog of available online omic resources for wheat and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in wheat.

Inherited cardiomyopathies are a diverse group of heart muscle diseases caused by genetic mutations that result in structural and functional abnormalities of the myocardium. Understanding genotype-phenotype correlations in these conditions is vital for personalized cardiac medicine, enabling targeted therapeutic strategies and predictive diagnostics. This review explores the major types of inherited cardiomyopathies—hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), arrhythmogenic right ventricular cardiomyopathy (ARVC), and restrictive cardiomyopathy (RCM)—and provides detailed insights into how different genetic mutations manifest as clinical features. The integration of multi-omics approaches and advanced disease modeling techniques has enhanced our ability to dissect these correlations. The review also discusses the implications of these findings for personalized medicine, including tailored therapeutic strategies, predictive diagnostics, and future research directions.

The utilization of Artificial Intelligence (AI) in biotechnology is widespread, addressing challenges such as elucidating disease pathophysiology and novel therapeutic approaches. AI plays a critical role in tasks such as drug manufacturing, chemical analysis, RNA and DNA sequencing, and enzyme studies by automating processes and expediting data collection and analysis. AI has particularly transformed the analysis of omics data for researchers, providing tools to handle complex and multifaceted datasets effectively. Through AI, integrative analysis of multi-omics data can be conducted in efficient ways. This article discusses the application of multi-omics and AI technologies in studying various diseases related to infection (COVID-19), mutation (cancer), and senescence (alopecia) to understand their pathophysiology. The applications of AI were performed as the aspect of the diagnosis, prognosis, and treatment for each disease. We introduce AI-driven analysis of pathophysiology can overcome traditional limitations in pathology, with diverse features showing potential in defining the causes of diseases, and potentially enhancing primary omics data in the distinguish the subtype of diseases. In this context, integrated approaches using multi-omics data and AI technology could provide fresh biological insights by comprehending the molecular mechanism of diseases and is instrumental in advancing precision medicine. We anticipate that the rapidly advancing AI-based multi-omics data analysis will significantly contribute to promoting healthy longevity.

Cancer is one of the leading causes of death, making timely diagnosis and prognosis very important. Utilization of AI (artificial intelligence) enables providers to organize and process patient data in a way that can lead to better overall outcomes. This review paper aims to look at the varying uses of AI for diagnosis and prognosis and clinical utility. PubMed and EBSCO databases were utilized for finding publications from January 1, 2013, to December 22, 2023. Articles were collected using key search terms such as “artificial intelligence” and “machine learning.” Included in the collection were studies of the application of AI in determining cancer diagnosis and prognosis using multi-omics data, radiomics, pathomics, clinical and laboratory data. The resulting 89 studies were categorized into eight sections based on the type of data utilized and then further subdivided into two subsections focusing on cancer diagnosis and prognosis, respectively. 8 studies integrated more than one form of omics, namely genomics, transcriptomics, epigenomics, and proteomics. Incorporating AI into cancer diagnosis and prognosis alongside omics and clinical data represents a significant advancement. Given the considerable potential of AI in this domain, ongoing prospective studies are essential to enhance algorithm interpretability and to ensure safe clinical integration.

Improvements in the treatment of childhood cancer have considerably enhanced survival rates over the last decades, to over 80% as per today. However, this great achievement has been accompanied by the occurrence of several early and long-term treatment-related complications major of which is the cardiotoxicity. The chemotherapeutic agents that have been implicated as a cause of cardiotoxicity, are mostly anthracyclines and mitoxantrone, alkylating agents, proteasome inhibitors and to a lesser extent anti-microtubule agents, cisplatin, monoclonal antibodies, small molecular tyrosine kinase inhibitors, and nucleotide synthesis inhibitors. Routine diagnosis and monitoring of cardiotoxicity rely on electrocardiography and echocardiography. For the early detection of cardiotoxicity, in recent years, major studies have been conducted using biomarkers such as troponin, N-terminal pro b-natriuretic peptide, etc. Despite refinements in diagnostics still severe limitations exist, due to the increase of the above-mentioned biomarkers, only after significant cardiac damage has occurred. Lately, research has been expanded by introducing new technologies and finding new markers by omics approach. These new markers could be used not only for early detection, but also for early prevention of cardiotoxicity. The omics science, which includes genomics, transcriptomics, proteomics, and metabolomics, offers new opportunities for biomarker discovery in cardiotoxicity and may provide understanding of mechanisms of cardiotoxicity, beyond traditional technologies. This article reviews the contemporary definition of cardiotoxicity, older and newer chemotherapeutic agents mainly involved in cardiotoxicity and the methods of early and preventive diagnosis, using omics technology.

Given the importance of menstrual blood in the pathogenesis of endometriosis and the multifunctional roles of menstrual mesenchymal stem cells (MenSCs) in regenerative medicine, this issue has gained prominence in the scientific community. Moreover, recent reviews highlight how robust the integrated assessment of omics data is for endometriosis. To our knowledge, no study has applied the multi-omics approaches to endometriosis MenSCs. It is a case-control study at a university-affiliated hospital. MenSCs transcriptome and proteome data were obtained by RNA-seq and UHPLC-MS/MS detection. Among the differentially expressed proteins and genes, we emphasize ATF3, ID1, ID3, FOSB, SNAI1, NR4A1, EGR1, LAMC3, and ZFP36 genes and MT2A, TYMP, COL1A1, COL6A2, and NID2 proteins that were already reported in the endometriosis. Our functional enrichment analysis reveals integrated modulating signaling pathways such as epithelial-mesenchymal transition (↑) and PI3K signaling via AKT to mTORC1 (↓in proteome), mTORC1 signaling, TGF beta signaling, TNFA signaling via NFkB, and response to hypoxia via HIF1A targets (↑in transcriptome). Our findings highlight primary changes in the endometriosis MenSCs, suggesting that the chronic inflammatory endometrial microenvironment can modulate these cells, providing opportunities for endometriosis etiopathogenesis. Moreover, they identify challenges for future research leveraging knowledge for regenerative and precision medicine in endometriosis.

High-throughput screening technologies continues to produce large amounts of multiomics data from different populations and cell types for various diseases, such as cancer. However, analysis of such data encounters difficulties due to cancer heterogeneity, further exacerbated by human biological complexity and genomic variability. There is a need to redefine the drug discovery development pipeline, bringing an Artificial Intelligence (AI)-powered informational view that integrates relevant biological information and explores new ways to develop effective anticancer approaches. Here, we show SynPred, an interdisciplinary approach that leverages specifically designed ensembles of AI-algorithms, links omics and biophysical traits to predict synergistic anticancer drug synergy. SynPred exhibits state-of-the-art performance metrics: accuracy – 0.85, precision – 0.77, recall – 0.75, AUROC – 0.82, and F1-score - 0.76 in an independent test set. Moreover, data interpretability was achieved by deploying the most current and robust feature importance approaches. A simple web-based application available online at http://www.moreiralab.com/resources/synpred/ was constructed to predict synergistic anticancer drug combinations requiring only the upload of the two drug SMILES to be tested, allowing easy access by non-expert researchers.

Rapid development of high-throughput omics technologies generates an increasing interests in algorithms for cutoff point identification. Existing cutoff methods and tools identify cutoff points based on association of continuous variables with another variable, such as phenotype, disease state or treatment group. These approaches are not applicable for descriptive studies in which continuous variables are reported without known association with any biologically meaningful variables. The most common shape of the ranked distribution of continuous variables in high-throughput descriptive studies corresponds to a biphasic exponential/super-exponential curve, where the first phase includes big number of variables with values slowly growing with rank and the second phase includes smaller number of variables rapidly growing with rank. This study describes an easy algorithm to identify the boundary between these phases to be used as a cutoff point. The major assumption of that approach is that small number of variables with high values dominate biological system and determine its major processes and functions. This approach was tested on three different datasets: genes in the human cerebral cortex, mammalian genes sensitive to chemical exposures, and proteins expressed in human heart. In every case, the described cutoff identification method produced shortlists of variables (genes, proteins) highly relevant for dominant functions/pathways of the analyzed biological systems. Thus, our described method for cutoff identification may be used to prioritize variables for a focused functional analysis, in situations where other methods of dichotomization of data are inaccessible.

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used to define the building blocks to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.

By providing useful tools to study host-pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches. In this review, we focus on the difficulties encountered when making use of omics approaches to study bacterial pathogenesis. Besides, we review different omics strategies (i.e. transcriptomics, proteomics and secretomics) and their applications for studying interactions of pathogens with their host.

A comprehensive understanding of the mechanisms underlying how Lentinula edodes handles heat stress (HS) is crucial for the development of superior HS-resistant strains. However, the mechanism by which the two sexually compatible haploid nuclei respond to heat stress remains largely unknown. Here, we examined the nuclei-specific (SP3 and SP30) HS-resistant mechanisms using integrated metabolomic and transcriptomic analysis. Results showed HS elicited the boost of ROS and hampered the mycelium growth for both monokaryons. Metabolome and transcriptome data demonstrated that the two sexually compatible monokaryons responded differently to HS. For SP3, the differentially expressed genes were significantly enriched in MAPK signaling, cell cycle and sugar metabolism, whereas those for SP30 were enriched in glyoxylate and dicarboxylate metabolism, and protein processing. The differentially accumulated metabolites of both strains were enriched in the glycerophospholipid metabolism, alpha-linolenic acid metabolism, biosynthesis of cofactors, etc, but with different regulatory modes. The enriched KEGG pathways for SP3 mostly tend to be down-regulated, whereas those in SP30 showed a contrary trend. The genes in MAPK signaling pathway might be associated with the glycerophospholipid metabolism in SP3, but not in SP30. Omics-integration analysis depicted distinguishable regulatory networks and discovered totally different hub genes of the two strains. Our findings revealed for the first time that the two sexually compatible nuclei responded to HS with different mechanisms and provided candidate metabolites, responsive genes and regulatory pathways for further experimental validation.

Arabidopsis and other model plants can help improve crops by providing a reference framework for assembling omics data from plants. Arabidopsis is extensively studied and has a well-curated and annotated genome, making it an excellent reference organism for comparative analysis. When there is no reference genome of the organism being investigated, using the genome of Arabidopsis may be an option thanks to the extensive knowledge we have about it. Crop improvement can help to increase crop yields, improve crop quality, and enhance resistance to pests, diseases, and environmental stresses. It can also help to reduce the use of pesticides and fertilizers, which can have negative impacts on the environment and human health. Therefore, crop improvement is essential to ensure food security and sustainability in the face of global challenges such as climate change, land degradation, and water scarcity. The assembly process of genomic, transcriptomic, and metabolomic data from plants using carefully selected information on Arabidopsis can lead to a deeper understanding of organisms and their potential for genetic improvement for crops. However, the successful integration of data requires expertise and experience to design more effective and precise crop improvement strategies.

Foods that are fermented have a crucial role in global diets, these foods benefit from the process of fermentation, which enhances nutrition, flavor, and safety through the use of probiotics, anti-aging compounds, and antibiotics. Traditional fermentation is based on the spontaneous activity of microorganisms, while modern methods utilize defined cultures for consistency. The microorganisms in cheese are important for the flavor and texture of the product. These microorganisms are either non-starter or starter bacteria, yeast, and mold. The advances in sequencing technology have facilitated an increase in our understanding of these communities and their contribution to the quality and safety of cheese. Despite the health benefits of fermented dairy products, such as yogurt, they can pose a risk of contamination with pathogens. New methods of management and sequencing are crucial to ensuring the safety and quality of fermented foods, combining traditional methods with modern advances.

Plant-microbe interactions are essential for ecosystem health and agricultural productivity. Metabolomics has revolutionized our understanding of these interactions by providing powerful methods to decipher the complex chemical signals involved. This review highlights the various metabolomics techniques used to study plant-microbe interactions, such as mass spectrometry, nuclear magnetic resonance spectroscopy, and advanced imaging technologies. We also discuss the role of contemporary bioinformatics tools, extensive databases, and the increasing influence of artificial intelligence and machine learning in the analysis of metabolomics data. Integrating metabolomics with other omics fields, including transcriptomics, proteomics, and metagenomics, allows for a comprehensive understanding of the molecular mechanisms underlying plant-microbe interactions. The review emphasizes the significance of fluxomics in elucidating the dynamic nature of metabolic networks. While there are challenges in data analysis, integration, and interpretation, metabolomics has profoundly expanded our knowledge of the role metabolites play in shaping plant-microbe interactions. As metabolomics technologies advance and integrate further with other omics approaches, we anticipate groundbreaking discoveries that will provide deeper insights into these complex interactions, ultimately leading to innovative strategies for sustainable agriculture and biotechnology.

A decade or so of research led to the conclusion, in 2022, that the Soil Realm is home to ~2.1 x 10²⁴ taxa and supports >99.9% of global species biodiversity, mostly Bacteria or other microbes based upon topographic field data. A subsequent 2023 soil biodiversity report tabulated a central value of just 1.04 × 10¹⁰ taxa and claimed soils had 59±15% (i.e., 44–74%) of total species on Earth, incidentally confirming upper values of ~90% for Bacteria. Incompatibility of these two studies is reviewed, supporting the prior global biodiversity data with a vast majority of species inhabiting soil, this despite excluding virus entities (now with >5 x 10³¹ virions and up to 10²⁶ species, 80–90% being in soils). The true status of Oligochaeta (earthworms) and other taxa marked “?” in the 2023 paper are clarified. Although soil biota totals are raised enormously, inordinate threats and the reality of species extinctions yet pertain, specifically to those biota – such as microbes and earthworms – essential for rich, healthy soils that house & nourish almost all the Tree of Life presently on Earth.

Rice, as a staple crop feeding billions, faces constant threats from various diseases jeopardizing global food security. Precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. Integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with better understanding of their functional roles in disease resistance. Improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can give a transformative impact on rice breeding for enhancing disease resistance.

The concept of omics-based technological approaches has promoted translational research by integrating knowledge from diverse areas to understand their dynamics by exploring the molecular mechanisms underlying various processes paving the way for further improvements in the crops quality by providing sound knowledge on controlling plant diseases. This area is not profoundly investigated a decade back and hence this knowledge has become exceedingly important in modern times as it has got potential for being utilized in crop improvement programs. In this review, the contributions of different omics technologies including genomics, transcriptomics, proteomics, and metabolomics in understanding and materializing the ways involved in the plant pathogen interaction (PPI) is discussed. Furthermore, opportunities, challenges, and perspectives of omics linked to signaling mechanisms have also been highlighted that are significantly linked to plant-microbe interactions.

Climate change has had a significant impact on many ecosystems worldwide, prompting native population species to adapt to the current weather patterns eventually. Pre-existing genetic variation in populations explains part of this adaptation. Still, recent studies have shown that new stable phenotypes can be generated through epigenetic modifications in just a few generations, thereby contributing to the stability and survival of plants in their natural habitat as they eventually adjust to the surrounding impacts. The state of chromatin inside plant cells varies, allowing cells to fine-tune their transcriptional profiles to better adapt to stimuli from the external environment. Within a cell, chromatin state changes such as post-transcriptional histone modifications and variations, DNA methylation, and non-coding RNA activity are all examples of chromatin state alterations that may epigenetically dictate certain transcriptional outputs. Recent advances in the field of ‘Omics’ in major crops has made it easier to identify epigenetic changes and their impact on plant responses to environmental stresses. These epigenetic mechanisms thus play an important role in improving crop adaptation and resilience to changing environments. This variation that has emerged can thus be exploited in crop breeding, ultimately leading to the generation of stable climate-resilient genotypes.

Increased severity of droughts, due to anthropogenic activities and global warming has imposed a severe threat on agricultural productivity ever before. This has further advanced the need for some eco-friendly approaches to ensure global food security. In this regard, application of plant growth-promoting rhizobacteria (PGPR) can be beneficial. PGPR through various mechanisms viz. osmotic adjustments, increased antioxidant, phytohormone production, regulating stomatal conductivity, increased nutrient uptake, releasing Volatile organic compounds (VOCs), and Exo-polysaccharide (EPS) production, etc not only ensures the plant’s survival during drought but also augment its growth. This review, extensively discusses the various mechanisms of PGPR in drought stress tolerance. We have also summarized the recent molecular and omics-based approaches for elucidating the role of drought responsive genes. The manuscript presents an in-depth mechanistic approach to combat the drought stress and also deals with designing PGPR based bioinoculants. Lastly, we present a possible sequence of steps for increasing the success rate of bioinoculants.

Bioethanol has been considered as an excellent alternative to fossil fuels since it importantly contributes to the reduced consumption of the crude oil and to the alleviation of environmental pollution [1]. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds [2]. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over the others, e.g. it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars) [3], tolerate to high temperature, toxin [4,5] and a wide range of pH values [6], and produce volatile short-chain ester [2]. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species [7]. These attributes make K. marxianus a promise as an industrial host for the biosynthesis of biofuels and other valuable chemicals.

The present work offers a contemporary synthesis of the application of the Oxford Nanopore^® MinION^™ within the context of cultural heritage biodeterioration investigations, while also providing a comprehensive discussion of possible future perspectives for their utilization in this research field. Owing to the distinctive characteristics of this device, the past few years have witnessed the consistent increase on the application of this system in a variety of cultural heritage materials. In fact, the technique has been useful to understand microbial biodeteriogens diversity and some of their metabolic and biodeteriogenic features. Considering the immense potential for application of this system, this manuscript explores and discusses further possibilities of the technique, focusing on helping understand critical questions on the cultural heritage biodeterioration area. Its application in various differential contexts, has opened doors for prospective applications on other interesting sub-areas of research meriting future investigations, including: biodeteriogens genome and transcriptome analysis, metatranscriptomics, biodeteriorative metabolism studies, inter and intra kingdom interactions analysis, resistome profiling, object history and context studies, in situ applications, bioprospecting and biotechnology.

Acetamiprid is a broad-spectrum neonicotinoid insecticide used in agriculture to control aphids. While recent studies have documented resistance to acetamiprid in several aphid species, the underlying mechanisms are still not fully understood. In this study, we analyzed the transcriptome and metatranscriptome of a laboratory strain of the pea aphid, Acyrthosiphon pisum (Harris, 1776), with reduced susceptibility to acetamiprid after nine generations of exposure to identify candidate genes and the microbiome involved in the adaptation process. Sequencing of the transcriptome of both selected (RS) and non-selected (SS) strains allowed the identification of 14858 genes and 4938 new transcripts. Most of the differentially expressed genes were associated with catalytic activities and metabolic pathways involving carbon and fatty acids. Specifically, the alcohol-forming fatty acyl-CoA reductase (FAR) and acyl-CoA synthetase (ACSF2), both involved in the synthesis of epidermal wax layer components, were significantly upregulated in RS, suggesting that adaptation to acetamiprid involves the synthesis of a thicker protective layer. Metatranscriptomic analysis revealed subtle shifts in the microbiome of RS. These results contribute to a deeper understanding of acetamiprid adaptation by the pea aphid and provide new insights for aphid control strategies.

Inflammatory Bowel Disease (IBD) is a chronic and progressive inflammatory disorder affecting the gastrointestinal tract (GT) caused by a wide range of genetic, microbial, and environmental factors. IBD is characterized by chronic inflammation, decreased gut microbial diversity and dysbiosis, with a lower amount of beneficial bacteria and a concomitant increase of pathogenic species. It is well known that dysbiosis is closely related to the induction of inflammation and oxidative stress, this last caused by an imbalance between reactive oxygen species (ROS) production and cellular antioxidant capacity that leads to cellular ROS accumulation. ROS are responsible for the intestinal epithelium oxidative damage and the increased intestinal permeability found in IBD patients and their reduction could represent a potential therapeutic strategy to limit the IBD progression and alleviate its symptom. Recent evidence highlighted that dietary polyphenols, natural antioxidants, are able to maintain redox equilibrium in the GT preventing gut dysbiosis, intestinal epithelium damage and radical inflammatory responses. Here, we suggest that the relatively new foodomics approaches, together with new technologies for promoting the antioxidative properties of dietary polyphenols, including novel delivery systems, chemical modifications and combination strategies, may provide critical insight to determine the clinical value of polyphenols for IBD therapy and a comprehensive perspective for implementing natural antioxidants as potential IBD candidate treatment.

The advancement of mass spectrometry technologies has revolutionised plant metabolomics research by enabling the acquisition of raw metabolomics data. However, the identification, analysis, and visualisation of these data require specialised tools. Existing solutions lack a dedicated plant-specific metabolite database and pose usability challenges. To address these limitations, we developed PlantMetSuite, a web-based tool for comprehensive metabolomics analysis and visualisation. PlantMetSuite encompasses interactive bioinformatics tools and databases specifically tailored for plant metabolomics data, facilitating upstream-to-downstream analysis in metabolomics and supporting integrative multi-omics investigations. PlantMetSuite can be accessed directly through a user's browser without the need for installation or programming skills. The tool is freely available at https://plantmetsuite.verygenome.com/ and will undergo regular updates and expansions to incorporate additional libraries and newly published metabolomics analysis methods. The tool's significance lies in empowering researchers with an accessible and customisable platform for unlocking plant metabolomics insights.

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current state-of-the-art and discusses key limitations underlying these emerging approaches, in particular, the limited functional knowledge they provide in understanding local proteomes / interactomes. This limitation is directly linked to the use of non-biologically- or non-pharmaceutically-relevant reactive intermediates in the course of covalently labeling the local proteomes. As such, these methods cannot report on specific functions of localized protein players, nor can they scrutinize whether the specific functions of such proteins/interactomes can be directly manipulated by pharmacologically-relevant small-molecule ligands. The latest data hint that precision localized electrophile delivery concept ushers a means to address this limitation with high spatiotemporal resolution, and ultimately, in relevant live animals.

The ability to read and quantify nucleic acids such as DNA and RNA using sequencing technologies has revolutionized our understanding of life. With the emergence of synthetic biology, these tools are now being put to work in new ways - enabling de novo biological design. Here, we show how sequencing is supporting the creation of a new wave of biological parts and systems, as well as providing the vast data sets needed for the machine learning of design rules for predictive bioengineering. However, we believe this is only the tip of the iceberg and end by providing an outlook on recent advances that will likely broaden the role of sequencing in synthetic biology and its deployment in real-world environments.

Despite medical advances, sepsis and septic shock remain one of the leading causes of mortality worldwide, with a high inter-individual variability in prognosis, clinical manifestations and response to treatment. Given the heterogeneity of sepsis and recent technological progress amongst machine learning analysis technique, a new, personalized approach in sepsis is being intensively studied. Despite the difficulties when tailoring a targeted approach, with the use of artificial intelligence-based pattern recognition, more and more publications are becoming available, highlighting novel factors that may intervene in the high heterogenicity of sepsis. This has led to the devise of a phenotypical approach in sepsis, further dividing patients based on host and trigger-related factors, clinical manifestations and progression towards organ deficiencies, dynamic prognosis algorithms and patient trajectory in the Intensive Care Unit (ICU). Host and trigger-related factors refer to patients’ comorbidities, body-mass index, age, temperature, immune response, type of bacteria and infection site. The progression to organ deficiencies refers to individual particularities of sepsis-related multiorgan failure. Finally, the patient’s trajectory in the ICU points out the need of a better understanding of interindividual response to various supportive therapies. This review aims to identify the main sources of variability in clustering septic patients in various clinical phenotypes, as a useful clinical tool for precision-based approach in sepsis and septic shock.

Cow’s Milk (CM) is a healthy food consumed worldwide by individuals of all ages. Unfortunately, 'lactase deficient' individuals cannot digest milk's carbohydrate lactose depriving themselves of highly beneficial milk proteins like casein, lactoalbumin and lactoglobulin, due to lactose intolerance (LI), while other individuals develop cow milk allergy specifically against these proteins (CMPA). The management of these conditions is distinctly different and an inappropriate diagnosis or treatment may have significant implications for the patients, especially if they are infants or very young children, resulting in unnecessary dietary restriction or avoidable adverse reactions. Omics technologies play a pivotal role in elucidating the intricate interactions between nutrients and the human body, spanning from genetic factors to the microbiota profile and metabolites. This comprehensive approach enables the precise delineation and identification of distinct cohorts of individuals with specific dietary requirements, so that tailored nutrition strategies can be developed. This is what is called personalized nutrition or precision nutrition (PN), the area of nutrition that focuses on the effects of the nutrients over the genome, proteome and metabolome, promoting well-being and health, preventing diseases, reducing chronic disease incidence, and so increasing life expectancy. Here, we report the scientific community opinion proposing to replace the approach “one size fits all” with tailor-made nutrition programs, designed by integrating nutrigenomic data together with clinical parameters and microbiota profiles, taking into account the individual lactose tolerance threshold and needs in terms of specific nutrients intake. This customized approach could help LI patients to improve their quality of life, overcoming depression or anxiety, often resulting from the individual perception of this condition as different from a normal state.

A heterogeneous disease like cancer is activated through multiple pathways and different perturbations. Depending upon the activated pathway(s), patients’ survival vary significantly and show different efficacy to various drugs. Therefore, cancer subtype detection using genomics level data is a significant research problem. Subtype detection is often a complex problem, and in most cases, needs multi-omics data fusion to achieve accurate subtyping. Different data fusion and subtyping approaches have been proposed, such as kernel-based fusion, matrix factorization, and deep learning autoencoders. In this paper, we compared the performance of different deep learning autoencoders for cancer subtype detection. We performed cancer subtype detection on four different cancer types from The Cancer Genome Atlas (TCGA) datasets using four autoencoder implementations. We also predicted the optimal number of subtypes in a cancer type using the silhouette score. We observed that the detected subtypes exhibit significant differences in survival profiles. Furthermore, we also compared the effect of feature selection and similarity measures for subtype detection. To evaluate the results obtained, we selected the Glioblastoma multiforme (GBM) dataset and identified the differentially expressed genes in each of the subtypes identified by the autoencoders; the obtained results coincide well with other genomic studies and can be corroborated with the involved pathways and biological functions. Thus, it shows that the results from the autoencoders, obtained through the interaction of different datatypes of cancer, can be used for the prediction and characterization of patient subgroups and survival profiles.

The world faces two seemingly unrelated challenges—a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.

Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer-review and increases the impact of datasets by enhancing their visibility, accessibility, and re-usability. We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivise researchers to publish high-quality data sets, we created a workflow for streamlined import of omics metadata directly into a data paper manuscript. An omics data paper template was designed by defining key article sections which encourage the description of omics datasets and methodologies. The workflow was based on REpresentational State Transfer services and Xpath to extract information from the European Nucleotide Archive, ArrayExpress and BioSamples databases, which follow community-agreed standards. The workflow for automatic import of standard-compliant metadata into an omics data paper manuscript facilitates the authoring process. It demonstrates the importance and potential of creating machine-readable and standard-compliant metadata. The omics data paper structure and workflow to import omics metadata improves the data publishing landscape by providing a novel mechanism for creating high-quality, enhanced metadata records, peer reviewing and publishing of these. It constitutes a powerful addition for distribution, visibility, reproducibility and re-usability of scientific data. We hope that streamlined metadata re-use for scholarly publishing encourages authors to improve the quality of their metadata to achieve a truly FAIR data world.

The objective of this study was to determine the effects of supplementing L-isoleucine (L-Ile) on milk protein synthesis, using an immortalized bovine mammary epithelial (MAC-T) cell line. In this case, the cells were treated with 0, 0.3, 0.6, 0.9, 1.2 and 1.5 mM of supplemental Isoleucine (Ile), and the most efficient time for protein synthesis for each amino acid was determined by measuring the cell, medium and total protein at 0, 24, 48, 72 and 96 h. Confirmatory tests showed that 48h incubation time and 0.6 mM dosage of L-Ile are considered as the optimal time and dosage. The mechanism of milk protein synthesis was elucidated through proteomics analysis to clarify the metabolic pathway. When the L-Ile was supplemented, extracellular protein (medium protein) reached a peak at 48h, whereas in the case of the intracellular cell protein, it was shown to have reached to its peak at 24h in all L-Ile dosage treatments. In total, it is noted that there were 63 upregulated and 52 downregulated proteins. The results of the protein pathway analysis showed that the L-Ile group stimulated insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade, insulin/IGF pathway-protein kinase B signaling cascade, p53 pathway, de novo purine biosynthesis, Wnt signaling pathway, glycolysis, pentose phosphate pathway, and ATP synthesis which are pathways involved and related to protein and energy metabolism. Together, these results demonstrate that L-Ile supplementation was effective in stimulating β-casein synthesis by stimulating genes and pathways which are significantly related to protein and energy metabolism.

Gene regulation is vital for cellular function and homeostasis, involving diverse mechanisms controlling specific gene products and contributing to tissue-specific gene expression. Dysregulation leads to diseases, emphasizing the need for understanding these mechanisms. Non-coding regions, notably enhancers and super-enhancers (SEs), act as crucial gene regulators, orchestrating transcriptional activity via transcription factors (TFs). SEs, with high activity, are pivotal in cell identity and disease progression. Current computational approaches focus on individual regulators like TFs and miRNAs, neglecting SE interactions. We emphasize incorporating SEs into models to enhance understanding. Experimental studies have recently linked miRNAs and TFs to SEs. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) provides valuable SE information. In this review, we categorize computational methods leveraging TF and miRNA data into three areas and explore challenges integrating enhancers/SEs. These include unraveling indirect regulatory networks, identifying network motifs, and enriching pathway identification by dissecting gene regulators, including SEs. We hypothesize that addressing these challenges will enhance our understanding of gene regulation, aiding in identifying therapeutic targets and disease biomarkers. We believe that understanding the role of ChIP-Seq data in predicting the effect of miRNA on gene regulation is crucial to construct statistical/computational model that would tackle these challenges.

Once discovered, cancer stem cells have become a hot topic in the research of cancer therapy. These cells possess stem cell-like self-renewal and differentiation capacities and are important factors that dominate cancer metastasis, therapy- resistance and recurrence. What's worse, their own characteristics make them difficult to be eliminated. Colorectal cancer is the third most common cancer and the second leading cause of cancer death worldwide. Targeting colorectal cancer stem cells (CRCSCs) can inhibit colorectal cancer metastasis, enhance therapeutic efficacy, and reduce recurrence. Here, we introduced the origin, marker proteins, identification, cultivation and research techniques of CRCSCs, summarized the signaling pathways that regulate the stemness of CRCSCs, such as Wnt, JAK/STAT3, Notch, and Hh signaling pathway. In addition to these, we also reviewed anti-CRCSC drugs targeting signaling pathways，markers，and other regulators in recent years. These will help researchers gain insight into the current agents targeting to CRCSCs, explore new cancer drugs, and propose potential therapy.

Demonstrating biosimilarity entails comprehensive analytical evaluations, clinical pharmacolo-gy profiling, and efficacy testing for at least one medical indication in patients. These require-ments are stipulated by the U.S. Biologics Price Competition and Innovation Act (BPCIA). The costliest element—efficacy testing—can be waived if other compliance benchmarks are satisfied, including comparing functional pharmacodynamic (PD) biomarkers, even when they do not di-rectly correlate with clinical outcomes. Most biological drugs, such as monoclonal antibodies (mAbs), lack identifiable PD biomarkers. The FDA has employed various 'omics' technologies to identify potential PD biomarkers, including proteomics, glycomics, transcriptomics, genomics, epigenomics, and metabolomics. Although these efforts provide a robust scientific basis for estab-lishing biosimilarity, they are neither practical nor necessarily superior to existing functional biomarkers, such as receptor binding and mode-of-action outcomes. As we report for the first time, these functional biomarkers can effectively serve as PD indicators for all FDA-licensed bio-logical drugs. We recommend that the FDA consider officially listing these functional biomarkers to expedite and reduce the cost of biosimilar development, thereby increasing the accessibility of biological drugs. PD surrogates, like the receptor binding and pharmacokinetic profiles, are more robust and offer a rational solution to finding PD markers to compare for establishing biosimi-larity.

The COVID-19 pandemic has presented an unprecedented challenge to the healthcare system. Identifying the genomics and clinical biomarkers for effective patient stratification and management is critical to controlling the spread of the disease. Omics datasets provide a wealth of information that can aid in understanding the underlying molecular mechanisms of COVID-19 and identifying potential biomarkers for patient stratification. Artificial intelligence (AI) and machine learning (ML) algorithms have been increasingly used to analyze large-scale omics and clinical datasets for patient stratification. In this manuscript, we demonstrate the recent advances and predictive accuracies in AI and ML-based patient stratification modeling linking omics and clinical biomarker datasets, focusing on COVID-19 patients. Our ML model not only demonstrates that clinical features are enough an indicator of COVID-19 severity and survival but also infers what clinical features are more impactful, which makes our approach a useful guide for clinicians for prioritization of best-fit therapeutics for a given cohort of patients. Moreover, with weighted gene network analysis, we are able to provide insights into gene networks that have a significant association with COVID-19 severity and clinical features. Finally, we have demonstrated the importance of clinical biomarkers in identifying high-risk patients and predicting disease progression.

The global threat of COVID-19 has led to the increasing use of metabolomics to study SARS-CoV-2 infection in humans and animals. Despite this, understanding SARS-CoV-2's metabolome during infection remains difficult and incomplete. Here, metabolic responses were characterized from sampled nasal washes collected from an asymptomatic ferret model (n = 20) at different time points before and after the SARS-CoV-2 challenge using an LC-MS-based metabolomics approach. Multivariate analysis of the nasal wash metabolome data resulted in several statistically significant features being observed. Despite no effects of gender or interaction between gender and time on the time course of SARS-CoV-2 infection, 16 metabolites were significantly different at every time point post-infection. Among these altered metabolites, the relative abundance of taurine was elevated post infection which could be an indication of hepatotoxicity, while the accumulation of sialic acids could indicate SARS-CoV-2 invasion. The pathway analysis identified several pathways influenced by SARS-CoV-2 infection. Of these, sugar, glycan, and amino acid metabolisms were the key altered pathways in the upper respiratory channel during infection. These findings provide some new insights into the progression of SARS-CoV-2 infection in ferrets at the metabolic level which could be useful for the development of early clinical diagnosis tools and new or repurposed drug therapies.

Abstract: Since ancient times aging has also been regarded as a disease, and humankind has always strived to extend the natural lifespan. Analyzing the genes involved in aging and disease allows for finding important indicators and biological markers for pathologies and possible therapeutic targets. An example of the use of omics technologies is the research regarding aging and the rare and fatal premature aging syndrome progeria (Hutchinson-Gilford progeria syndrome, HGPS). In our study, we focused on the in silico analysis of differentially expressed genes (DEGs) in progeria and aging, using a publicly available RNA Seq dataset (GEO dataset GSE113957) and a variety of bioinformatics tools. We identified several genes that appear to be involved both in natural aging and progeria (KRT8, KRT18, ACKR4, CCL2, UCP2, ADAMTS15, ACTN4P1, WNT16, IGFBP2). Further analyzing these genes and the pathways involved confirmed their possible roles in aging, suggesting the need for further in vitro and in vivo research. The graphical abstract illustrates the analysis workflow we used and will introduce in the following as an example to demonstrate the power of omics and bioinformatics.

The endothelium has multiple functions from maintaining vascular homeostasis, providing nutrition and oxygen to tissues, to evocating inflammation, under adverse conditions, and determining endo-thelial barrier disruption resulting in dysfunction. Endothelial dysfunction represents the typical condition associated with the pathogenesis of all the diseases of cardiovascular system, as well as of diseases of all the other human body’s systems, also including sepsis, acute respiratory distress syn-drome and COVID-19 respiratory distress. Such evidence is leading to identifying potential bi-omarkers and therapeutic targets for preserving, reverting, or restoring endothelium integrity and functionality by early treating its dysfunction. Here, it stresses some strategies for achieving these goals, even if diverse challenges exist and require a significant bench work associated with an in-creased number of clinical studies.

In the era of multi-omic sciences, dogma on singular cause-effect in physio-pathological processes is overcome and system biology approaches have been providing new perspectives to see through. In this context, extracellular vesicles (EVs) are offering a new level of complexity, given their role in cellular communication and their activity as mediators of specific signals to target cells or tissues. Indeed, their heterogeneity in terms of content, function, origin and potentiality contribute to the cross-interaction of almost every molecular process occurring in a complex system. Such features make EVs proper biological systems being, therefore, optimal targets of omic sciences. Currently, most studies focus on dissecting EVs content in order to either characterize it or to explore its role in various pathogenic processes at transcriptomic, proteomic, metabolomic, lipidomic and genomic levels. Despite valuable results are being provided by individual omic studies, the categorization of EVs biological data might represent a limit to be overcome. For this reason, a multi-omic integrative approach might contribute to explore EVs function, their tissue-specific origin and their potentiality. This review summarizes the state-of-the-art of EVs omic studies, addressing recent research on the integration of EVs multi-level biological data and challenging developments in EVs origin.

The indigenous communities across the globe especially in the rural areas consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many of the traditional food plants are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. TFPs are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in times of pandemics and other situations like COVID-19. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realising the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of traditional food plants for their improvements, further cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in few TFPs. This suggests that there is ample scope of integrated use of modern omics and editing tools/techniques for improvement of TFPs and their use for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Polycyclic aromatic hydrocarbons (PAHs), which consist of low-molecular-weight PAHs (LMW-PAHs) and high-molecular-weight PAHs (HMW-PAHs), form an important class of pollutants. Pyrene and benzo[a]pyrene (BaP) are the main pollutants belonging to HMW-PAHs, and their degradation by microorganisms remains an important strategy for their removal from the environments. Extensive studies have been carried out on the isolation and characterisation of microorganisms that actively degrade LMW-PAHs, and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of “omics” approaches

The exponential growth of publicly available omics data presents both an opportunity and a challenge for biomedical researchers, particularly those in low- and middle-income countries (LMICs). The Collective Omics Data to Knowledge (CD2K) initiative aims to address this challenge by providing an accessible framework for biomedical research training. This review describes the development and implementation of the CD2K program, which comprises three core modules: COD1 (reductionist interpretation of collective omics data), COD2 (creation of curated dataset collections), and COD3 (re-analysis of omics data on a global scale). The CD2K approach emphasizes the reuse and reinterpretation of public data, integrating literature mining and emerging technologies like Large Language Models (LLMs). A key feature of the program is its focus on accessibility, designed to make the exploitation of large-scale datasets amenable to researchers without extensive data science skills. The curriculum aims to equip trainees with a range of skills, from basic data interpretation to more advanced bioinformatics analysis, with an emphasis on producing tangible outputs such as peer-reviewed publications, which directly address career development needs. The CD2K initiative has involved researchers from multiple institutions across several countries, resulting in several publications and publicly available dataset collections. While still in its early stages, the program shows promise in providing a structured framework for leveraging public omics data in biomedical research. This review also discusses the current limitations of the CD2K approach and ongoing efforts to expand its reach. By offering an accessible model for building research capacity, the CD2K initiative represents a step towards fostering data-driven discovery in global biomedical research, particularly in resource-limited settings.

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits by genomic selection (GS), and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state applications of the omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.

Maternal obesity and over/undernutrition can have a long-lasting impact on offspring health during critical periods in the first 1000 days of life. Children born to mothers with obesity have reduced immune responses to stimuli which increase susceptibility to infections. Recently, maternal western-style diets (WSD), high in fat and simple sugars, have been associated with skewing neonatal immune cell development, and recent evidence suggests that dysregulation of innate immunity in early life has long-term consequences on metabolic diseases and behavioral disorders in later life. Several factors contribute to abnormal innate immune tolerance or trained immunity, including changes in gut microbiota, metabolites, and epigenetic modifications. Critical knowledge gaps remain regarding the mechanisms whereby these factors impact fetal and postnatal immune cell development, especially in precursor stem cells in bone marrow and fetal liver. Components of the maternal microbiota that are transferred from mothers consuming a WSD to their offspring are understudied and identifying cause and effect on neonatal innate and adaptive immune development needs to be refined. Tools including single-cell RNA-sequencing, epigenetic analysis, and spatial location of specific immune cells in liver and bone marrow are critical for understanding immune system programming. Considering the vital role of immune function plays in offspring health, it will be important to understand how maternal diets can control developmental programming of innate and adaptive immunity.

As the era of omics continues to expand, omics-based experiments have become popular in industrial biotechnology. They promise deeper biological understanding, which may be leveraged to develop novel solutions to bioprocess optimization and cell line engineering strategies. Despite this expansion, naivety about what omic data offers and how to best handle such data can challenge the extraction of actionable value. However, the value of omic experiments in biotechnology research and development can be maximized with deliberate application of omic approaches and forethought about analysis techniques. Here we describe important considerations when designing and implementing omic-based experiments, and discuss how systems biology analysis strategies can enhance efforts to obtain actionable insights in biomanufacturing.

Metabolomics is now considered to be a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense response to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in molecular breeding and genome editing programs to develop superior next generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted method. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) and matrix-assisted laser desorption/ionization (MALDI) have speed up metabolic profiling in plants. Further, we deliver a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.

The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV-1-host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV-host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV-human protein-protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies may represent a basis for developing new anti-HIV therapeutic strategies such as new small-molecule drugs preventing infection of CD4+ cells and viral replication, effective vaccines, "shock and kill" and "block and lock" approaches to cure latent infection.

Cancer is the second major cause of disease-related dead worldwide, and its accurate early diagnosis and therapeutic intervention are fundamental for saving the patient’s life. Cancer, as a complex and heterogeneous disorder, results from disruption and alteration of a wide variety of biological entities, including genes, proteins, mRNAs, miRNAs, and metabolites that eventually emerge as clinical symptoms. Traditionally, diagnosis is based on clinical examination, blood tests for biomarkers, histopathology of biopsy, and imaging (MRI, CT, PET, US). Additionally, omics biotechnologies help to further characterize the genome, metabolome, microbiome traits of the patient that could have an impact on the prognosis and patient’s response to the therapy. The integration of all these data relies on gathering of several experts and may require considerable time, and, unfortunately, it is not without the risk of error in the interpretation and therefore in the decision. Systems biology algorithms exploit Artificial Intelligence (AI) combined with omics technologies to perform a rapid and accurate analysis and integration of patient’s big data and support the physician in making diagnosis and tailoring the most appropriate therapeutic intervention. However, AI is not free from possible diagnostic and prognostic errors in the interpretation of images or biochemical-clinical data. Here, we first describe the methods used by systems biology for combining AI with omics and then discuss the potential, challenges, limitations, and critical issues in using AI in cancer research.

Endometrial cancer (EC), a prevalent gynecological malignancy, presents significant challenges due to its genetic complexity and heterogeneity. The genomic landscape of EC is underpinned by genetic alterations, such as mutations in PTEN, PIK3CA, and ARID1A, and chromosomal abnormalities. The identification of molecular subtypes—POLE-ultramutated, microsatellite instability (MSI), copy-number low, and copy-number high—illustrates the diverse genetic profiles within EC and underscores the need for subtype-specific therapeutic strategies. The integration of multi-omics technologies such as CRISPR gene editing, single-cell genomics, and spatial transcriptomics, have revolutionized our understanding and approach to studying EC, and offers a holistic perspective that enhances the ability to identify novel biomarkers and therapeutic targets. The translation of these multi-omics findings into personalized medicine and precision oncology is increasingly feasible in clinical practice. Targeted therapies such as PI3K/AKT/mTOR inhibitors have demonstrated the potential for improved treatment efficacy tailored to specific genetic alterations. Despite these advancements, challenges persist in terms of variability in patient responses, the integration of genomic data into clinical workflows, and ethical considerations. This review explores the genomic underpinnings of EC, from genes to clinical practice. It highlights the ongoing need for multidisciplinary research and collaboration to address the complexities of EC and improve diagnosis, treatment, and patient outcomes.

The primary considerations while producing rice (Oryza sativa L.) include improving its nutritional quality and production. To tackle widespread hunger globally, better nutritional, high-yielding rice cultivars need to be developed. The conventional ways are to increase the production of rice and add balanced nutrients in the daily diet to fulfill the need of yield and nutrient quality. This article focuses on nutritional strategies for rice and illustrates the availability of omics technologies. Current advancements providing many methodologies and approaches for exploring genetic resources and for understanding the molecular mechanisms involved in trait formation have been highlighted. Studying the genetic influences of various characteristics has been proven to expedite crop breeding processes. In this perspective, genome-wide association research, genome selection (GS), and QTL mapping are all genetic analysis that helps in increasing the nutritional content of rice. Implementation of several omic techniques are effective approaches to enhance and regulate the nutritional quality of rice cultivars. Advancements in different types of omics including genomics and pangenomics, transcriptomics, metabolomics, nutrigenomics, and proteomics are also relevant to rice development initiatives. This review article compiles genes, locus, mutants and all omic approaches for rice enhancement. This knowledge will be very useful for now and for the future regarding rice studies.

Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and Amyotrophic Lateral Sclerosis are heterogeneous, progressive diseases with frequently overlapping symptoms characterized by a loss of neurons. Studies suggested relations between neurodegenerative diseases for many years, e.g., regarding the aggregation of toxic proteins or triggering endogenous cell death pathways. Within this study, publicly available genomic, transcriptomic and proteomic data were gathered from 188 studies and more than one million patients to detect shared genetic patterns between the neurodegenerative diseases and the analyzed omics-layers within conditions. The results show a remarkably high number of shared genes between the transcriptomic and proteomic levels for all diseases while showing a significant relation between genomic and proteomic data only in some cases. A set of 139 genes was found to be differentially expressed in several transcriptomic experiments of all four diseases. These 139 genes showed overrepresented GO-Terms and pathways mainly involved in stress response, cell development, cell adhesion, and the cytoskeleton. Furthermore, the overlap of two and three omics-layers per disease were used to search for overrepresented pathways and GO-Terms. Taken together, we could confirm the existence of many relations between Alzheimer's disease, Parkinson's disease, Huntington's disease, and Amyotrophic Lateral Sclerosis on the transcriptomic and proteomic level by analyzing the pathways and GO-Terms arising in these intersections. The significance of the connection between the transcriptomic and proteomic data for all four analyzed neurodegenerative diseases showed that exploring these omics-layers simultaneously holds new insights that do not emerge from analyzing these omics-layers separately. Our data therefore suggests addressing human patients with neurodegenerative diseases as complex biological systems by integrating multiple underlying data sources.

Rice, a globally important food crop, faces significant challenges due to salt and drought stress. These abiotic stresses severely impact rice growth and yield, manifesting as reduced plant height, decreased tillering, reduced biomass, and poor leaf development. Recent advances in molecular biology and genomics have uncovered key physiological and molecular mechanisms that rice employs to cope with these stresses, including osmotic regulation, ion balance, antioxidant re-sponses, signal transduction, and gene expression regulation. Transcription factors such as DREB, NAC, and bZIP, as well as plant hormones like ABA and GA, have been identified as crucial reg-ulators. Utilizing CRISPR/Cas9 technology for gene editing holds promise for significantly en-hancing rice stress tolerance. Future research should integrate multi-omics approaches and smart agriculture technologies to develop rice varieties with enhanced stress resistance, ensuring food security and sustainable agriculture in the face of global environmental changes.

Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with themselves, their environment, and hosts via metabolites and signaling molecules. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metagenomics methods, and modeling formalisms. Furthermore, the review explains model building, examples of microbiome model applications for prediction, optimization, and control. It concludes with guidelines, software, and repositories for modeling. Each section provides entry-level information, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.

Births occurring before thirty-seven weeks of gestation are referred to as preterm births (PTBs), which is the primary cause of neonatal mortality and long-term disabilities. The unknown mechanism behind PTB makes diagnosis difficult, yet early detection is necessary for controlling and averting related consequences. The primary focus of this work is to provide an overview of the known risk factors associated with preterm labor and the conventional and advanced procedures for early detection of PTB, including multi-omics and artificial intelligence (AI)/machine learning (ML)-based approaches. It also discusses the principles of detecting various proteomic biomarkers based on lateral flow immunoassay and microfluidic chips, along with the commercially available point-of-care testing (POCT) devices and associated challenges. After briefing the therapeutic and preventive measures of PTB, the review summarizes with an outlook.

The molecular basis of Down syndrome (DS) predisposition to leukemia is not fully understood but involves various factors such as chromosomal abnormalities, oncogenic mutations, epigenetic alterations, and changes in selection dynamics. Myeloid leukemia associated with DS (ML-DS) is preceded by a preleukemic phase called transient abnormal myelopoiesis driven by GATA1 gene mutations and progresses to ML-DS through additional mutations in cohesin genes, CTCF, RAS, or JAK/STAT pathway genes. DS-related ALL (ALL-DS) differs from non-DS ALL in terms of cytogenetic subgroups and genetic driver events and aberrant expression of CRLF2, JAK2 mutations, and RAS pathway activating mutations are frequent in ALL-DS. Recent advancements in single-cell multi-omics technologies have provided unprecedented insights into the cellular and molecular heterogeneity of DS-associated hematologic neoplasms. Single-cell RNA sequencing and digital spatial profiling enable the identification of rare cell subpopulations, characterization of clonal evolution dynamics, and exploration of the tumor microenvironment's role. These approaches may help identify new druggable targets and tailor therapeutic interventions based on distinct molecular profiles, ultimately improving patient outcomes with the potential to guide personalized medicine approaches and the development of targeted therapies.

To further understand the role of phosphorylation in ISGF3- and STAT2/IRF9-mediated constitutive and long-term IFN-I-stimulated transcriptional responses, we performed RNA-Seq and ChIP-Seq, in combination with phosphorylation inhibition and anti-viral experiments. First, we identified a group of ISRE-containing ISGs that were commonly regulated in IFNα treated WT and STAT1-KO cells. Thus, in 2fTGH and Huh7.5 WT cells IFNα-inducible transcription and anti-viral activity relied on the recruitment of the ISGF3 components STAT1, STAT2 and IRF9 in a phosphorylation- and time-dependent manner. Likewise, in ST2-U3C and Huh-STAT1KO cells lacking STAT1, ISG expression correlated with DNA-binding of phosphorylated STAT2/IRF9. This pointed to a dominant role of classical ISGF3 and STAT2/IRF9, and not U-ISGF3 or U-STAT2/IRF9, in the regulation of early and prolonged ISG expression and viral protection, in WT and STAT1-KO cells. In addition, comparative experiments in U3C (STAT1-KO) cells overexpressing all ISGF3 components (ST1-ST2-IRF9-U3C), revealed a threshold-dependent role of U-ISFG3, and potentially U-STAT2/IRF9, in the regulation of constitutive and possibly long-term IFNα-treated ISG expression and anti-viral activity.

The topic of predictive toxicology has been greatly influenced by recent progress in comprehending drug toxicity processes and enhancing medication development. The integration of omics technologies, such as transcriptomics, proteomics, and metabolomics, with traditional toxicological assessments has yielded extensive knowledge about the biological pathways implicated in drug-induced toxicity. The utilization of a multi-omics method amplifies the ability to identify biomarkers that can detect toxicity at an early stage, hence enhancing the safety profile of novel therapeutic medicines. Machine learning and in silico models, such as QSAR models and multi-task deep learning algorithms, have become essential tools. They have shown great accuracy in predicting toxicity endpoints and have helped in the identification of new biomarkers and therapeutic targets. The introduction of microphysiological systems and PBPK modeling has enhanced the transfer of preclinical discoveries to clinical results, providing more precise forecasts of human reactions to medications. Notwithstanding these progressions, obstacles such as the diversity of data and the complex nature of omics data require sophisticated computational techniques for efficient analysis. Continued cooperation and established procedures are crucial to fully utilize these technologies, guaranteeing the creation of safer and more efficient medicinal agents.

Quorum Sensing (QS) and Machine Learning (ML) hybrid systems represent a groundbreaking innovation in synthetic biology, offering unprecedented control and adaptability in microbial gene regulation and metabolic processes. QS, a microbial communication mechanism, is crucial for coordinating gene expression in response to population density, impacting behaviors such as biofilm formation, virulence, and resource optimization. However, traditional QS systems are constrained by their reliance on static, pre-programmed feedback loops, limiting their flexibility in dynamic, complex environments. This review highlights how integrating advanced ML algorithms—such as reinforcement learning and deep learning—into QS systems can overcome these limitations by enabling real-time data processing, predictive modeling, and dynamic feedback control. Through these innovations, QS-ML systems can autonomously adjust gene expression and metabolic outputs, making them more efficient and scalable in applications ranging from pathogen control to precision medicine and industrial biomanufacturing. Key case studies illustrate the successful deployment of QS-ML systems to combat antimicrobial resistance, optimize bio-production, and enhance therapeutic precision in cancer and immune modulation. Despite the clear advantages, challenges remain in data integration, system robustness, and regulatory oversight. Addressing these hurdles through interdisciplinary collaboration and developing scalable, multi-omics data platforms will be critical for advancing QS-ML systems from experimental settings to real-world applications. This review underscores the transformative potential of QS-ML systems in revolutionizing synthetic biology, with profound implications for personalized medicine, sustainable biomanufacturing, and environmental health.