Cross-organism analysis using InterMine.

Molecular biology experiments are generating an unprecedented amount of information from a variety of different experimental modalities. DNA sequencing machines, proteomics mass cytometry and microscopes generate huge amounts of data every day. Not only is the data large, but it is also multidimensional. Understanding trends and getting actionable insights from these data requires techniques that allow comprehension at a high level but also insight into what underlies these trends. Lots of small errors or poor summarization can lead to false results and reproducibility issues in large data sets. Hence it is essential we do not cherry-pick results to suit a hypothesis but instead examine all data and publish accurate insights in a data-driven way. This article will give an overview of some of the problems faced by the researcher in understanding epigenetic changes (which are related to changes in the physical structure of DNA) when presented with raw analysis results using visualization methods. We will also discuss the new challenges faced by using machine learning which can be helped by visualization.

Metabolic markers are the core of metabonomic surveys. Hence selection of differential metabolites is of great importance for either biological or clinical purpose. Here, a feature selection method was developed for complex metabonomic data set. As an effective tool for metabonomics data analysis, support vector machine (SVM) was employed as the basic classifier. To find out meaningful features effectively, support vector machine recursive feature elimination (SVM-RFE) was firstly applied. Then, genetic algorithm (GA) and random forest (RF) which consider the interaction among the metabolites and independent performance of each metabolite in all samples, respectively, were used to obtain more informative metabolic difference and avoid the risk of false positive. A data set from plasma metabonomics study of rat liver diseases developed from hepatitis, cirrhosis to hepatocellular carcinoma was applied for the validation of the method. Besides the good classification results for 3 kinds of liver diseases, 31 important metabolites including lysophosphatidylethanolamine (LPE) C16:0, palmitoylcarnitine, lysophosphatidylethanolamine (LPC) C18:0 were also selected for further studies. A better complementary effect of the three feature selection methods could be seen from the current results. The combinational method also represented more differential metabolites and provided more metabolic information for a “global” understanding of diseases than any single method. Further more, this method is also suitable for other complex biological data sets.

BackgroundLong non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. Only a few plant lncRNA studies focus on understanding their evolutionary history, which is crucial for an in-depth understanding of lncRNAs. Therefore, the integration of large volumes of plant lncRNA data is required to deeply investigate the evolution of lncRNAs.ResultsWe present a large-scale evolutionary analysis of lncRNAs in 25 flowering plants. In total, we identified 199,796 high-confidence lncRNAs through data integration analysis, and grouped them into 5497 lncRNA orthologous families. Then, we divided the lncRNAs into groups based on the degree of sequence conservation, and quantified the various characteristics of 756 conserved Arabidopsis thaliana lncRNAs. We found that compared with non-conserved lncRNAs, conserved lncRNAs might have more exons, longer sequence length, higher expression levels, and lower tissue specificities. Functional annotation based on the A. thaliana coding-lncRNA gene co-expression network suggested potential functions of conserved lncRNAs including autophagy, locomotion, and cell cycle. Enrichment analysis revealed that the functions of conserved lncRNAs were closely related to the growth and development of the tissues in which they were specifically expressed.ConclusionsComprehensive integration of large-scale lncRNA data and construction of a phylogenetic tree with orthologous lncRNA families from 25 flowering plants was used to provide an oversight of the evolutionary history of plant lncRNAs including origin, conservation, and orthologous relationships. Further analysis revealed a differential characteristic profile for conserved lncRNAs in A. thaliana when compared with non-conserved lncRNAs. We also examined tissue specific expression and the potential functional roles of conserved lncRNAs. The results presented here will further our understanding of plant lncRNA evolution, and provide the basis for further in-depth studies of their functions.

The purpose of the study was to provide the pipeline for processing of publicly available unprocessed data on gene expression via integration and differential gene expression analysis. Data collection from open gene expression databases, normalization and integration into a single expression matrix in accordance with metadata and determination of differentially expressed genes were fulfilled. To demonstrate all stages of data processing and integrative analysis, there were used the data from gene expression in the human placenta from the first and second trimesters of normal pregnancy. The source code for the integrative analysis was written in the R programming language and publicly available as a repository on GitHub. Four clusters of functionally enriched differentially expressed genes were identified for the human placenta in the interval between the first and second trimester of pregnancy. Immune processes, developmental processes, vasculogenesis and angiogenesis, signaling and the processes associated with zinc ions varied in the considered interval between the first and second trimester of placental development. The proposed sequence of actions for integrative analysis could be applied to any data obtained by microarray technology.

Artificial intelligence (AI) is reshaping healthcare and personalized medicine, particularly in the pharmaceutical industry. This review provides a comprehensive examination of current AI applications across various stages of the drug development pipeline, including drug discovery, clinical trial design, patient stratification, diagnosis, and treatment personalization. By employing advanced computational approaches such as machine learning, deep learning, and natural language processing, AI enables the integration and analysis of large and complex biological and clinical datasets, including genomic, proteomic, and electronic health record data. These capabilities facilitate the identification of novel therapeutic targets and support the development of individualized treatment strategies. The review also addresses critical considerations such as data quality, algorithmic transparency, ethical challenges, and regulatory frameworks that influence the safe and effective deployment of AI technologies. Furthermore, it highlights the growing need for robust data integration, interpretation strategies, and interdisciplinary collaboration to fully realize AI’s potential in advancing personalized medicine. Future perspectives emphasize AI’s role as a transformative tool for innovation in patient-centered pharmaceutical care.

Digital transformation and the adoption of ICT technologies in the factory of the future are growing faster and faster. In particular, data exploration methods and techniques are enabling the development of data-intensive Remote Monitoring Services for anomaly detection and predictive maintenance purposes. Remote Monitoring Services involve different actors across organizations. The Original Equipment Manufacturer explores high volume of data collected by sensors on the monitored machines to provide anomaly detection and predictive maintenance services. Insurance agencies may provide support to sustain maintenance costs. Spare parts suppliers can schedule the delivery of mechanical parts required for maintenance interventions. In this scenario, trust among participants becomes a critical issue. On the one hand, providers of anomaly detection and predictive maintenance services as well as insurance agencies must trust the way machines have been used by collecting and analysing sensors data. On the other hand, owners of monitored machines must trust the use of collected data to implement services, based on which maintenance costs are calculated. The goal of this paper is to leverage blockchain and smart contracts to ensure the required level of trust when implementing data exploration for Remote Monitoring Services. Events occurring on the monitored machines are stored as transactions in a blockchain-based system, to ensure non repudiation. Moreover, trust-demanding services are implemented as smart contracts, to guarantee the required level of trustworthiness among participants. The approach is integrated with a tool for data exploration in the digital factory, and has been validated taking into account performances and cost requirements.

Never before in history data is generated and collected at such high volumes as it is today. As the volumes of data available to business people, scientists, and the public increase, their effective use becomes more challenging. Keeping up to date with the flood of data, using standard tools for data analysis and exploration, is fraught with difficulty. The field of visual analytics seeks to provide people with better and more effective ways to explore and understand large datasets, while also enabling them to act upon their findings immediately. Visual analytics integrates the analytic capabilities of the computer and the perceptual and intellectual abilities of the human analyst, allowing novel discoveries and empowering individuals to take control of the analytical process. Visual analytics enables unexpected insights, which may lead to beneficial and profitable innovation. The talk presents the challenges of visual analytics and exemplifies them with several application examples, which illustrate the exiting potential of current visual analysis techniques but also their limitations.

This demonstration will be presented at the 2004 National Conference on Digital Government Research. The third year results of the project Digitalization of Coastal Management and Decision Making Supported by Multi-Dimensional Geospatial Information and Analysis will be presented. Mobile wireless communications, internet web services, and web GIS are integrated into a web-based decision-making system for coastal management. Employing three-dimensional visualization technology, athe system also provides a visualization tool for multisource spatial-temporal data integration and uncertainty analysis. Also demonstrated is an interactive QuickBird image processing subsystem used for high resolution DEM and three-dimensional shoreline extraction of Tampa Bay.The goal of this project is to develop technologies to enhance the operational capabilities of federal, state, and local agencies responsible for coastal management and decision making. The pilot test site is along the Lake Erie coastline from Port Clinton to East Cleveland, Ohio. Research strategies are currently being applied to Painesville, OH and Tampa Bay, Florida. The demonstration will include the following sections.

During the past two decades, computational analysis has become paramount for biological research. Advancements in high-throughput methods and computational tools resulted in the generation of large amounts of data from different omics fields (multi-omics), such as genomics, epigenomics, transcriptomics, and metabolomics. This plethora of large scale and diverse omics data is being driven by the understanding that a single-omic type does not provide adequate information and integrative analysis of multi-omics data is optimal to gain sufficiently meaningful insights into the actual biological mechanisms. Although various open-source tools have been developed for this purpose, multi-omics data integration and analysis are still beset by a number of problems, including software compatibility, complex parameter selection and creation of functional pipelines with multiple steps of analyses. In this work we present GenOptics, a novel visual analytics platform that aims to facilitate the integration and subsequent analysis of diverse multi-omics datasets as well as meta-data (e.g., clinical data), through a fully interactive environment. The platform comprises of two separate parts. The first incorporates asynchronous analyses of Next-Generation Sequencing raw data, including RNA-, Whole exome-, and ChIP-Seq, using workflows implemented with the Common Workflow Language (doi:10.6084/m9.figshare.3115156.v2) and Docker containers to automate software installation and confer cross-platform portability. The second part constitutes the analytical platform itself, designed to facilitate the execution of robust bioinformatics analyses by life scientists with minimal or no knowledge of programming. GenOptics constitutes an open source (https://genoptics.github.io/), computational biology platform for novel pattern and biomarker detection.

In this paper we give an account of a new change of perspective in non-linear modelling and prediction as applied to smooth systems. The core element of these developments is the Gamma test a non-linear modelling and analysis tool which allows us to examine the nature of a hypothetical input/output relationship in a numerical data-set. In essence, the Gamma test allows us to efficiently calculate that part of the variance of the output which cannot be accounted for by the existence of any smooth model based on the inputs, even though this model be unknown. A key aspect of this tool is its speed: the Gamma test has time complexity O( $M \log M$ ), where M is the number of data-points. For data-sets consisting of a few thousand points and a reasonable number of attributes, a single run of the Gamma test typically takes a few seconds. Around this essentially simple procedure a new set of analytical tools has evolved which allow us to model smooth non-linear systems directly from the data with a precision and confidence that hitherto was inaccessible. In this paper we briefly describe the Gamma test, its benefits in model identification and model building, and then in more detail explain and motivate the procedures which facilitate a Gamma analysis. We briefly report on a case study applying these ideas to the practical problem of predicting level and flow rates in the Thames valley river basin. Finally we speculate on the future development and enhancement of these techniques into areas such as datamining and the production of complex non-linear models directly from data via graphical representations of process charts and automated Gamma analysis of each input-output node.

The integration of neuroimaging and transcriptomics data has revolutionized our understanding of complex brain phenomena and holds promise for linking molecular level genetic markers to brain dynamics and function. However, the involved data differ strongly across biological scales and acquisition modalities, presenting significant preprocessing and analytical challenges. In this context, multi-modal brain data exploration software offers a low-threshold, holistic, and non-biased approach to hypothesis generation that is complementary to literature search. This review assesses current data exploration tools that combine transcriptomic and neuroimaging data, evaluating them based on species coverage, data modalities, data integration approaches, visualization capabilities, and user data integration. We highlight the potential of these tools by discussing their applicability for example research questions and identify yet unaddressed workflows and promising approaches to support imaging transcriptomics analyses. This comprehensive survey aims to inform researchers in their selection of suitable software for their specific research needs and to guide the development of more effective multi-modal brain data exploration tools.

Kvik is an open-source system that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Existing data exploration tools do not provide all the required functionality for such multi-study data exploration. We have therefore developed the Kvik framework which makes it easy to implement specialized data exploration tools for specific projects. Applications in Kvik follow the three-tier architecture commonly used in web applications, with REST interfaces between the tiers. This makes it easy to adapt the applications to new statistical analyses, metadata, and visualizations. Kvik uses R to perform on-demand data analyses when researchers explore the data. In this note, we describe how we used Kvik to develop the Kvik Pathways application to explore gene expression data from healthy women with high and low plasma ratios of essential fatty acids using biological pathway visualizations. Researchers interact with Kvik Pathways through a web application that uses the JavaScript libraries Cytoscape.js and D3. We use Docker containers to make deployment of Kvik Pathways simple.

We present novel optimization-based classification models that are general purpose and suitable for developing predictive rules for large heterogeneous biological and medical data sets. Our predictive model simultaneously incorporates (1) the ability to classify any number of distinct groups; (2) the ability to incorporate heterogeneous types of attributes as input; (3) a high-dimensional data transformation that eliminates noise and errors in biological data; (4) the ability to incorporate constraints to limit the rate of misclassification, and a reserved-judgment region that provides a safeguard against over-training (which tends to lead to high misclassification rates from the resulting predictive rule); and (5) successive multi-stage classification capability to handle data points placed in the reserved judgment region. Application of the predictive model to a broad class of biological and medical problems is described. Applications include: the differential diagnosis of the type of erythemato-squamous diseases; genomic analysis and prediction of aberrant CpG island meythlation in human cancer; discriminant analysis of motility and morphology data in human lung carcinoma; prediction of ultrasonic cell disruption for drug delivery; identification of tumor shape and volume in treatment of sarcoma; multistage discriminant analysis of biomarkers for prediction of early atherosclerosis; fingerprinting of native and angiogenic microvascular networks for early diagnosis of diabetes, aging, macular degeneracy and tumor metastasis, and prediction of protein localization sites. In all these applications, the predictive model yields correct classification rates ranging from 80% to 100%. This provides motivation for pursuing its use as a medical diagnostic, monitoring and decision-making tool.

Parallel processing on large redundant biological data sets: Protein structures classification with CEPAR

Network inference utilizes experimental high-throughput data for the reconstruction of molecular interaction networks where new relationships between the network entities can be predicted. Despite the increasing amount of experimental data, the parameters of each modeling technique cannot be optimized based on the experimental data alone, but needs to be qualitatively assessed if the components of the resulting network describe the experimental setting. Candidate list prioritization and validation builds upon data integration and data visualization. The application of tools supporting this procedure is limited to the exploration of smaller information networks because the display and interpretation of large amounts of information is challenging regarding the computational effort and the users' experience. The Ondex software framework was extended with customizable context-sensitive menus which allow additional integration and data analysis options for a selected set of candidates during interactive data exploration. We provide new functionalities for on-the-fly data integration using InterProScan, PubMed Central literature search, and sequence-based homology search. We applied the Ondex system to the integration of publicly available data for Aspergillus nidulans and analyzed transcriptome data. We demonstrate the advantages of our approach by proposing new hypotheses for the functional annotation of specific genes of differentially expressed fungal gene clusters. Our extension of the Ondex framework makes it possible to overcome the separation between data integration and interactive analysis. More specifically, computationally demanding calculations can be performed on selected sub-networks without losing any information from the whole network. Furthermore, our extensions allow for direct access to online biological databases which helps to keep the integrated information up-to-date.