Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism

10.1186/s12864-015-1256-3BMC Genomics16114

Real Time Sentiment Change Detection of Twitter Data Streams

In the past few years, there has been a huge growth in Twitter sentiment analysis having already provided a fair amount of research on sentiment detection of public opinion among Twitter users. Given the fact that Twitter messages are generated constantly with dizzying rates, a huge volume of streaming data is created, thus there is an imperative need for accurate methods for knowledge discovery and mining of this information. Although there exists a plethora of twitter sentiment analysis methods in the recent literature, the researchers have shifted to real-time sentiment identification on twitter streaming data, as expected. A major challenge is to deal with the Big Data challenges arising in Twitter streaming applications concerning both Volume and Velocity. Under this perspective, in this paper, a methodological approach based on open source tools is provided for real-time detection of changes in sentiment that is ultra efficient with respect to both memory consumption and computational cost. This is achieved by iteratively collecting tweets in real time and discarding them immediately after their process. For this purpose, we employ the Lexicon approach for sentiment characterizations, while change detection is achieved through appropriate control charts that do not require historical information. We believe that the proposed methodology provides the trigger for a potential large-scale monitoring of threads in an attempt to discover fake news spread or propaganda efforts in their early stages. Our experimental real-time analysis based on a recent hashtag provides evidence that the proposed approach can detect meaningful sentiment changes across a hashtags lifetime

An Ensemble Feature Selection Approach for Analysis and Modeling of Transcriptome Data in Alzheimer’s Disease

Data-driven analysis and characterization of molecular phenotypes comprises an efficient way to decipher complex disease mechanisms. Using emerging next generation sequencing technologies, important disease-relevant outcomes are extracted, offering the potential for precision diagnosis and therapeutics in progressive disorders. Single-cell RNA sequencing (scRNA-seq) allows the inherent heterogeneity between individual cellular environments to be exploited and provides one of the most promising platforms for quantifying cell-to-cell gene expression variability. However, the high-dimensional nature of scRNA-seq data poses a significant challenge for downstream analysis, particularly in identifying genes that are dominant across cell populations. Feature selection is a crucial step in scRNA-seq data analysis, reducing the dimensionality of data and facilitating the identification of genes most relevant to the biological question. Herein, we present a need for an ensemble feature selection methodology for scRNA-seq data, specifically in the context of Alzheimer’s disease (AD). We combined various feature selection strategies to obtain the most dominant differentially expressed genes (DEGs) in an AD scRNA-seq dataset, providing a promising approach to identify potential transcriptome biomarkers through scRNA-seq data analysis, which can be applied to other diseases. We anticipate that feature selection techniques, such as our ensemble methodology, will dominate analysis options for transcriptome data, especially as datasets increase in volume and complexity, leading to more accurate classification and the generation of differentially significant features

Exploring Promising Biomarkers for Alzheimer’s Disease through the Computational Analysis of Peripheral Blood Single-Cell RNA Sequencing Data

Alzheimer’s disease (AD) represents one of the most important healthcare challenges of the current century, characterized as an expanding, “silent pandemic”. Recent studies suggest that the peripheral immune system may participate in AD development; however, the molecular components of these cells in AD remain poorly understood. Although single-cell RNA sequencing (scRNA-seq) offers a sufficient exploration of various biological processes at the cellular level, the number of existing works is limited, and no comprehensive machine learning (ML) analysis has yet been conducted to identify effective biomarkers in AD. Herein, we introduced a computational workflow using both deep learning and ML processes examining scRNA-seq data obtained from the peripheral blood of both Alzheimer’s disease patients with an amyloid-positive status and healthy controls with an amyloid-negative status, totaling 36,849 cells. The output of our pipeline contained transcripts ranked by their level of significance, which could serve as reliable genetic signatures of AD pathophysiology. The comprehensive functional analysis of the most dominant genes in terms of biological relevance to AD demonstrates that the proposed methodology has great potential for discovering blood-based fingerprints of the disease. Furthermore, the present approach paves the way for the application of ML techniques to scRNA-seq data from complex disorders, providing new challenges to identify key biological processes from a molecular perspective

Detecting Perturbed Subpathways towards Mouse Lung Regeneration Following H1N1 Influenza Infection

It has already been established by the systems-level approaches that the future of predictive disease biomarkers will not be sketched by plain lists of genes or proteins or other biological entities but rather integrated entities that consider all underlying component relationships. Towards this orientation, early pathway-based approaches coupled expression data with whole pathway interaction topologies but it was the recent approaches that zoomed into subpathways (local areas of the entire biological pathway) that provided more targeted and context-specific candidate disease biomarkers. Here, we explore the application potential of PerSubs, a graph-based algorithm which identifies differentially activated disease-specific subpathways. PerSubs is applicable both for microarray and RNA-Seq data and utilizes the Kyoto Encyclopedia of Genes and Genomes (KEGG) database as reference for biological pathways. PerSubs operates in two stages: first, identifies differentially expressed genes (or uses any list of disease-related genes) and in second stage, treating each gene of the list as start point, it scans the pathway topology around to build meaningful subpathway topologies. Here, we apply PerSubs to investigate which pathways are perturbed towards mouse lung regeneration following H1N1 influenza infection

OLYMPUS: An automated hybrid clustering method in time series gene expression. Case study: Host response after Influenza A (H1N1) infection

10.1016/j.cmpb.2013.05.025Computer Methods and Programs in Biomedicine1113650-661CMPB

Tensor-Based Semantically-Aware Topic Clustering of Biomedical Documents

Biomedicine is a pillar of the collective, scientific effort of human self-discovery, as well as a major source of humanistic data codified primarily in biomedical documents. Despite their rigid structure, maintaining and updating a considerably-sized collection of such documents is a task of overwhelming complexity mandating efficient information retrieval for the purpose of the integration of clustering schemes. The latter should work natively with inherently multidimensional data and higher order interdependencies. Additionally, past experience indicates that clustering should be semantically enhanced. Tensor algebra is the key to extending the current term-document model to more dimensions. In this article, an alternative keyword-term-document strategy, based on scientometric observations that keywords typically possess more expressive power than ordinary text terms, whose algorithmic cornerstones are third order tensors and MeSH ontological functions, is proposed. This strategy has been compared against a baseline using two different biomedical datasets, the TREC (Text REtrieval Conference) genomics benchmark and a large custom set of cognitive science articles from PubMed

Assessing and Modelling of Post-Traumatic Stress Disorder Using Molecular and Functional Biomarkers

Post-traumatic stress disorder (PTSD) is a complex psychological disorder that develops following exposure to traumatic events. PTSD is influenced by catalytic factors such as dysregulated hypothalamic-pituitary-adrenal (HPA) axis, neurotransmitter imbalances, and oxidative stress. Genetic variations may act as important catalysts, impacting neurochemical signaling, synaptic plasticity, and stress response systems. Understanding the intricate gene networks and their interactions is vital for comprehending the underlying mechanisms of PTSD. Focusing on the catalytic factors of PTSD is essential because they provide valuable insights into the underlying mechanisms of the disorder. By understanding these factors and their interplay, researchers may uncover potential targets for interventions and therapies, leading to more effective and personalized treatments for individuals with PTSD. The aforementioned gene networks, composed of specific genes associated with the disorder, provide a comprehensive view of the molecular pathways and regulatory mechanisms involved in PTSD. Through this study valuable insights into the disorder’s underlying mechanisms and opening avenues for effective treatments, personalized interventions, and the development of biomarkers for early detection and monitoring are provided