Improved prediction of missing protein interactome links via anomaly detection

NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation

Transcription factor (TF) coordination plays a key role in target gene (TG) regulation via protein-protein interactions (PPIs) and DNA co-binding to regulatory elements. Single-cell technologies facilitate gene expression measurement for individual cells and cell-type identification, yet the connection between TF coordination and TG regulation of various cell types remains unclear. To address this, we have developed a novel computational approach, Network Regression Embeddings (NetREm), to reveal cell-type TF-TF coordination activities for TG regulation. NetREm leverages network-constrained regularization using prior knowledge of direct and/or indirect PPIs among TFs to analyze single-cell gene expression data. We test NetREm by simulation data and benchmark its performance in 4 real-world applications that have gold standard TF-TG networks available: mouse (mESCs) and simulated human (hESCs) embryonic stem (ESCs), human hematopoietic stem (HSCs), and mouse dendritic (mDCs) cells. Further, we use NetREm to prioritize valid novel TF-TF coordination links in human Peripheral Blood Mononuclear cell (PBMC) sub-types. We apply NetREm to analyze various cell types in both central (CNS) and peripheral (PNS) nerve system (NS) (e.g. neuronal, glial, Schwann cells (SCs)) as well as in Alzheimers disease (AD). Our findings uncover cell-type coordinating TFs and identify new TF-TG candidate links. We validate our top predictions using Cut&Run and knockout loss-of-function expression data in rat/mouse models and compare results with additional functional genomic data, including expression quantitative trait loci (eQTL) and Genome-Wide Association Studies (GWAS) to link genetic variants (single nucleotide polymorphisms (SNPs)) to TF coordination.

Social media analytics of the Internet of Things

The Internet of Things technology offers convenience and innovation in areas such as smart homes and smart cities. Internet of Things solutions require careful management of devices and the risk mitigation of potential vulnerabilities within cyber-physical systems. The Internet of Things concept, its implementations, and applications are frequently discussed on social media platforms. This research illuminates the public view of the Internet of Things through a content-based and network analysis of contemporary conversations occurring on the Twitter platform. Tweets can be analyzed with machine learning methods to converge the volume and variety of conversations into predictive and descriptive models. We have reviewed 684,503 tweets collected in a 2-week period. Using supervised and unsupervised machine learning methods, we have identified trends within the realm of IoT and their interconnecting relationships between the most mentioned industries. We have identified characteristics of language sentiment which can help to predict the popularity of IoT conversation topics. We found the healthcare industry as the leading use case industry for IoT implementations. This is not surprising as the current COVID-19 pandemic is driving significant social media discussions. There was an alarming dearth of conversations towards cybersecurity. Recent breaches and ransomware events denote that organizations should spend more time communicating about risks and mitigations. Only 12% of the tweets relating to the Internet of Things contained any mention of topics such as encryption, vulnerabilities, or risk, among other cybersecurity-related terms. We propose an IoT Cybersecurity Communication Scorecard to help organizations benchmark the density and sentiment of their corporate communications regarding security against their specific industry.