Abstract High school English teachers often encounter barriers to assembling diverse, thematically aligned text sets due to limited planning time and pedagogical resources. To address this need, we present T-TExTS (Teaching Text Expansion for Teacher Scaffolding), a knowledge graph (KG)-based recommendation system that suggests Literature texts based on pedagogical merit rather than surface-level metadata. We construct a domain-specific ontology using the Knowledge Acquisition and Representation Methodology (KNARM), instantiate it as a knowledge graph with separate Terminological Box (TBox) and Assertional Box (ABox) components, and evaluate four graph embedding strategies (DeepWalk, biased random walk, hybrid embedding, and Node2Vec) across three dataset configurations (98, 196, and 351 texts) and two relation-weighting schemes. The experimental results reveal that traversal-level expert weighting alone does not outperform algorithmic structural tuning: Node2Vec achieves the highest Area Under the Curve (AUC) at every dataset size (0.9642–0.9750) and the strongest ranking metrics (Hits@K, MRR, nDCG) at larger scales. Combining structural and pedagogical signals through embedding concatenation, however, preserves both interpretability and competitive ranking quality, with the hybrid model maintaining a high AUC across all scales (0.9122–0.9350) and remaining within a few percentage points of Node2Vec on every ranking metric. These findings highlight the value of ontology-driven knowledge graph embeddings for educational recommendation systems and demonstrate that T-TExTS can meaningfully ease the burden of English Literature text selection for secondary educators, supporting more informed and inclusive curricular decisions. The source code for T-TExTS is available at https://github.com/koncordantlab/TTExTS .

Understanding the complex mechanisms of drugs' therapeutic effects is essential for advancing precision medicine and optimizing treatment strategies. However, systematically distinguishing between drugs that address root causes (etiological mechanisms) and those that alleviate symptoms (palliative mechanisms) using modern Artificial Intelligence (AI)-based strategies remains underexplored. We present a novel computational framework for classifying drug Mechanisms of Action (MoA) as etiological or palliative, comparing three approaches: (i) Fine-tuning Science Bidirectional Encoder Representations from Transformers (SciBERT) with drug descriptions; (ii) Training various Graph Neural Networks (GNNs) on a constructed heterogeneous network of drugs, genes, and diseases; and (iii) Developing DruGNNosis-MoA, which integrates GNN with our fine-tuned SciBERT embeddings as node features. DruGNNosis-MoA excelled (F1-score 0.94) at identifying drug MoA. DruGNNosis-MoA characterizes drug mechanisms for subsequent pharmacological studies, thereby advancing precision medicine and therapeutic development.

BACKGROUND: PubMed contains millions of abstracts that co-mention terms that describe drugs with other biomedical terms such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating them with other drug-drug similarity resources such as the Library of Integrated Network-based Cellular Signatures (LINCS) L1000 signatures to develop novel hypotheses. RESULTS: DrugShot is a web-based server application and an Appyter that enables users to enter any biomedical search term into a simple input form to receive ranked lists of drugs and other small molecules based on their relevance to the search term. To produce ranked lists of small molecules, DrugShot cross-references returned PubMed identifiers (PMIDs) with DrugRIF or AutoRIF, which are curated resources of drug-PMID associations, to produce an associated small molecule list where each small molecule is ranked according to total co-mentions with the search term from shared PubMed IDs. Additionally, using two types of drug-drug similarity matrices, lists of small molecules are predicted to be associated with the search term. Such predictions are based on literature co-mentions and signature similarity from LINCS L1000 drug-induced gene expression profiles. CONCLUSIONS: DrugShot prioritizes drugs and small molecules associated with biomedical search terms. In addition to listing known associations, DrugShot predicts additional drugs and small molecules related to any search term. Hence, DrugShot can be used to prioritize drugs and preclinical compounds for drug repurposing and suggest indications and adverse events for preclinical compounds. DrugShot is freely and openly available at: https://maayanlab.cloud/drugshot and https://appyters.maayanlab.cloud/#/DrugShot .

MOTIVATION: Micro-blogging with Twitter to communicate new results, discuss ideas and share techniques is becoming central. While most Twitter users are real people, the Twitter API provides the opportunity to develop Twitter bots and to analyze global trends in tweets. RESULTS: EnrichrBot is a bot that tracks and tweets information about human genes implementing six principal functions: (i) tweeting information about under-studied genes including non-coding lncRNAs, (ii) replying to requests for information about genes, (iii) responding to GWASbot, another bot that tweets Manhattan plots from genome-wide association study analysis of the UK Biobank, (iv) tweeting randomly selected gene sets from the Enrichr database for analysis with Enrichr, (v) responding to mentions of human genes in tweets with additional information about these genes and (vi) tweeting a weekly report about the most trending genes on Twitter. AVAILABILITY AND IMPLEMENTATION: https://twitter.com/botenrichr; source code: https://github.com/MaayanLab/EnrichrBot. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Mechanistic molecular studies in biomedical research often discover important genes that are aberrantly over- or under-expressed in disease. However, manipulating these genes in an attempt to improve the disease state is challenging. Herein, we reveal Drug Gene Budger (DGB), a web-based and mobile application developed to assist investigators in order to prioritize small molecules that are predicted to maximally influence the expression of their target gene of interest. With DGB, users can enter a gene symbol along with the wish to up-regulate or down-regulate its expression. The output of the application is a ranked list of small molecules that have been experimentally determined to produce the desired expression effect. The table includes log-transformed fold change, P-value and q-value for each small molecule, reporting the significance of differential expression as determined by the limma method. Relevant links are provided to further explore knowledge about the target gene, the small molecule and the source of evidence from which the relationship between the small molecule and the target gene was derived. The experimental data contained within DGB is compiled from signatures extracted from the LINCS L1000 dataset, the original Connectivity Map (CMap) dataset and the Gene Expression Omnibus (GEO). DGB also presents a specificity measure for a drug-gene connection based on the number of genes a drug modulates. DGB provides a useful preliminary technique for identifying small molecules that can target the expression of a single gene in human cells and tissues. AVAILABILITY AND IMPLEMENTATION: The application is freely available on the web at http://DGB.cloud and as a mobile phone application on iTunes https://itunes.apple.com/us/app/drug-gene-budger/id1243580241? mt=8 and Google Play https://play.google.com/store/apps/details? id=com.drgenebudger. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: Genome-wide gene expression profiling of mammalian cells is becoming a staple of many published biomedical and biological research studies. Such data is deposited into data repositories such as the Gene Expression Omnibus (GEO) for potential reuse. However, these repositories currently do not provide simple interfaces to systematically analyze collections of related studies. RESULTS: Here we present GENE Expression and Enrichment Vector Analyzer (GEN3VA), a web-based system that enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO. Each tagged collection of signatures is presented in a report that consists of heatmaps of the differentially expressed genes; principal component analysis of all signatures; enrichment analysis with several gene set libraries across all signatures, which we term enrichment vector analysis; and global mapping of small molecules that are predicted to reverse or mimic each signature in the aggregate. We demonstrate how GEN3VA can be used to identify common molecular mechanisms of aging by analyzing tagged signatures from 244 studies that compared young vs. old tissues in mammalian systems. In a second case study, we collected 86 signatures from treatment of human cells with dexamethasone, a glucocorticoid receptor (GR) agonist. Our analysis confirms consensus GR target genes and predicts potential drug mimickers. CONCLUSIONS: GEN3VA can be used to identify, aggregate, and analyze themed collections of gene expression signatures from diverse but related studies. Such integrative analyses can be used to address concerns about data reproducibility, confirm results across labs, and discover new collective knowledge by data reuse. GEN3VA is an open-source web-based system that is freely available at: http://amp.pharm.mssm.edu/gen3va .

High-level spinal cord injury (SCI) in humans causes paralysis below the neck. Functional electrical stimulation (FES) technology applies electrical current to nerves and muscles to restore movement, and controllers for upper extremity FES neuroprostheses calculate stimulation patterns to produce desired arm movement. However, currently available FES controllers have yet to restore natural movements. Reinforcement learning (RL) is a reward-driven control technique; it can employ user-generated rewards, and human preferences can be used in training. To test this concept with FES, we conducted simulation experiments using computer-generated “pseudo-human” rewards. Rewards with varying properties were used with an actor-critic RL controller for a planar two-degree-of-freedom biomechanical human arm model performing reaching movements. Results demonstrate that sparse, delayed pseudo-human rewards permit stable and effective RL controller learning. The frequency of reward is proportional to learning success, and human-scale sparse rewards permit greater learning than exclusively automated rewards. Diversity of training task sets did not affect learning. Long-term stability of trained controllers was observed. Using human-generated rewards to train RL controllers for upper-extremity FES systems may be useful. Our findings represent progress toward achieving human-machine teaming in control of upper-extremity FES systems for more natural arm movements based on human user preferences and RL algorithm learning capabilities.