Biology subjects

Abid, A.

Publications and source records attributed to Abid, A..

6 recordsLinked to original sources

bioRxiv2026

Metagenomic Evidence for Horizontal Gene Transfer and Functional Convergence in the Oral Microbiome of Cohabiting Dogs and Owners

The intimate cohabitation between humans and their pets facilitates bidirectional microbial exchange, yet the extent and functional consequences of this transfer within the oral niche remain underexplored. Here, we employed metagenomic sequencing to characterize the oral microbiome of dogs and their owners across distinct geographic regions in China, integrating taxonomic, gene-centric, and functional analyses using public databases (BacMet, CARD, eggNOG, KEGG) to assess microbe-host associations. We found that dog-owner pairs exhibited significantly higher gene-level similarity compared to unrelated individuals, indicating a strong cohabitation-driven microbial linkage. While no major taxonomic shifts were observed in the human oral microbiome associated with pet ownership, we identified a marked enrichment of antibiotic resistance genes (ARGs)--particularly those conferring resistance to peptides, fluoroquinolones, antiseptics, diaminopyrimidines, cephalosporins, and carbapenems--in cohabiting pairs. This enrichment, together with the identification of exclusively shared ARGs (e.g., mdtF, macB, RanA), suggests the potential for horizontal gene transfer (HGT) between pet- and human-associated microbiomes. Functional profiling further revealed greater similarity in microbial metabolic pathways between cohabiting pairs than between unrelated individuals, reinforcing the likelihood of HGT as a mechanism underlying functional convergence. Collectively, these findings reveal that cohabitation with dogs reshapes the human oral microbiome at the genetic and functional levels, with potential implications for antimicrobial resistance transmission. This study provides a foundational framework for assessing the health risks associated with pet-human microbial exchange in shared living environments.

microbiology↗

bioRxiv2025

Genomic characterization of heat related QTLs of wheat using SNPs

Withdrawal StatementThe authors have withdrawn their manuscript because the manuscript requires substantial revision. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

plant biology↗

bioRxiv2024

The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity

The NHGRI-EBI GWAS Catalog serves as a vital resource for the genetic research community, providing access to the most comprehensive database of human GWAS results. Currently, it contains close to 7,000 publications for more than 15,000 traits, from which more than 625,000 lead associations have been curated. Additionally, 85,000 full genome-wide summary statistics datasets - containing association data for all variants in the analysis - are available for downstream analyses such as meta-analysis, fine-mapping, Mendelian randomisation or development of polygenic risk scores. As a centralised repository for GWAS results, the GWAS Catalog sets and implements standards for data submission and harmonisation, and encourages the use of consistent descriptors for traits, samples and methodologies. We share processes and vocabulary with the PGS Catalog, improving interoperability for a growing user group. Here, we describe the latest changes in data content, improvements in our user interface, and the implementation of the GWAS-SSF standard format for summary statistics. We address the challenges of handling the rapid increase in large-scale molecular quantitative trait GWAS and the need for sensitivity in the use of population and cohort descriptors while maintaining data interoperability and reusability.

genetics↗

bioRxiv2024

Sex differences in change-of-mind neuroeconomic decision-making is modulated by LINC00473 in medial prefrontal cortex

Changing ones mind involves re-appraisals between past-costs versus future-value and may be altered in psychopathology. Long intergenic non-coding RNA LINC00473 in medial prefrontal cortex (mPFC) can induce stress-resilience in a sex-dependent manner, but its role in cognition is unknown. We characterized decision-making behavior in male and female mice in the neuroeconomic paradigm Restaurant Row following virus-mediated expression of LINC00473 in mPFC. Mice foraged for food among varying temporal-costs and subjective-value while on a limited time-budget. Without affecting primary deliberative decisions, LINC00473 selectively influenced re-evaluative choices in a sex-dependent manner. This included changing how mice (i) cached value with the passage of time and (ii) weighed prior mistakes, which underlie the computational bases of sensitivity to sunk costs and regret. These findings suggest a common value function is shared between these neuroeconomic processes and reveal a bridge between molecular drivers of stress-resilience and psychological mechanisms underlying sex-specific proclivities in negative rumination.

neuroscience↗

bioRxiv2021

A curated collection of human vaccination response signatures

Recent advances in high-throughput experiments and systems biology approaches have resulted in hundreds of publications identifying "immune signatures". Unfortunately, these are often described within text, figures, or tables in a format not amenable to computational processing, thus severely hampering our ability to fully exploit this information. Here we present a data model to represent immune signatures, along with the Human Immunology Project Consortium (HIPC) Dashboard (www.hipc-dashboard.org), a web-enabled application to facilitate signature access and querying. The data model captures the biological response components (e.g., genes, proteins, cell types or metabolites) and metadata describing the context under which the signature was identified using standardized terms from established resources (e.g., HGNC, Protein Ontology, Cell Ontology). We have manually curated a collection of >600 immune signatures from >60 published studies profiling human vaccination responses for the current release. The system will aid in building a broader understanding of the human immune response to stimuli by enabling researchers to easily access and interrogate published immune signatures.

bioinformatics↗

bioRxiv2019

Deep Learning Interpretation of Echocardiograms

Echocardiography uses ultrasound technology to capture high temporal and spatial resolution images of the heart and surrounding structures and is the most common imaging modality in cardiovascular medicine. Using convolutional neural networks on a large new dataset, we show that deep learning applied to echocardiography can identify local cardiac structures, estimate cardiac function, and predict systemic phenotypes that modify cardiovascular risk but not readily identifiable to human interpretation. Our deep learning model, EchoNet, accurately identified the presence of pacemaker leads (AUC = 0.89), enlarged left atrium (AUC = 0.85), normal left ventricular wall thickness (AUC = 0.75), left ventricular end systolic and diastolic volumes(R2 = 0.73 and R2 = 0.68), and ejection fraction (R2 = 0.48) as well as predicted systemic phenotypes of age (R2 = 0.46), sex (AUC = 0.88), weight (R2 = 0.56), and height (R2 = 0.33). Interpretation analysis validates that EchoNet shows appropriate attention to key cardiac structures when performing human-explainable tasks and highlight hypothesis-generating regions of interest when predicting systemic phenotypes difficult for human interpretation. Machine learning on echocardiography images can streamline repetitive tasks in the clinical workflow, standardize interpretation in areas with insufficient qualified cardiologists, and more consistently produce echocardiographic measurements.

bioengineering↗