Biology subjects

Mathlouthi, N. E. H.

Publications and source records attributed to Mathlouthi, N. E. H..

3 recordsLinked to original sources

bioRxiv2026

Quantum Encoding Strategies for Drug Response Prediction: An Exhaustive Benchmark on a 20-Qubit Superconducting QPU

We present the first systematic, hardware-executed benchmark of twelve distinct quantum data-encoding strategies for drug-response prediction on a real superconducting quantum processing unit (QPU). All experiments were conducted on the IQM Garnet 20-qubit QPU via the IQM Resonance cloud platform, using the Qrisp quantum-software framework (v 0.8.2). Each encoding was evaluated on n = 50 stratified samples drawn from the Genomics of Drug Sensitivity in Cancer dataset (GDSC2, 242 036 drug-cell-line pairs), targeting the natural-log IC50 response variable. Variational weights were optimised offline with the gradient-free COBYLA algorithm before hardware submission. Every circuit was executed with 1024 shots; the regression signal is the zero-qubit Pauli expectation value [<]Z0[>]. Results show that the QAOA-inspired encoding achieves the best RMSE of 3.314 and is statistically superior (p < 0.05, Wilcoxon signed-rank test) to six of the remaining eleven encodings. Hardware-efficient entanglement structures--specifically alternating cost and mixer layers--provide a systematic advantage over purely rotational or diagonal encodings under realistic noise conditions. This work constitutes a reproducible baseline for noise-aware quantum machine learning on pharmaceutical data; all code, data, and raw QPU outputs are publicly released.

bioinformatics↗

bioRxiv2026

First Survey of Publicly Available Metagenomic Sequencing Data Across 24 Middle Eastern and North African Countries: The MENA Microbiome Database

Microbiome research has expanded globally, yet the Middle East and North Africa (MENA) region remains severely under-represented in international sequencing repositories. Here we present the MENA Microbiome Database, the first systematically harmonized catalog of publicly available metagenomic sequencing data from 24 MENA countries, consolidating 60,126 runs across 51,365 biological samples and 2,373 BioProjects deposited between 2008 and 2026. Records were retrieved from ENA, NCBI SRA, and PubMed, enriched with BioSample and study-level metadata, and classified into microbiome subtypes using a 73-rule keyword-based harmonization framework. Amplicon sequencing accounted for 80.6% of runs, with Illumina platforms dominating at 92.7%. Geographic coverage is highly skewed: Saudi Arabia and Turkey together contribute over half of all records, while five countries (Libya, Syria, Palestine, Yemen, and South Sudan) remain critically under-sampled. Metadata completeness averaged 73.97% under a MIxS-MIMS proxy framework, with geographic coordinates available for fewer than 15% of runs. Ecological analyses revealed that country-level factors significantly structure environmental, animal-associated, and plant-associated microbiomes, but not human-associated microbiomes. Spatial autocorrelation confirmed non-random clustering of sampling effort around Red Sea coastal and eastern Mediterranean hotspots. This open, reproducible resource, comprising harmonized data files, analysis code, and an interactive browsing platform, establishes a foundational infrastructure for regional microbiome science and equitable global comparative studies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/722303v1_ufig1.gif" ALT="Figure 1000"> View larger version (69K): org.highwire.dtl.DTLVardef@16ebcd3org.highwire.dtl.DTLVardef@12ed2d1org.highwire.dtl.DTLVardef@112b5b1org.highwire.dtl.DTLVardef@156b8a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

The microbiota of fresh unfermented date palm sap: a culturomics and metagenomics investigation.

Palm sap is an artisanal fermented beverage, the consumption of which has been historically attested for millennia. Despite this, the underlying fermentative microbiota is poorly known. Here, three date palm sap samples collected and bought in Tunisia were investigated for bacteria, methanogenic archaea, and fungi using culturomics and molecular detection techniques, including metagenomics. Metagenomics yielded 250 bacteria, two fungi, and no archaea. Culturomics yielded 36 bacteria, eight fungi, and no archaea. Taken together, these approaches detected 250 bacteria and nine fungi, including 28 bacteria and eight fungi which had been previously unreported in date palm sap, in addition to three potentially new bacteria. Specifically, the bacteria Zymomonas mobilis and Leuconostoc mesenteroides and the fungus Saccharomyces cerevisiae were the most abundant, fermentative species found in the three samples, by culturomics and metagenomics. While determining the source of these microbes of interest was beyond the scope of the study, the data reported here may pave the way for a better understanding of the organic and organoleptic qualities of date palm sap in productive countries. IMPORTANCEThis study provides valuable insights into the microbial composition of date palm sap, a traditional fermented beverage with deep historical roots. Despite its widespread consumption and cultural importance, the microbes driving its fermentation remain largely unexplored. Using advanced methods like metagenomics and culturomics, we uncovered a diverse array of bacteria and fungi, including species crucial for fermentation, such as Zymomonas mobilis, Leuconostoc mesenteroides, and Saccharomyces cerevisiae. Moreover, the discovery of previously unreported microbes highlights the potential for further research into their roles in sap fermentation and quality. Improving our understanding of the microbial communities involved in the fermentation of date palm sap underscores its importance to the field of applied and environmental microbiology.

microbiology↗