M. Ali

Modeling cardiac microcirculation for the simulation of coronary flow and 3D myocardial perfusion

The paper develops a mathematical model of coronary microcirculation to simulate hyperemic blood flow and 3D myocardial perfusion in clinical cases.

Genes acquired by horizontal gene transfer share common regulatory patterns in Photorhabdus laumondii

The paper shows that plasmid-induced stress increases natural product biosynthesis in Photorhabdus laumondii by inducing gene clusters.

Mutation-specific CAR T cells as precision therapy for IGLV3-21R110 expressing high-risk chronic lymphocytic leukemia

This study develops CAR T cells targeting a specific mutation in CLL to selectively kill cancer cells while sparing healthy B cells.

The tissue-resident regulatory T cell pool is shaped by transient multi-tissue migration and a conserved residency program

The paper analyzes tissue-resident regulatory T cells (Tregs) in non-lymphoid organs, showing they share phenotypes, transient residency, and TCR sequences, with tissue-agnostic re-entry capabilities.

Targeted protein editing with an antibody-based system

This paper introduces an antibody-based system for post-translational modification of endogenous proteins in complex environments, demonstrating its use on green fluorescent protein and beta-2 microglobulin.

Dysregulated Platelet Function in Patients with Post-Acute Sequelae of COVID-19

This study examines platelet function and thrombotic risk in PASC patients, finding dysregulated platelet responses and reduced thrombosis under shear conditions.

Tomato CYP94C1 terminates jasmonate signaling during fruit ripening by inactivating bioactive jasmonoyl-L-isoleucine

This study identifies CYP94C1 as a key enzyme in tomato that terminates jasmonate signaling during ripening by converting bioactive JA-Ile to an inactive form, thereby reducing susceptibility to necrotrophic pathogens.

AbNatiV: VQ-VAE-based assessment of antibody and nanobody nativeness for hit selection, humanisation, and engineering

AbNatiV assesses antibody and nanobody nativeness using a VQ-VAE model, enabling hit selection, humanisation, and engineering with improved performance over conventional methods.

Asparagine availability controls B cell homeostasis

The paper shows asparagine metabolism is critical for B cell function and germinal centre homeostasis, with Asn deprivation impairing survival, proliferation, and immune responses.

Perception and Readiness Towards Inter-Professional Education Among Different Health Care Disciplines at Khyber Medical University Peshawar

This study assesses perception and readiness towards interprofessional education among healthcare students at Khyber Medical University, finding strong positive correlations between perception and readiness.

The 3-Dimensional Genome Drives the Evolution of Asymmetric Gene Duplicates via Enhancer Capture-Divergence

This paper shows that enhancer capture-divergence (ECD) is a significant evolutionary mechanism for asymmetric, distally duplicated genes, using Drosophila HP6/Umbrea as an example.

Development and Evolution of Drosophila Chromatin Landscape in a 3D genome context

This study characterizes the developmental and evolutionary dynamics of chromatin states in Drosophila pseudoobscura, revealing how transposable elements contribute to genome organization and regulation across different stages and tissues.

Comparative multi-OMICS single-cell atlas of five COVID-19 (rAdVV and mRNA) vaccines describe unique and distinct mechanisms of action

This study compares the mechanisms of action of five COVID-19 vaccines using multi-omics single-cell data, revealing distinct immune responses and cell-type-specific effects.

Dynamic mitochondrial transcription and translation in B cells control germinal centre entry and lymphomagenesis

This study shows that mitochondrial transcription and translation in B cells are critical for germinal centre entry and lymphomagenesis, with TFAM playing a key role.

Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

The paper uses phage-based screening to identify 1,712 virus-host interactions mimicking host short linear motifs, revealing therapeutic targets for broad-spectrum antivirals.

Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation

The paper uses multi-omics and 3D-imaging to show that calvaria bone marrow has a distinct molecular profile and contributes to neuroinflammation.

High-throughput UHPLC-MS to screen metabolites in feces for gut metabolic health

This study develops a high-throughput UHPLC-MS method to screen fecal metabolites for gut metabolic health, identifying 28 metabolites with quantitative profiles in patients with alcohol-related liver disease and healthy controls.

Proteomics of spatially identified tissues in whole organs

This paper introduces DISCO-MS, a method for spatial proteomics of whole organs, and shows it provides proteomics data comparable to fresh tissues in rodent and human samples.

Sugar Beet Extract Acts as a Natural Bio-Stimulant for Physio-Biochemical analysis of Hordeum Vulgare L. under Induced Salinity Stress

This study evaluates sugar beet extract's ability to mitigate salinity stress effects on barley growth and physiological traits.

Maturation of Human Long-lived Plasma Cells Results in Resistance to Apoptosis by Transcriptional and Epigenetic Regulation

This study shows human blood ASCs undergo transcriptional and epigenetic changes in the BM microniche to become apoptotic-resistant LLPC.

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

The paper identifies coronavirus-host protein interaction motifs, revealing SARS-CoV-2 specific mechanisms and a peptide-based inhibitor that blocks infection.

Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome

The paper introduces HD2, a proteome-scale method for identifying and characterizing SLiM-mediated protein interactions with amino acid resolution, and provides tools for analyzing the results.

Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya

The study investigates typhoid dynamics in Kenya, finding high multidrug-resistant H58 S. Typhi prevalence in both cases and controls, suggesting carriers contribute to community spread.

Effect of exogenously applied alpha-tocopherol on vital agronomic, physiological and biochemical attributes of Lentil (Lens culinaris Medik.) under induced drought stress

This study shows that applying alpha-tocopherol to lentils under drought stress improves growth, physiological, and biochemical traits by reducing oxidative stress and enhancing stress tolerance.

Feeding Experimentation Device version 3 (FED3): An open-source home-cage compatible device for measuring food intake and operant behavior

The paper introduces FED3, an open-source device for measuring food intake and operant behavior in rodents, demonstrating its utility in quantifying intake, meal patterns, and operant learning across multiple institutions.

Short linear motif based interactions and dynamics of the ezrin, radixin, moesin and merlin FERM domains

The paper identifies and characterizes short linear motifs binding to FERM domains of ERM proteins and merlin, revealing allosteric regulation between ligands.

Cytoplasmic short linear motifs in ACE2 and integrin beta3 link SARS-CoV-2 host cell receptors to endocytosis and autophagy

Affinity measurements confirmed binding of short linear motifs in the cytoplasmic tails of ACE2 and integrin β3, linking these receptors to endocytosis and autophagy.

Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

This study compares gene expression dynamics during floral transition in Arabidopsis and Brassica rapa, revealing differences in regulatory networks and synchronization of gene expression.

A comparative study of stress responses elicited by misfolded proteins targeted by bipartite or matrix-targeting signal sequences to yeast mitochondria

This study compares stress responses in yeast mitochondria caused by misfolded proteins targeted to the IMS or matrix using different signal sequences, revealing compartment-specific adaptations.

Inhibition of histone readers bromodomain extra-terminal proteins alleviates skin fibrosis in experimental models of scleroderma

This study shows that inhibiting BET proteins, particularly BRD4, reduces skin fibrosis in scleroderma models by affecting calcium signaling and gene expression.