David Zeevi

Global microbial DNA signatures of temperature and nutrient limitation across ecosystems

Tomer Antman, Ohad Lewin‐Epstein, Tamir Yerushalmi, Yonatan Broder et autres

il, us (code pays fourni par la source)

KGOT: Unified Knowledge Graph and Optimal Transport Pseudo-Labeling for Molecule-Protein Interaction Prediction

Jiayu Qin, Zhengquan Luo, Guy Tadmor, Changyou Chen et autres

Predicting molecule-protein interactions (MPIs) is a fundamental task in computational biology, with crucial applications in drug discovery and molecular function annotation. However, existing MPI models face two major challenges. First, the scarcity of labeled molecule-protein pairs significantly limits model performance, as available …

Local-Curvature-Aware Knowledge Graph Embedding: An Extended Ricci Flow Approach

Zhengquan Luo, Guy Tadmor, Or Amar, David Zeevi et autres

Knowledge graph embedding (KGE) relies on the geometry of the embedding space to encode semantic and structural relations. Existing methods place all entities on one homogeneous manifold, Euclidean, spherical, hyperbolic, or their product/multi-curvature variants, to model linear, symmetric, or hierarchical patterns. Yet …

Learning the DNA syntax of human microbiomes to infer health and disease

Ana Mejia-Fleisacher, Noa Bossel Ben Moshe, Tomer Antman, David Zeevi et autres

Abstract The human microbiome is a key factor in human health and alterations in community structure are associated with diverse pathological conditions. However, defining universal criteria to distinguish healthy from altered microbiome configurations remains challenging due to inter- and intra-individual variability, database-dependent …

il (code pays fourni par la source)

Synergy in viral-bacterial coinfection expedites algal bloom demise

Eliran Soffer, Constanze Kuhlisch, Jean‐Baptiste Raina, Noa Barak-Gavish et autres

Algal blooms are hotspots for diverse microbial interactions affecting bloom dynamics. Viral infections often regulate the demise of these blooms, recycling >25% of oceanic fixed carbon. Although these blooms collapse synchronously, only 10-30% of algal cells show active viral infection, suggesting additional …

il, fr, pf, ch, nl (code pays fourni par la source)

Metagenomic co-assembly uncovers mobile antibiotic resistance genes in airborne microbiomes

Burak Adnan Erkorkmaz, David Zeevi, Yinon Rudich

Antibiotic resistance poses a major global threat to health and ecosystems. Genes that confer resistance and can move between microbes, known as mobile antibiotic resistance genes, are especially concerning, as they can spread into disease-causing bacteria. While many pathways for gene dispersal …

il (code pays fourni par la source)

Global DNA signatures of temperature and nutrient limitation in prokaryotes

Tomer Antman, Ohad Lewin‐Epstein, Tamir Yerushalmi, Yonatan Broder et autres

Abstract Microorganisms adapt to their environment through changes in both their genes and overall genome composition. However, identifying universal principles of genomic adaptation remains challenging because different environments present multiple, overlapping selective pressures. To overcome this challenge, we analyzed DNA composition patterns …

il, us (code pays fourni par la source)

Dust storm-driven dispersal of potential pathogens and antibiotic resistance genes in the Eastern Mediterranean

Burak Adnan Erkorkmaz, David Zeevi, Yinon Rudich

il (code pays fourni par la source)

Metagenomic co-assembly reveals mobile antibiotic resistance genes in airborne microbiomes in the Eastern Mediterranean

Burak Adnan Erkorkmaz, David Zeevi, Yinon Rudich

Abstract Antibiotic resistance is a significant threat to global ecological health. Mobile resistance genes are of particular concern due to their ability to transfer between organisms. In environmental settings and within the microbiota of humans and animals, these genes can sometime move …

il (code pays fourni par la source)

Dust storm-driven dispersal of potential pathogens and antibiotic resistance genes in the Eastern Mediterranean

Burak Adnan Erkorkmaz, David Zeevi, Yinon Rudich

Abstract The atmosphere hosts a microbiome that connects distant ecosystems yet remains relatively unexplored. In this study, we tested the hypothesis that dust storms enhance the spread of pathogenic microorganisms and whether these microorganisms carry antibiotic resistance and virulence-related genes in the …

il, ru (code pays fourni par la source)

Spec2Class: Accurate Prediction of Plant Secondary Metabolite Class using Deep Learning

В В Полторак, Nir Shachaf, Asaph Aharoni, David Zeevi

Abstract Mass spectrometry (MS)-based data is commonly used in studying metabolism and natural products, but typically requires domain-specific skill and experience to analyze. Existing computational tools for non-targeted metabolite analysis (i.e., metabolomics) mostly rely on comparison to reference MS spectral libraries for …

ru, il (code pays fourni par la source)

Competitive fungal commensalism mitigates candidiasis pathology

Jarmila Sekeresova Kralova, Catalina Donic, Bareket Dassa, Ilana Livyatan et autres

The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here, we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from …

il, de (code pays fourni par la source)