Kalai Mathee

Alternative to invasive bronchoscopy: validating tracheal aspirates for microbiome profiling in intensive care unit pneumonia patients

Parshatd Govindasamy, Jun Yeun Cho, Jiyoul Yang, Bumhee Yang et autres

Pneumonia causes significant mortality in intensive care unit (ICU) patients, yet traditional culture-based pathogen detection lacks sufficient sensitivity. While bronchoalveolar lavage fluid (BAL) provides optimal diagnostic yield, bronchoscopy is often contraindicated in critically ill patients. This study compares the respiratory microbiome profiles …

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BiMba: using Vision Mamba to predict protein sites that bind other proteins

Azam Shirali, Parshatd Govindasamy, Vitalii Stebliankin, Jimeng Shi et autres

MOTIVATION: Identifying protein binding sites in protein-protein complexes is a central challenge in structural biology. Binding sites, consisting of groups of residues, govern how proteins recognize, and interact with protein partners. Thus, identifying them is essential for understanding biological function and guiding …

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ME ditome : Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes

Arpit Mehta, Vitalii Stebliankin, Kalai Mathee, Giri Narasimhan

RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. …

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EMoMiS: A pipeline for epitope-based molecular mimicry search in protein structures with potential applications to SARS-CoV-2

Vitalii Stebliankin, Rajeshwari Chellappan, Prabin Baral, Christian A. Balbin et autres

The Epitope-based Molecular Mimicry Search (EMoMiS) pipeline developed in this study provides a valuable computational tool for predicting molecular mimicry between antigens. The novelty of the tool includes a prediction of antibody cross-reactivity, which can have beneficial or detrimental effects on the …

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MetaEdit: Computational Identification of RNA Editing in Microbiomes

Arpit Mehta, Vitalii Stebliankin, Kalai Mathee, Giri Narasimhan

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Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA

Daniel Ruiz-Perez, Isabella Gimon, Musfiqur Rahman Sazal, Kalai Mathee et autres

A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state of the …

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Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus

Eric I. Nayman, Brooke A. Schwartz, Michaela Polmann, Alayna C. Gumabong et autres

Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome …

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Genomic and metabolic versatility of Pseudomonas aeruginosa contributes to its inter-kingdom transmission and survival

Sakthivel Ambreetha, Diansy Zincke, Dananjeyan Balachandar, Kalai Mathee

Pseudomonas aeruginosa is one of the most versatile bacteria with renowned pathogenicity and extensive drug resistance. The diverse habitats of this bacterium include fresh, saline and drainage waters, soil, moist surfaces, taps, showerheads, pipelines, medical implants, nematodes, insects, plants, animals, birds and …

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In memoriam: Vincent Olubunmi Rotimi (1943–2023) – a luminary of medical microbiology

Olufunlola Rotimi, Kalai Mathee

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks …

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Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks using METALICA

Daniel Ruiz-Perez, Isabella Gimon, Musfiqur Rahman Sazal, Kalai Mathee et autres

ABSTRACT A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state-of-the-art in …

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Detection of SARS-CoV-2 in high-efficiency particulate air (HEPA) filters of low-cost air purifiers in community-based organizations

Rachel D. Clarke, Nana Aisha Garba, Manuel Alejandro Barbieri, Leonardo Acuña et autres

This study aims to investigate the presence of SARS-CoV-2 in public spaces and assess the utility of inexpensive air purifiers equipped with high-efficiency particulate air (HEPA) filters for viral detection. Samples were collected from six community-based organizations in underserved minority neighborhoods in …

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Microbiome depiction through user-adapted bioinformatic pipelines and parameters

Eric I. Nayman, Brooke A. Schwartz, Fantaysia C. Polanco, Alexandra Firek et autres

Microbial compositions generated based on the 16S rRNA marker gene should be interpreted with caution. To improve microbial community profiling, bioinformatic protocols must be user-adapted. Analysis should be performed with consideration for the select target amplicon, pipelines and parameters used, and taxa …

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