AIMC Topic: Gastrointestinal Microbiome
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Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.
Communications biology
Aug 6, 2025
Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of trans...
A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.
NPJ systems biology and applications
Aug 5, 2025
We present MBPert, a generic computational framework for inferring species interactions and predicting dynamics in time-evolving ecosystems from perturbation and time-series data. In this work, we contextualize the framework in microbial ecosystem mo...
Personalized colorectal cancer risk assessment through explainable AI and Gut microbiome profiling.
Gut microbes
Aug 4, 2025
The clinical adenoma - carcinoma progression represents a well-established framework for understanding colorectal cancer (CRC) development, although the molecular mechanisms underlying this transition remain only partially understood. Increasing evid...
Combining mucosal microbiome and host multi-omics data shows prognostic potential in paediatric ulcerative colitis.
Nature communications
Aug 4, 2025
Current first-line treatments of paediatric ulcerative colitis (UC) maintain a 6-month remission in only half of the patients. Relapse prediction at diagnosis could enable earlier introduction of immunosuppressants. We collected intestinal biopsies f...
Gut microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC.
NPJ biofilms and microbiomes
Jul 28, 2025
The role of gut dysbiosis in shaping immunotherapy responses is well-recognized, yet its effect on the therapeutic efficacy of chemotherapy and immunotherapy combinations remains poorly understood. We analyzed gut microbiota in non-small cell lung ca...
Application of image guided analyses to monitor fecal microbial composition and diversity in a human cohort.
Scientific reports
Jul 19, 2025
The critical role of gut microbiota in human health and disease has been increasingly illustrated over the past decades, with a significant amount of research demonstrating an unmet need for self-monitor of the fecal microbial composition in an easil...
Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.
Journal of proteome research
Jul 18, 2025
A major challenge in mass-spectrometry-based metaproteomics is accurately identifying and quantifying biological functions across the full taxonomic lineage of microorganisms. This issue stems from what we refer to as the "shared confidently identifi...
Microbiome-based prediction of allogeneic hematopoietic stem cell transplantation outcome.
Genome medicine
Jul 17, 2025
BACKGROUND: Allogeneic hematopoietic stem cell transplantation (HSCT) is potentially curative for hematologic malignancies but is frequently complicated by relapse and immune-mediated complications, such as graft-versus-host disease (GVHD). Emerging ...
Extensive novel diversity and phenotypic associations in the dromedary camel microbiome are revealed through deep metagenomics and machine learning.
PloS one
Jul 17, 2025
The dromedary camel, also known as one-humped camel or Arabian camel, is iconic and economically important to Arabian society. Its contemporary importance in commerce and transportation, along with the historical and modern use of its milk and meat p...
Integrative analysis of multi-omics data and gut microbiota composition reveals prognostic subtypes and predicts immunotherapy response in colorectal cancer using machine learning.
Scientific reports
Jul 12, 2025
Colorectal cancer (CRC) exhibits substantial heterogeneity in molecular subtypes and clinical outcomes. We performed an integrative analysis of multi-omics data from 274 CRC patients to investigate the impact of gut microbiota composition on prognosi...
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