Gut microbiome, big data and machine learning to promote precision medicine for cancer

Search and clustering orders of magnitude faster than BLAST

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Metagenomic biomarker discovery and explanation

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The UK Biobank resource with deep phenotyping and genomic data

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The human microbiome project

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Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors

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Diversity, stability and resilience of the human gut microbiota

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Role of the microbiota in immunity and inflammation.

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Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients

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Machine Learning in Medicine

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Helicobacter pylori Infection and the Risk of Gastric Carcinoma

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Data Analytics and Data Visualization for the Pharmaceutical Industry

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Machine learning in applied microbiology, from data quality to model validation and implementation

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Modulating drug response through the gut microbiome: pathways to precision therapy

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Artificial intelligence: Ways and means for central nervous system (CNS) delivery

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Bibliometric and visual analysis of human microbiome—breast cancer interactions: current insights and future directions

Zhou, Y., Jiang, M., Li, X., Shen, K., Zong, H., Lv, Q., & Shen, B. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1490007 · Cited by 4

Big data for neuroscience in the context of predictive, preventive, and personalized medicine

Bajinka, O., Ouédraogo, S. Y., Li, N., & Zhan, X. (2024) · The EPMA Journal · doi:10.1007/s13167-024-00393-1 · Cited by 4

Gut microbiota dysbiosis: the hidden roles in human aging and age-related diseases

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AI-aided Data Mining in Gut Microbiome: The Road to Precision Medicine

Jiang, X., Xu, C., Guo, Q., & Zhu, H. (2021) · International Congress on Image and Signal Processing (CISP) · doi:10.1109/cisp-bmei53629.2021.9624432 · Cited by 4

Optimisation of Cancer Status Prediction Pipelines using Bio-Inspired Computing

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Three-dimensional breast imaging using Artificial-Intelligence-Based Automatic Measurement System

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HGMT: a database of human gut microbiota for tumors and immunotherapy response

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The intratumor microbiome and cancer immunity: from pathogenesis to therapeutic opportunities through artificial intelligence

Honcharyuk, I., Caridi, B., Pinco, P., Ferri, S., Giani, A. D., Baeri, A., Amoroso, C., Massironi, S., & Facciotti, F. (2025) · Expert Review of Clinical Immunology · doi:10.1080/1744666x.2025.2602537 · Cited by 3

From 16S rRNA to deep learning: Evolution of computational approaches in human microbiome studies

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AI without borders: The rise of cross-disciplinary machine learning

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Data bias in precision medicine

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Detection of Hepatocellular Carcinoma Using Optimized miRNA Combinations and Interpretable Machine Learning Models

Long, Z., & Zhang, L. (2025) · IEEE Access · doi:10.1109/access.2025.3559105 · Cited by 3

Predictive Microbiology and Machine Learning by Optimization Productive Process: Metanalysis

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Big Data Bot with a Special Reference to Bioinformatics

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Biocenosis of the vagina. Norm. Disruption. Restoration

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MiTree: A Unified Web Cloud Analytic Platform for User-Friendly and Interpretable Microbiome Data Mining Using Tree-Based Methods

Kim, J., & Koh, H. (2023) · Microorganisms · doi:10.3390/microorganisms11112816 · Cited by 3

Got the Munchies for an Egg Sandwich? The Effects of Cannabis on Bowel Motility and Beyond

Gunther, R. S., Farrell, M. B., & Banks, K. P. (2024) · Journal of Nuclear Medicine Technology · doi:10.2967/jnmt.123.266816 · Cited by 3

Understanding the Role of the Microbiome in Cancer Diagnostics and Therapeutics by Creating and Utilizing ML Models

Cekikj, M., Jakimovska, M., Kalajdzhiski, S., Özcan, O., & Sezerman, O. U. (2022) · Applied Sciences · doi:10.3390/app12094094 · Cited by 4

The human gut metacommunity as a conceptual aid in the development of precision medicine

Tannock, G. W. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1469543 · Cited by 2

Machine learning in solid organ transplantation: Charting the evolving landscape

Rawashdeh, B., Al‐Abdallat, H., Arpalı, E., Thomas, B. S., Dunn, T. B., & COOPER, M. M. (2024) · World Journal of Transplantation · doi:10.5500/wjt.v15.i1.99642 · Cited by 2

Sparse identification of nonlinear economic dynamical model

Li, J., Li, K., & Lin, Z. (2025) · Physica A Statistical Mechanics and its Applications · doi:10.1016/j.physa.2025.130861 · Cited by 2

Artificial Intelligence for Predicting Immunotherapy Efficacy in Non-Small Cell Lung Cancer

Cao, P., Jia, X., Yang, Y., Wang, X., Zhu, J., Li, X., Yang, Z., & Wen, Q. (2026) · Journal of Inflammation Research · doi:10.2147/jir.s581764 · Cited by 2

The interplay between Peptostreptococcus and Fusobacterium as novel signatures in colorectal cancer recurrence

Zhang, Y., Zhang, B., Pang, W., Gu, W., Wang, X., Yuan, H., Fang, S., Zhang, J., Li, X., Xing, X., et al. (2026) · Microbiome · doi:10.1186/s40168-026-02378-w · Cited by 2

Advancing Drug Discovery with AI: Machine and Deep Learning Strategies for Target Identification and Precision Nanomedicine

Chakraborty, A., Gholap, A. D., Khuspe, P. R., Sundaram, G., Webster, T. J., Khalid, M., Haris, M. S., & Faiyazuddin, M. (2026) · International Journal of Nanomedicine · doi:10.2147/ijn.s600651 · Cited by 2

The gut microbiome in colorectal cancer: molecular paradigms and translational frontiers

Liu, Y., & Mei, D. (2026) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2026.1864299 · Cited by 2

Recommendation of precision medicine application in Indonesia from multiple perspective: a review

Hisan, U. K., & Amri, M. M. (2022) · International Journal of Public Health Science (IJPHS) · doi:10.11591/ijphs.v12i1.22010 · Cited by 7

The principle of uncertainty in biology: Will machine learning/artificial intelligence lead to the end of mechanistic studies?

de Lorenzo, V. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002495 · Cited by 2

Understand how machine learning impact lung cancer research from 2010 to 2021: A bibliometric analysis

Chen, Z., Liu, Y., Lin, Z., & Huang, W. (2024) · Open Medicine · doi:10.1515/med-2023-0874 · Cited by 2

Artificial Intelligence in Organ Transplantation: Surveying Current Applications, Addressing Challenges and Exploring Frontiers

Rawashdeh, B. (2024) · Artificial intelligence · doi:10.5772/intechopen.114356 · Cited by 2

mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics

Sankaran, K., & Jeganathan, P. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012196 · Cited by 3

Risk prediction model for pneumothorax or pleural effusion after microwave ablation in patients with lung malignancy

Wang, Z., Liu, Y., Cao, X., Liu, M., Wang, L., & Zhong, L. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e38422 · Cited by 3

Integrating Biological Domain Knowledge with Machine Learning for Identifying Colorectal-Cancer-Associated Microbial Enzymes in Metagenomic Data

Bakır-Güngör, B., Ersöz, N. Ş., & Yousef, M. (2025) · Applied Sciences · doi:10.3390/app15062940 · Cited by 2

The impact of postmenopausal hormone therapy on the duodenal microbiome

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Predicting Overall Survival in Patients with Nonmetastatic Gastric Signet Ring Cell Carcinoma: A Machine Learning Approach

Li, X., Chen, Z., Lin, J., Wang, S., & Song, C. (2022) · Computational and Mathematical Methods in Medicine · doi:10.1155/2022/4862376 · Cited by 2

ML-based predictive gut microbiome analysis for health assessment

Sorribes, M. G., Leoni, G., Gallardo, A. P., Petrillo, M., Consoli, S., Gómez, V., & Ceresa, M. (2024) · Procedia Computer Science · doi:10.1016/j.procs.2024.06.318 · Cited by 2

A Bibliometric Study of Machine Learning in BiofilmPreprint

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Plant-derived Molecules as Potent Anti-skin Cancer Agents

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The gut microbiome in personalized precision medicine

Buschmann, M. M., & Gilbert, J. A. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-98808-7.00012-6 · Cited by 1

Discovering microbiota functions via chemical probe incorporation for targeted sequencing

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Instrumental variable estimation for compositional treatments

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Assessment of spatial and temporal variability in fecal contamination patterns within urbanized bay shellfish growing area utilizing community-based microbial source tracking approaches

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Challenges and Future Perspectives in Microbiota-Based Precision Medicine: Standardization of Profiling Methods, Ethical Considerations and the Potential for Pre-emptive Healthcare

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Peripheral Blood TCR Clonotype Diversity as a Biomarker for Colorectal Cancer

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Deep Learning-Driven Multi-Objective Clustering for Neuroblastoma Omics Data with NSGA-II

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Cultivation in a bottom-up manner: a new way to explore environmental microbiome

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Implementing microbiome analysis in clinical practice: overcoming challenges

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Gut microbiota

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Real-time data transmission of cross-border e-commerce based on big data considering data complexity

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Current Progress of Bioinformatics for Human Health

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The Application of AI in Precision Oncology: Tailoring Diagnosis, Treatment, and the Monitoring of Disease Progression to the Patient

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Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques

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Search-based health status detection and disease classification using species-level profiles of metagenomes

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Machine learning reveals the interplay between muscle fatty acids and the gut microbiota: implications for high-quality porkPreprint

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The Potential of Microbiome Big Data in Precision Medicine: Predicting Outcomes Through Machine Learning

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Reply to Klann et al

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Analysis of next- and third-generation RNA-Seq data reveals the structures of alternative transcription units in bacterial genomesPreprint

Wang, Q., Liu, Z.-Q., Yan, B., Chou, W., Ettwiller, L. M., Ma, Q., & Liu, B. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.02.425006

A novel computational framework for genome-scale alternative transcription units prediction

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Deep Learning for Enhancing Precision Medicine

Oh, M. (2021) · VTechWorks (Virginia Tech)

Novel Approaches to Marker Gene Representation Learning Using Trained Tokenizers and Jointly Trained Transformer Models

Manuele, A. (2021) · DalSpace (Dalhousie University)

Corps atypiques. Jeu : Revue de théâtre, no. 151, 2014

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Impact of the Microbiome on Oral Biopharmaceutics

McCoubrey, L. E., Batchelor, H. K., Basit, A. W., Gaisford, S., & Orlu, M. (2021) · Wiley eBooks · doi:10.1002/9781119678366.ch17

Machine Learning Predicts the Impact of Antibiotic Properties on Composition and Functions of Bacterial Community in Aquatic HabitatPreprint

Kang, J., Zhang, Z., Chen, Y., Zhou, Z., Zhang, J., Xu, N., Zhang, Q., Lu, T., & Qian, H. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3969067

Analysis of Big Data Embedded Mapping Model Oriented to Prediction of Subordinate Relationship

Xu, H. (2021) · Journal of Physics Conference Series · doi:10.1088/1742-6596/1982/1/012181

Lower abundance of human gut virus species is associated with cancer cachexiaPreprint

Stang, A., Weilert, H., Illig, T., Schmidt, R., Burbach, K., Gronauer, R., & Seifert, M. (2022) · Research Square · doi:10.21203/rs.3.rs-1756753/v1

Foldercase: A Science-Focused Platform Supporting Collaborative ResearchPreprint

Schwarz, E. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4174576

Construction and Validation of Early Warning Model of Lung Cancer Based on Machine Learning: A Retrospective Study

Ye, S., Pan, J., Ye, Z., Cao, Z., Cai, X., Zheng, H., & Ye, H. (2022) · Technology in Cancer Research & Treatment · doi:10.1177/15330338221136724 · Cited by 1

Research Trends of Medical Big Data: A Bibliometric Analysis (Preprint)Preprint

Wang, Y. J., Xu, L., Dong, J., Li, Y., Lai, S., Peng, Y.-H., Jiang, Z., & Hao, L. (2023) · doi:10.2196/preprints.48846

Application of intestinal microecological preparations in the health of the elderly

Lin, J., & Wang, H. (2023) · International Conference on Modern Medicine and Global Health (ICMMGH) · doi:10.1117/12.2692641

Embracing Big Data in Medical Education in Malaysia: Overcoming Challenges and Seizing Opportunities

Junaini, S. N., & Chew, K. S. (2023) · Malaysian Journal of Medicine and Health Sciences · doi:10.47836/mjmhs.19.4.49

Translational Efforts in Precision Medicine to Address Disparities

Davis, M. B., Ford, M., Martini, R. N., & Newman, L. A. (2023) · Springer eBooks · doi:10.1007/978-3-031-37638-2_4

Entity Matching Analysis using SIF, RNN, Attention and Hybrid Methods for Research Article Similarity

Muzammil, M. A. A., Raditya, E., & Rakhmawati, N. A. (2023) · International Conference on Cybernetics and Intelligent System (ICORIS) · doi:10.1109/icoris60118.2023.10352251

Type 2 Diabetes Mellitus Prediction with Gut Microbes Using Machine Learning Through Shotgun Metagenomic Sequencing

Sharma, A., Bhardwaj, S., Srivastava, D. K., & Srivastava, P. (2024) · Lecture notes in networks and systems · doi:10.1007/978-981-99-8349-0_3

Additional file 4 of Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants

Zhang, Q., Zhang, Z., Lu, T., Yu, Y., Peñuelas, J., Zhu, Y., & Qian, H. (2021) · Figshare · doi:10.6084/m9.figshare.16714010

Machine learning models of human tissue microbiomes for tissue-of-origin predictionPreprint

Mahmoudabadi, G., & Quake, S. R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.06.592823

CoPR: Collective Pattern Recognition—a Framework for Microbial Community Activity AnalysisPreprint

Vidanaarachchi, R., Tang, S. L., & Halgamuge, S. K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.30.601456

Single cell genomics unleashed: exploring the landscape of endometriosis with machine learning, gene expression profiling, and therapeutic target discovery

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MDSGCN: Predicting Multiple Types of Mutation-Drug Association Through Signed Graph Convolution Network

Feng, H., Wang, X., & Lin, F. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3548695

The Importance of Big Data Preparation in Microbial Colony Classification

Priscilla, H., Wairooy, I. K., Ghazali, K. N., & Makalew, B. A. (2024) · International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS) · doi:10.1109/icimcis63449.2024.10957685

Microbiology

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Clinical efficacy of the symbiotic drug Lotardi-A in the complex therapy of patients with irritable bowel syndrome in metabolic-associated fatty liver disease

Sirchak, Y. S. (2025) · ScienceRise Medical Science · doi:10.15587/2519-4798.2025.329828

Record Linkage as a Pre-processing Tool in Big Data Applications Using Machine Learning

Subramanian, K., Thangarasu, G., & Kannan, K. N. (2025) · Lecture notes in networks and systems · doi:10.1007/978-981-96-5220-4_5

Healthy gut: A wellness factor for humans

Das, M., Santra, S., Khamaru, D., Jayaseelan, P., Lalsangi, S. B., & Banerjee, R. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-33351-4.00010-6

The role of urokinase type plasminogen activator in colorectal cancer: innovative therapies and cutting-edge technologies

Muruganantham, J. K., Jayakumar, S., & Veerabathiran, R. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26635-5.00053-5

Biodiversity

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Managing Digital Transformation in the Healthcare Sector: Big Data Influencing Patient Outcomes, Costs, and Efficiency Improvement

Ljepava, N., Tarabasz, A., & Skibinska, E. (2025) · Advances in Science, Technology & Innovation/Advances in science, technology & innovation · doi:10.1007/978-3-031-92135-3_9 · Cited by 1

Additional file 2 of Artificial intelligence learning landscape of triple-negative breast cancer uncovers new opportunities for enhancing outcomes and immunotherapy responses

Li, S., Zhang, N., Zhang, H., Zhou, R., Li, Z., Yang, X. Y., Wu, W., Li, H., Luo, P., Wang, Z., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26613155

Additional file 4 of Gut microbiome features and metabolites in non-alcoholic fatty liver disease among community-dwelling middle-aged and older adults

Zeng, F., Su, X., Liang, X., Liao, M., Zhong, H., Xu, J., Gou, W., Zhang, X., Shen, L., Zheng, J.-S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26690359

Additional file 2 of XGBoost-based and tumor-immune characterized gene signature for the prediction of metastatic status in breast cancer

Li, Q., Yang, H., Wang, P., Liu, X., Lv, K., & Ye, M. (2022) · Figshare · doi:10.6084/m9.figshare.19613671

Additional file 3 of Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants

Zhang, Q., Zhang, Z., Lu, T., Yu, Y., Peñuelas, J., Zhu, Y.-G., & Qian, H. (2021) · Figshare · doi:10.6084/m9.figshare.16714007

Additional file 3 of Artificial intelligence learning landscape of triple-negative breast cancer uncovers new opportunities for enhancing outcomes and immunotherapy responses

Li, S., Zhang, N., Zhang, H., Zhou, R., Li, Z., Yang, X., Wu, W., Li, H., Luo, P., Wang, Z., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26613158

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Additional file 2 of Gut microbiome features and metabolites in non-alcoholic fatty liver disease among community-dwelling middle-aged and older adults

Zeng, F., Su, X., Liang, X., Liao, M., Zhong, H., Xu, J., Gou, W., Zhang, X., Shen, L., Zheng, J.-S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25367488

Additional file 5 of Gut microbiome features and metabolites in non-alcoholic fatty liver disease among community-dwelling middle-aged and older adults

Zeng, F., Su, X., Liang, X., Liao, M., Zhong, H., Xu, J., Gou, W., Zhang, X., Shen, L., Zheng, J.-S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26690362

Additional file 1 of XGBoost-based and tumor-immune characterized gene signature for the prediction of metastatic status in breast cancer

Li, Q., Yang, H., Wang, P., Liu, X., Lv, K., & Ye, M. (2022) · Figshare · doi:10.6084/m9.figshare.19613668

Additional file 1 of Gut microbiome features and metabolites in non-alcoholic fatty liver disease among community-dwelling middle-aged and older adults

Zeng, F., Su, X., Liang, X., Liao, M., Zhong, H., Xu, J., Gou, W., Zhang, X., Shen, L., Zheng, J.-S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25367299

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