Chapter 12: Human Microbiome Analysis

Morgan, Xochitl C., Huttenhower, Curtis·2012·PLoS Computational Biology

Cited by (491)

Items 301–400 of 491

  1. The oral microbiome
    Liam P. Shaw, Andrew Mark Smith, Adam Paul Roberts · 2017 · Emerging Topics in Life Sciences
  2. High-dimensional Causal Mediation Analysis with a Large Number of Mediators Clumping at Zero to Assess the Contribution of the Microbiome to the Risk of Bacterial Pathogen Colonization in Older Adults
    Wei Liu, John Patrick Haran, Arlene S. Ash, Jeroan J. Allison, Shangyuan Ye, Jennifer Tjia, Vanni Bucci, Bo Zhang · 2019 · Current Bioinformatics
  3. Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation
    Ana Rubio‐García, Aldert Zomer, Ruoshui Guo, John W. A. Rossen, Jan H. van Zeijl, Jaap A. Wagenaar, Roosmarijn E. C. Luiken · 2023 · PLoS ONE
  4. Updates and Current Challenges in Reproductive Microbiome: A Comparative Analysis between Cows and Women
    Amanda Fonseca Zangirolamo, Anne Kemmer Souza, Deborah Nakayama Yokomizo, Ana Karolyne Alves Miguel, Márcio Costa, Amauri Alcindo Alfieri, Marcelo Marcondes Seneda · 2024 · Animals
  5. The Microbiome in Obesity, Diabetes, and NAFLD: What is Your Gut Telling Us?
    Leon Anton Adams, Mark Morrison · 2016 · Current Hepatology Reports
  6. Fermentation of Dietetic Fiber from Green Bean and Prickly Pear Shell by Pure and Mixture Culture of Lactobacillus acidophilus LA-5 and Bifidobacterium bifidum 450B
    Y. N. Mora-Cura, Norma Paola Meléndez-Rentería, Mario Delgado-García, Juan Carlos Contreras‐Esquivel, Jesús A. Morlett-Chávez, Cristóbal N. Aguilar, Raúl Rodrı́guez-Herrera · 2017 · Current Microbiology
  7. El holobionte enfermo, el ejemplo de la esclerosis múltiple
    Federico Castillo-Álvarez, María Eugenia Marzo-Sola · 2018 · Medicina Clínica
  8. Comparison of Microbiota Variation in Korean Healthy Adolescents with Adults Suggests Notable Maturity Differences
    Joo-Wook Kim, Jin Sook Lee, Jung Ho Kim, Joo-Won Jeong, Dae Ho Lee, Seungyoon Nam · 2018 · OMICS A Journal of Integrative Biology
  9. Interaction of microbiome and immunity in tumorigenesis and clinical treatment
    Yue Yu, Wen Zhong · 2022 · Biomedicine & Pharmacotherapy
  10. Using the Human Gastrointestinal Microbiome to Personalize Nutrition Advice: Are Registered Dietitian Nutritionists Ready for the Opportunities and Challenges?
    Ruth Harvie, Ryan M. Chanyi, Jeremy P. Burton, Michael Schultz · 2016 · Journal of the Academy of Nutrition and Dietetics
  11. Microbial Forensics: A Present to Future Perspective on Genomic Targets, Bioinformatic Challenges, and Applications
    Rachel Shadoff, Mary Anne Panoyan, Nicole M.M. Novroski · 2022 · Forensic Genomics
  12. The microbiome and aging
    Isabel Abadías‐Granado, Javier Sánchez‐Bernal, Yolanda Gilaberte · 2022 · Plastic and Aesthetic Research
  13. Gut microbiome diversity measures for metabolic conditions: a systematic scoping review
    Chatpol Samuthpongtorn, Tanawin Nopsopon, Krit Pongpirul · 2021 · medRxiv
  14. Intestinal biomarkers, microbiota composition, and genetic predisposition to inflammatory bowel disease as predictors of Parkinson's disease manifestation
    Zhi Chai, Yuxia Ouyang, Anketse Debebe, Mellissa Picker, Wonjun Lee, Seth Fenton, Anouck Becker, Kerstin Augustin-Emmerichs, Andreas Schwiertz, Susanne Nicole Weber et al. · 2025 · Journal of Parkinson s Disease
  15. Microbiomics: An Approach to Community Microbiology
    Pankaj Sharma, Vijaya Brahma, Anamika Sharma, Rama Kant Dubey, Gurupkar Singh Sidhu, Pawan Kumar Malhotra · 2015 · Springer eBooks
  16. Mixed group of Rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness.
    Shyh‐Ching Lo, Guo-Chiuan Hung, Bingjie Li, Haiyan Lei, Tianwei Li, Kenjiro Nagamine, Shien Tsai, Mark Jay Zucker, Ludmilla Olesnicky · 2015 · PubMed Central
  17. Bioinformatic Analysis of Microbiome Data
    Yinglin Xia, Jun Sun, Ding‐Geng Chen · 2018 · ICSA book series in statistics
  18. Next-Generation Sequencing: The Enabler and the Way Ahead
    Sonja Pavlović, Kristel Klaassen, Biljana Stanković, Maja Stojiljković, Branka Zukić · 2020 · Elsevier eBooks
  19. Fermentation revival in the classroom: investigating ancient human practices as CUREs for modern diseases
    Jennifer K Lyles, Monika W. Oli · 2020 · FEMS Microbiology Letters
  20. Bacterioplankton community assembly in migratory fish habitat: a case study of the southern East China Sea
    Shizhan Zheng, Shouheng Zhou, Betina Lukwambe, Regan Nicholaus, Wen Yang, Zhongming Zheng · 2022 · Environmental Science and Pollution Research
  21. MG7: Configurable and scalable 16S metagenomics data analysis
    Alexey Alekhin, Evdokim Kovach, Marina Manrique, Pablo Pareja-Tobes, Eduardo Pareja, Raquel Tobes, Eduardo Pareja-Tobes · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
  22. Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis
    Jocelyn Reynolds, Jeong‐Yeol Yoon · 2025 · Microchimica Acta
  23. Integrated multi-omics identifies pathways governing interspecies interaction between A. fumigatus and K. pneumoniae
    Tamires A. Bitencourt, Filomena Nogueira, Sabrina Jenull, Trinh Phan-Canh, Michael Tscherner, Karl Kuchler, Thomas Lion · 2024 · Communications Biology
  24. Effect of dietary fibre on the gastrointestinal microbiota during critical illness: A scoping review
    Angaj Ghosh, Calum J. Walsh, Matthew J. Maiden, Timothy P. Stinear, Adam M. Deane · 2024 · World Journal of Critical Care Medicine
  25. GUT MICROBIOTA AND ITS IMPORTANCE FOR HUMAN HEALTH
    Сафина Диляра Дамировна, Sayar R. Abdulkhakov, NAIL B. AMIROV · 2021 · The Bulletin of Contemporary Clinical Medicine
  26. Ophthalmic viscoelastics commonly used in cataract surgery: A microbiota investigation
    Kourtney K. Dowler, Aida I. Vientós‐Plotts, Elizabeth A. Giuliano, Zachary L. McAdams, Rebecca A. Dorfmeyer, Carol R. Reinero, Aaron C. Ericsson · 2023 · Veterinary Ophthalmology
  27. Tumor-mediated microbiota alteration impairs synaptic tagging/capture in the hippocampal CA1 area via IL-1β production
    Ying Zhu, Yu Mei, Nimmi Baby, Huey Yee Teo, Zuhairah Binte Hanafi, Siti Nazihah Mohd Salleh, Sreedharan Sajikumar, Haiyan Liu · 2023 · Communications Biology
  28. Organism and Microbiome Analysis
    Ashleigh A. Halderman, Andrew P. Lane · 2017 · Otolaryngologic Clinics of North America
  29. Integrative Review of Gut Microbiota and Expression of Symptoms Associated With Neonatal Abstinence Syndrome
    Stephanie D. Sealschott, Rita H. Pickler, Christine A. Fortney, Michael T. Bailey · 2020 · Nursing Research
  30. A Minireview on Gastrointestinal Microbiota and Radiosusceptibility
    Aihong Mao, Chao Sun, Takanori Katsube, Bing Wang · 2020 · Dose-Response
  31. The Lung Microbiome in Carcinogenesis and Immunotherapy Treatment
    Kathleen J. Kennedy, Karam Khaddour, Nithya Ramnath, Frank D. Weinberg · 2023 · The Cancer Journal
  32. Microbiome in Chronic Lung Diseases
    Manoj J. Mammen, Sanjay Sethi · 2017 · Barcelona Respiratory Network
  33. The Gut Microbiome Beyond the Bacteriome—The Neglected Role of Virome and Mycobiome in Health and Disease
    Charikleia Stefanaki · 2019 · Elsevier eBooks
  34. An Approach to Analyze Longitudinal Zero-Inflated Microbiome Count Data Using Two-Stage Mixed Effects Models
    Jian Wang, Cielito C. Reyes‐Gibby, Sanjay S. Shete · 2020 · Statistics in Biosciences
  35. Infant Nasopharyngeal Microbiota Subphenotypes and Early Childhood Lung Function: Evidence from a Rural Ghanaian Pregnancy Cohort
    Kathryn Dubowski, Seyram Kaali, Darby W. Jack, Rebecca Kyerewaa Dwommoh Prah, José C. Clemente, Theresa Afia Serwaa Tawiah, Mohammed Nuhu Mujtaba, Louisa Fatahiya Iddrisu, Daniel Carrión, Dennis Gyasi Konadu et al. · 2021 · International Journal of Environmental Research and Public Health
  36. The evolutionary signal in metagenome phyletic profiles predicts many gene functions
    Vedrana Vidulin, Tomislav Šmuc, Sašo Džeroski, Fran Supek · 2018 · Microbiome
  37. TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data
    Qingrong Shen, Xiaoqian Fan, Yangyang Sun, Hao Gao, Xiaoquan Su · 2025 · BMC Bioinformatics
  38. Applications of NGS in DNA Analysis
    Kelly M. Elkins, Hannah E. Berry, Kashiya R. Reese · 2022 · Springer eBooks
  39. Metagenomics vs metaproteomics: A review of their application on anaerobic digestion in biogas generation
    Tze-Kang Lam · 2023 · Bioresource Technology Reports
  40. Uncovering the microbiome landscape in sashimi delicacies
    Cheng-Wei Ho, Peiying Chen, Yi-Ting Liao, Yen‐Fu Cheng, Han‐Hsing Tsou, Tsung‐Yun Liu, Kung‐Hao Liang · 2024 · Scientific Reports
  41. GEMimp: An Accurate and Robust Imputation Method for Microbiome Data Using Graph Embedding Neural Network
    Ziwei Sun, Kai Song · 2024 · Journal of Molecular Biology
  42. Improved Detection of Culprit Pathogens by Bacterial DNA Sequencing Affects Antibiotic Management Decisions in Severe Pneumonia
    Daniel G. Dunlap, C. W. Marshall, Adam C. Fitch, Sarah F. Rapport, Vaughn S. Cooper, Bryan J. McVerry, Alison Morris, Georgios D. Kitsios · 2018 · American Journal of Case Reports
  43. Investigation of Adiposity Measures and Operational Taxonomic unit (OTU) Data Transformation Procedures in Stool Samples from a German Cohort Study Using Machine Learning Algorithms
    Martina Troll, Stefan Brandmaier, Sandra Reitmeier, Jonathan Adam, Sapna Sharma, Alice Sommer, Marie‐Abèle Bind, Klaus Neuhaus, Thomas Clavel, Jerzy Adamski et al. · 2020 · Microorganisms
  44. Leveraging random forest techniques for enhanced microbiological analysis: a machine learning approach to investigating microbial communities and their interactions
    Daria Chrobak, Maciej Kołodzieczak, Polina Kozlovska, Adrianna Krzemińska, Tymoteusz I. Miller · 2023 · InterConf
  45. Carbohydrates for glycemic control: functional and microbiome aspects
    Fabiana Andréa Hoffmann Sardá, Eliana Bistriche Giuntini · 2023 · Current Opinion in Clinical Nutrition & Metabolic Care
  46. Interplay between Human Intestinal Microbiota and Gut-to-Brain Axis: Relationship with Autism Spectrum Disorders
    Francisco Javier Díaz‐García, Saúl Flores‐Medina, Diana Mercedes Soriano-Becerril · 2019 · IntechOpen eBooks
  47. Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics
    Hendrick Gao-Min Lim, Shih-Hsin Hsiao, Yuan-Chii Gladys Lee · 2021 · Biology
  48. Microbial characteristics of dental caries in HIV positive individuals
    Dunstan Kalanzi, Harriet Mayanja‐Kizza, Damalie Nakanjako, Fred Semitala, Gerald Mboowa, Muhammad Mbabali, Edgar Kigozi, Fred Ashaba Katabazi, Ivan Sserwadda, David Patrick Kateete et al. · 2022 · Frontiers in Oral Health
  49. Metagenomics for Gut Microbes
    Ranjith N. Kumavath · 2018 · InTech eBooks
  50. Metabolomics and proteomics as tools to advance the understanding of exercise responses: The emerging role of gut microbiota in athlete health and performance
    Caimari Antoni, Noemí Boqué, Canela Nuria, Pol Herrero, Mayneris-Perxachs Jordi, Lluı́s Arola, Francesc Puiggròs · 2019 · Elsevier eBooks
  51. Concept and Scientific Background of Personalized Medicine
    Thomas R.M. Bieber · 2015 · Springer eBooks
  52. Relationship Between Gut Microbiota and Pancreatitis: A Systematic Review
    Xu Zhang, Tcheudjeu Temagna Armel, Gaurav Tyagi · 2024 · Apollo Medicine
  53. A Review: Composition of Neonatal Meconium Microbiota and Its Role for Potential Probiotic
    Devi Oktaviyani, Raden Zulfa 'Alawiyyah, Putri Nusaiba, Amarila Malik · 2021 · Pharmaceutical Sciences and Research
  54. Gut Microbiome and Neurodegeneration: A Bioinformatics Approach
    Swetanshu, Pratichi Singh · 2022 · Nutritional neurosciences
  55. Emerging Insights Into Microbiome Therapeutics for Urinary Tract Infections: A Narrative Review
    Hoonhee Seo, Md Abdur Rahim, Indrajeet Barman, Mohammed Solayman Hossain, Hanieh Tajdozian, Fatemeh Ghorbanian, Md Sarower Hossen Shuvo, Jiho Choi, Sukyung Kim, Hee Jo Yang et al. · 2025 · Urogenital Tract Infection
  56. Bioprinting Using Aqueous Two-Phase System
    Brendan M. Leung, Joseph M. Labuz, Christopher Moraes, Shuichi Takayama · 2015 · Elsevier eBooks
  57. Metagenomics in Deciphering Microbial Communities Associated with Medicinal Plants
    Hira Amna Saleem, Hareem Mohsin, Azka Asif, Rabia Tanvir, Yasir Rehman · 2020 · Environmental and microbial biotechnology
  58. Comparison of enrichment methods for isolating Enterohemorrhagic Escherichia coli in kimchi
    Myeong-Kyo Jeong, Gun Woo Nam, Eun Jeong Heo, Mi-Gyeong Kim, Hyo‐Sun Kwak, Soon Han Kim, Soo Hwan Suh · 2022 · Journal of Microbiological Methods
  59. NoC Architectures as Enablers of Biological Discovery for Personalized and Precision Medicine
    Paul Bogdan, Turbo Majumder, Arvind Ramanathan, Yuankun Xue · 2015 · IEEE/ACM International Symposium on Networks-on-Chip (NOCS)
  60. Metagenomic Approaches for Investigating the Role of the Microbiome in Gut Health and Inflammatory Diseases
    Rodrigo Dias de Oliveira Carvalho, Fillipe Luiz Rosa Do Carmo, Sara Heloísa da Silva, Bárbara Fernandes Cordeiro, Aline B.M. Vaz, Enrico G. T. Gimenez, Luis Goulart, Aristóteles Goés‐Neto, Yves Le Loir, Gwénaël Jan et al. · 2018 · InTech eBooks
  61. Disease of the holobiont, the example of multiple sclerosis
    Federico Castillo-Álvarez, María Eugenia Marzo-Sola · 2019 · Medicina Clínica (English Edition)
  62. The Possible Role of Gut Microbiota and Microbial Translocation Profiling During Chemo-Free Treatment of Lymphoid Malignancies
    Valentina Zuccaro, Andrea Lombardi, Erika Asperges, Paolo Sacchi, P. Marone, Alessandra Gazzola, Luca Arcaini, Raffaele Bruno · 2019 · International Journal of Molecular Sciences
  63. Functional Metagenomics for Rhizospheric Soil in Agricultural Systems
    Estefanía Garibay-Valdéz, Kadiya Calderón, Francisco Vargas‐Albores, Asunción Lago‐Lestón, Luis Rafael Martínez‐Córdova, Marcel Martínez‐Porchas · 2019 · Springer eBooks
  64. Microbiota - The Unseen Players in Adult Asthmatic Airways
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  65. The Gut Microbiome and Antimicrobial Resistance in Companion Animals
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  66. Host trait prediction from human microbiome data for Colorectal Cancer
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  67. Emerging clinical pharmacology topics in drug development and precision medicine
    Qi Liu, Jack A. Gilbert, Hao‐Jie Zhu, Shiew Mei Huang, Elizabeth Kunkoski, Promi Das, Kimberly L. Bergman, Mary M. Buschmann, M. Khair ElZarrad · 2021 · Elsevier eBooks
  68. Deep ensemble learning over the microbial phylogenetic tree (DeepEn-Phy)
    Wodan Ling, Youran Qi, Xing Hua, Michael C. Wu · 2021 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  69. Microbial Biofilms
    Chaminda Jayampath Seneviratne, Neha Srivastava, Intekhab Islam, Patrick Allen · 2017 · CRC Press eBooks
  70. Invited Commentary: The Microbiome and Population Health—Considerations for Enhancing Study Design and Data Analysis in Observational and Interventional Epidemiology
    Ryan T. Demmer · 2018 · American Journal of Epidemiology
  71. The in vitro faecal evaluation of prebiotic effects of rooibos phenolic compounds on the gut microbiota of vervet monkeys (Chlorocebus pygerythrus)
    Noluxabiso Mangwana · 2020
  72. A flexible mixed-membership model for community and enterotype detection for microbiome data
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  73. Understanding the intricate interactions between microbiota and host
    Aiysha Siddiq Khan, Mohan Kamthan, Asghar Ali · 2025 · World Journal of Experimental Medicine
  74. Host and microbiota interaction in depression syndrome
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  75. Assessing the Relationship Between Nitrate-Reducing Capacity of the Oral Microbiome and Systemic Outcomes
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  76. Effects of Maternal Pre-Pregnancy BMI on Preterm Infant Microbiome and Fecal Fermentation Profile—A Preliminary Cohort Study
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  77. Human Microbiome and Bacteriophages: Impacts on Health and Disease
    Muhammad Abdullah Sheraz, Hongyan Shi, Santasree Banerjee · 2025 · Current Clinical Microbiology Reports
  78. Porphyromonas somerae in urinary microbiome and its potential metabolic role in bladder cancer
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  79. The microbiome and lung cancer: microbial effects on host immune responses and treatment outcomes
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  80. The Use of Big Data in the Modern Biology: The Case of Agriculture
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  81. What we have learned to date from the omics approach to non-Alzheimer's dementias
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  82. Microbiome differences related to metformin intolerance among Black individuals with diabetes, a pilot cross-sectional study
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  83. Alterations in microbiome of COVID-19 patients and its impact on forensic investigations
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  84. Multi-omics in Gut Microbiome
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  85. Beyond the tumor: the gut microbiome as a key player in immunotherapy efficacy and resistance
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  86. A New Dirichlet‐Multinomial Mixture Regression Model for the Analysis of Microbiome Data
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  87. Microbiome of the upper airway focusing on chronic rhinosinusitis and allergic rhinitis
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  88. Microbiota and cancer (review of literature)
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  89. The Importance of the Microbiome in the Gut
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  90. Microbiome Data Mining for Microbial Interactions and Relationships
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  91. Microbiome: Current Status and Future Applications
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  92. Metagenomic Analysis and Their Application
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  94. Symbiotic association of gut microbiome in health and diseases at ageing
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  95. Understanding the impact of radical changes in diet and the gut microbiota on brain function and structure: rationale and design of the EMBRACE study
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  96. Microbiome and Human Health: Recent Insights and Future Directions
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  97. The gastrointestinal microbiome in critical illness: A Clinician's guide to mechanisms, emerging tools, and therapeutic questions
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  98. Explore impact of inhaled glucocorticoids/β₂-agonists on the oropharyngeal microbiota in asthma patients impact of GCs/β₂-agonists on oropharyngeal microbiota in asthma
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  99. The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians
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  100. Gut Microbiota-Immune Interactions in Endometrial Cancer: Causal Mediation and Subtype-Specific Mechanisms
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