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Hire Khoi Nguyen .

Canada

USD 59 /hr

5+ yrs Microbiome Data Scientist | 10+ yrs Academic Publishing | Bioinformatics, Statistics & Writing Expert

Profile Summary

I am an experienced Microbiome Data Scientist with over 5 years of professional experience in microbiome analysis and 10+ years of academic research and publication experience in Microbiome, Human Nutrition, Biotechnology. I hold dual MSc degrees in Human Nutrition & Metabolism (University of Alberta, Canada) and Biotechnology (VNU-HCM, Vietnam). Currently working at Microbiome Insights Inc. (Canada), I specialize in analyzing complex microbiome, clinical, and omics datasets to address research questions and support scientific publications. I have extensive experience in designing microbiome studies, leading data analysis, developing automated pipelines, and delivering clear, actionable results to clients worldwide. Also, I am working as a Research Assistant at Xia Lab, Institute of Parasitology, McGill University (Canada). At McGill, I am involved in multiple microbiome and multi-omics projects, including developing functional modules for web platforms, applying AI tools in data analysis, and contributing to the development of an Omic Data Science textbook. 📝 Key Skills & Expertise: Programming & Data Analysis: Proficient in R, Unix Shell, HTML, cloud storage Bioinformatics & Biostatistics: Sequencing data cleaning, multivariate analysis, regression models, machine learning (Random Forest, ROC, clustering) Data Visualization: Publication-ready figures, infographics, storytelling dashboards Wet Lab Experience: Molecular biology techniques, DNA extraction, ELISA, antimicrobial testing 🌎 Featured Projects: Mediterranean Diet & Breast Cancer Risk (Germany, 2020-2022): Identified key metabolites linking diet and intestinal permeability using mediation analysis & machine learning. Weight-loss Program Clinical Trial (Germany, 2022-2025): Discovered predictive phosphatidylcholine biomarkers using Dynamic Bayesian Network & Gradient Boosting. HIV Drug Side Effects Study (Belgium, 2022-2024): Linked bacterial profiles to antiretroviral drug side effects using advanced visualization techniques. Obesity & Metabolic Syndrome Trials (Ireland-Canada, 2016–Present): Identified microbial groups linked to fiber treatment outcomes using clustering and network analysis. 🌐 I have collaborated with research teams in Germany, Ireland, Belgium, Canada, and the U.S., contributing to multiple peer-reviewed publications and ongoing clinical trials. Whether you need microbiome data analysis, academic writing, statistical consulting, or bioinformatics support, I deliver high-quality, reliable, and publication-ready work.

Subject Matter Expertise

• ★ Data Analysis
• ★ Meta-Analysis
• ★ R
• ☆ Biostatistics
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Cluster Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Machine Learning
• ☆ Data Mining
• ☆ Data Cleaning
• ☆ Neural Networks
• ☆ Pattern Recognition
• ☆ Statistics
• ☆ Applied Statistics
• ☆ Regression Analysis
• ☆ Multivariate Analysis
• ☆ Nonlinear Regression
• ☆ Bayesian Statistics
• ☆ Correlation Analysis
• ☆ Study Design
• ☆ Statistical Review
• ☆ Bioinformatics
• ☆ Systems Biology
• ☆ Taxonomy/Classification
• ☆ SQL
• ☆ Clinical Trials
• ☆ Clinical Trial Design
• ☆ Clinical Trials Data Analysis
• ☆ Precision Medicine
• ☆ Gastroenterology & Hepatology
• ☆ Colorectal Cancer
• ☆ Crohn's Disease
• ☆ Irritable Bowel Syndrome (IBS)

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Clinical Trial Documentation, Technical Writing

Research Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Data Visualization, Data Mining, Data Cleaning, Data Processing, Data Insights

Work Experience

Microbiome Data Scientist

Microbiome Insights Inc

February 2020 - Present

Independent Researcher

n/a

January 2020 - Present

Researcher

International University

March 2014 - March 2016

Education

Master of Science in Nutrition and Metabolism (Agricultural, Food & Nutritional Science)

University of Alberta

September 2016 - January 2020

Master of Science in Biotechnology (School of Biotechnology)

International University

November 2012 - April 2015

Biotechnology Engineer (School of Biotechnology)

International University

September 2007 - August 2011

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Nguyen Khoi Nguyen, Julia Montenegro, Camila L P Oliveira, Anissa M Armet, Aloys Berg, Arya M Sharma, Laurie Mereu, Cristiane Cominetti, Sunita Ghosh, Caroline Richard, et al. (2023). Impact of a Powdered Meal Replacement on Metabolism and Gut Microbiota (PREMIUM) in individuals with excessive body weight: a study protocol for a randomised controlled trial . BMJ Open.

Edward C. Deehan and Zhengxiao Zhang and Alessandra Riva and Anissa M. Armet and Maria Elisa Perez-Mu{\~{n}}oz and Nguyen K. Nguyen and Jacqueline A. Krysa and Benjamin Seethaler and Yuan-Yuan Zhao and Janis Cole and Fuyong Li and Bela Hausmann and Andreas Spittler and Julie-Anne Nazare and Nathalie M. Delzenne and Jonathan M. Curtis and Wendy V. Wismer and Spencer D. Proctor and Jeffrey A. Bakal and Stephan C. Bischoff and Dan Knights and Catherine J. Field and David Berry and Carla M. Prado and Jens Walter(2022). Elucidating the role of the gut microbiota in the physiological effects of dietary fiber . Microbiome. 10. (1). Springer Science and Business Media {LLC}

Stephan C. Bischoff, Nguyen K. Nguyen, Benjamin Seethaler, Julia Beisner, Philipp Kügler, Thorsten Stefan (2022). Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy . Nutrients.

Khoi Nguyen Nguyen, Stephan Bischoff, Benjamin Seethaler, Julia Beisner, Philipp Kügler, Thorsten Stefan (2022). Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy . Nutrients.

Kiran Preet Padda and Akshit Puri and Nguyen Khoi Nguyen and Timothy J. Philpott and Chris P. Chanway(2022). Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance . Plant and Soil. Springer Science and Business Media {LLC}

Deehan, Edward C., Zhang, Zhengxiao, Riva, Alessandra, Armet, Anissa M., Perez-Munoz, Maria Elisa, Nguyen, Nguyen K., Krysa, Jacqueline A., Seethaler, Benjamin, Zhao, Yuan-Yuan, Cole, Janis, et al. (2022). Elucidating the role of the gut microbiota in the physiological effects of dietary fiber . Microbiome.

Seethaler, Benjamin, Nguyen, Nguyen K., Basrai, Maryam, Kiechle, Marion, Walter, Jens, Delzenne, Nathalie M., Bischoff, Stephan C. (2022). Short-chain fatty acids are key mediators of the favorable effects of the Mediterranean diet on intestinal barrier integrity: data from the randomized controlled LIBRE trial . The American Journal of Clinical Nutrition.

Padda, K.P., Puri, A., Nguyen, N.K., Philpott, T.J., Chanway, C.P.(2022). Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance . Plant and Soil. 474. (1-2). p. 213-232.

Bischoff, S.C., Nguyen, N.K., Seethaler, B., Beisner, J., Kügler, P., Stefan, T.(2022). Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy . Nutrients. 14. (15).

Deehan, E.C., Zhang, Z., Riva, A., Armet, A.M., Perez-Muñoz, M.E., Nguyen, N.K., Krysa, J.A., Seethaler, B., Zhao, Y.-Y., Cole, J., et al.(2022). Elucidating the role of the gut microbiota in the physiological effects of dietary fiber . Microbiome. 10. (1).

Seethaler, B., Nguyen, N.K., Basrai, M., Kiechle, M., Walter, J., Delzenne, N.M., Bischoff, S.C.(2022). Short-chain fatty acids are key mediators of the favorable effects of the Mediterranean diet on intestinal barrier integrity: data from the randomized controlled LIBRE trial . American Journal of Clinical Nutrition. 116. (4). p. 928-942.

Padda, Kiran Preet, Puri, Akshit, Nguyen, Nguyen Khoi, Philpott, Timothy J., Chanway, Chris P. (2022). Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance . Plant and Soil.

Nguyen K. Nguyen and Edward C. Deehan and Zhengxiao Zhang and Mingliang Jin and Nami Baskota and Maria Elisa Perez-Mu{\~{n}}oz and Janis Cole and Yunus E. Tuncil and Benjamin Seethaler and Ting Wang and Martine Laville and Nathalie M. Delzenne and Stephan C. Bischoff and Bruce R. Hamaker and In{\'{e}}s Mart{\'{\i}}nez and Dan Knights and Jeffrey A. Bakal and Carla M. Prado and Jens Walter(2020). Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate . Microbiome. 8. (1). Springer Science and Business Media {LLC}

Edward C. Deehan and Chen Yang and Maria Elisa Perez-Mu{\~{n}}oz and Nguyen K. Nguyen and Christopher C. Cheng and Lucila Triador and Zhengxiao Zhang and Jeffrey A. Bakal and Jens Walter(2020). Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production . Cell Host & Microbe. 27. (3). p. 389--404.e6. Elsevier {BV}

Deehan, E.C., Yang, C., Perez-Muñoz, M.E., Nguyen, N.K., Cheng, C.C., Triador, L., Zhang, Z., Bakal, J.A., Walter, J.(2020). Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production . Cell Host and Microbe. 27. (3). p. 389-404.e6.

Nguyen, N.K., Deehan, E.C., Zhang, Z., Jin, M., Baskota, N., Perez-Muñoz, M.E., Cole, J., Tuncil, Y.E., Seethaler, B., Wang, T., et al.(2020). Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate . Microbiome. 8. (1).

Effects of Lactobacillus casei and Alterations in Fermentation Conditions on Biosynthesis of Glucuronic Acid by a Dekkera bruxellensis-Gluconacetobacter intermedius Kombucha Symbiosis Model System Nguyen Khoi Nguyen, Huong Thuy Nguyen & Phu Hong Le (2015) Effects of Lactobacillus casei and Alterations in Fermentation Conditions on Biosynthesis of Glucuronic Acid by a Dekkera bruxellensis-Gluconacetobacter intermedius Kombucha Symbiosis Model System, Food Biotechnology, 29:4, 356-370, DOI: 10.1080/08905436.2015.1092446 . Food Biotechnology.

Nguyen Khoi Nguyen, Phuong Bang Nguyen, Huong Thuy Nguyen, Phu Hong Le(2015). Screening the optimal ratio of symbiosis between isolated yeast and acetic acid bacteria strain from traditional kombucha for high-level production of glucuronic acid . LWT - Food Science and Technology. 64. (2). p. 1149--1155. Elsevier {BV}

(2015). Lactic acid bacteria: promising supplements for enhancing the biological activities of kombucha . SpringerPlus.

Nguyen, N.K., Dong, N.T.N., Nguyen, H.T., Le, P.H.(2015). Lactic acid bacteria: promising supplements for enhancing the biological activities of kombucha . SpringerPlus. 4. (1). p. 1-6.

Nguyen Khoi Nguyen, Ngan Thi Ngoc Dong, Huong Thuy Nguyen, Phu Hong Le (2015). Lactic acid bacteria: promising supplements for enhancing the biological activities of kombucha . SpringerPlus.

Nguyen, N.K., Nguyen, H.T., Le, P.H.(2015). Effects of lactobacillus casei and alterations in fermentation conditions on biosynthesis of glucuronic acid by a dekkera bruxellensis-gluconacetobacter intermedius kombucha symbiosis model system . Food Biotechnology. 29. (4). p. 356-370.

Nguyen Khoi Nguyen, Huong Thuy Nguyen, Phu Hong Le (2015). Effects of Lactobacillus casei and Alterations in Fermentation Conditions on Biosynthesis of Glucuronic Acid by a Dekkera bruxellensis-Gluconacetobacter intermedius Kombucha Symbiosis Model System . Food Biotechnology.

Nguyen, N.K., Nguyen, P.B., Nguyen, H.T., Le, P.H.(2015). Screening the optimal ratio of symbiosis between isolated yeast and acetic acid bacteria strain from traditional kombucha for high-level production of glucuronic acid . LWT - Food Science and Technology. 64. (2). p. 1149-1155.

Nguyen Khoi Nguyen, Phuong Bang Nguyen, Huong Thuy Nguyen, Phu Hong Le (2015). Screening the optimal ratio of symbiosis between isolated yeast and acetic acid bacteria strain from traditional kombucha for high-level production of glucuronic acid . LWT - Food Science and Technology.