Profile Details

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Hire Dr. Daniel J.

United Kingdom

USD 50 /hr

PhD Microbiology & Bioinformatics Expert | Python/R | Remote Research Suppor

Profile Summary

PhD Microbiology & Bioinformatics Specialist with over 10 years of experience in research, metagenomics, and bacterial genomics. Proven track record in designing and implementing 16S rRNA and shotgun metagenomics pipelines, analyzing microbiome data, and translating findings into actionable insights for academic and industry projects. Key Strengths: ✔ Bioinformatics: Expertise in WGS, 16S amplicon sequencing, transcriptomics (tools: DADA2, Phyloseq, DESeq2, Kraken, Python/R). ✔ Microbiology: Specialized in probiotic mechanisms, antibiotic resistance, and bacterial pathogenesis (BSL-2 lab experience). ✔ Data to Publications: Published 7+ peer-reviewed studies on gut microbiome modulation, IBS, and probiotic efficacy. ✔ Remote Collaboration: Experienced in managing distributed projects, from data analysis to scientific writing. How I Can Help You: Develop custom bioinformatics pipelines for microbiome studies. Analyze and interpret metagenomic/16S datasets for clinical or commercial applications. Support grant writing, manuscript preparation, or statistical analysis. Passionate about leveraging data-driven approaches to advance microbiome research—let’s collaborate to elevate your project!

Subject Matter Expertise

• ☆ Microbiology
• ☆ Microbiome Research
• ☆ Data Analysis
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Cluster Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Data Management
• ☆ Data Manipulation
• ☆ Machine Learning
• ☆ Data Cleaning
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Structural Bioinformatics
• ☆ Python
• ☆ R

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Fact Checking, Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Data Visualization, Big Data Analytics, Data Cleaning, Data Processing

Work Experience

Cultech (United Kingdom)

June 2021 - Present

Postdoctoral Researcher

Uppsala University

June 2019 - January 2021

University research assistant

Swansea University

March 2018 - June 2018

Clinical Informatics Scientist

PRA Health Sciences

September 2013 - October 2014

Education

PhD Microbiology and Infectious diseases

Swansea University

October 2014 - January 2019

Certifications

• PhD Certificate

  Swansea University

  January 2019 - Present

Publications

JOURNAL ARTICLE

Sophie E. Thomas, Joshua Kerry-Smith, Susan F. Plummer, Jack P. Bate, Daniel A. John, Evie Lawrence, Lydia Powell, Jordanna Dally, Ryan Moseley, Daryn R. Michael (2024). The ability of the Lab4 probiotic consortium to impact upon the functionality of serum deprived human keratinocytes in vitro . Frontiers in Microbiomes.

Benjamin Mullish, D. R. Michael, M. Dabcheva, T. S. Webberley, N. Coates, D. A. John, D. Wang, Y. Luo, S. F. Plummer, J. R. Marchesi (2024). Authors' reply to letter: He who controls Clostridia and Bacteroidia controls the gut microbiome: The concept of targeted probiotics to restore the balance of keystone taxa in irritable bowel syndrome . Neurogastroenterology & Motility.

Benjamin Mullish, D. R. Michael, M. Dabcheva, T. S. Webberley, N. Coates, D. A. John, D. Wang, Y. Luo, S. F. Plummer, J. R. Marchesi (2024). A double‐blind, randomized, placebo‐controlled study assessing the impact of probiotic supplementation on the symptoms of irritable bowel syndrome in females . Neurogastroenterology & Motility.

Daniel John, Daryn Michael, Maya Dabcheva, Eleri Hulme, Julio Illanes, Tom Webberley, Duolao Wang, Sue Plummer (2024). A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome . Frontiers in Microbiomes.

Daniel John, Harry Tracey, Niall Coates, Eleri Hulme, Daryn Robert Michael, Susan Frances Plummer (2023). Insights into the enumeration of mixtures of probiotic bacteria by flow cytometry . BMC Microbiology.

B.H. Mullish, D.R. Michael, T.S. Webberley, D. John, G. Ramanathan, S.F. Plummer, D. Wang, J.R. Marchesi (2023). The gastrointestinal status of healthy adults: a post hoc assessment of the impact of three distinct probiotics . Beneficial Microbes.

Daniel John, Thomas S. Webberley, Giulia Masetti, Ryan J. Bevan, Joshua Kerry-Smith, Alison A. Jack, Daryn R. Michael, Sophie Thomas, Maria Glymenaki, Jia Li, et al. (2022). The Impact of Probiotic Supplementation on Cognitive, Pathological and Metabolic Markers in a Transgenic Mouse Model of Alzheimer’s Disease . Frontiers in Neuroscience.

Daniel A. John, Lisa K. Williams, Venkateswarlu Kanamarlapudi, Thomas J. Humphrey, Thomas S. Wilkinson (2017). The Bacterial Species Campylobacter jejuni Induce Diverse Innate Immune Responses in Human and Avian Intestinal Epithelial Cells . Frontiers in Microbiology.