My Portfolio

About

Omics Expert & Computational Biologist

Passionate about microbiome research and multi-omics

Date of birth: 6 July 1990
Email: menia.gavr@gmail.com
Phone: +31 620607736
City: Wageningen, The Netherlands

Degree: PhD
Expertise: Omics, NGS,Microbiome Research
ORCID: https://orcid.org/0000-0003-0204-2223

As a computational biologist, I specialize in omics and microbiome research, with a strong background in data analysis and interpretation. Proficient in utilizing advanced computational tools and bioinformatics techniques to uncover valuable insights from complex biological datasets. Accomplished in executing analytical pipelines, as well as collaborating with interdisciplinary teams to drive impactful research in the fields of (meta)genomics, (meta)transcriptomics, proteomics, and microbiome analysis. Harnessing data-driven approaches to enhance our understanding of microbial communities and their interactions with their host environments is my passion!

Facts

My expertise lies in handling and analyzing large-scale microbiome datasets, including data preprocessing, quality control, statistical analysis and integration from diverse sources. My enthusiasm stems from the potential to contribute to groundbreaking discoveries in (micro)biology, ultimately advancing our knowledge of the intricacies of life at a molecular level.

Publications in scientific journals, preprint servers, international symposia and conferences

Check them out!

Citations in peer-reviewed scientific journals

EU Projects and Consortia supported my research

Years of experience working in multidisciplinary teams in various universities and research institutes

Skills

NGS Data Analysis

Preprocessing and quality control of raw data
Sequence alignment and mapping
Assembly of (meta)genomes and (meta)transcriptomes
Metagenome binning and comparative genomics
Taxonomic assignment and phylogenomics
Functional annotation and Metabolism reconstruction
Database manipulation
Proteomics data analysis
Biological interpretation of large-scale microbiome datasets

Unix/Linux Operation

File manipulation and navigation
Advanced shell scripting (Bash)
Package and environment management (e.g., Conda)
Utilization of bioinformatic tools and pipelines
High-Performance and Cloud Computing (AWS)

Programming

R: Data manipulation (dplyr, tidyr), statistical analysis (Bioconductor), data visualization (ggplot2, plotly), and data reporting (R Markdown)
Python: Data manipulation and analysis (pandas), data visualization (seaborn, matplotlib), statistical analysis (scipy), and numerical computing (numpy)

Other software

Illustration tools (Adobe Illustrator, Adobe Photoshop, Inkscape)
Version control with Github and Git
Code editing with VS code, Submlime Text and Notepad++
Microsoft office suite

Scientific Communication

Technical Report & Research Article writing
Project Report writing for international & national research collaborations
Present research findings at meetings, symposia & conferences
Peer-reviewed articles for high-impact factor scientific journals

Analytical & Interpersonal skills

Teamwork
Proactivity
Critical thinking
Problem solving
Pattern recognition
Attention to detail
Time management

Resume

Professional Experience

Postdoctoral Researcher

2022 - Present

Wageningen, The Netherlands

Led and conducted multi-omics projects focusing on microbial and host-microbe interactions in human and animal health, nutrition and biotechnological applications
Analysed high-throughput sequencing data employing advanced bioinformatic tools and workflows
Facilitated collaborations across disciplines to ensure successful translation of microbiome research
Mentored PhD students in research question formulation, experimental design and data analysis
Contributed to high-impact publications, peer-reviewed journals and presented findings at scientific conferences
Drafted and contributed to grant proposals and project applications
Data management according to data science best practices
Tutorial development on NGS data analysis

Marie Skłodowska-Curie Early Stage Researcher (ESR)

2017 - 2022

Wageningen, The Netherlands

Conducted metagenomic analysis to unravel host-microbiome interactions
Utilized various bioinformatic tools and pipelines for metagenome binning and comparative genomics
Performed taxonomic profiling to reconstruct the phylogeny of host-associated microbiomes
Assessed the functional potential by mining metagenomes and single genomes for metabolic pathways, carbohydrate-active enzymes and biosynthetic gene clusters
Published analyses and findings in peer-reviewed scientific journals
Presented results in consortia meetings, symposia and international conferences

Education

PhD in Microbiology

2017 - 2022

Laboratory of Microbiology, Wageningen University & Research, The Netherlands

Master of Science in Environmental Biology

2014 - 2016

University of Crete, Greece

Minor: Management of Marine Biological Resources

Bachelor of Science in Biology

2008 - 2013

Aristotle University of Thessaloniki, Greece

List of Projects

Human Gut Microbiome Profiling in High-Risk Diabetes

Analysed metagenomes to study microbial community structure and functional potential in individuals with type 2 diabetes risk, focusing on dietary interventions with fibre intake

Impact of Prebiotic Oligosaccharides on Pediatric Gut Health

Developed statistical analysis plans for two clinical trials. Performed statistical analysis of clinical data and analysis of 16S rRNA sequencing data to evaluate the effect of prebiotics on gut microbiota in children with functional constipation

Functional Analysis of Microbial Fermentation of Dietary Fibers

Conducted metatranscriptomic analysis to assess the impact of dietary fibres on microbial diversity and metabolic activity, providing insights into human gut health

Dietary Supplement Effects on Gut Microbiota in Osteoarthritis Patients

Analysed gut microbiota composition and functional profiles using 16S rRNA and metagenomic sequencing to understand the role of dietary supplements in modulating gut health