Marcus Alvarez Portfolio Website

These awards reflect my dedication to both the challenging and routine aspects of my journey. For me, they are simply milestones that remind me that, regardless of good or bad days, the work needs to be done.

1st Place in the XXXVII class of the Animal Science program at UNESP (preview)
Awarded by Rotary Club of Botucatu - Dec 2017
1st Place in Professionalizing Course of the Animal Science program at UNESP (preview)
Awarded by the Regional Veterinary Medicine Council of São Paulo - Dec 2017
Best Performance in Mandatory Courses at the Department of Animal Production, UNESP (preview)
Awarded by the Faculty of Veterinary Medicine and Animal Science, UNESP, Botucatu - Dec 2017
1st Place - Best Scientific Work Award at the 3rd COSBRAPIM (preview)
Awarded by the 3rd COSBRAPIM - South Brazilian Apiculture and Meliponiculture Congress and the 36th ECAM – Santa Catarina Beekeepers and Meliponists Meeting

Welcome to my Gallery of Work, a curated collection of figures and plots from various projects I've worked on. Here, you’ll find insights from biological data, displayed through charts, graphs, and visual representations. These works showcase highlights uncovered through careful data analysis. Feel free to explore, and click on any image to learn more about the analysis behind it.

All figures were generated using code I wrote. I mainly use ggplot2 (tidyverse) package for R, allowing me to create fully customizable, high-definition plots. Here is a concise list (but not exhaustive) of third-party programs I have worked with for data analysis, and the list continues to grow:

Abyss AMRfinder antiSMASH Arlequin Augustus bedtools BLAST Bowtie Busco BWA CrisprCasFinder Diamond edgeR FastQC Flash GATK HTSeq IntegronFinder Kraken2 MAFFT OrthoFinder PlasmidFinder PLINK prodigal Prokka Qiime2 Resfinder SAMtools seqkit Seqtk snpEff SPAdes Stacks Trimmomatic TrinityRnaSeq VCFtools Velvet Vsearch

Click on images to show or hide description and high-definition viewing.

I had the pleasure of being invited in 2019 to lecture on "Introduction to NGS Data Analysis" in the postgraduate program in Genetics at São Paulo State University (UNESP). The topics I covered included:
- Types of file formats used in bioinformatics
- Sequencing quality and processing
- Sequencing-based genotyping
- Genome assembly and assembly statistics
- BLAST and gene annotation

I had the pleasure of being invited again in 2020 to lecture on "Introduction to NGS Data Analysis" in the postgraduate program in Genetics at São Paulo State University (UNESP).

As a relevant addition, I completed a teaching internship (2021) in the course "Scientific Experimentation" as part of the Animal Science undergraduate program at São Paulo State University (UNESP). During this internship, I conducted classes of R Programming Language Fundamentals and data analysis.

I was honored to be invited by CONBIT'22 − Biotechnology Organizing Committee, National League of Biotechnology Students from Brazil, to lead the workshop minicourse "Getting to Know NCBI Platform" at the NÚCLEO'22 (2022) event. The topics I covered included:
- What is NCBI
- Common file formats used in bioinformatics and NCBI databases
- Exploring the platform interface
- NCBI tools available online
- Data submission and retrieval on NCBI
- Hands-on: Using the BLAST tool offline

I delivered a short duration training course titled "Linux and RStudio basics" for the Fundação de Apoio à Pesquisa Agrícola (Foundation for Support to Agricultural Research from Brazil, 2024). The course focused on introducing participants to essential Linux commands and basic RStudio functionalities.

In July 2025, I had the pleasure of being invited to give a lecture entitled "Bioinformatics and Diversity Indices — Bioinformatics approaches for assessing microbial diversity", in the discipline of "Microbiota and mucosal immune system interaction" in the postgraduate program in General and Applied Biology at the São Paulo State University (UNESP). The topics I covered included:
- Bioinformatics workflow in Metabarcoding
- Sampling Sufficiency: Rarefaction Curves
- Alpha Diversity Indices
- Beta Diversity Indices
- Inferential analyses in microbial diversity

I was honored to be invited to speak at the Bioprocess Engineering and Biotechnology Workshop (WEBB 2025) held at the São Paulo State University, Botucatu campus (FCA). The title of the talk was: "From Biology to Programming: The Importance of Computational Analysis in Biological Sciences."

Data Analysis

Processing biological data using bioinformatics tools to extract meaningful insights for research or business purposes.

Data Visualization

Creating clear visual representations of complex data and delivering comprehensive reports to support decision-making.

Custom Solutions

Integrating bioinformatics tools into existing systems or developing custom scripts to meet specific client needs.

Consultation and Training

Providing expert advice on project strategies and offering training sessions to upskill teams in bioinformatics techniques.

Fast Computing Solutions

Delivering quick and precise analyses using high-performance on-premise technology or scalable cloud computing resources to meet tight deadlines.

Troubleshooting

Identifying issues in existing workflows, fixing errors, and optimizing processes to improve performance and accuracy in bioinformatics analyses.

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Marcus Alvarez

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Marcus Vinicius Niz Alvarez

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