Luigui Gallardo-Becerra

luiguimichelgallardo@gmail.com

Computational Biologist and Software Engineer with 6+ years of experience building backend systems, automating complex workflows, and designing scalable data pipelines. Proficient in Python, C#, ASP.NET Core, and SQL, with a strong background in bioinformatics, HPC environments, and cloud-native development. Contributed to 14 peer-reviewed publications through machine learning models and large-scale multi-omics analysis.

Below are the links to my LinkedIn, GitHub, and ResearchGate profiles. You can also download my resume here.

Página con tutoriales de bioinformática en español.

Experience

Graduate Research Assistant (Data Science & Bioinformatics)

January 2019 - July 2025
Institute of Biotechnology, UNAM

Led and contributed to genomics and microbiome research projects by integrating molecular biology workflows with scalable computational pipelines and web tooling to support high-impact scientific findings.

  • Developed reproducible NGS analysis pipelines (Python, R, Bash, Snakemake, Nextflow) for metagenomics, metatranscriptomics, RNA-seq, and 16S datasets, reducing analysis time from days to hours.
  • Analyzed high-throughput sequencing datasets (>2 TB) using HPC and Linux systems, optimizing compute environments and improving workflow efficiency for 10+ research members.
  • Designed and implemented custom ETL and data-processing tools (Python, R, Bash, Perl) to solve research-specific challenges in microbiome and microbial genomics studies.
  • Used Git and GitHub for version control, documentation, and collaborative development in multidisciplinary teams.
  • Co-authored 14+ peer-reviewed publications in journals including Microbial Ecology, Scientific Reports, and Genes, contributing to experimental design, data analysis, and manuscript preparation.

Data Engineer

October 2016 - December 2018
Appen

Worked as an independent contractor supporting data sourcing and annotation projects for clients in technology and machine learning.

  • Collected, curated, and preprocessed structured and unstructured datasets for ML and analytics teams.
  • Prepared weekly deliverables and maintained documentation for project managers and clients.
  • Provided translation and linguistic annotation (Spanish–English) to support data quality requirements.

Software Engineer (Internship)

May 2016 - July 2016
Department of Computer Science, CUCEI (UDG)

Assisted in the development of a clinical record management web application.

  • Built REST APIs using ASP.NET Core (C#) and implemented frontend components with Angular, HTML, CSS, and JavaScript.

Data Scientist | Bioinformatician (Internship)

January 2016 - July 2016
Institute of Biotechnology, UNAM

Supported a microbiome research project analyzing bacterial community composition under different aquaculture conditions.

  • Processed and analyzed 16S rRNA sequencing datasets using Linux, HPC environments, Bash, and R.
  • Developed ETL scripts (Python, Bash, Perl) for preprocessing and feature extraction.
  • Generated visualizations and statistical analyses for publication and presentations.
  • Co-authored a peer-reviewed article published in Nature Scientific Reports.

Mathematics Teacher

January 2014 - December 2015
Student Coaching

Provided part-time mathematics instruction for high school and college-preparatory students.

  • Developed custom lesson plans and provided individual and group tutoring.
  • Designed weekly assessments to measure and improve student performance.

Research & Portfolio

Below is a selection of peer-reviewed publications I have co-authored. For each work, I briefly describe my main contributions and provide a link to the published article.

Bioactive Plasmid- and Phage-Encoded Antimicrobial Peptides (AMPs) in the Human Gut: A Metatranscriptome–Virome Profiling Reveals Exploratory Links to Metabolic Human Diseases (2025)

  • Defined the main research question; performed raw data preprocessing; developed the bioinformatics pipeline and custom tools; generated figures; and contributed to manuscript writing.
AMP discovery pipeline

Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective (2025)

  • Helped define the research question; performed raw data preprocessing; built the bioinformatics pipeline and analysis workflows; created figures; and contributed to manuscript writing.
hologenome perspective

Environmental Enrichment Prevents Gut Dysbiosis Progression and Enhances Glucose Metabolism in High-Fat Diet-Induced Obese Mice (2024)

  • Performed raw sequencing data preprocessing; designed and executed the bioinformatics pipeline; generated figures; and contributed to manuscript preparation.
environmental enrichment mice

Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota (2023)

  • Led the conceptual design; performed data preprocessing; developed analysis pipelines and custom tools; created figures; and co-wrote the manuscript.
antimicrobial peptides

Complete genome sequence and characterization of a novel Enterococcus faecium with probiotic potential isolated from the gut of Litopenaeus vannamei (2023)

  • Preprocessed raw sequencing data, supported genome analysis, created figures, and contributed to manuscript writing.
enterococcus

White spot syndrome virus impact on the expression of immune genes and gut microbiome of black tiger shrimp Penaeus monodon (2023)

  • Performed raw data preprocessing, supported downstream analyses, generated figures, and contributed to manuscript drafting.
white spot syndrome

The Two-Faced Role of crAssphage Subfamilies in Obesity and Metabolic Syndrome: Between Good and Evil (2023)

  • Preprocessed sequencing data; developed project-specific software tools; created figures; and co-authored the manuscript.
crAssphage

Transcriptome Analysis of Soursop (Annona muricata L.) Fruit under Postharvest Storage Identifies Genes Families Involved in Ripening (2022)

  • Preprocessed RNA-seq data; developed the analysis pipeline; generated figures; and contributed to manuscript writing.
soursop transcriptome

Agavin induces beneficial microbes in the shrimp microbiota under farming conditions (2022)

  • Preprocessed raw sequencing data; implemented bioinformatics workflows; created figures; and participated in manuscript preparation.
agavin shrimp

Protocol for the isolation, sequencing, and analysis of the gut phageome from human fecal samples (2022)

  • Designed and implemented the bioinformatics pipeline; generated figures; and co-wrote sections of the protocol.
phageome protocol

Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome (2021)

  • Helped define the research question; performed data preprocessing; built analysis pipelines and custom tools; generated figures; and co-authored the manuscript.
gut virome

Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children (2020)

  • Contributed to defining the research question; performed biochemical work to obtain RNA and prepare NGS libraries; preprocessed sequencing data; developed bioinformatics pipelines and tools; created figures; and co-wrote the manuscript.
secrebiome

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota (2018)

  • Helped define the research question; collected and curated raw data; performed preprocessing; built bioinformatics workflows and custom tools; created figures; and contributed to manuscript writing.
shrimp meta-analysis

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions (2017)

  • Preprocessed sequencing data; developed analysis pipelines; generated figures; and contributed to manuscript preparation.
shrimp microbiome

Metagenomic Workflow with Snakemake

  • Implemented a Snakemake workflow to align metagenomic samples with BWA-MEM, compute relative abundances, and generate summary plots for downstream interpretation.
snakemake workflow snakemake results

Airbnb Seattle Data Analysis

  • Downloaded and cleaned public Airbnb data for Seattle; performed exploratory and statistical analyses; and created visualizations to answer business-driven questions and build a coherent data story.
airbnb analysis 1 airbnb analysis 2 airbnb analysis 3

Applications and Pipelines

LittleVet – Veterinary Clinic Management Web Application

  • Developed using Python, Django, HTML, and CSS.
  • Designed a full-stack system for managing clients, pets, appointments, and clinic records.
  • Implemented secure authentication and structured data models for scalable workflow management.

DESeq2 Differential Expression Analysis Tool

  • Developed using R, Shiny, and RStudio.
  • Automates differential expression analysis from metadata and read-count matrices.
  • Generates publication-ready volcano plots and correlation visualizations (SVG format).

Pearson and Spearman Correlation Analysis Tool

  • Built using Shiny and R for interactive correlation analysis.
  • Accepts tabular input and computes Pearson or Spearman correlations with statistical significance.
  • Provides downloadable, publication-ready correlation plots in SVG format.

Nextflow Pipeline for 16S rRNA Profiling Analysis

  • Developed using Nextflow to automate reproducible 16S rRNA workflows.
  • Processes Illumina paired-end reads through QC, OTU clustering, taxonomy assignment, and diversity analyses.
  • Generates standardized outputs compatible with downstream visualization platforms.

Education

National Autonomous University of Mexico (UNAM)

Ph.D. in Computational Biology
Thesis Research
January 2019 – July 2025

National Autonomous University of Mexico (UNAM)

Master of Science in Computational Biology
Thesis Research
August 2016 – January 2019

University of Guadalajara (UDG)

Bachelor of Science in Molecular Biology
Thesis Research
August 2012 – January 2016

Skills

Software Engineer with a strong background in backend development, cloud-native solutions, and scalable data systems. Experienced in building web applications with ASP.NET Core, designing ETL pipelines, and automating complex workflows. Fast learner with excellent problem-solving abilities and strong adaptability across diverse technologies.

Programming Languages & Tools
  • C#, ASP.NET Core, Python, SQL, Bash, JavaScript, R, HTML/CSS
  • Architecture: Clean Architecture, REST APIs, ETL Pipelines
  • Linux, Docker, AWS, Git/GitHub, CI/CD workflows
  • Databases: SQL Server, MySQL, PostgreSQL, Dapper
Bioinformatics & Computational Biology
  • NGS workflows: RNA-seq, WGS, 16S, metagenomics, metatranscriptomics, viromics
  • Pipeline development with Snakemake, Nextflow, Bash, Python, and R
  • Genome & transcriptome assembly (Trinity, SPAdes) and annotation
  • Differential expression, taxonomic profiling, pathway analysis
  • Sequence alignment & QC: Bowtie2, HISAT2, BWA, samtools, fastp, Kraken2
  • ETL automation and custom tool development for multi-omics data
Data Engineering & Cloud
  • ETL pipeline design and automation (Python, Bash, Apache Spark)
  • HPC / SLURM, Nextflow, Snakemake workflow orchestration
  • AWS cloud infrastructure, containerization with Docker
Languages
  • English – Full professional proficiency
  • Spanish – Native

Interests

I enjoy outdoor activities such as hiking, camping, and mountain biking, which help me stay active and connected to nature. At home, I appreciate classic films and television series as a way to unwind. I also dedicate time to exploring new developments in informatics, biotechnology, and scientific research, continually expanding my knowledge in these fast-evolving fields.

Awards & Certifications

  • FullStack Academy – Software Development Bootcamp (2023)
  • Google Data Analytics Specialization (2022)
  • Data Scientist: Machine Learning Specialization – Codecademy (2021)
  • Maximum Cum Laude – Bachelor’s Degree (2017)
  • First Place – XVI State Contest of Physics Devices and Experiments (2011)
  • Honorable Mention – ExpoCiencias Nacional, Tlaxcala (Science Dissemination Project, 2010)
  • Second Place – XXIII Mexican Mathematics Olympiad, State Competition (2010)
  • Third Place – XIX University Mathematics Olympiad (2009)
  • Second Place – XXI University Mathematics Olympiad, State Competition (2009)