Luigui Gallardo-Becerra

Software engineer

As a software developer specializing in .NET technologies, I contributed to various research projects in data science and bioinformatics, leveraging my skills in:

• Development of .NET applications: designed and implemented robust software solutions using C# and .NET Framework/Core.
• Database integration: integrated and optimized databases (SQL Server) for efficient data storage and retrieval.
• Web development: built responsive web applications using ASP.NET MVC, Razor Pages, and front-end technologies like HTML, CSS, and JavaScript.
• API development: created RESTful APIs using ASP.NET Web API for seamless integration with other systems.
• Version control and CI/CD: maintained Git repositories and implemented continuous integration/delivery pipelines using tools like Azure DevOps.
• Testing and debugging: performed unit testing and debugging to ensure software quality and reliability.
• Documentation and reporting: documented software design, implementation, and maintenance processes using tools such as Markdown and Microsoft Office.

Graduate Research Assistant (Data Science & Bioinformatics)

I was part of different research projects, from the beginning obtaining or creating the raw data to the final report or publication. The tasks that I carried out includes the following:

• Management of research projects: participated in the creation of main and secondary objectives and research questions from different projects to obtain novel biological information useful for the scientific community
• Server management (HPC): managed the Laboratory's server, installed Linux operative systems and specific software/packages, avoided server slowdowns, and built secure server environments.
• Creation of pipelines: created pipelines to avoid repetitive workflows and make reproducible analysis using bash, python, Snakemake, and Rabix Composer
• Software development: developed several software tools to solve and achieve specific goals using bash, python, Perl, and R
• Creation of plots: using R, Rstudio, Jupyter Notebooks, Excel, Graphpad, and Tableau
• Maintenance of GitHub account (CI/CD): creation and maintenance of GitHub repositories
• Creation of reports/publications: using Markdown and Word, I delivered weekly and biannual reports to the members of the Laboratory. Also, I co-authored peer-reviewed publications that are highly cited in their respective areas
• Presentations to the general public and academic events: participated in scientific dissemination, specialized seminars, and congresses

Data Analyst

I was an independent contractor and participated in several projects providing Data Sourcing and Annotation for different Appen clients (browsers, social networks, etc.). The tasks I performed were the following:

• Data collection and Preprocessing: obtention of raw data and its preprocessing before passing it to the final client or the Machine Learning Department
• Creation of weekly deliverables: for the final client or project manager
• Content translation: from Spanish to English or English to Spanish

Software Engineer (Internship)

I participated in the creation of a web application. The tasks that I carried out included:

• Creation of web app: using ASP.NET Core (C#) and Angular (JavaScript, HTML, and CSS), I created an API to save patients records and images.

Data Scientist | Bioinformatician (Internship)

I participated in the research project "Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions". The tasks that I performed were:

• Big Data Analysis: using a HPC, Linux and bash, I analyzed the 16S rRNA information of several samples
• Creation of plots: using R, Rstudio, Excel, and Python
• Software development: I developed several tools for ETL data using bash, python and Perl
• Creation of paper: with the data obtained from this internship, I co-authored this paper

Mathematics teacher

As a part-time teacher, I taught middle and high school students math classes to increase their grades or for college admission tests.

• Prepared group and individualized classes and lessons
• Applied weekly assessments to each student

This is a detailed list of the peer-reviewed publications that I co-authored. In each of them, I explain the tasks performed and highlighted relevant figures. Also, there is a link you can follow to get the published manuscript.

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

Raw data preprocessing, creation of plots, and publication writing.

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

Raw data preprocessing, creation of plots, and publication writing.

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

Raw data preprocessing, software development of specific tools, creation of plots, and publication writing.

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

Raw data preprocessing, creation of bioinformatic pipeline, creation of plots, and publication writing.

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

Raw data preprocessing, creation of bioinformatic pipeline, creation of plots, and publication writing.

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

Creation of bioinformatic pipeline, creation of plots, and publication writing.

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

Establishment of main research question, raw data preprocessing, creation of bioinformatic pipeline, software tool development, creation of plots, and publication writing.

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

Establishment of main research question, biochemical analyzes to obtain RNA, creation of Next Generation Sequencing libraries, raw data preprocessing, creation of bioinformatic pipeline, software tool development, creation of plots, and publication writing.

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

Establishment of main research question, raw data collection, raw data preprocessing, creation of bioinformatic pipeline, software tool development, creation of plots, and publication writing.

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

Raw data preprocessing, creation of bioinformatic pipeline, creation of plots, and publication writing.

Metagenomic workflow with Snakemake

In this workflow with Snakemake, I aligned metagenomic samples with bwa-mem, obtained their relative abundances, and plot the final result.

Airbnb Seattle

In this project, I downloaded the public information from Airbnb with the available rooms/apartments/houses in Seattle. With this information, I answered data questions with statistical analysis and visualizations and finally created final reports.

LittleVet webapp:

Created with HTML, CSS, Python and Django.

Created this Django web app to have a database for a little pet hospital. With this web app you can administrate Owners, Patients (Pets) and Appointments.

DESeq2 differential expression analysis:

Created with Shiny and Rstudio.

It takes two files as input (metadata and features/genes readcount). Calculate the Differential expression between groups and create a Volcano Plot in SVG format.

At the end, you can download the correlation plot of interest in SVG format.

Pearson and Spearman correlations:

Created with Shiny and Rstudio.

It takes a table as input, makes the calculation of coefficients and p-values depending on the correlation method.

At the end, you can download the correlation plot of interest in SVG format.

Nextflow pipeline for 16S profiling analysis:

Created with Nextflow.

It takes rawdata from 16S Illumina paired end sequening. It makes the quality control, the OTU clustering, the taxonomic assignation and the creation of plots, and alpha and beta diversity analysis.

National Autonomous University of Mexico, (UNAM)

Computational Biology

National Autonomous University of Mexico, (UNAM)

Computational Biology

University of Guadalajara, (UDG)

Molecular Biology