Bioinformatics · Mathematics · Open Science

Joaquin Auzenne

Interdisciplinary scientist from UT Austin bridging quantitative theory and experimental execution — at the intersection of mathematics, computation, and biology.

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Joaquin Auzenne
Dual B.S.
Mathematics, Computational Biology
5+
Years Research
4
Previous Research Roles
Bilingual
English, French
Metabarcoding Transcriptomics Neurolinguistics Predictive Modeling Statistical Learning Dynamical Systems
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About Me

I’m Joaquin — a recent graduate (‘25) from the University of Texas at Austin with a B.S. in Mathematics and a B.S. in Computational Biology, along with a Certificate in Scientific Computation and Data Sciences.

I’m an interdisciplinary scientist focused on engineering high-fidelity solutions for complex biological systems. My work treats biological data as a mathematical landscape to be decoded through predictive modeling and robust pipeline engineering — whether building eDNA metabarcoding workflows for conservation, designing metabolic pathways for sustainable chemistry, or forecasting pharmaceutical logistics.

I’m currently interested in metabarcoding for conservation and species identification, the evolution of language in primates and neurolinguistics, and tackling hard interdisciplinary problems through applications of mathematics — statistics, modeling, analysis, and beyond.

I support open science and the FAIR principles: scientific data should be Findable, Accessible, Interoperable, and Reusable for all. I’m always looking to collaborate on exciting research projects!

Pronouns: he / him · ⚡ I love learning languages through music, film, and reading!

Currently Learning
  • Dialectical Biologist by Richard Levins, Richard Lewontin
  • Functional Analysis for Applied Math by Todd Arbogast
  • Topics in Algebra by I.N. Herstein
Research Interests
  • eDNA Metabarcoding & Conservation
  • Primate Neurolinguistics
  • Transcriptomics & 'Omics Data
  • GenAI & LLM Applications with RAG
Languages
English Native
French Fluent
Spanish Conversational
Japanese Novice
Education
  • B.S. Mathematics · UT Austin '25
  • B.S. Computational Biology · UT Austin '25
  • Cert. Scientific Computation & Data Sciences
  • Polymathic Scholars Honors
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Experience & Education

Download CV
Dec 2024 – Present Austin, TX
Bioinformatic Assistant
DiFiore Lab, University of Texas at Austin
  • Developed a mammalian metabarcoding pipeline for pre-processing and consensus sequence clustering of Nanopore MinION-sequenced environmental DNA (83 soil samples, ~6M reads) in Shell script for taxonomic assignment via BLAST+.
  • Integrated multiple public domain databases (NCBI, IUCN) using the GBIF Metabarcoding Data Toolkit API for comprehensive species identification and interactive species-range visualization (ArcGIS).
  • Established a curated DNA reference library of mammals identified along the Magdalena River in Colombia, focusing on rRNA genetic markers (12S, 16S).
  • Delivered consensus sequences ready for longitudinal population and dispersal analyses using MinION MKICN Nanopore sequencing, MultiQC, NGSpeciesID read clustering, and megaBLAST taxonomic assignment.
Jan 2022 – Sept 2023 Austin, TX
Undergraduate Researcher & Teaching Mentor
FRI EvoDevOmics, University of Texas at Austin
  • Designed high-throughput transcriptomic pipelines (preprocessing, quality control, alignment) in R on BRCF HPC clusters to reveal the basis of embryonic diversification in Dendrobatid frogs via differential gene expression analyses (DESeq2, WGCNA, PCA, nearest-neighbors clustering).
  • Employed Python tool IdMiner for automated literature searches through the PaperBLAST database (PubMed, NCBI) to functionally annotate 40+ differentially expressed genes.
  • Served as Teaching Assistant for a computational biology course of 20+ students, covering next-generation sequencing, omics data analysis, FAIR digital resource stewardship, and career readiness under Rebecca Young, PhD.
  • Presented weekly lessons on statistical methods (MANOVA, PCA, WGCNA) to student cohorts, translating complex bioinformatic concepts for undergraduate audiences.
Feb 2020 – May 2021 Denton, TX
Undergraduate Research Assistant
Henard Lab, University of North Texas BioDiscovery Institute
  • Awarded $500 competitive grant to design a shikimate biosynthesis pathway in plasmid-modified E. coli (Gibson assembly) as a "green chemistry" alternative for nylon precursor production in a scalable methane-fed bioreactor.
  • Maintained E. coli and methanotrophic cultures; evaluated methane production within continuous-stirred tank reactors; performed qRT-PCR confirmation of engineered shikimate-pathway constructs.
  • Conducted daily hood upkeep, sterility checks, liquid chromatography analysis, and detailed laboratory record-keeping.
  • Adapted "Muconic acid production from methane using rationally-engineered methanotrophic biocatalysts" (Henard et al.) for Frontiers for Young Minds, translating advanced metabolic engineering concepts for a younger audience.
Oct 2019 – Jun 2020 Denton, TX
Reptile Care & Research Assistant
Crossley Lab, University of North Texas Integrative Biology
  • Oversaw daily feeding, tank maintenance, and husbandry for 30+ tanks of large laboratory reptiles (Alligator mississippiensis, Chelydra serpentina); provided on-call emergency support including animal restraint, transport, and surgical assistance.
  • Conducted cardiorespiratory physiological study of alligators and snapping turtles birthed under normoxic and hypoxic conditions via controlled treadmill exercise and blood gas centrifugation.
Jan 2024 – Aug 2024 Austin, TX
Consultant Machinist
Paradigm Robotics
  • Fabricated and assembled mechanical components for fire-resistant robotic systems (FireBot), translating CAD designs into G-code and operating mill/lathe equipment; collaborated with engineers on design iterations and equipment modifications.
May 2023 – Aug 2023 Dakar, Senegal
Data Analysis Intern
Tanel Health (Heman Sweatt Center for Black Males, UT Austin)
  • Implemented gradient boosting and regression (XGBoost, SARIMA) on pharmaceutical sales data to improve back-end inventory forecasting on AWS, with projected waste reduction of up to 20% across 200+ in-network enterprises.
  • Created technical reports justifying predictive model selections to shareholders, including associated performance metrics and visualizations (Python: matplotlib, Plotly).
  • Digitized prescriptions and integrated a two-factor QR-based prescription authentication system into a 10,000+ customer database, improving compliance and fraud prevention.
  • Collaborated with an interdisciplinary team of healthcare providers and software developers in a cross-cultural environment, adhering to strict data privacy standards.
Aug 2021 – Nov 2022 Austin, TX
CNC Machinist & Programmer
Carr Lane Manufacturing
  • Trained new CNC machinists, performed GD&T quality inspections, and maintained 5S standards while machining on HAAS/DMG Mori mills and lathes; programmed overnight production runs increasing weekly machining output by 24+ hours.
  • Led evening shift operations, maintaining detailed maintenance logs for tool performance, inventory tracking, and equipment status; documented procedures in SOPs for consistent quality and safety compliance.
  • Performed preventive maintenance on CNC equipment including coolant system monitoring, chip evacuation checks, and tool audits to ensure optimal machine performance and prevent unplanned downtime.
  • Collaborated with the engineering team to troubleshoot process issues and recommend equipment modifications, communicating technical problems and proposed solutions to improve production efficiency.
Aug 2021 – May 2025 Austin, TX
B.S. Mathematics & B.S. Computational Biology
University of Texas at Austin · Certificate in Scientific Computation and Data Sciences
  • College of Natural Sciences Polymathic Scholars Honors
  • Thesis: DNA Metabarcoding of Soil Samples from the Magdalena River Valley
  • Courses: Applied Data Analysis, Bioinformatics, Predictive Analytics, Mathematical Modeling, Systems Biology of Stem Cells, Functional Analysis, Social and Biological Networks, Scientific Computing in Numerical Analysis, Environmental Epigenetics, Microbial Genetics, Language and the Brain
Aug 2019 – May 2021 Denton, TX
Pre-Major Studies in Biology & Chemistry
University of North Texas (transferred to UT Austin)
  • Research at Henard Lab (metabolic engineering) and Crossley Lab (reptile cardiorespiratory physiology)
2022 – 2023 Austin, TX
SIAM Directed Reading Program
University of Texas at Austin
  • Engaged in advanced independent study in applied mathematics under faculty mentorship, culminating in a formal literature review presentation.
Certifications
Professional Certifications
Industry Training
  • MSSC Certified Production Technician
  • Lean Six Sigma White Belt
  • OSHA-10 General Industry Safety Certification
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Skills & Toolkit

Programming
Python pandas scikit-learn PyTorch TensorFlow R tidyverse ggplot2 Shiny MCMCglmm nlme SQL Bash / Shell MATLAB (PINNs) Java HTML / CSS C++ SLURM / HPC
Bioinformatics
Illumina (NextSeq, NovaSeq) ONT MinION / MKICN Cutadapt FastQC / MultiQC NanoPlot STAR / Salmon Kallisto NGSpeciesID BWA-MEM2 DESeq2 WGCNA AlphaFold2 Variant Calling Benchling (LIMS)
Data Analysis
SAS SPSS Tableau PCA ANCOVA MLE XGBoost SARIMA NLP GenAI / LLM RAG ggplot2 matplotlib Plotly AWS FAIR Data Management
Wet Lab
PCR / qPCR / ddPCR DNA / RNA Extraction SDS-PAGE Media Preparation Gibson Assembly CRISPR / Cas iPSC Anaerobic Culture (Coy) Light Microscopy Gram Staining Plate Preparation Transfection Centrifugation Blood Gas Analysis Cleanroom Operations
Animal & Field Work
Laboratory Animal Handling Behavioral Observations Physiological Data Collection Specimen Transport Animal Restraint Environmental DNA Sampling
Manufacturing & Engineering
CNC (HAAS / DMG Mori) G-Code GD&T AutoCAD SolidWorks 3D Printing Carbon Fiber Fabrication Lean Six Sigma OSHA-10
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Selected Projects

Project 01
COVID-19 Spatiotemporal Network Dynamics
Dept. of Integrative Biology · UT Austin · Oct–Dec 2024

Built spatial network time-series models of U.S. COVID-19 spread (32M cases, Apr 2020–Apr 2021) with R/Shiny interactive maps, dashboards, and weighted network centrality statistics to identify transmission hubs and inform public health intervention strategies.

R / Shiny Network Analysis Time Series Epidemiology
Project 02
IdMiner — Bioinformatic Literature Search Tool
FRI EvoDevOmics · UT Austin · 2022–2023

Co-developed a Python-based automated literature mining tool using BeautifulSoup to query PaperBLAST (1M+ papers across PubMed and NCBI) for gene-associated publications, validating 40+ differentially expressed gene annotations in frog embryonic transcriptomics research.

Python PaperBLAST Web Scraping Functional Annotation Transcriptomics
Project 03
Longhorn Racing — Composites Division
LHR Combustion Team · UT Austin · Sep 2021–May 2022

Fabricated carbon fiber and fiberglass structural components for Formula SAE race cars, developing precision handling techniques under strict quality and safety standards. Designed a lightweight carbon fiber steering wheel and other structural components optimized for weight reduction and heat dissipation.

Carbon Fiber Composites SolidWorks Formula SAE
Project 04
Mammalian Metabarcoding & Species-Range Visualization Platform
DiFiore Lab · UT Austin · Dec 2024–Present

Developed an interactive web application presenting Nanopore eDNA genomic analyses as user-friendly interfaces for both scientific and public audiences, integrating sequencing results with geospatial species-range data for the Magdalena River Valley.

eDNA ONT MinION Bash megaBLAST ArcGIS Conservation
Project 05
Methanotroph Metabolic Engineering
Henard Lab · UNT BioDiscovery Institute · 2020–2021

Awarded $500 to design a shikimate biosynthesis pathway for plasmid-modified E. coli (Gibson assembly) as a green-chemistry alternative for nylon production in a scalable methane-fed bioreactor. Adapted "Muconic acid production from methane using rationally-engineered methanotrophic biocatalysts" (Henard et al.) for Frontiers for Young Minds.

Metabolic Engineering Gibson Assembly qRT-PCR Science Communication
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Get in Touch

I'm always open to collaborating on exciting research projects, discussing bioinformatics, applied mathematics, philosophy, or anything else! Feel free to reach out through any of the channels below.

Work auzenne.work@gmail.com Academic joaquinauzenne@utexas.edu LinkedIn linkedin.com/in/auzenneworks GitHub github.com/joaquinauzenne Phone +1 (512) 228-2719
Location
Austin, TX
Affiliation
University of Texas at Austin
Pronouns
He / Him
Open To
Research collaborations, interdisciplinary projects, open science initiatives
References
Dr. Anthony Di Fiore · Dr. Rebecca Young · Dr. Calvin Henard