Open to opportunities

Ignacio Ibarra

@ignacioibarra

Message

Computational biologist and ML researcher focused on generative modeling.

Germany

Message

What I'm looking for

I seek hands-on roles building and deploying ML models for genomics, with collaborative teams, clear impact, and opportunities to lead technical roadmaps and mentor junior scientists.

I am a computational biologist and machine learning researcher with over a decade of experience across academia and startups, specializing in generative modeling, single-cell genomics, and functional genomics. I have led multidisciplinary projects, shipped production-ready ML workflows, coordinated international consortia, and contributed to numerous high-impact publications cited widely.

As a hands-on scientist-engineer, I develop models in Python/PyTorch, build reproducible omics pipelines, and drive technical roadmaps that deliver MVPs and improve computing performance. I enjoy mentoring teams, obtaining grant funding, and translating advanced ML methods into translational medicine solutions.

Experience

Work history, roles, and key accomplishments

Current

Independent ML Consultant

Current

Ignacio L. Ibarra

Mar 2025 - Present (6 months)

Provide ML consulting and production-ready algorithmic workflows for biotech and startups, delivering solutions with 100% client approval and reducing deployment costs in iterative projects.

Python PyTorch CI CD Bioinformatics Algorithm Design

Director

Bioptimus

Sep 2024 - Feb 2025 (5 months)

Led development of a 'ChatGPT for Biology' MVP, defined technical roadmap, and shipped a working product within two quarters while building the early biotech team.

Product Roadmap Python PyTorch Model Interpretability Team Leadership Software Development Git

Postdoctoral Fellow

Helmholtz München

Sep 2024 - Feb 2025 (5 months)

Developed generative models for transcriptomic perturbations and benchmarked single-cell atlas workflows, improving compute times by 50% and coordinating multi-lab consortium projects.

Generative Models Python PyTorch AWS Benchmarking

Predoctoral Fellow

EMBL Heidelberg

Sep 2015 - Feb 2020 (4 years 5 months)

Developed QC-approved omics workflows (scATAC/scRNA/ChIP/SELEX), led international collaborations, and published multiple high-impact papers with widely reused methods.

QC Pipelines R Python Publications Bioinformatics

Research Assistant

CABD Seville

Mar 2015 - Oct 2015 (7 months)

Developed DP-algorithms for protein structure alignment, reducing computation time in structural comparisons by over 25%.

Algorithm Design Dynamic Programming Python Performance Optimization Computational Biology

Research Assistant

Pontifical Catholic University of Chile

Jan 2012 - Sep 2014 (2 years 8 months)

Built structural bioinformatics models and algorithms for protein-DNA studies, contributing to method development during doctoral training.

Bioinformatics Algorithm Development Biochemistry Python

Intern

BII Singapore

Aug 2011 - Dec 2011 (4 months)

Modeled DNA and protein–DNA structures via spatial restraints and provided structural models to accelerate experimental docking studies.

Structural Biology Spatial Restraints Python

Education

Degrees, certifications, and relevant coursework

EMBL Heidelberg

Doctor of Philosophy, Computational Biology

2015 - 2019

Grade: 1.1 (magna cum laude)

Activities and societies: Thesis work, international collaborations, publications and consortium project coordination.

Joint PhD in Computational Biology with Ruprecht-Karls-Universität Heidelberg focusing on integrative modeling of transcription factor cooperativity and phenotypic variability; graduated magna cum laude.