Alejandro Gil Gómez 💻

Alejandro Gil Gómez

Computational Scientist

Stony Brook Medicine and Research Computing

Professional Summary

Alejandro Gil Gómez, Ph.D., is a Computational Scientist at Stony Brook Medicine and Research Computing focused on clinical and translational research. His expertise spans end-to-end bioinformatics, AI/ML workflows, and high-performance computing (HPC). He specializes in developing scalable, reproducible pipelines for a wide array of data types, including RNA-seq differential expression, genomic variant analysis, proteomics, and spatial omics. Experienced in processing HIPAA-regulated clinical datasets, he bridges advanced computational workflows with practical biomedical discovery. He holds a Ph.D. in Ecology and Evolution from Stony Brook University and has also taught bioinformatics and mentored students in data-intensive research.

Education

PhD Ecology and Evolution

2018-08-23
2025-05-01

Stony Brook University

BSc in Biology

2013-09-23
2017-05-01

Universidad Autónoma de Madrid

Interests

Clinical and Translational Bioinformatics RNA-seq, Proteomics and Spatial Omics Reproducible Pipelines (Nextflow, nf-core) High-Performance Computing Evolution of Antibiotic Biosynthesis and Resistance Phylogenetics and Network Biology
📚 My Research

As a computational scientist with a Ph.D. in Ecology and Evolution, my mission is to study the intricate evolutionary patterns between bacteria, antibiotics, and biomolecules. Through computational methods, I explore the evolution of antibiotic resistance and their biosynthetic pathways. My work not only enhances our understanding of these fundamental processes but also holds promise for practical applications.

Areas of Focus:

Antibiotic Resistance: I focus on the genetic and molecular mechanisms behind bacterial resistance to antibiotics. By deciphering these adaptations, I contribute to the fight against drug-resistant infections.

Biosynthesis: Biomolecules are the building blocks of life. I investigate how bacteria synthesize essential compounds, uncovering novel pathways and potential targets for drug development.

Education and Mentorship: Beyond research, I am passionate about nurturing the next generation of scientists. I engage with students, fostering curiosity and creativity in the dynamic field of biology.

Collaboration Invitation:

If you share my enthusiasm for biological mysteries or have ideas for collaboration, please reach out! Let’s explore new frontiers together.

Featured Publications

Oxygen-sensing regulatory architecture structures mammalian diversification

Oxygen-sensing regulatory architecture across 239 mammalian species tracks life history, atmospheric O2, ecological specializations and cancer resistance.

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Proteome remodeling in the zoospore-to-vegetative cell transition of the stramenopile Aurantiochytrium limacinum reveals candidate ectoplasmic network proteins featured image

Proteome remodeling in the zoospore-to-vegetative cell transition of the stramenopile Aurantiochytrium limacinum reveals candidate ectoplasmic network proteins

Proteomics of the zoospore-to-vegetative cell transition in Aurantiochytrium limacinum identifies candidate proteins of the ectoplasmic network.

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Alejandro Gil Gómez
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Molecular Evolution and Systems-Level Consequences of Natural Antibiotic Biosynthesis in Bacteria

PhD dissertation on the evolution of natural antibiotics and their targets.

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Alejandro Gil Gómez
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Phylogenetic reconciliation of BGCs unveils an acceleration in evolutionary and HGT rates after the evolution of aminocoumarin antibiotics

Phylogenetic reconciliation of biosynthetic gene clusters shows an acceleration in evolutionary and horizontal gene transfer rates after the evolution of aminocoumarin antibiotics.

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Alejandro Gil Gómez
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Wiring between close nodes in molecular networks evolves more quickly than between distant nodes featured image

Wiring between close nodes in molecular networks evolves more quickly than between distant nodes

As species diverge, a wide range of evolutionary processes lead to changes in protein-protein interaction networks and metabolic networks. The rate at which molecular networks …

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Alejandro Gil Gómez
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Recent & Upcoming Talks
NVwulf Open OnDemand training featured image

NVwulf Open OnDemand training

Hands-on training with Alejandro Gil Gómez and Arshad Mehmood on NVwulf's OnDemand apps for tissue imaging and on running the MCMICRO pipeline.

Recent News
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Get in touch
Questions, ideas or collaborations? Send me a message.