Gabriel - CV

CURRICULUM

VITAE

WORK EXPERIENCE
Genome language model trainingFour stacked transformer blocks on the left feed four GPU nodes on the right via gradient-sync arrows, with a 2B parameter callout.2B

January 2024 — Present

HEAD OF MACHINE LEARNING AND BIOINFORMATICS

TRIPLEBAR

  • Designed and trained 2B-parameter genome language model on 4,000 fungal genomes using multi-node distributed training (16 GPUs), achieving 15% improvement in variant effect prediction.
  • Fine-tuned 8B foundation models for genotype-phenotype prediction, implementing custom PyTorch workflows with gradient checkpointing and mixed-precision training.
  • Applied protein structure prediction (Boltz, ESM) and diffusion-based design (RFDiffusion) to develop naïve antibody screening strategies, reducing costs by 40%.
  • Architected cloud-native genomic analysis pipeline processing 200+ whole genomes weekly, reducing variant calling time from 72 to 2 hours using GATK and NVIDIA Parabricks on GCP Vertex AI.
Multi-omics integrationThree horizontal lanes representing genomics, proteomics, and metabolomics converge into a single candidate gene node on the right.GPM

December 2021 — December 2023

DATA SCIENTIST III

AMYRIS

  • Built end-to-end multi-omics data platform integrating genomics, proteomics, and metabolomics for candidate gene identification.
  • Developed unsupervised learning pipeline for metabolite clustering using dimensionality reduction (UMAP, t-SNE) and hierarchical clustering.
  • Implemented automated feature extraction from mass spectrometry data using convolutional neural networks, achieving 92% accuracy in compound classification.
LC-MS spectral matchingChromatogram peaks at the top feed a small convolutional neural network box, producing a spectral match score shown as peaks at the bottom.CNN

March 2020 — November 2021

SENIOR SCIENTIST, COMPUTATIONAL METABOLOMICS

HEXAGON BIO

  • Developed high-throughput metabolomics pipeline processing 4+ TB of LC-MS/MS data, reducing analysis time from weeks to days.
  • Built deep learning models for retention time prediction and spectral matching, improving accuracy by 35%.
  • Accelerated natural product discovery pipeline by 5x through integration of computational predictions with experimental validation.
Forager bioactive discovery funnelA funnel narrows from twenty thousand candidate compounds down to fifty bioactives, with a one hundred times throughput callout.100x

February 2018 — February 2020

LEAD SCIENTIST, COMPUTATIONAL METABOLOMICS

BRIGHTSEED

  • Architected 'Forager' AI platform achieving 100x increase in phytonutrient identification throughput for 20,000+ compounds.
  • Developed custom molecular fingerprinting and supervised learning models to identify 50+ novel bioactive molecules.
  • Led initiatives connecting computational predictions to experimental design, resulting in 2 patent applications.
Real-time QC gateThree factory floor nodes on the left feed a machine learning decision gate on the right, with a ninety percent QC throughput callout.90%

January 2016 — January 2018

SENIOR SCIENTIST, MASS SPECTROMETRY SPECIALIST

MONDELEZ INTERNATIONAL

  • Developed machine learning-based QC algorithms reducing mass spectrometry analysis time by 90% across 3 global manufacturing facilities.
  • Implemented automated decision systems for real-time quality control at industrial scale.
EDUCATION

2014 — 2015

POSTDOCTORAL RESEARCHER, IRACDA FELLOW

UNIVERSITY OF CALIFORNIA, SAN DIEGO

2008 — 2013

PHD IN CHEMISTRY, NSF GRFP FELLOW

UNIVERSITY OF CALIFORNIA SANTA CRUZ

2004 — 2008

BACHELOR OF SCIENCE IN CHEMICAL BIOLOGY

UNIVERSITY OF CALIFORNIA BERKELEY

SKILLS

FOUNDATION MODELS & ML

  • Pre-training, fine-tuning, evaluation framework design
  • Genomic & Protein Language Models (Evo2, ESM, Boltz)
  • Diffusion Models (RFDiffusion) for antibody design
  • Distributed training (DDP, FSDP, Megatron-LM), Multi-GPU clusters

COMPUTATIONAL BIOLOGY

  • Variant calling (GATK, Parabricks), Genome assembly
  • LC-MS/MS analysis (targeted & untargeted), Antibody design
  • Biological Databases: NCBI, UniProt, PDB, MassIVE
  • Chemistry: RDKit, molecular fingerprinting, SAR analysis

SOFTWARE & INFRASTRUCTURE

  • Python, R, SQL, Bash, JavaScript, Java
  • PyTorch, Lightning, BioNeMo, Scikit-learn
  • Cloud: GCP (Vertex AI), AWS, Docker, Kubernetes
  • DevOps: Git, CI/CD, reproducible workflows
PATENTS

2023

EXTRACT, CONSUMABLE PRODUCT AND METHOD FOR ENRICHING BIOACTIVE METABOLITE IN AN EXTRACT

Chae, L. H., Flatt, J., Herrmann, A. M., Navarro, G., Ochoa, J. L.

VIEW PATENT →

2016

METHODS FOR MAKING AND USING NOVEL SEMI-SYNTHETIC SMALL MOLECULES FOR THE TREATMENT PARASITIC DISEASE

Roger R Linington, Gabriel Navarro, Khanitha Pudhom, James McKerrow

VIEW PATENT →

2015

SEMI-SYNTHETIC SMALL MOLECULES FOR THE TREATMENT PARASITIC DISEASE

Roger Linington, Gabriel Navarro, Khanitha Pudhom, James McKerrow

VIEW PATENT →

2014

NOVEL SEMI-SYNTHETIC SMALL MOLECULES FOR THE TREATMENT PARASITIC DISEASE

Khanitha Pudhom, Gabriel Navarro, James McKerrow, Roger Linington

VIEW PATENT →
PUBLICATIONS

TAU OLIGOMERS MODULATE SYNAPSE FATE BY ELICITING PROGRESSIVE BIPARTITE SYNAPSE DYSREGULATION AND SYNAPSE LOSS

Pareja-Navarro, K. A., King, C. D., Kauwe, G., Ngwala, Y. Y., Lokitiyakul, D., Wong, I., Vira, A., Chen, J. H., Sharma, M., Navarro, G.

bioRxiv (Under Review: Molecular Neurodegeneration), 2026

PORTOBELAMIDES A AND B AND CACIQUEAMIDE, CYTOTOXIC PEPTIDIC NATURAL PRODUCTS FROM A CALDORA SP. MARINE CYANOBACTERIUM

Demirkiran, O., Almaliti, J., Leao, T., Navarro, G., Byrum, T., Valeriote, F. A., Gerwick, L., Gerwick, W. H.

Journal of Natural Products, 84(8), 2081-2093, 2021

EVALUATING NITROGEN-CONTAINING BIOSYNTHETIC PRODUCTS PRODUCED BY SALTWATER CULTURING OF SEVERAL CALIFORNIA LITTORAL ZONE GRAM-NEGATIVE BACTERIA

Lorig-Roach, N., Still, P. C., Coppage, D., Compton, J. E., Crews, M. S., Navarro, G., Tenney, K., Crews, P.

Journal of Natural Products, 80(8), 2304-2310, 2017

BIOFILM FORMATION AND DETACHMENT IN GRAM-NEGATIVE PATHOGENS IS MODULATED BY SELECT BILE ACIDS

Sanchez, L. M., Cheng, A. T., Warner, C. J. A., Townsley, L., Peach, K. C., Navarro, G., Shikuma, N. J., Bray, W. M., Riener, R. M., Yildiz, F. H.

PLoS One, 11(3), e0149603, 2016

KALKIPYRONE B, A MARINE CYANOBACTERIAL Γ-PYRONE POSSESSING CYTOTOXIC AND ANTI-FUNGAL ACTIVITIES

Bertin, M. J., Demirkiran, O., Navarro, G., Moss, N. A., Lee, J., Goldgof, G. M., Vigil, E., Winzeler, E. A., Valeriote, F. A., Gerwick, W. H.

Phytochemistry, 122, 113-118, 2016

SALINIPOSTINS A–K, LONG-CHAIN BICYCLIC PHOSPHOTRIESTERS AS A POTENT AND SELECTIVE ANTIMALARIAL CHEMOTYPE

Navarro, G., Schulze, C. J., Ebert, D., DeRisi, J., Linington, R. G.

The Journal of Organic Chemistry, 80(3), 1312-1320, 2015

ABYSSOMICIN 2 REACTIVATES LATENT HIV-1 BY A PKC- AND HDAC-INDEPENDENT MECHANISM

Navarro, G., León, B., Dickey, B. J., Stepan, G., Tsai, A., Jones, G. S., Morales, M. E., Barnes, T., Ahmadyar, S., Tsiang, M.

Organic Letters, 17(2), 262-265, 2015

ISOLATION OF POLYCAVERNOSIDE D FROM A MARINE CYANOBACTERIUM

Navarro, G., Cummings, M. E., Lee, J., Moss, N., Glukhov, E., Valeriote, F. A., Gerwick, L., Gerwick, W. H.

Environmental Science & Technology Letters, 2(7), 166-170, 2015

MASS SPECTROMETRY TOOLS FOR SCREENING OF MARINE CYANOBACTERIAL NATURAL PRODUCTS

Knaan, T. L., Garg, N., Peng, Y., Alexandrov, T., Navarro, G., Glukhov, E., Gerwick, L., Gerwick, W. H., Dorrestein, P. C.

Planta Medica, 81(11), PQ6, 2015

HONAUCIN A, MECHANISM OF ACTION AND ROLE AS A POTENTIAL CANCER PREVENTION AGENT

Gerwick, L., Mascuch, S. J., Navarro, G., Boudreau, P., Carland, T. M., Gaasterland, T., Gerwick, W. H.

Planta Medica, 81(11), PW2, 2015

IMAGE-BASED 384-WELL HIGH-THROUGHPUT SCREENING METHOD FOR THE DISCOVERY OF SKYLLAMYCINS A TO C AS BIOFILM INHIBITORS AND INDUCERS OF BIOFILM DETACHMENT IN PSEUDOMONAS AERUGINOSA

Navarro, G., Cheng, A. T., Peach, K. C., Bray, W. M., Bernan, V. S., Yildiz, F. H., Linington, R. G.

Antimicrobial Agents and Chemotherapy, 58(2), 1092-1099, 2014

HIT-TO-LEAD DEVELOPMENT OF THE CHAMIGRANE ENDOPEROXIDE MERULIN A FOR THE TREATMENT OF AFRICAN SLEEPING SICKNESS

Navarro, G., Chokpaiboon, S., De Muylder, G., Bray, W. M., Nisam, S. C., McKerrow, J. H., Pudhom, K., Linington, R. G.

PLoS Neglected Tropical Diseases (or similar), 2012

AN IMAGE-BASED 384-WELL HIGH-THROUGHPUT SCREENING METHOD FOR PHENOTYPIC DISCOVERY OF BIOFILM INHIBITORS IN PSEUDOMONAS AERUGINOSA

Navarro, G., Peach, K. C., Cheng, A., Bray, W. M., Yildiz, F. H., Linington, R. G.

Planta Medica, 78(11), PD145, 2012

VERSATILE METHOD FOR THE DETECTION OF COVALENTLY BOUND SUBSTRATES ON SOLID SUPPORTS BY DART MASS SPECTROMETRY

Sanchez, L. M., Curtis, M. E., Bracamonte, B. E., Kurita, K. L., Navarro, G., Sparkman, O. D., Linington, R. G.

Organic Letters, 2011

HIGHLIGHTS OF MARINE INVERTEBRATE-DERIVED BIOSYNTHETIC PRODUCTS: THEIR BIOMEDICAL POTENTIAL AND POSSIBLE PRODUCTION BY MICROBIAL ASSOCIANTS

Radjasa, O. K., Vaske, Y. M., Navarro, G., Vervoort, H. C., Tenney, K., Linington, R. G., Crews, P.

Bioorganic & Medicinal Chemistry, 2011

BIOMIMETIC SYNTHESIS OF THE SHIMALACTONES

Sofiyev, V., Navarro, G., Trauner, D.

Organic Letters, 10(1), 149-152, 2008

GABRIEL

Computational biology × foundation models

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© 2026 Gabriel Navarro

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