Hi, my name is

Daniel J. Gomez

I find answers to clinical research questions.

Bioinformatics Scientist focusing on Clinical Computational Science at Stanford.

Daniel Gomez
Daniel J. Gomez

About Me

I am Daniel Joseph Gomez, a Graduate Researcher in the Snyder Lab at Stanford Genetics.

My research focuses on:

  • Multi-omics Analysis
  • Digital Twins & AI Virtual Cells and Tissue
  • Spatial-omics & Single-cell Genomics
  • Exercise Interorgan Crosstalking Maps
  • Large-scale Datasets from innovative consortia: MoTrPAC, HuBMAP, HTAN, Human Cell Atlas

I build computational frameworks to translate high-throughput data into clinical insights.

Core Research & Tech Stack:

  • Spatial Multi-omics
  • Generative AI / Virtual Cells
  • Bioinformatics (R/Python)
  • Computational Systems Immunology
  • Single-cell Analysis
  • Clinical Digital Twins

Experience

Graduate Research Fellow

@ Stanford (Snyder Lab)
2023 – Present
  • Leading the computational integration of multiple next-generation computational tools for spatial multi-omics analysis.
  • Developing AI Virtual Cells and digital twins for personalized clinical predictions.
  • Generating Spatial Maps for large-scale data in consortia HuBMAP, HTAN, and PsychENCODE.
  • Analyzing single-cell genomics data to bridge molecular physiology and immunotherapy.
  • Collaborating on MoTrPAC and other large-scale multi-omics consortium projects.

Teaching Associate

@ California State University - East Bay
Aug 2022 - Jan 2023
Hayward, CA
  • Clinical Microbiology (BIO230): Taught lab sections covering identification and culture techniques of microorganisms for health sciences and nursing majors.
  • Human Anatomy and Physiology I (BIO270): Led lab analysis of skeletal, muscular, nervous, cardiovascular, and respiratory systems.
  • Managed sections of ~20 university students and collaborated with faculty on curriculum delivery.

Lab Assistant II

@ Roche
May 2022 - Aug 2022
Pleasanton, CA
  • Antibody Formulation: Assisted in molecular assay development and execution within the Roche Tissue Diagnostics (RTD) Global Operations.
  • Supported the development of Companion Diagnostics and IVD products for personalized healthcare.
  • Executed quality control of lab reagents and performed precise buffer preparation for tissue diagnostic protocols.

Formulations Operator II

@ Thermo Fisher Scientific
2019 – 2022
Pleasanton, CA
  • TAPP Robotics Lab: Operated high-throughput robotics including Hamilton Microlab Star, TECAN, and Bravo Velocity for NGS panel manufacturing.
  • Oligonucleotide Production: Manufactured custom primers and NGS panels following strict SOPs and batch records.
  • Provided technical troubleshooting for automated lab equipment and evaluated non-routine test results to ensure product quality.


Associate Manufacturing Technician

  • Custom Primers Lab: Manufacture Oligonucleotides/Custom Primers for use in the biotech industry by following established protocols and SOPs. Operate semi-automated and automated basic lab equipment. Regularly evaluate non-routine test results and either fail the product or allow it to continue through the production cycle.
  • Understand scientific principles in order to problem solve, troubleshoot test results, evaluate alternative choices and exercise independent judgment in selecting the best solution. Provide multiple decision options and corresponding logic/data behind the decisions. Proactively identifies production problems.
  • Provides feedback and contributes ideas and suggestions to new and/or improved lab techniques, protocols, processes, special handling of the product and equipment.
  • Balance multiple tasks. Demonstrate knowledge in the use of basic lab techniques and basic computer knowledge. Demonstrate the ability to meet standards as defined by the manufacturing process.
  • Inform appropriate people about problems/questions; be prepared to discuss problems/questions clearly. Work in a safe manner. Work with team members to overcome obstacles. Collaborate, support and consult with other team members as necessary. Give and receive constructive feedback
  • Occupies a significant role in mainstream oligonucleotide production. The role requires the ability to exercise judgment within generally defined practices and policies in selecting methods and techniques for obtaining solutions.

Research Assistant

@ UH John A. Burns School of Medicine
Jan 2013 - Nov 2013
Honolulu, HI
  • NeuroAIDS Research: Conducted autoimmune molecular mechanism studies on chronic neuroinflammation in HAND patients under Dr. Bruce Shiramizu.
  • Advanced Microscopy: Captured and analyzed data using Light, Fluorescent, and Confocal Microscopy.
  • Technical Protocols: Performed FFPE immunohistochemistry, RNA in situ hybridization (QuantiGene ISH), and PBMC transmigration assays in BBB models.

Assistant Researcher

@ UC San Diego - School of Medicine
Jan 2014 - Jun 2014
La Jolla, CA
  • Cardiac Physiology: Conducted ex vivo heart perfusion studies in Mus musculus utilizing the Langendorff heart apparatus.
  • Surgical Protocols: Executed precise mouse surgical protocols for organ isolation and established Isolated Heart Stand assays.
  • Metabolomics: Performed advanced metabolic profiling of cardiomyocyte cell cultures using the Seahorse XF Extracellular Flux Analyzer.
  • Biochemical Assays: Evaluated cardiac response and signaling through somatostatin assays to study physiological health and performance.

Teaching Assistant

@ University of Hawaii at Manoa
2011 – 2012
Honolulu, HI
  • General Chemistry I: Lectured undergraduates on laboratory protocols, chemical concepts, and safety procedures.
  • Managed reagent preparation, supervised lab sessions, and designed weekly quizzes to assess student progress.
  • Responsible for grading lab reports and managing end-of-semester grade calculations for all students.

Education

Master of Science, Biology

California State University, East Bay
Aug 2022 – May 2026
Hayward & Stanford, CA

Principal Thesis Advisor: Michael Snyder, PhD (Stanford University School of Medicine)

Research & Internships:

  • Graduate Student Intern (2023): Snyder Lab, Stanford Cancer Institute (SCI), Stanford Medicine. Focused on multi-omics integration and precision oncology.
  • Snyder Lab (Department of Genetics): Thesis concentration on Single-cell Spatial Mapping, Exercise Multiomics, and Biomedical Data Science.

Spatial Biology Training:

  • Contextualizing Cellular Physiology Workshop: NIH NIDDK (National Institute of Diabetes and Digestive and Kidney Diseases).
  • 2nd Annual Spatial Biology Workshop: Stanford School of Medicine, Department of Pathology (Professor Michael Angelo Lab). Specialized in spatially resolved transcriptomics.

Structural Biology & Graduate Training:

  • Kasper Rogala Lab (Department of Structural Biology, Department of Chemical and Systems Biology): Internship in Structural Biology* Stanford University (SSRL): RapiData 2023. Specialized in macromolecular X-Ray diffraction and data processing at synchrotron beamlines.
  • Stanford-SLAC Cryo-EM Center (S2C2): Single Particle Analysis (SPA) and Cryo-ET image processing (Relion, CryoSPARC).

Core Competencies: Systems Biology, AI/ML in Precision Medicine, Spatially Resolved Technologies, Pathology, Genomics, Structural Biology, Bioengineering, CRISPR/Cas Systems, and Cancer.

Bachelor of Science, Cell/Cellular and Molecular Biology

San Francisco State University
Aug 2020 – May 2022
San Francisco, CA

Research Experience:

  • Lab of Prof. Dr. Nicole Salazar Velmeshev: Investigated Cancer Chemokine Signaling (G protein-coupled receptor superfamily).
  • Lab of Prof. Dr. Scott Roy: Bioinformatics research focusing on SRSF proteins, alternative splicing, and intron evolution.
  • Honors Genetics: Mentored by Prof. Dr. Michael Goldman.

Post-Baccalaureate & Specialized Coursework:

  • University of Hawaii John A. Burns School of Medicine (Grade: A+): Graduate research in Neurovirology and Immunohistochemistry (IHC) under Dr. Mukesh Kumar and Dr. Bruce Shiramizu.
  • Johns Hopkins University School of Medicine (Grade: A): Translational Research in NeuroHIV and Mental Health (TRNAMH) with Prof. Dr. Amanda Brown.
  • University of Hawaii at Manoa: Molecular Cell Biology and Immunology under Dr. Paul Patek.

High School Diploma

Modesto High School
2003 – 2007
Modesto, CA

MHETT Program (Technical Theatre and Design): Specialized in Theatre Design and Technology. Served as Technical Director, Stage Manager, Lighting Designer, and Director for various productions.

Music & Arts:

  • Modesto High Orchestra: 1st and 2nd Violin.
  • Active participant in the local technical theatre and design community.

Achievements

Advanced Certifications

2025-2026
AI/ML Fundamentals in Precision Medicine

Stanford University School of Medicine

2024
Fundamentals of Data Science & Cloud Computing

Stanford Data Ocean

2023
RapiData 2023: X-Ray Diffraction

SLAC National Accelerator Laboratory

Invited Talks

International Webinar on Cancer Research

Topic: Human Retroviruses in Neuro-Oncology

Guest Speaker (2022)
MDPI Cells 2023 Conference

Topic: Golgi Apparatus Dysfunction in Cancer

Conference Speaker (2023)
CSU Northridge Seminar

Topic: Data-Driven Discovery in Oncology

Invited Speaker (2022)