Hi, my name is
Daniel J. Gomez
I find answers to clinical research questions.
Bioinformatics Scientist focusing on Clinical Computational Science at Stanford.


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)
- 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
- 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
- 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
- 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
- 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
- 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
- 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
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
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
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
AI/ML Fundamentals in Precision Medicine
Stanford University School of Medicine
Fundamentals of Data Science & Cloud Computing
Stanford Data Ocean
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)