Daniel J. Gomez
Daniel J. Gomez

I am daniel gomez ORCID iD icon, I'm conducting independent or collaborative research and developing impactful innovations that address challenges across multiple research initatives (MoTrPAC, HuBMAP, Human Cell Atlas, PsychENCODE, Space Omics), projects, or diseases and conditions, building generative solutions in disease, genetics, exercise immunology, pregnancy, maternal and children's health, astroimmunology, digital biology, multi-omics, bioinformatics, generative models, LLMs, and foundational models, AIVCs, and observational and experimental methods in novel spatial omics, single-cell genomics, translational science, has the ability to communicate my findings in physical activity signaling exercise medicine pathways, immunotherapy, personalized medicine, and map organs that discover novel exerkines. My work recently won an award for "Multiscale System Modeling and Cross-Organ Modeling" won Most Innovative Project Award in the Whole Person Physiome Hackathon 2026. I'm a scientist in the Snyder Lab at Stanford University School of Medicine Department of Genetics doing innovative biological science research and testing, learning, generating hypothesis, implementing single-cell technologies in molecular and cellular science. I completed requirements for a M.S. in Biological Sciences at the California State University, East Bay. I got a certification in the Fundamentals of Data Science in Precision Medicine and Cloud Computing at Stanford University School of Medicine, and completed my second certification in Fundamentals of AI/ML in Precision Medicine at Stanford Data Ocean, Stanford Deep Data Research Center. Previously, I completed a structural biology course on how to use Synchrotron radiation and determine macromolecular structures and macromolecular crystallography at Stanford-SLAC RapiData 2023 at SSRL in addition to earning a Cybersecurity for Lab Users certificate from CS 100 at SLAC National Accelerator Laboratory. I conduct RNA and protein engineering design experiments that are able to inverse design generate sequences, structures, and biomolecules from RNA to protein and back to RNA, I also work with several DNA Language Models (DLMs), Genomics Language Models (gLMs), Codon Language Models (cLMs), Protein Language Models (pLMs), and single-cell Foundational Models (scFMs). I'm also working on my single cell multi-omics model that has the capability to handle exerkine sequence generation and design. I earned my Bachelor's of Science degree in Biology: Concentration in Cell and Molecular Biology from San Francisco State University. More information is available in my CV.

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Recent Events and Invited Talks
Research

Research Assistant, Genetics, Pathology, Immunology

My thesis research is on exerkines, exercise multiomics, health and disease, mechanobiology, astroimmunology, building 3D atlases with single-cell spatial maps at single-cell resolution with machine learning and sc/snRNAseq, spatial omics using computational next-generation tools. This novel research makes a big impact in multiple research communities (i.e., consortia): Molecular Transducers of Physical Activity (MoTrPAC), Genotype-Tissue Expression (GTEx) project, Human Biomolecular Atlas Project (HuBMAP), Human Tumor Atlas Network (HTAN), Gut Cell Atlas, Human Cell Atlas.

I'm interested in multiomics disciplines of medicine and biosciences, molecular biology, genetics, biomedical data science, computational biology, integrative multiomics, pathology, bioinformatics, biomedical data science/machine learning (AI/ML), single-cell and spatial biology, chemistry, structural biology, biophysics and immunophysics, tissue and organ architecture.

*Denotes co-first authorship

Consortium Publications

MoTrPAC Publications
HuBMAP Publications Portal

Co-Infection and Cancer: Host-Pathogen Interaction between Dendritic Cells and HIV-1, HTLV-1, and Other Oncogenic Viruses
Tania Mulherkar*, Daniel J. Gomez* Grace Sandel, Pooja R. Jain
Viruses, 2022  
CSU ScholarWorks / Drexel University Libraries Conference Proceeding / pdf / Poster / Presentation / 22nd Microbiology Student Group Symposium in Krutch Theater at Clark Kerr UC Berkeley Campus

We reviewed dendritic cells (DCs) interactions during co-infections with several malignancies as well as oncogenic viruses and their current respective therapeutics.

Pioneering Organelle Structural Biology
Daniel Gomez
Preprints, 2022     pdf

Conference Paper, 2023     video
Conference Paper MDPI AG | Biology and Life Science Forum / Cells 2023 Submission / Cells 2023 Conference Session 2: Organelle Function

Keywords: cancer; Golgi; organelle structural biology; nanoimages; tomograms; therapeutics; cryo-ET; SXT; CLEM; structural biology; organelles; Golgi Apparatus (GA); Parkinsons disease (PD); cryo-ET; alpha-synuclein; neurodegenerative diseases; soft X-ray tomography (SXT); cancer; NDDs

Recorded Talks
CRISPR-Cas

CRISPR-Cas Genomics Techniques

CRISPR-Cas functional genomics technique applications.

The long non-coding-RNA landscape of EET

The Long Non-Coding-RNA Landscape of Endurance Exercise Training

Long non-coding-RNA structure and function mechanisms, and the MoTrPAC rat study of lncRNA endurance exercise training.

Immuno-onocology: Immunotherapy and Precision Cancer Vaccines

Immuno-onocology: Immunotherapy and Precision Cancer Vaccines

Mechanisms of Precision Immuno-Oncology in immunotherapy, cancer vaccines, Immunomind data.


Research and Teaching Experience


Stanford Unviersity Seal

Research Assistant

Auditor, GENE211: Genomics, Winter 2024

Affiliate, Stanford University School of Medicine, Department of Genetics, 2023 - 2025

Intern, Stanford University School of Medicine, Summer 2023

Certificate, Fundamentals of Data Science in Precision Medicine and Cloud Computing (Bioinformatics), Department of Genetics, Stanford Medicine, Stanford Data Ocean, Stanford Deep Data Research Center

Visiting Scientist, SLAC National Acceleratory Laboratory

Certificate, SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource (SSRL) RapiData 2023: Data Collection and Structure Solving

Image Processing Workshop for Cryo-Electron Microscopy, S2C2 Cryo-ET Preparation, Stanford-SLAC Cryo-EM Center

Auditor, BIOE320: Cryogenic Electron Microscope and Tomography, Winter 2023

Teaching Lab

Teaching Responsibilities

I have taught Chemistry and Biology undergraduates in General Chemistry I Laboratory, Clinical Microbiology Lab, and Human Anatomy and Physiology Lab.

CSU East Bay Logo

Teaching Associate, BIOL230: Introduction to Clinical Microbiology Lab, Fall 2022

Teaching Associate, BIOL270: Human Anatomy and Physiology I Lab, Fall 2022

University of Hawaii Logo

Teaching Assistant, CHEM161L: General Chemistry I Lab, Spring 2011

Grant Funding

Successfully influencing and applying grant funding demonstrates my ability to develop and lead research projects, as well as my expertise in grant writing, timeline forecasting, project managment and budget management.

Funding Image

Graduate Project Funded Research

MoTrPAC

HuBMAP

HTAN

Human Gut Cell Atlas

Other Human Cell Atlases

PsychENCODE


Grantsmanship Training

R03 Grant, Stanford

Novartis Graduate Training Program, Stanford

Undergraduate Grants for Research

Undergraduate Research Opportunities Program (UROP)
Molecular Cell Biology Undergrad Program at UH Mānoa
Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A Burns School of Medicine, University of Hawaii at Mānoa

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