About Me

Research fields: Precision Exercise Medicine, Computational Biology and Bioinformatics, Exerkines

Current Mission: Learn advanced multiomics, bioinformatics, computational biology, and data analysis in the GTEx and the MoTrPAC Data Hub for the purpose of mapping exerkines to support human health, resilence, and disease prevention. I am constructing an exerkine map with ligand-receptor-target interaction networks, and find the biomarkers of exercise in preclinial and human databases. I inquiry multiple bioinformatic databases including genotype-to-tissue gene expression and carry that onward to phenomic (genotype-to-phenotype) analysis of tissue maps. I'm analyzing the multi-omics of rodents and humans and will map exerkines at transcriptome, proteins, and metabolites. These exerkines are to be mapped across all organs in the rat and relevant human organs while keeping focused on the endurance exercise training in rodents and correlated human spatial single-cell architectural multiomics maps. In this way, it'll contribute to the molecular map of exercise where we can understand how exercise and physical activity improves human health.

Positions

  1. Graduate Research Student (Snyder Lab)
    Stanford Genome Technology Center (SGTC)
    Department of Genetics
    Stanford University School of Medicine
    Department of Biological Sciences, Califonia State University, East Bay
  2. Volunteer Neuroscientist and Neurosurgery Researcher (Steinberg Lab)
    Department of Neurosurgery
    Stanford University School of Medicine
    Wu Tsai Neurosciences Institute
  3. Virtual Volunteer Associate Fellow
    Institute of Molecular Medicine and Infectious Diseases (IMMID)
    Department of Microbiology & Immunology, Drexel Medicine
  4. Vice President (VP) of Science, Technology, Engineering, Mathematics (STEM) Programs at Myplaceisahappy1 (MPH1) (501c3 non-profit)

Education


Graduate Studies
University Thesis at Stanford Genetics
The Snyder Lab, Department of Genetics, Stanford University School of Medicine
M.S. Biological Sciences: Computational Biology, Bioinformatics, and Genomics
California State University, East Bay, CSUEB, 2022 - Present (Anticipated 2024)


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


From Genomics to Therapeutics: Integrative Multiomics and Translational Medicine Graduate Training

Bioinformatics and Systems Biology

  • Multiomics data analyses, Exerkine Translational Research
  • MoTrPAC (integrative multiomics, network data analysis)
  • GTEx (single cell data, genotype-tissue gene expression)
  • HuBMAP and Human Reference Atlas
  • Human Cell Atlas and Human Protein Atlas


  • Spatial Biology

    2023 2nd Annual Spatial Biology Workshop (Angelo Lab) Stanford School of Medicine, Li Ka Shing Learning and Knowledge Center (LKSC)
    • Cell Detection and Classification
    • Applications of Spatial Biology I & II
    • De Novo Mass Spectrometry
    • The Scientific Spectrum of Spatial Analysis
    • Workshop: H&E bootcamp
    • Follow-up virtual-learning


    Structural Biology

    Structural Biology and Chemical & Systems Biology Graduate Intern, Summer 2022
    Stanford Cancer Institute Stanford Medicine

    Cryo-Electron Microscopy and Tomography (CryoEM and CryoET)

  • BioE 320 - Biological cryogenic microscopy and tomography
    Stanford Bioengineering Schools of Engineering & Medicine
  • 2023 Image Processing Workshop for Cryo-Electron Microscopy
    S2C2 | Stanford-SLAC Cryo-EM Center | SCSC Sample Preparation for Cryo-Electron Tomography
  • 2023 Tomography and Cryo-FIB Workshop
    UW-Madison | Midwest Center for Cryo Electron Tomography (MCCET)
  • CEMRC Dragonfly Practical Workshop: Application to Tomography Data
    Penn State College of Medicine | UW-Madison CEMRC and MCCET
  • JoVE protocol for deep learning-based segmentation of cryo-electron tomography (Heebner et al 2022)
  • 42nd Steenbock Symposium: “Opening the Doors to Cryo-EM"
    UW-Madison, Department of Biochemistry, UW-Madison Cryo-Electron Microscopy Research Center (CEMRC) and Midwest Center for Cryo Electron Tomography (MCCET)

  • Macromolecular Crystallography (MX)

  • RapiData 2023 at SSRL | Certificate
    Structural Molecular Biology (SMB) Division | Macromolecular Crystallography
    Stanford Synchrotron Radiation Lightsource (SSRL)


  • Neuroscience and Neurosurgery

    Stanford Neurosurgery, 2022-2024
    1. Neurosurgery & Neurology
    2. Neuroimaging & Neuroradiology
    3. Neurosciences Preclinical Imaging Laboratory (NPIL)
    4. Neurodegeneration (Acute & Chronic)
    5. MRI-FLAIR Neuroimaging
    6. Spatial Transcriptomics
    7. Endovascular Neurointervention
    Endovascular Neurointerventional Research in Neurosurgerical oncology and neurosurgery while providing Multimodal Neuronavigation and neuroimaging. My research interests lie in the application of cutting-edge techniques in organelle structural biology and bioengineering to develop new and more effective therapies for diseases. Specifically, I am interested in studying the therapeutic cells, radiobiological nuclides, and small molecules in precision medicine and health. I also aim to explore novel approaches like MRI data processing, computational neurobiology and bioinformatics for macromolecular engineering and drug design. Additionally, I am fascinated by the study of organelles and their roles in cellular function and disease, and I am learning cutting-edge imaging techniques: expansion microscopy (ExM & ExA-SPIM), molecular/cryogenic electron microscopy (EM) and tomography (ET) for high-resolution bioimaging of organelles in live cells and tissue to enable new diagnostic and therapeutic approaches for diseases: aging, cancer, neurodegenerative disorders, and infectious diseases.
    JABSOM & Johns Hopkins Schools of Medicine, 2012-2013 Undergraduate
    B.S. Biology: Cell and Molecular Biology
    San Francisco State University, SFSU, 2020 - 2022
    Molceular Cell Biology
    University of Hawaii at Mānoa, UHM, 2010 - 2013
    Ohlone College, 2008 - 2015
    Modesto Junior College, MJC, 2003 - 2009

    Research: Projects
    Lectures: Presentations

    Research

    Project IV: Mapping Exerkines Network Physiomes in Human and Rats of Endurance Exercise Training (EET) in Young Rats and Translational Human Biology
    Topic: This thesis project aims to construct a comprehensive molecular and functional exerkine map, transcending tissue and species boundaries. Major: Computational Multiomics Biology
    Thesis Lab: Professor and Chairman, Dr. Micahel P. Snyder
    Timeline: Present - December 2024
    Stanford Genome Technology Center (SGTC)
    Department of Genetics, Stanford University School of Medicine
    Department of Biological Sciences, California State University, East Bay

    Project III: Virophysics (Computational Structural Predictions) and Organelle Structural Biology
    Institutions: SLAC National Accelerator Laboratory, Stanford University, California State University, East Bay
    Theme: This research project focuses on exploring the field of virophysics with an emphasis on computational structural predictions. Additionally, the project delves into organelle structural biology to understand the intricate architecture of cellular components and its implications in various physiological processes.
    Summary: The project involves the application of computational methods to predict the structural dynamics of viral components, contributing to the field of virophysics. Simultaneously, the investigation into organelle structural biology aims to unravel the complexities of cellular structures and their roles in health and disease. The project integrates experimental and computational approaches to advance our understanding of virus-host interactions and cellular architecture.

    Publications
    1. Gómez DJ*. (2023) 'Untangling the Microscopic World of Organelles, Cells, Tissues, and Organs: A Focus on the Dysfunctional Golgi Apparatus in Disease Research †'. Biology and Life Sciences Forum.
    2. Gómez DJ*. (2022) 'Unraveling the Structural Dynamics of Human Pegivirus-1 RNA-Dependent RNA Polymerase Using Computational Methods'. ResearchGate.
    3. Gómez D*. (2022) 'Pioneering Organelle Structural Biology: Golgi Apparatus Dysfunction in Parkinson’s Disease, Neurodevelopmental Disorders, and Cancer'. Preprints. 2022100383.

    Project II: Coinfections and Cancer: Host-Pathogen Interactions in Dendritic Cells and the Host-Virus-Tumor Interface
    Institutions: Drexel University School of Medicine, California State University, East Bay Theme: This research project focuses on investigating the mechanisms of host-pathogen interactions in the context of disease development. The project involves both experimental and computational methods to illustrate the molecular and cellular basis of disease pathogenesis.
    Summary: The research project encompasses several posters and publications that highlight different aspects of host-pathogen interactions and organelle dysfunction in disease research. The posters presented at the Microbiology Student Group Symposium and the AACR-JCA Joint Conference focus on co-infection and cancer, specifically the role of viral oncogenesis in liver, blood, and brain cancer by host-pathogen interactions. The publications delve into the co-infection and cancer in dendritic cells as well as other oncogenic viruses. The project aims to advance our understanding of the coinfection and cancer mechanisms underlying their disease development and to identify potential targets for therapeutic intervention.

    Posters
    1. Gómez DJ* . 22nd Microbiology Student Group Symposium Poster / Poster presentation at 22nd Annual Microbiology Student Symposium in Krutch Theater at Clark Kerr UC Berkeley Campus (2023, In-person)
    2. Gómez DJ, Mulherkar T, Sandel G, Jain P.* "Co-infection and cancer: Viral oncogenesis in humans result in liver, blood, and brain cancer by host-pathogen interactions" Poster presentation at 12th Annual AACR-JCA Joint Conference. (2022, Virtual)
    Publications
    1. Gómez DJ+, Mulherkar T+, Sandel G, and Jain P*. (2022) 'Co-Infection and Cancer: Host–Pathogen Interaction between Dendritic Cells and HIV-1, HTLV-1, and Other Oncogenic Viruses'. Viruses.

    Project I: Undergraduate Research Opportunities Program (UROP)
    Institutions: John A. Burns School of Medicine, University of Hawai'i at Mānoa Title: Interleukin-17 Production in CNS by Infiltrating T Cells and Glial Cells in the HIV-1-Infected Brain
    Summary: Despite effective combined anti-retroviral therapy (cART) for HIV-1-infected individuals, neurocognitive complications persist in patients, leading to negative impacts on daily functioning. The central nervous system (CNS) is affected in multiple ways during HIV infection, as HIV-infected cells cross the blood-brain-barrier (BBB) and initiate events causing CNS damage and neurocognitive problems. This study aims to investigate the role of interleukin-17 (IL-17) in HIV-associated neurocognitive disorders (HAND), as IL-17 can disrupt the BBB. The researchers will analyze brain specimens and cerebrospinal fluid (CSF) samples from HAND patients with HIV encephalitis (HIVE) and compare them to samples from HIV-infected individuals with normal cognition (NC). The hypothesis is that IL-17A will be found in subcortical structures, specifically in the medium-spiny neurons of the basal ganglia and interneurons in the hippocampus, and that astrocytic secretion of the TH17 cell chemokine (CCL20) and cytokine (IL-17) will be detected in CSF samples of HAND patients with HIVE.

    Proposal
    1. Gómez DJ*, Shiramizu, B. (2013) 'IL-17 in HIV-1-Infected CNS'. 28 Mar. 2013. JABSOM, UH Mānoa, Honolulu, HI. TRMD499: Directed Research and Reading.

    Volunteer Researching
    [Summer 2022 - Present] Virtual Volunteer Associate Fellow, Microbiology & Immunology, Drexel College of Medicine
    [Spring 2014] Research Assistant, Anesthesia, UC San Diego School of Medicine
    [Fall 2020] Research Assistant, Physiological Sciences, UF College of Veterinary Medicine

    Presentations

    Presentations and Talks

    Gene Editing, Therapy & Genome Engineering

    Computational Biology + Molecular Biology

    Upcoming: Precision bioinformatics

    1. Advancing Your Expertise: Bioinformatics Training for NGS and Single-Cell RNA Sequencing
    2. Expanding Horizons: Bioinformatics Training for Mass Spectrometry and Spatial Biology
    3. Advancing Healthcare: Bioinformatics Training for Precision and Preventative Medicine

    Structural Biology

    Cancer Neuroscience & Tumor Virology

    Community

    Listen to my podcast episodes on Spotify:

    Hallmarks of Cancer: The New Dimension (Review)

    Teaching Assistant/Associate and Tutoring
    [Fall 2022] Clinical Microbiology, CSU East Bay
    [Fall 2022] Human Anatomy and Physiology, CSU East Bay
    [2011 - 2014] Private Tutor: (O. Chem) Chemistry and Biology
    [Summer 2011] Tutor, Learning Emporium, College of Natural Sciences, UH Manoa
    [Spring 2011] General Chemistry I Lab, University of Hawaii at Mānoa

    Mentorship
    [2022-23] CSUEB Biology students
    [2022-23] UF MHPMP Mentor, Pre-Health Club
    MHPMP (Minority Health Professional Mentorship Program)

    Outreach and Volunteering
    [2022-23] Volunteer Reviewer, MDPI
    Journals: cells, biology, cancers, viruses, IJMS, pharmaceuticals
    [2022-] Vice President of STEM Programs, Myplaceisahappy1
    Scientific Programs and Diversity and Health Equity
    [2022] St. Michael's Church
    [2021] Assistant Lighting Designer, College of Sequoias
    [2014] Comunity Wellness Advocate, American Cancer Society
    [2013] Physician Shadow, City of Hope

    Equity & Inclusion
    Society of Latinx Engineers (SOLE) "Estanfor"
    Health Equity Research (HER) Lab Latinx Community