We foster dialogue between data scientists and researchers in clinics and laboratories in order to drive excellence in health care research at Stanford.
About the Data Studio
The Data Studio is a collaboration between Spectrum (The Stanford Center for Clinical and Translational Research and Education) and the Department of Biomedical Data Science. The Data Studio is open to the Stanford community engaged in biomedical research. We expect it to have educational value for students and postdocs interested in biomedical data science. The Data Studio features DBDS faculty and staff who offer the following services: workshops, office hours, and one-to-one consultations. When you complete the Data Studio request form, our coordinator and consultants will work with you to choose the right service for your research project. Appointments may be requested by completing the required form.
Workshops are an extensive and in-depth consultation for a Medical School researcher based on research questions, data, statistical models, and other material prepared by the researcher with the aid of our facilitator. During the Data Studio Workshop, the researcher explains the project, goals, and needs. Experts in the related topic from across campus will be invited and contribute to the brainstorming. After the meeting, the facilitator will follow up, helping with immediate action items and summary of the discussion. Ultimately, we strive to pair each PI with a data scientist for long-term collaboration.Office Hours are brief consultations for Medical School researchers during the last session of each month. DBDS faculty are available to advise about your research questions. Consult the schedule below to complete the Office Hour registration form. Once you have registered, you will receive a calendar invitation with the date, time, and location of the session. Bring any data, prior analyses, or other materials that you have. Our consultants may even recommend your project for a Workshop if it is appropriate.
One-to-one consultations for Medical School researchers are available year-round. Our facilitator assigns each request to a data scientist with the relevant expertise.
Partners
General questions about statistical issues may be brought to the STAT390 Consulting Workshop. This is a class offered by the Department of Statistics during each academic quarter that is staffed by graduate students and directed by a faculty instructor. The service typically consists of a single meeting with the researcher to address a specific concern, such as planning of experiments and data analysis. For more information, consult the STAT390 Consulting Workshop web page.
Researchers who are members of the Stanford Cancer Institute (SCI) conducting research projects related to cancer may request assistance from the SCI Biostatistics Shared Resource.
The Genetics Bioinformatics Service Center (GBSC) offers an end-to-end bioinformatics consulting service (BaaS) that provides high performance computational infrastructure and cutting-edge bioinformatics services for the Stanford community. The team consults on genomics, transcriptomics, proteomics, epigenetics, and metabolomics projects, and also develop custom workflows. For consulting and hands-on bioinformatics help with your projects please reach out to gbsc-baas-team@lists.stanford.edu to set up an initial meeting.
Schedule
The Data Studio is held each Wednesday from 3:00 until 4:30 pm during the fall, winter, and spring quarters of the academic year. Consult the schedule below for the location of each session. Students may participate by enrolling in BMDS 291 for an introduction to the art of statistical consultation and practicum working on projects with a biomedical researcher. All are welcome to attend. Click here to sign up for our mailing list.
The currently scheduled topic is listed below.
TITLE: Intestinal Stem Cell and Regulatory T-Cell Interaction Lead to Immunomodulation and Tissue Regeneration
INVESTIGATORS
Neetu Saini (1)
Rosa Bacchetta (1)
Michael J. Rosen (2)
- Pediatric Stem Cell Transplantation and Regenerative Medicine
- Pediatric Gastroenterology
DATE: Wednesday, 4 February 2026
TIME: 3:00–4:30 PM
LOCATION: Room R358, Edwards Building, 300 Pasteur Drive, Stanford, CA
WEBPAGE: https://dbds.stanford.edu/data-studio/
ABSTRACT
The Data Studio Workshop brings together a biomedical investigator with a group of experts for an in-depth session to solicit advice about statistical and study design issues that arise while planning or conducting a research project. This week, the investigator(s) will discuss the following project with the group.
INTRODUCTION
Pediatric Crohn’s disease (CD) is a rare but serious inflammatory bowel disease (IBD) shaped by genetic, immune, and environmental factors. Children with CD experience stunted growth, reduced quality of life, and progressive intestinal damage that can become irreversible and require surgery. Current therapies rely on broad reduction of symptoms; these often fail to achieve durable remission and, critically, do not directly promote repair of the damaged gut, even though gut injury is central to disease progression. Currently, there is a lack of targeted restorative therapies. Thus, pediatric CD patients are in urgent need of a treatment option that could alleviate the disease symptoms with minimal side effects and support development and growth.
Regulatory T-cells (Tregs) are immune “brakes” that prevent harmful inflammation. In healthy individuals, Tregs maintain immune regulation in different tissues, including in the gut, but these cells are less functional in CD patients. Treg-based cell therapies are being developed to treat autoimmune and inflammatory conditions, but their use is limited by the challenge of isolating, expanding, and keeping these cells stable in the gut. In this study, we propose the use of engineered, stable Treg-like cells (CD4LVFOXP3), a patient-specific “living drug” that can control excess inflammation in the gut and support gut repair. CD4LVFOXP3 cells developed in our laboratory are in Phase I clinical trials for a different disease, also involving the gut, supporting the applicability of these cells in the clinic. Gut-repair capacity of CD4LVFOXP3 is investigated in this proposal by combining CD4LVFOXP3 cells with patient-derived gut-tissue culture. The Aims in the proposal are designed to generate the mechanistic and preclinical evidence needed to support IND-enabling work and launch a Phase I clinical trial of CD4LVFOXP3 therapy for pediatric CD.
HYPOTHESIS & AIM
Our central hypothesis is that, in addition to their immune-regulatory functions, CD4LVFOXP3 will promote intestinal stem cell (ISC) renewal and regeneration by secreting soluble factors that activate stem cell repair pathways. This central hypothesis will be tested by the following specific aims:
Aim 1: Identify and validate soluble factors secreted by CD4LVFOXP3 cells that promote ISC renewal and regeneration in damaged enteroids.
Aim 2: Determine the transcriptomic changes underlying enteroid regeneration induced by CD4LVFOXP3.
Aim 3: Investigate the dual immunomodulatory and regenerative function of allogenic CD4LVFOXP3 in fully formed organoids.
DATASET
We will study continuous response variables in matched pairs of enteroids and organoids (CD4LVFOXP3 vs. CD4act or untreated) from patients with CD and unmatched healthy donors (HD). We plan to do an autologous co-culture of enteroids and CD4LVFOXP3 vs. CD4act of 15-20 CD patients (irrespective of their age, sex, disease status, and treatment) and analyze the following parameters:
Enteroids co-culture
| Enteroids alone or co-culture with CD4LVFOXP3 or CD4act | Organoids alone or co-culture with CD4LVFOXP3 or CD4act |
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STATISTICAL MODELS
In the enteroids set of co-cultures, we would like to see consistent changes (in the readout as listed above: Transcriptome, Secretome) induced by CD4LVFOXP3 as compared to enteroids only or co-culture with CD4act to determine how CD4LVFOXP3 modulates the gut stem cells and organoids towards more regenerative and renewal signatures.
STATISTICAL QUESTIONS
- How to quantify “consistent” effects across patients or more specifically, “For how many patients is the direction of change consistent with a regenerative phenotype (e.g., increased TEER, increased stemness score, reduced death score), and is that proportion greater than expected by chance?”
- What effect size will be meaningful for each primary endpoint?
- TEER: absolute change (Ω-cm²) or percentage change vs baseline/control.
- Secretome: log2 fold-change (FOXP3 vs CD4act / vs alone).
- scRNA-seq
i. log2 fold-change in pseudobulk within a cell type; or
ii. change in a predefined pathway/stemness score.
- Given an autologous, patient-paired design with approximately 15-20 CD donors (+/- HD comparators) and three culture conditions (no T cells, CD4LVFOXP3, CD4act), what is the most defensible statistical analysis plan and the corresponding power/detectable effect size calculations (including assumptions about within-patient variance and expected culture/scRNA dropout) that would be acceptable for a grant and a manuscript?
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