Stanford - Department of Biomedical Data Science

James Zou at the DeSci Foundation: Large language models and future of science.
2024-01-22 08:00 - 22:00 (America/Los_Angeles)
James Zou will be presenting at the DeSci Foundation The Future of Science Seminar Series on the topic of Large language models and future of science.
The event will be held on Wednesday 22th January 2024 at 8am PST and is free to attend. A recording will be made available to those who register in advance.
Abstract
In this talk, we will explore the transformative potential of large language models (LLMs) such as ChatGPT in reshaping scientific inquiry and communication through several vignettes. First, we will discuss how LLM can provide informative feedback to improve scientific manuscripts. Then we will show how to use LLMs to organize biomedical images to make it easier for clinicians and researchers to retrieve relevant information. Finally we will investigate using LLMs for outreach and education.

For more information: https://cassyni.com/events/4fJ1CwqCNeC73oLJQsG7yX

DBDS Collaboration and Careers Forum
2024-01-23 08:30 - 13:30
We’d like to invite you to the annual DBDS Collaboration and Careers Forum:
Tuesday, January 23rd from 8:30am to 1:30pm
Stanford University, Alumni Center
This Forum is designed to engage leaders from companies, government agencies and other organizations external to Stanford with DBDS faculty, graduate students, postdocs and staff scientists. It offers a unique opportunity to discuss advancements in AI, data science and multimodal data integration, and to explore collaboration.
The program will include:

Overview of DBDS Initiatives and 2024 Plans, from Department Chair, Sylvia Plevritis
Faculty lightning talks in areas such as spatial biology, clinical data science, imaging, digital health, and translational bioinformatics
Interactive Session to explore research collaborations with outside organizations, and for students to discuss job and internship opportunities
Industry panel discussion
Time for networking and making new connections

More information will be coming soon. We hope to see you there!

Weekly Seminar: Daniel Mukasa
2024-01-25 13:30 - 15:00 | MSOB Conference Room
Date: 1/25/24
Time: 1:30-3 pm
Daniel Mukasa
Title:Computationally Design of Wearable Chemical Sensors for Personalized Healthcare
More info here

Faculty Meeting: January 31, 2024
2024-01-31 11:30 - 13:00 | MSOB Conference Room
Lunch will be available.
Zoom link: https://stanford.zoom.us/j/97249583050?pwd=[REDACTED]

Weekly Seminar: Drago Plecko
2024-02-01 13:30 - 14:50 | MSOB Conference Room
Thursday, February 1, from 1:30-2:50, MSOB, Rm 303

Causal Health Equity – Toward a Taxonomy
Drago Plecko
Postdoctoral Scholar, Department of Computer Science, Columbia University

More information here: http://dbds.stanford.edu/wp-content/uploads/2024/01/Seminar-Series-Flier-Drago-Plecko.pdf

SEMINAR: Predicting and Discovering Protein Dynamics
2024-02-05 15:00 - 16:00
HANNAH WAYMENT-STEELE, PhD, BRANDEIS UNIVERSITY
Monday, February 5, 2024
3-4 PM
ChEM-H / Neuro Research
Complex, Room E153
Entrance across from the pub

CCBS Seminar Series: Roles of systemic immunity in tumor metastasis and effective immunotherapy, Nathan Reticker-Flynn
2024-02-16 13:00 - 14:00
Please join us at our next monthly CCSB Seminar, Friday, February 16, at 1:00 PM. Our Seminar Series in systems biology of cancer aims to bring together experimental and computational researchers.
We are pleased to announce our upcoming speaker, Assistant Professor Nathan Reticker-Flynn.
Title: Roles of systemic immunity in tumor metastasis and effective immunotherapy
Abstract: The majority of cancer-associated deaths result from distant organ metastases rather than primary tumors, yet few therapies exist to treat this stage of disease. Recent advances in tumor immunotherapies, such as immune checkpoint blockade, have shown promise for patients with metastatic disease, yet most patients remain unresponsive to these treatments. Here, we investigate the roles of systemic immunity in metastatic progression and response to immunotherapies. We demonstrate that lymph node colonization plays a critical role in metastatic progression by imparting tumor-specific immune tolerance within the immune repertoire of the involved lymph nodes. This tolerance becomes systemic across the host and facilitates metastatic seeding of distant sites. Furthermore, using mouse models and systems approaches, we demonstrate that the generation of effective anti-tumor immune responses to immunotherapies requires activation of immunity in secondary lymphoid organs. Together, these findings demonstrate the critical roles of lymph nodes in facilitating metastatic progression and driving responses to immunotherapy.
Bio: Nathan Reticker-Flynn is a tumor immunologist and Biomedical Engineer working at the interfaces of cancer metastasis, tumor evolution, adaptive immunity, and immunotherapy. He received his PhD from the Massachusetts Institute of Technology while working with Dr. Sangeeta Bhatia as part of the Harvard-MIT Division of Health Sciences and Technology. His doctoral studies focused upon developing screening platforms for interrogating interactions between tumors and extracellular matrix during metastatic progression and led to the discovery of aberrant glycosylation motifs that promote metastasis. Dr. Reticker-Flynn performed his postdoctoral studies in the laboratory of Dr. Edgar Engleman at Stanford University School of Medicine. There, his work has focused on using systems approaches and mouse models to investigate tumor-immune interactions during metastasis and responses to immunotherapies. His discoveries include the revelation that effective immunotherapies require systemic activation of anti-tumor immunity and that lymph node metastases serve to reeducate adaptive immune responses in a manner that promotes distant metastasis. Dr. Reticker-Flynn is currently an Assistant Professor at Stanford University in the Department of Otolaryngology and a member of the Stanford Cancer Institute. His lab uses systems approaches, combining patient samples and mouse models, to elucidate the mechanisms of tumor-immune tolerance during metastatic progression and develops novel immunotherapies that reverse tumor-specific tolerance to treat patients with metastatic disease.
When: Friday, February 16, from 1:00-2:00pm
Location: James H. Clark Center, Room S360, 3rd floor next to the Coffee Shop
Or Online: Zoom link
Subsequent seminars will continue to take place on the 3rd Friday of each month from 11:00am to 12:00pm (please note the time change), same room and Zoom link.
Please contact Corinne Beck if you have any questions and please feel free to forward this announcement and flyer as you see fit.

Black History Month Happy Hour and Laurel Stell Celebration
2024-02-29 16:30 - 17:30 | MSOB lounge
Black History Month Happy Hour and Laurel Stell Celebration
Congratulations to Laurel Stell!!!
Stanford School of Medicine HRG JEDI selected our Laurel Stell in 2024 Cohort for BetterUp Coaching Program. They want every member of staff to feel like they can learn and grow, make an impact, and feel connected in their current role and is investing in staff, specifically, those wearing a DEI practitioner/volunteer hat, to recognize them for and enable their work, invest in their personal and professional growth, and increase resilience and retention.
Research identifies coaching as having a high impact on building leadership and professional skills, wellness, and resilience. Our BetterUp coaching program is specifically designed for School of Medicine Staff invested in JEDI, including as a practitioner, and aligns to the Stanford Medicine Commission on Justice and Equity recommendations.
This program runs annually from late January – September, with 6 months of coaching access.

2/29 from 4:30-5:30pm – MSOB lounge

The Biomedical Data Science PhD admissions interviews
2024-03-07 - 2024-03-08
The Biomedical Data Science PhD admissions interviews will be in-person on March 7-8, 2024.

Women in Data Science Conference at Stanford
2024-03-08
Be in the Room
Early bird registration is now open for our annual conference at Stanford University. Join us in-person for this International Women’s Day tradition, which will be held on campus. Register before Dec 15 for a BIG discount. Email us if you’d like to become a sponsor.
https://www.eventbrite.com/e/women-in-data-science-wids-stanford-conference-2024-tickets-641480183497?aff=WiDSWorldwideNewsletters&mc_cid=06d111be5c&mc_eid=43175f7ae8

CCBS Seminar Series
2024-03-15 11:00 - 12:00 | Clark Center S360
Third Friday of the month with two exceptions: no seminar in August and in December the seminar will take place on the 13th
Regular Time (Feb-Dec): 11:00 AM – 12:00 PM
Location: Clark Center, S360 (behind the coffee shop)

Stanford CCSB Seminar Series: Gina Bouchard
2024-03-15 11:00 - 12:00
Please join us at our next monthly CCSB Seminar, Friday, March 15, from 11 AM to 12 PM. Clark Center, Room S360, or Zoom link.
Our Seminar Series in systems biology of cancer aims to bring together experimental and computational researchers.
Speaker: Dr. Gina Bouchard, Instructor in the Department of Biomedical Data Science
Title: Spatial biology of tumor-stroma assembloids reveals that “Nothing is lost, nothing is created, everything is reorganized.”
Abstract:
Spatial -omics technologies must be codeveloped with quantitative methods for comparing in vitro patient-derived models with histological specimens. We propose a quantitative approach to assess the extent of resemblance between patient-derived tumor models and human tumors’ cytoarchitecture. We introduce the “colocatome” as a spatial -omic cataloging statistically significant colocalizations between cell subpopulations or states, allowing for normalization and facilitating direct comparisons of spatial features between in vitro models and tissues. Our study involves colocatome analysis on multiplexed immunofluorescence images of human lung adenocarcinoma (LUAD) tumor-stroma assembloids constructed with epithelial organoids and Cancer-Associated Fibroblasts (CAFs) from the tumor edge vs core. We confirm that assembloids recapitulate LUAD’s tumor-stroma cytoarchitecture, affirming the relevance of patient-derived in vitro models for studying human tumors. Following drug perturbation of assembloids, we demonstrate that CAFs protect cancer cells from targeted oncogene treatment by uniquely reorganizing cytoarchitecture, rather than promoting cellular heterogeneity or selection. We identify drug-resistant cytoarchitecture patterns from assembloids, consistent with the more aggressive histologic growth patterns of treatment-naive LUAD samples. Overall, our colocatome analysis applied to in vitro patient-derived tumor models and transferred findings to cancer specimens can serve as a functional spatial readout to predict tissue reorganization in response to cancer treatment and is generalizable to other conditions.
Bio:
Dr. Bouchard received her bachelor’s degree in pharmacology and her doctorate in Radiation Science and Biomedical Imaging in the laboratory of Dr. Benoit Paquette at the University of Sherbrooke, Canada. During her thesis, Dr. Bouchard studied the effects of radiation on breast cancer cell migration and invasiveness. Dr. Bouchard received a postdoctoral fellowship from Stanford University to join the Cancer Systems Biology program with the primary goal of training cancer biologists for bioinformatics, and vice versa. During her postdoctoral research in Dr. Sylvia Plevritis’ laboratory, Dr. Bouchard investigated the intercommunication between cancer cells and fibroblasts from various sites of lung adenocarcinomas using a multi-omics approach. Dr. Bouchard is currently continuing her research as an Instructor in the Department of Biomedical Data Science at Stanford. Here, she utilizes 3D patient-derived assembloids to examine metabolic reprogramming in the stroma, employing a spatial biology approach. The primary objective is to identify spatial features associated with metabolic resistance and to optimize radiotherapy in cancer patients.
When: Friday, March 15, 11 AM – 12 PM
Location: James H. Clark Center, Room S360, 3rd floor next to the Coffee Shop
Or Online: Zoom link
Please contact Corinne Beck if you have any questions and feel free to subscribe to our mailing list to receive our announcements and updates .

CCSB Seminar Series
2024-04-19 10:00 - 23:00, 2024-06-21 11:00 - 12:00, 2024-07-19 11:00 - 12:00, 2024-09-20 11:00 - 12:00, 2024-10-18 11:00 - 12:00, 2024-11-15 11:00 - 12:00, 2024-12-13 11:00 - 12:00 | Clark Center S360
Third Friday of the month
Regular Time (Feb-Dec): 11:00 AM – 12:00 PM
Location: Clark Center, S360 (behind the coffee shop)

CCSB Symposium
2024-04-22 08:30 - 17:30
CCSB Symposium

Monday, April 22
8:30 AM – 5:30 PM
Location: Mackenzie Room, Huang Bldg., Science & Engineering Quad

DBDSFest: April 23, 2024
2024-04-23 08:30 - 17:00 | Alumni Center
DBDSfest 2024
Where Unity Creates Strength:
Celebrating People, Diversity and Data Science
DBDSfest Registration Link: https://forms.gle/yCY4K2sdjbaXFGnL7.
DBDSfest Poster Link: https://forms.gle/JGQKC9pQeS14BSBt8.
Click here for more details!

CCSB Seminar Series
2024-05-17 11:00 - 12:00

Generative AI and Healthcare VC Panel
2024-05-17 15:00 - 17:00
The panel will feature five venture capitalists and will focus on the latest trends, challenges, and success factors with AI in healthcare startups. This panel is open to all faculty, graduate students and postdocs. It is sponsored by DBDS and the course BIODS 295 Generative AI in Healthcare.
REGISTER HERE
When: May 17th, 3:00-4:30pm Panel; 4:30-5:30 Reception
Where: Chem H Building Room E153
Panelists:

Jay Rughani, a16z
Fern Mandelbaum, Emerson Collective
Cheryl Cheng, Vive Collective
Rafic Makki, Mubadala Capital
Eric Chen, OVO Fund
Moderator: Karen Matthys, Executive Director, DBDS

Read panelists’ bios here: http://dbds.stanford.edu/genai-vc-panel-bios/

Stanford CCSB Seminar Series: Aaron M. Newman, 11/15
2024-11-15 11:00 - 12:00 | Clark Center, S360, 3rd floor

Monday Student Talks: Speakers Bryan Bunning and Yixing Jiang
2024-11-18 12:15 - 13:15 | LK 120
DBDS Student Talks (BIOMEDIN 201) Autumn Quarter 2024-25
11/18/24
12:15-12:45: Bryan Bunning
12:45-1:15: Yixing Jiang
LK 120/or Zoom Link: https://stanford.zoom.us/j/97747187137?pwd=[REDACTED]
Password: [REDACTED]
Title: A Micro-Randomized Trial Design of Remote Patient Monitoring in Pediatric Type 1 Diabetes
Abstract: At Stanford Children’s Hospital, the standard-of-care for Type 1 Diabetes (T1D) in children now includes continuous glucose monitors (CGMs) and AI-enabled remote patient monitoring (RPM) to track blood sugar levels in real time. This initiative, known as the Teamwork, Targets, Technology, and Tight Control (4T) Program, aggregates patient glucose data, sends it to the cloud for analysis, and presents it to the care team via a dashboard to support timely insulin adjustments and patient triage.
In this study, we designed a micro-randomized trial embedded within the 4T Program for newly diagnosed pediatric T1D patients. The intervention involves increasing the RPM frequency for a subpopulation of patients who are not meeting their glucose targets. Through simulations, we assessed the impact of factors such as study duration, sample size, and clinic capacity. Clinic capacity, ie the working capacity for the staff to act and provide care from the remote data, is highlighted. This simulation-based approach provides a practical framework for designing effective RPM studies under real-world constraints. This trial may offer evidence to inform RPM billing policy standards in diabetes.

Yixing Jiang, 3rd Year PhD Student
(12:45pm-1:15pm)
Title: SmartAlert: Integrating Machine Learning and Alert Triggers into Live Electronic Medical Record Systems, Targeting Low-Yield Inpatient Lab Tests
Abstract: This study explores integrating machine learning into electronic medical record systems to predict stability of inpatient lab tests. A ‘smart alerts’ system was developed and tested at Stanford Hospital. The system identifies stable lab results, advising clinicians on test ordering. Live deployment showed desired precision at good recall in predicting test result stability, with suggestions for system optimization identified. This approach may significantly decrease low-yield testing and enhance personalized clinical decision-making.

Symposium on AI for Data Science Part 1: Integrating AI into the Data Scientist's Workflow
2024-12-03 09:00 - 15:00 | Li Ka Shing Conference Center, Berg Hall B&C
The focus: integrating AI into the data scientist’s workflow, discuss challenges and solutions, implications for the next generation, where we would address how the field is/should be evolving, how graduate programs should accommodate, and what is needed to support the training/education of the next generation.
Speakers/participants include Lloyd Minor, Ruth O’Hara, Michael Pencina from Duke, Sylvia Plevritis, Sara Singer, Melissa Bondy, Michelle Williams (former Dean of Harvard’s School of Public Health), Steve Goodman, and Nigam Shah
Tuesday, December 3, 2024 9:00AM-3:00PM
Li Ka Shing Conference Center, Berg Hall B&C, 291 Campus Drive, Stanford, CA 94305
REGISTER TODAY: https://bit.ly/3NOw4p6
This is a free event. Lunch and light refreshments will be served.
Special Guest Speakers
Panelists and Moderators
Register here: https://bit.ly/3NOw4p6

Dr. John Ioannidis, "Cities Facing Each Other: A Book Reading" 2/18
2025-02-18 18:00 - 19:30 | Stanford Humanities Center – Board Room, 424 Santa Teresa St, Stanford
Please join the Workshop in Poetics next Tuesday, February 18 at 6pm (Stanford Humanities Center Board Room) at for our first event of Winter Quarter! For more information and to RSVP please visit our website here.

We will be hosting Stanford professor of medicine, poet, and Poetics community member John P.A. Ioannidis, who will be reading from his two most recently published books in Greek and in English. Light snacks and refreshments will be served.
Event Details:
Tuesday, February 18, 2025
6:00pm – 7:30pm PST
Location Stanford Humanities Center – Board Room
424 Santa Teresa St
Stanford , CA
This event is open to: Alumni/Friends, Faculty/Staff, General Public, Members & Students
John Ioannidis, “Cities Facing Each Other: A Book Reading” | Stanford Center for Poetics

Frontiers in Biology: Patrick O'Brien, February 19th
2025-02-19 16:00 - 17:00 | Clark Center Auditorium
“Escape From the Planet of the Cows”

Zoom Meeting ID: 94002169959
Passcode: [REDACTED]

CCSB Seminar Series: Wesley Tansey, PhD, Assistant Professor at Memorial Sloan Kettering Cancer Center, 2/21
2025-02-21 11:00 - 12:00 | Clark Center, S360, 3rd floor

Bryan Bunning: “Research-In-Progress Talk," 2/24
2025-02-24 10:30 - 12:00
Title: A Micro-Randomized Trial Design of Remote Patient Monitoring in Pediatric Type 1 Diabetes
Abstract:
In this presentation, we highlight the methods development and rationale behind a micro-randomized trial of pediatric Type 1 Diabetic (T1D) patients. Through simulations, we assessed the impact of factors such as study duration, sample size, and clinic capacity. Clinic capacity, ie the working capacity for the staff to act and provide care from the remote data, is highlighted. This work builds upon a combination of methods including micro-randomization trial design and of index-based treatment allocation. A simulation-based approach provides a practical framework for designing effective RPM studies under real-world constraints. This trial may offer evidence to inform RPM billing policy standards in diabetes.
Monday, February 24th, 2025; 10:30 AM – 12 PM PST
3180 Porter Drive, Room B107/B136
Zoom link: https://stanford.zoom.us/j/95454685856?pwd=[REDACTED]
PW: [REDACTED]
