Stanford - Department of Biomedical Data Science

CCSB Seminar Series
2024-05-17 11:00 - 12:00 (America/Los_Angeles)
Third Friday of the month
Regular Time (Feb-Dec): 11:00 AM – 12:00 PM
Location: Clark Center, S360 (behind the coffee shop)

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 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

CCSB Seminar Series
2024-04-19 10:00 - 23:00 | Clark Center S360

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 .

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)

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

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.

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

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.

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

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

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=S20vUFFTOEppazZpbGFiVktCZ3lYQT09&from=addon#success

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

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!

James Zou at the DeSci Foundation: Large language models and future of science.
2024-01-22 08:00 - 22:00
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

CCSB Seminar Series
2024-01-19 10:00 - 11:00
Seminar Series:

Third Friday of the month with two exceptions: no seminar in August and in December the seminar will take place on the 13th
First seminar
10:00- 11:00 AM
Location: Clark Center, S360 (behind the coffee shop)

Weekly Seminar: 1/18
2024-01-18 08:00 - 17:00
Date: 1/18/24
Adit Radhakrishnan
Title: How do neural networks learn features from data?
1:30-3:00 pm in MSOB x303
More info here.

Alex Derry's Dissertation Defense
2023-12-08 10:00 - 12:00
The Department of Biomedical Data Science invites you to a Dissertation Defense
Alex Derry
Friday, December 8th, 2023
10:00 am PST
Location: Y2E2 111
Deep learning on local sites for protein structure and function analysis
Understanding how the three-dimensional structure of a protein leads to its function is important for determining disease mechanisms, developing targeted therapeutics, and engineering new proteins with desired functional characteristics. The expansion of protein structure databases due to experimental and computational advances provides an unprecedented opportunity to learn structure-function relationships in a data-driven manner. Deep learning methods that operate on protein structures have shown promise for specific tasks, but their utility for functional analysis has been limited due to inconsistencies in model training and evaluation, lack of labeled proteinfunction data, and an inability to reconcile global predictions with local biochemical mechanisms. In this dissertation, I explore these challenges and propose a framework for protein analysis based on learning on local sites rather than the entire protein structure. First, to establish standards for model development and evaluation, I present work on (1) developing a suite of benchmark datasets, processing tools, and baseline models, and (2) quantifying the effect of differing structure compositions in the training data. I then describe a self-supervised learning method that leverages evolutionary relationships to learn general-purpose representations of local structural sites and show how these representations enable improved performance on downstream tasks involving classification, search, and annotation of functional sites. By clustering millions of sites, I propose a framework for protein analysis based on conserved structural motifs which enables the discovery of functional relationships across protein classes. Finally, I present a method for explainable function annotation that predicts the overall function of a protein as well as the individual residues which are responsible.
Zoom: https://stanford.zoom.us/j/95316385692
(PW: 271506)

DBDS Holiday Extravaganza
2023-12-07 17:00 - 20:00
December 7, 2023; Stanford Faculty Club
More info to come!

Faculty Meeting: (November + December) December 6, 2023
2023-12-06 11:30 - 13:00 | MSOB Conference Room
Lunch will be provided.
Zoom link: https://stanford.zoom.us/j/97249583050?pwd=S20vUFFTOEppazZpbGFiVktCZ3lYQT09&from=addon#success

Kevin Wu: Medical AI After Deployment: Data-driven analyses and methods for clinically viable AI
2023-11-08 14:00 - 15:00 | CCSR 0235
Wednesday, November 8th, 2023
2:00 pm – 3:00 pm PST
CCSR 0235
Zoom Link: https://stanford.zoom.us/j/95984592133?pwd=MDRXcyt4eTlCVlZhdHZYZ0prLzBGZz09
Title: Medical AI After Deployment: Data-driven analyses and methods for clinically viable AI
Abstract: Medical AI algorithms have undergone significant development and regulatory approval, with over 600 FDA-approved medical AI devices currently. However, their actual clinical safety and impact remain unclear. First, we analyze FDA submission documents and find that the majority of FDA approvals do not report multi-site evaluation, and nearly none have prospective analyses. Second, we track the occurrences of newly released AI billing codes in a nationwide insurance claims database and find that only a handful of products have meaningful clinical adoption. Finally, we systematically track device updating in FDA submissions and find that the majority of devices have not had updates to model weights since initial approval. Given these limitations, we propose several methods to address common issues with algorithmic deployment. First, we present a framework for understanding the marginal contribution of distribution shifts to overall model degradation. Second, we present a method for efficient missing data collection in the context of fixed models. Finally, we present ways to improve the robustness of evaluating medical LLMs.

Faculty Development Committee Meeting
2023-11-08 12:00 - 13:00
Wednesday, November 8, 2023 from 12:00 PM to 1:00 PM
https://stanford.zoom.us/j/98257342544?pwd=VWNJa0l0S05YTGZSbkxtaUozVkNyUT09&from=addon
Attendees: Olivier Gevaert; Theresa McCann-Packer; Iain M Johnstone; Manisha Desai; Teri Klein; James Zou; Julia Adela Palacios; Lu Tian; Ni Deng; Daniel Rubin

Workshop on GenAI in Healthcare: Red Teaming
2023-10-25 15:00
Please join us for an interaction session to test GenAI models for potential issues with biases, inaccuracies, and other matters related to healthcare. Red-teaming is a form of evaluation that elicits model vulnerabilities that might lead to undesirable behaviors. We will be looking for such behaviors on healthcare-related tasks.
All faculty, graduate students and postdocs are welcome. We will break into groups with table leaders from Stanford Healthcare, School of Medicine, CS and external partners providing technical and clinical insights. At the end we’ll have a read-out of findings, and then continue the conversations during happy hour.
REGISTER HERE
Date: October 25th
Location: Chem-H Building Room E241
Agenda:
3:00pm | Check in begins
3:15pm | Table groups begin Red Teaming
4:45pm | Happy hour
6:00pm | Event concludes
If you have questions, please contact Roxana Daneshjou or Karen Matthys. Faculty, if you’re interested in leading a table group please let us know.

DBDS Retreat September 18-20 Asilomar Conference Center
2023-09-15 08:00 - 17:00
BMI 2023 Retreat Agenda
September 18-20, 2023 | Asilomar Conference Center | Pacific Grove, CA
Monday, September 18

Time
Activity
Where

3:30-5:00 PM
Check In and Welcome Reception
The Meadows/BBQ Area

5:00-5:45 PM
Group Photo & Headshots
Back steps of Hearst Social Hall

6:00-7:00 PM
Dinner
Seascape Room

7:00-7:45 PM
State of the Department
Seascape Room

7:45-8:45 PM
Alumni Fireside Chat
With Serge Saxonov and Iwei Yeh
Seascape Room

8:45-11:00 PM
Bonfire
The Meadows/BBQ Area

Tuesday, September 19

Time
Activity
Where

7:30-8:20 AM
Breakfast
Seascape Room

8:20-8:30 AM
Break

8:30-9:30 AM
Faculty Lightning Talks
Merrill Hall

9:30-9:45
Break

9:45-10:45 AM
Ice Breaker
Merrill Hall

10:45-11:00 AM
Break

11:00-12:00 PM
Poster Session I
Merrill Hall

12:00-1:00 PM
Lunch
Seascape Room

1:00-1:10 PM
Break

1:10-2:10 PM
Faculty Lightning Talks
Merrill Hall

2:10-3:00 PM
Casual Faculty Forum
Surf and Sand

2:10-5:00 PM
Sandcastle Competition (optional)
Asilomar Beach Area

5:00-6:00 PM
Poster Session II
Merrill Hall

6:00-7:10 PM
Dinner
Seascape

7:00-7:10 PM
Break

7:10-9:00 PM
Community Game Night
Merrill Hall

Wednesday, September 20

Time
Activity
Where

7:30-8:30 AM
Breakfast
Seascape

Please check out of your room by 11 AM

8:30-9:30 AM
Faculty Lightning Talks
Merrill Hall

9:30-10:30 AM
Roadmap Overview and Breakouts

10:30-11:45 AM
New Student Orientation

11:00-11:45 AM
Returning students Cohort Huddles

11:45 AM
New Student Lunch
Merrill Hall
