Stanford - Department of Biomedical Data Science

DBDSFest: April 23, 2024
2024-04-23 08:30 - 17:00 (America/Los_Angeles) | 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
Third Friday of the month
Regular Time (Feb-Dec): 11:00 AM – 12:00 PM
Location: Clark Center, S360 (behind the coffee shop)

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/

CCSB Seminar Series
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

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]

Monday Student Talks: 2/24 Suhana Bedi; Sohaib Hassan
2025-02-24 12:15 - 13:15 | Alway M114/ZOOM
DBDS Student Talks (BIOMEDIN 201) Winter Quarter 2024-25 in Alway M114/ZOOM. Lunch will be provided for the talks.
Upcoming 2/24 Monday Talk Speakers:

DATE
12:15-12:45
12:45-1:15

2/24/2025
Bedi, Suhana
Hassan, Sohaib

Attendance will be taken weekly on a Google sheet. Please sign your name on the sheet when you attend the Monday Talks via Zoom or in-person.
–Hybrid model, with both in-person and remote attendance via Zoom.
–If you require any special accommodations, please reach out to DBDS Student Services in advance before the date of your talk.
Zoom Link: https://stanford.zoom.us/j/97615772092?pwd=[REDACTED]
Password: [REDACTED]

Grand Rounds: Nigam Shah, 2/25
2025-02-25 09:00 - 10:00
Upcoming Grand Rounds
Date: Tuesday, February 25, 2025
Time: 9:00-10:00am PT
Format: Live webinar presentation and Q&A
Registration: Open to the Stanford and AIMI affiliate community
Register Here
Speaker:

Nigam Shah, MBBS, PhD: Professor of Medicine, and of Biomedical Data Science; Chief Data Scientist, Stanford Healthcare; Associate Dean for Research, School of Medicine; Associate Director, Stanford Center for Biomedical Informatics Research, Stanford University
Title: Responsible AI at Stanford Healthcare
About: Dr. Shah is Professor of Medicine at Stanford University, and Chief Data Scientist for Stanford Health Care. His research is focused on bringing AI into clinical use, safely, ethically and cost-effectively. Dr. Shah is an inventor on eight patents, has authored over 300 scientific publications, and has co-founded three companies. Dr. Shah was inducted into the American College of Medical Informatics (ACMI) in 2015 and the American Society for Clinical Investigation (ASCI) in 2016. He holds an MBBS from Baroda Medical College, India, a PhD from Penn State University and completed postdoctoral training at Stanford University.

2025 CEHG Symposium featuring the first Cavalli-Sforza Lecture
2025-03-03 08:30 - 17:00 | Paul Brest Hall
Please mark your calendars for the return of the CEHG Symposium – the first since 2020! The event will take place on March 3rd, 2025 in Paul Brest Hall from 8:30 AM – 5 PM.

CEHG is proud to host Mary-Claire King as the speaker for the first Cavalli-Sforza Lecture in memory of Luigi Luca Cavalli-Sforza, a scientist celebrated for his groundbreaking work in genetics and human evolutionary history. Professor Cavalli-Sforza was a distinguished member of the Stanford faculty from 1971 to 1992, and remained an influential emeritus faculty member until 2008.

CCSB Seminar Series: Kyle Daniels, PhD, March 21
2025-03-21 11:00 - 12:00 | Clark Center S360
Stanford Center for Cancer Systems Biology
– Seminar Series – 2025
Kyle Daniels, PhD
Assistant Professor of Genetics and, by courtesy, of Neurosurgery, Stanford University
Mapping the structure-signaling-phenotype landscape in CAR T cells using synthetic signaling protein arrays and machine learning

Chimeric antigen receptor (CAR) T cells are powerful therapeutics for cancers. These CAR T cell therapies can be improved by providing JAK/STAT signaling to increase CAR T cell survival, proliferation, and anti-tumor activity. To design proteins that enhance CAR T cell efficacy, we sought to map the structure of JAK/STAT signaling domains to cell signaling and resulting CAR T cell phenotype. We recombined 14 signaling motifs to construct library of ~30,000 constitutively active synthetic cytokine receptors (SCRs) with intracellular domains composed of novel signaling motif combinations that activate different signaling cascades. We experimentally tested ~530 SCRs which generated a range of CAR T cell memory, cytotoxicity, and proliferation. To map the structure-signaling-phenotype landscape we trained models to predict CAR T cell signaling and phenotype that result from various motif combinations. Modeling also revealed a trade-off between memory and cytotoxicity, with a Pareto front defined by cell signaling. We identified signaling features associated with memory, cytotoxicity, or a balance between the two. SCRs with balanced pSTAT1/3/5 signaling encoded balanced memory and cytotoxicity to enhance CAR T cell tumor control in a mouse model of osteosarcoma. We also identified signaling features that promote unsafe autonomous CAR T cell proliferation. These findings demonstrate that combinatorial screening and machine learning can be combined to map the structure-signaling-function landscape of synthetic proteins in therapeutic immune cells. This approach and the resulting models may enable rational design of CAR T cells with improved cytotoxicity, memory, and safety profiles.
Friday, March 21, 2025
Clark Center, S360, 3rd floor
11:00AM -12:00PM
Refreshments will be provided

QSU Research Methods Seminar: Robert Tibshirani, Ph.D. 4/1
2025-04-01 12:00 - 13:00
QSU Research Methods Seminar
Tuesday, April 1, at 12:00 pm PST
join the seminar at 3180 Porter Dr. (combined Room B107 & B136)
*Lunch will be provided*
Zoom Link: Meeting ID: 996 4643 5133
Password: [REDACTED]
Robert Tibshirani, Ph.D.
Professor of Biomedical Data Science and of Statistics
Stanford University
Univariate-guided Sparse Regression
In this talk Dr. Tibshirani will introduce “UniLasso”, a novel statistical method for sparse regression. This two-stage approach preserves the signs of the univariate coefficients and leverages their magnitude. Both of these properties are attractive for stability and interpretation of the model. Through comprehensive simulations and applications to real-world datasets, we demonstrate that UniLasso outperforms Lasso in various settings, particularly in terms of sparsity and model interpretability. We prove asymptotic support recovery and mean-squared error consistency under a set of conditions different from the well-known irrepresentability conditions for the Lasso. Extensions to generalized linear models (GLMs) and Cox regression are also discussed. A special case of lasso, “uniReg” is an interesting competitor to good ol’ least squares regression (Legendre, 1805).
This is joint work with Sourav Chatterjee and Trevor Hastie.
We welcome any suggestions or questions about the seminar series – please contact Cyra June Ente cyraente@stanford.edu
We look forward to seeing you!

Jure Leskovec: From Data to Discovery: How Foundation Models Transform Biology 4/2
2025-04-02 16:00 - 17:00
Wednesday, April 2, 2025 4:00pm – 5:30pm PDT
Simonyi Conference Center, CoDa, 389 Jane Stanford Way, Stanford, CA 94305
Abstract: Foundation models are revolutionizing biology by learning the underlying structure of complex biological data and transforming how we analyze, interpret, and generate scientific knowledge. In this talk, we explore how these models accelerate discovery by integrating vast datasets, uncovering biological organization, and guiding hypothesis-driven research. We begin with models that learn universal representations of cells across tissues and species. Without explicit supervision, these models capture fundamental biological organization, allowing researchers to analyze, compare, and annotate cells with unprecedented precision. This ability to model biological diversity naturally leads to the next challenge: how to generate and test new biological hypotheses. Large language models, trained on vast scientific literature, can play a crucial role in this process.
For more information: https://datascience.stanford.edu/events/scientific-discovery-age-data-ai/jure-leskovec-stanford

Experimental Design: AI for Science 4/3-4/4
2025-04-03 09:00 - 17:00 | Mackenzie Room, Jen-Hsun Huang Engineering Center
Only a Month Away – Don’t Miss Out! Registration Filling Fast!
We are excited to invite you to the workshop “Experimental Design: AI for Science” happening at Stanford University on 3rd and 4th April 2025. The workshop focuses on theory and methodology of AI based experimental design and its application to addressing scientific problems. We have an exciting lineup of speakers including David Baker, Jennifer Chayes, Ashia Wilson, Stefano Ermon, Jennifer Listgarten, Aaron Streets, Andreas Krause, Brian Trippe, Yisong Yue, Jure Lesokvec and Kyunghyun Cho.
We also invite students and postdocs to submit abstracts about their research for consideration to present at the workshop. The topics can be broadly related to experimental design and AI for science, and are outlined in Call For Abstracts (deadline Mar. 15).
Website: edai4science.github.io
Registration for the workshop.
Submit abstracts before Mar. 15.

Innovators in Computational Biology & AI
2025-04-04 13:30 - 14:30 | Edwards, R358
We are excited to introduce a new seminar series – “Innovators in Computational Biology & AI,” sponsored by the Warren Alpert CBAI Scholars Program. Our inaugural speaker, Dr. Sarah McGough from Genentech, will share her experience transitioning from graduate school to industry, offering valuable insights into biotech, work culture, and career opportunities. Don’t miss her tips on navigating the job application process and career prospects. Please RSVP to help us plan for the event.
Speaker: Dr. Sarah McGough (Genentech)
Date: Friday. April 4th, 1:30-2:30PM
Location: Edwards Building, R358
Refreshments will be provided
If you have any questions or concerns, feel free to reach out to xsitu@stanford.edu.

For Graduate Students: Resource Fair! 4/11
2025-04-11 12:00 - 13:30 | Alumni Lawn, School of Medicine
Graduate Spring Resource Fair – Grow Your Grad Garden!
Friday, April 11, 2025
12:00pm – 1:30pm PDT
Location: Alumni Lawn, School of Medicine – Map Link
You’re invited! Check out Stanford’s third annual Graduate Spring Resource Fair – Grow Your Grad Garden! Bring your friends and grow your “grad garden” by getting to know over 40 different campus resources available to graduate students, including resources for mental health and well-being, learning and academic support systems, and diverse grad life communities. We will be offering free pizza lunch, speed friending, and lots of swag!

Welcome to the Edwards Building, DBDS! 4/14
2025-04-14 16:00 - 17:00
The Department of Pathology, chaired by Dr. Thomas Montine, will host the “Welcome Event” on April 14 for all members of DBDS.

Decoding Cancer Heterogeneity Through Multi-Modal Biomedical Data With Yuanning "Eric" Zheng, PhD
2025-04-18 11:00 - 12:00 | Clark Center, S360, 3rd floor
Stanford Center for Cancer Systems Biology
2025 Seminar Series
Join us at 11:00am on Friday, April 18, 2025, in the Clark Center (Room S360) or remotely at this Zoom link as Dr. Zheng discusses his research on addressing the challenges of cancer heterogeneity by developing bioinformatics tools and AI models to identify clinically relevant disease phenotypes.

Please see flyer for more information about the talk. We encourage you to attend in-person to best engage with the speaker and enjoy some refreshments.

Stanford 2025 Center for Cancer Systems Biology (CCSB) Symposium on May 1
2025-05-01 09:00 - 16:00
Stanford 2025 Center for Cancer Systems Biology (CCSB) Symposium

Thursday, May 1
9:00 am to 4:00 pm
ChEM-H and Neurosciences Building, Rotunda, E241, 2nd Floor. Poster session starts at 12:00pm.

The symposium is designed for participants to explore systems biology approaches to understanding cancer progression and treatment response. Talks covering computational and imaging innovations will focus on decoding the tumor microenvironment, analyzing spatial dynamics in metastasis, mapping cell-cell interactions, and advancing therapeutic and diagnostic strategies.
Registration is now open and free to all. Please register using this link or scan QR code in the flyer. We are finalizing the agenda and will share the full speaker lineup soon. In the meantime, please visit the symposium website for the draft agenda and additional details here.

DBDS Open House
2025-05-06 16:00 - 18:00 | Edwards Building, 300 Pasteur Drive, 3rd floor, Stanford, CA, United States
Dear DBDS Community,
We’re excited to announce DBDS OPEN HOUSE 2025 – and we’d love for you to join us!
Date: May 6, 2025
Time: 4pm-6pm
Location: Edwards Building, 300 Pasteur Drive, 3rd floor, Stanford, CA 94305
We look forward to seeing you at this exciting event!

Stat4One Annual Symposium 5/16-5/17
2025-05-16 08:00 - 17:00
Join us at the Stat4Onc Annual Symposium, where clinical and quantitative scientists will engage in interdisciplinary discussions on cancer clinical trials. Researchers from academia, industry, and regulatory agencies are invited to share new research, explore novel ideas, and collaborate on solutions for improving trial design, drug development, and patient care. Oncologists and statisticians will discuss key topics such as trial methodologies, precision oncology, master protocols, and real-world data.
Key areas of focus include training future statisticians and clinicians, pediatric oncology, population-based research, biomarkers, and increasing diversity in oncology studies. We are grateful for the support of the National Cancer Institute (NCI) through an NCI R13 grant.
Save Big Before 4/15! REGISTER NOW!
Don’t miss out on the opportunity to register early and take advantage of discounted rates.
Conference Registration Rates May 15 and May 16, 2025
For Stanford, U Chicago, U Conn, OHSU, and Government:

Before 4/15: $30.00
After 4/15: $60.00

For Academia and Non-Profit:

Before 4/15: $100.00
After 4/15: $200.00

Short Course Rates
One Day Course:

For Stanford, U Chicago, U Conn, OHSU, and Government:

Before 4/15: $50.00
After 4/15: $100.00

For Academia and Non-Profit:

Before 4/15: $150.00
After 4/15: $250.00

Half Day Course:

For Stanford, U Chicago, U Conn, OHSU, and Government:

Before 4/15: $25.00
After 4/15: $50.00

For Academia and Non-Profit:

Before 4/15: $80.00
After 4/15: $150.00

Don’t Delay!
Take advantage of these great early registration rates and save before 4/15! Secure your spot today!
