News & Events
Public Meeting Materials from the 2025 FaceBase Forum (30 June 2025)
The 2025 FaceBase Annual Community Forum, held on June 3 & 4 at the Information Sciences Institute in Marina del Rey, CA, demonstrated the newly emerging capabilities of FaceBase to support not only dental, oral and craniofacial (DOC) research and studies across the translational spectrum, but also in related health domains and systems. We introduced new collaborations with the National Institute of Deafness and Communication Disorders (NIDCD), explored integrating clinical elements into FaceBase with the description of an upcoming pilot, introduced the cutting edge technology of Dynamic MRI, discovered advances in basic DOC research and much, much more. FaceBase also announced their exciting roadmap for the next four years, emphasizing data integration, AI and machine learning applications, and future goals for enhancing research capabilities.
Below you will find comprehensive materials from the one-and-half-days event.
Slides and Webcasts from Presentations and Panels
| Presentation | Presenter(s) | Slides | Webcast/Video |
|---|---|---|---|
| Introduction | Yang Chai, D.D.S., Ph.D. (USC) | Slides | Webcast |
| FACEBASE: Empowering Data-Driven Research to Achieve Oral Health for All | Jennifer Webster-Cyriaque, D.D.S., Ph.D. (NIDCR/NIH) | Slides | Webcast |
| An Introduction to FaceBase’s Newest Partner: NIDCD… and the Temporal Bone | Debara L. Tucci, M.D., M.S., M.B.A. (NIDCD/NIH) | Slides | Webcast |
| FaceBase PI Community Forum | Susan Gregurick, Ph.D. (ODSS/NIH) | Webcast | |
| FaceBase 4 Roadmap | Carl Kesselman, Ph.D. and Rob Schuler, Ph.D. (USC) | Slides | Webcast |
| The Need for High Quality Data for Data Reuse and Machine Learning | Helen M. Berman, Ph.D. (USC) | Slides | Webcast |
| Long Range Gene Regulation of the Developing Human Face | Justin Cotney, Ph.D. (CHOP) | Slides | |
| Beaks, Bones, and Beyond: Using Avian Models to Study Development | Samantha Brugmann, Ph.D. (Cincinnati Children's Hospital) | Slides | |
| Panel: Incorporating Relevant Clinical Elements into FaceBase | Webcast | ||
| From panel: Bridging Repositories and Clinical Decision-Making | Anette Vistoso Monreal, D.D.S., M.S. (USC) | Slides | |
| From panel: myTMJ - A Digital Solution for Orofacial Pain | Mohammad Khalifeh, D.D.S., M.S. (USC) | Slides | |
| Approaches to Integration of Clinical Data into FaceBase | Thomas Peterson, Ph.D. (UCSF) | Slides | Webcast |
| AI in TMD and Orofacial Pain Diagnosis | Glenn Clark, D.D.S, M.S. and Anette Vistoso Monreal, D.D.S., M.S. (USC) | Slides | Webcast |
| Dynamic MRI to Study TMD and Craniofacial Conditions | Krishna S. Nayak, Ph.D. (USC) | Slides | Video Demo |
| Vision for Data Science in Craniofacial Research | Axel Visel, Ph.D. (LBNL) | Slides | Webcast |
| How FaceBase Data Helped Develop Pediatric Respirators | Christopher Nemeth, Ph.D. (ARA) and Benedikt Hallgrímsson, Ph.D. (U Calgary) | Slides | Webcast |
| Panel: Leveraging FaceBase in Related Health Domains | Carl Kesselman, Yang Chai, Benjamin Xu, Jennifer Kalish, Axel Visel | Webcast |
Poster Session Presenters
| Poster Title | Presenter(s) | Poster PDF | Abstract |
|---|---|---|---|
| Ameloblastin Multitargeting Domain Influences Ameloblast Gene Expression During Enamel Formation | Rucha A. Bapat (University of Southern California) | Not available | Not available |
| FaceBase: Data Resources for Craniofacial and Dental Development, Molecular Genetics, and Genomics | Alejandro Bugacov (Information Sciences Institute) | Poster PDF | Abstract |
| High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development | Jifan Feng (University of Southern California) | Poster PDF | Abstract |
| Trp53 Coordinates with Hippo Signaling During Tooth Root Development | Tingwei Guo (University of Southern California) | Poster PDF | Abstract |
| Dysregulated chondrocyte formation as a novel mechanism of lambdoid synostosis | Fenglei He (Tulane University) | Poster PDF | Abstract |
All our thanks go to those esteems speakers and panelists and to all who joined us! Looking forward to seeing you at next year’s Forum!
Data release: SHH expression in the Frontonasal Ectodermal Zone (21 May 2025)
We are excited to announce a new data release from a PLOS Genetics paper on SHH expression in the Frontonasal Ectodermal Zone that depicts a new enhancer element!
PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms Principal Investigators: Licia Selleri and Ralph S. Marcucio (University of California, San Francisco)
Citation:
Mok CH, Hu D, Losa M, Risolino M, Selleri L, Marcucio RS (2025) PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms. PLoS Genet 21(5): e1011315. https://doi.org/10.1371/journal.pgen.1011315
FaceBase Dataset:
Description:
Facial development is orchestrated by complex molecular interactions among signaling molecules and transcription factors, a class of proteins that regulate gene expression. Disruption of these interactions can lead to congenital facial malformations, affecting the lives of patients and their families. Understanding the molecular basis of these interactions during embryonic facial development will provide key insights into the origin of these disorders and may ultimately provide novel therapeutic targets. SHH is one of the key genes encoding a signaling molecule that regulates facial development. During early embryonic development, SHH is expressed in a signaling center in the surface cell layer that covers part of the face. This signaling center regulates proliferation to control proper outgrowth of the upper jaw. In the present study, we demonstrated that PBX1 and PBX3 transcription factors control expression of SHH at the molecular level. We identified a DNA element, SFE1, located in a regulatory region of the SHH locus. SFE1 induces SHH transcription when associated with PBX1 and represses transcription when associated with PBX3. These findings highlight the intricate molecular mechanisms underlying regulation of SHH expression and advance current knowledge of the regulatory pathways that control midfacial development.
This figure was generated from the ChIP-seq and ATAC-seq data in this study, submitted to FaceBase, and it shows the location of SFE1, a new enhancer element that we identified from this study.
Data release: TGF-β Signaling and Craniofacial Morphogenesis (20 May 2025)
We are excited to announce new data releases from a Nature Communications paper on TGF-β Signaling and Craniofacial Morphogenesis featuring high resolution spatial genomics data!
High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development (2 datasets) Principal Investigator: Yang Chai (University of Southern California)
Citation:
Feng, Jifan & Janeckova, Eva & Guo, Tingwei & Ziaei, Heliya & Zhang, Mingyi & Geng, Jessica & Cha, Sa & Araujo-Villalba, Angelita & Liu, Mengmeng & Ho, Thach-Vu & Chai, Yang. (2025). High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development. Nature Communications. 16. 10.1038/s41467-025-59206-2.
The authors employed scRNA-seq analysis alongside a seqFISH-based spatial genomics approach for high-resolution visualization of spatially resolved gene expression profiles for the developing palate and other craniofacial regions in the mouse embryos. The raw and processed scRNA-seq data from embryonic palatal tissue at different developmental stages (E12.5, E13.5, E14.5, E15.5, and E18.5) generated in this study has been deposited in FaceBase under the DOI 10.25550/62-QZ1A. The raw and processed sequencing-FISH data for anterior and posterior embryonic heads at E12.5, E13.5, and E15.5 are available in the FaceBase database under the DOI 10.25550/62-Y0VT.
FaceBase Achieves CoreTrustSeal Certification (26 March 2025)
FaceBase has officially been awarded the CoreTrustSeal certification. This recognition affirms our commitment to maintaining a trusted, sustainable, and FAIR (Findable, Accessible, Interoperable, Reusable) data repository for the dental, oral, and craniofacial research community.
The CoreTrustSeal is an internationally recognized certification that evaluates data repositories based on 16 rigorous requirements related to sustainability, data integrity, and long-term accessibility.
This milestone reflects our ongoing efforts to support open science, facilitate data sharing, and enhance research reproducibility.
To learn more about the CoreTrustSeal certification and what it means for FaceBase, visit CoreTrustSeal or read our CoreTrustSeal application.
Join us at AADOCR in New York City this week! (11 March 2025)
If you’re at AADOCR conference in New York City at the Javits Center this week, come say Hi!
Exhibit Hall: Booth #124: March 13-15, 9am to 5pm We’ll have new merch and FaceBase team members who would love to answer your questions, give demos and talk about your data.
Also:
NIDCR Trainee Poster session: Room 1A08 - March 12, 9am to 12pm Alejandro Bugacov will have a poster and a table where he can talk one on one with postdocs and give demos