April 11^th Agenda

April 12^th Agenda

Integrative Modeling of Multiscale Single-Cell Spatial Epigenome  

Jian Ma | Ray and Stephanie Lane Professor of Computational Biology, School of Computer Science, Carnegie Mellon University

Abstract: Despite significant advancements in high-throughput data acquisition in genomics and cell biology, our understanding of the diverse cell types within the human body remains limited. Particularly, the principles governing intracellular molecular spatial organization and cellular spatial organization within complex tissues are still largely unclear. A major challenge lies in developing computational methods capable of integrating heterogeneous and multiscale molecular, cellular, and tissue information. In this talk, I will discuss our recent work on creating integrative approaches for single-cell spatial epigenomics and transcriptomics. These methods hold the potential to reveal new insights into the fundamental genome structure and cellular function, as well as the spatial organization of cells within complex tissues, across a wide range of biological contexts in health and disease.

Bio: Jian Ma is the Ray and Stephanie Lane Professor of Computational Biology at the School of Computer Science at Carnegie Mellon University. His lab focuses on developing computational methods to study the structure and function of the human genome and cellular organization and their implications for evolution, health and disease. He currently leads a multi-disciplinary NIH Center, as part of the NIH 4D Nucleome Program. His recent work has been supported by NIH, NSF, CZI, Google, and the Mark Foundation. He has received several awards, including an NSF CAREER Award and a Guggenheim Fellowship (in Computer Science), and is an elected Fellow of AAAS.

Visit the Ma Lab Website

Is Spatial Omics the New Single Cell Omics?

Jasmine Plummer | Director, Center for Spatial OMICs, St. Jude Children’s Research Hospital

Abstract: Genomics has changed scientific research by allowing us to understand the interplay between genes and their environment. Like others in the field, Dr. Plummer adopted single cell genomics when the technology first arose as a means to better understand genetic perturbations and how they contribute to disease pathogenesis. She will be discussing the potential of spatial omics to being even more informative in the discovery in this area. Dr. Plummer will provide examples from her own research of how spatial omic technologies have offered insight into her work where single cell was limited. This session will contectualize what spatial omics can to help assess the spatial organization and cell types within niches and understand their intercellular communication.

 Bio: Dr. Jasmine Plummer  received her PhD in Molecular Genetics from the University of Toronto and completed a Master’s degree in neuroscience with a speciality in comparative neurobiology and neurodevelopment at Dalhousie University in Nova Scotia, Canada.

 Dr. Plummer’s postdoctoral work at Children’s Hospital Los Angeles implemented a systems biology approach to examine the genetic risk of neurodevelopmental disorders. As an Autism Speaks postdoctoral fellow, her research concentrated on the discovery and functional characterization of gene regulatory networks implicated in the development of autism. 

Throughout her career, Dr. Plummer has used a multi-omics approach to examine genetic risk as a factor of oncogenesis across cancers, including ovarian, breast, and prostate, and neurodevelopmental disorders. As Director of the Center for Spatial Omics, Dr. Plummer leverages her extensive research experience and knowledge of data integration, computational pipeline implementation, and program management to lead an omics-centered approach that advances research of pediatric catastrophic diseases.

Spatial Omics Lab at St. Jude's

Spatial Tissue Profiling: From a Novelty to a Discovery Powerhouse

Ioannis Vlachos | Assistant Professor of Pathology, Harvard Medical School

Abstract: Spatial tissue profiling has come with a promise to revolutionize research and clinical decision making. In this talk, I will be presenting efforts empowered with such technologies as well as internal, national, and international initiatives aiming to bring spatial tissue profiling into an era of maturity.

 Bio: Ioannis Vlachos, Ph.D., is Associate Professor of Pathology, Harvard Medical School (HMS), and the Director of the Spatial Technologies Unit of the HMS Initiative for RNA Medicine. He also directs the Bioinformatics Unit of the Precision RNA Medicine Core. Ioannis is the co-Director of the Bioinformatics Program of the Cancer Research Institute (CRI), a Member of the Dana Farber / Harvard Cancer Center, and an Associate Faculty of the Broad Institute of MIT & Harvard.

Dr. Vlachos’ research focuses on the optimal use of cutting-edge technologies for reverse translation, including bulk, single cell, and spatial tissue profiling to inform clinical decision making. To this end, his team is developing and applying novel technologies and AI/ML methodologies for data integration and target or biomarker prioritization. His group is creating the necessary data and methods to bring these novel approaches in precision medicine applications.

To enable the community gain access and benefit from the spatial tissue profiling revolution, he established the Spatial Technologies Unit (www.spatialtechnology.org) , with support from the Commonwealth of Massachusetts, Beth Israel Deaconess Medical Center, and the HMS Initiative for RNA Medicine. It is a center of excellence for spatial tissue profiling, providing access to technology, education, and support for entrepreneurship. Dr. Vlachos is working in rendering Spatial Tissue Profiling into a powerhouse for discovery, innovation, and clinical breakthroughs. His team in the Spatial Technologies Unit is transforming research-focused spatial technologies into robust, automated, and highly repeatable production-grade methods.

In 2023 Dr. Vlachos co-founded the Global Alliance for Spatial Technologies (GESTALT, www.globalspatial.org), in an effort to bring together the spatial tissue profiling community and to support world-wide efforts for standards in the field.

Dr. Vlachos work is supported by funding from diverse sources, including NIH (R01, P01, U54), the DoD, foundations, and collaborations with the industry. He is co-PI of a Human Biomolecular Atlas Project (HuBMAP, hubmap.org) Tissue Mapping Center, where his team is using cutting-edge single cell and spatial tissue profiling to interrogate the role of human lymphatic vasculature in health and disease.

10 of his publications are within the 1% most cited as evaluated by ISI/Web of Science.

Ioannis Vlachos Non-coding Research Lab

Studying Single Cells Through Multi-Omics & Spatiotemporal Context

Xiuwei Zhang | J.Z. Liang Early-Career Assistant Professor, School of Computational Science and Engineering, Georgia Institute of Technology

Abstract: With the advances in single cell technologies, cells are profiled through multiple modalities, and data on samples from an increasing number of individuals are obtained. Data integration methods across batches and modalities are being developed to learn representations of cells in a unified space. I will discuss how we learn biological insights in addition to building integrated datasets through integration methods developed in our lab. In addition, cells were generated in a temporal process and exist in a spatial context. I will discuss how we learn the temporal process and how to leverage temporal information when analyzing spatial data.

Bio: Xiuwei Zhang is a J.Z. Liang Early Career Chair Assistant Professor at the School of Computational Science & Engineering at Georgia Tech. She obtained her PhD in computer science from EPFL (École Polytechnique Fédérale de Lausanne) in Switzerland, and conducted postdoctoral research at Cambridge, UK and UC Berkeley. Her research focuses on developing methods to analyze single cell genomics and spatial data, including methods to study cell temporal dynamics, to perform data integration and to infer molecular interactions. She is a recipient of an NSF CAREER Award and the NIH Maximizing Investigators’ Research Award.

Zhang Group @GT