HuBMAP and Akoya: Mapping the Human Body One Cell at a Time
Original Air Date: May 2022
In this webinar series, you’ll hear from the HuBMAP researchers, bioinformaticians, and computer scientists behind this extraordinary effort, see how Akoya spatial phenotyping data is driving discovery, and learn how you can contribute.
In this roundtable moderated by Dr. Niro Ramachandran of Akoya, HuBMAP investigators will discuss the goals of the HuBMAP consortium, what they’ve accomplished thus far, share their vision for HuBMAP and similar cell atlas consortia, and provide an overview of the working groups developing new protocols. They’ll also discuss how HuBMAP researchers can work with biotechnology companies like Akoya to advance our understanding of human health and disease.
Panelists
Garry Nolan, PhD
HuBMAP Principal Investigator, Stanford TMC
Biography
Dr. Garry Nolan is a spatial biology pioneer, who has focused his research efforts on developing novel technologies and computational methods for research into cancer, leukemia, immunology and autoimmune disease. A co-inventor of the CODEX technology, which forms the basis of the PhenoCycler platform, and co-founder of Akoya Biosciences, Garry is a prolific inventor and has been honored as one of the top 25 inventors at Stanford University. He’s a member of the Parker Institute for Cancer Immunotherapy and the HuBMAP Consortium.
Jeannie Camarillo, PhD
HuBMAP Rapid Technology Implementation Team
Biography
Elizabeth Neumann, PhD
HuBMAP Researcher, Vanderbilt TMC
Biography
Dr. Elizabeth Neumann is an early career researcher in the process of starting her own lab at UC Davis. She was previously a postdoctoral NIH fellow working on HuBMAP-related projects at Vanderbilt University, where she championed an initiative to develop a Kidney Cell Atlas. She earned her PhD in Analytical Chemistry from the University of Illinois at Urbana-Champaign. Elizabeth has expertise in multiplex spatial proteomics, single-cell mass spectral analysis, and 3D imaging mass spectrometry. She has a passion for scientific mentorship, diversity, and education within STEM.
Andrea Radtke, PhD
HuBMAP Rapid Technology Implementation Team
Biography
Dr. Andrea Radtke is an immunologist specializing in spatial proteomics, single-cell biology, and multiplexed antibody-based imaging. At the NIH, she is the lead scientist for the Center for Advanced Tissue Imaging (CAT-I), where she develops and optimizes tissue imaging techniques and manages laboratory operations. She is a member of the HuBMAP Affinity Reagents Working Group and leads the consortium’s Organ Mapping Antibody Panels project. Andrea received her PhD in Molecular Microbiology and Immunology from Johns Hopkins School of Public Health.
Organ Cell Atlas Initiatives: Inside HuBMAP Tissue Mapping Centers
In this webinar, you’ll hear from two HuBMAP investigators who are working on organ cell atlas initiatives. Learn how HuBMAP tissue mapping centers collect samples, design spatial phenotyping experiments, upload highly multiplexed imaging data to the HuBMAP repository, and analyze their data to gain a deeper understanding of the function of single cells and cellular neighborhoods within different organs — enabling further insights into human health and disease.
Speakers
Elizabeth Neumann, PhD
HuBMAP Researcher, Vanderbilt TMC
Biography
Dr. Elizabeth Neumann is an early career researcher in the process of starting her own lab at UC Davis. She was previously a postdoctoral NIH fellow working on HuBMAP-related projects at Vanderbilt University, where she championed an initiative to develop a Kidney Cell Atlas. She earned her PhD in Analytical Chemistry from the University of Illinois at Urbana-Champaign. Elizabeth has expertise in multiplex spatial proteomics, single-cell mass spectral analysis, and 3D imaging mass spectrometry. She has a passion for scientific mentorship, diversity, and education within STEM.
John Hickey, PhD
HuBMAP Researcher, Stanford TMC
Biography
Dr. John Hickey is an ACS Postdoctoral Fellow in Dr. Garry Nolan’s lab at Stanford University School of Medicine. He received his PhD in Biomedical Engineering from Johns Hopkins University, where he engineered biomaterials to solve challenges facing T cell immunotherapies. He currently uses CODEX multiplexed imaging alongside other single cell multiomic technologies to characterize biological processes in healthy tissues, cancer, and cancer therapies. As part of the HuBMAP Tissue Mapping Center at Stanford, John is helping to develop an organ atlas for healthy human small bowel and colon.
A Framework for Cell Atlas Initiatives: The Information Science Behind HuBMAP
In this roundtable moderated by Dr. Grady Carlson of Akoya, HuBMAP bioinformaticians will discuss computational and logistical challenges and resources required to drive HuBMAP efforts to collect and curate information from numerous resource groups. They will discuss standards and processes they rely on, and provide an overview of the computational approaches HuBMAP uses to integrate, visualize and analyze data from many different assays.
Panelists
Jonathan Silverstein, MD, MS, FASC, FACMI
HuBMAP Principal Investigator, HIVE Infrastructure and Engagement Component
Biography
Dr. Jonathan Silverstein serves as Chief Research Informatics Officer and Professor of Biomedical Informatics at University of Pittsburgh School of Medicine. He is internationally known for his expertise, and federally funded research, in the application of advanced computing architectures to biomedicine and on the design, implementation and evaluation of high-performance collaboration and visualization environments for anatomic education and surgery. He is a senior member of the HuBMAP leadership team, and he is the principal investigator for a Rapid Technology Implementation Project focused on renewable and specific affinity reagents for mapping proteoforms in human tissues. Jonathan earned his medical degree from Washington University in St. Louis and his Master of Science from the Harvard School of Public Health. Additionally, he is a Fellow of the American College of Surgeons and a Fellow of the American College of Medical Informatics.
Nils Gehlenborg, PhD
Biography
Dr. Nils Gehlenborg, PhD, is an Associate Professor in the Department of Biomedical Informatics at Harvard Medical School, Director of the Master in Biomedical Informatics program, and Director of the Biomedical Informatics and Data Science Research Training (BIRT) program. He is the principal investigator for the HUBMAP tools component working group, which provides a suite of cloud-based data visualization, exploration, and analysis tools for HuBMAP data. Nils received his PhD in Bioinformatics from the University of Cambridge.
Katy Börner, PhD
Biography
Dr. Katy Börner is the Victor H. Yngve Professor of Engineering & Information Science in the Department of Intelligent Systems Engineering & Information and Library Science, School of Informatics, Computing, and Engineering at Indiana University in Bloomington, IN. She leads the mapping component of the HuBMAP Integration, Visualization & Engagement working group, which is developing a common coordinate framework to catalog and support spatial and semantic searches of cell types, functions, and spatial relationships. Katy holds PhD in Computer Science from the University of Kaiserslautern.
John Hickey, PhD
HuBMAP Researcher, Stanford TMC
Biography
Dr. John Hickey is an ACS Postdoctoral Fellow in Dr. Garry Nolan’s lab at Stanford University School of Medicine. He received his PhD in Biomedical Engineering from Johns Hopkins University, where he engineered biomaterials to solve challenges facing T cell immunotherapies. He currently uses CODEX multiplexed imaging alongside other single cell multiomic technologies to characterize biological processes in healthy tissues, cancer, and cancer therapies. As part of the HuBMAP Tissue Mapping Center at Stanford, John is helping to develop an organ atlas for healthy human small bowel and colon.
