Introduction to Plant Cell Atlas
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A ~20 minute presentation by Dr. Sue Rhee on the goals and vision of the Plant Cell Atlas initiative.
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2025 Workshop Videos
Plant Cell Identity Webinar Series - November 2024 - September 2025
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Date: November 12, 2024 Speaker: Dr. Dennis Stevenson (New York Botanical Gardens) Talk Title: "Plant Anatomy in the Age of Genomics" Moderators: Dr. Natanella Illouz-Eliaz and Dr. Trevor Nolan Date: December 10, 2024 Speakers: Dr. Rachel Shahan and Dr. Geoff Schiebinger Talk Titles: "Investigating cell fates and states over time with the Arabidopsis root" and "Towards a mathematical theory of development" Moderator: Dr. Kaisa Kajala Date: February 11, 2025 Speakers: Dr. Kenneth Birnbaum and Dr. Kaisa Kajala Talk Titles: "Cell Types and Cell States: Measuring the Difference Between Cells" and "Evolution of Plant Cell Types - Exodermis, A Root Barrier Cell Type, as a Case Study" Moderator: Dr. Olivia Wilkins Date: March 11, 2025 Speakers: Dr. Keiko Torii and Dr. Justin Walley Talk Titles: "Cell States During Cell Development" and "Proteomic Approaches to Defining Cell Types and States" Moderator: Gergo Palfalvi Date: April 8, 2025 Speakers: Dr. Nemanja Vukašinović Talk Title: "Live Imaging Reveals New Cell States in Root Meristems." Moderator: Mingyuan Zhu Date: May 5, 2025 Speakers: Dr. Alex Marand Talk Title: "The Effects of Regulatory Diversity on Cell Identity." Moderator: Benjamin Cole Date: September 16, 2025 Panelists: Olivia Wilkins, PhD - University of Manitoba Bas Bargmann, PhD - Virginia Tech Marc Libault, PhD - University of Missouri Title: The Open Panel Discussion Moderators: Kaisa Kajala, PhD - Utrecht University Benjamin Cole, PhD - DOE - Joint Genome Institute |
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Plant Cell Atlas Spatial Metabolomics Workshop Part II - March 5, 2025
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Speaker: Dr. Marco Vicari - KTH Royal Institute of Technology Talk Title: Spatial Multimodal Analysis: Performing Mass Spectrometry Imaging and Spatial Transciptomics on the Same Tissue Section Host: Dr. Chris Anderton |
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Imaging Workshop Webinar Series - September 2025
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Date: September 24, 2025 Workshop Title: FIJI Basics for Visualizing and Quantifying Plant Images Hosts: Dr. Ivan Radin, University of Minnesota and Dr. Kirk J Czymmek, Donald Danforth Plant Science Center |
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2024 Workshop Videos
Spatial Omics Workshop - May 9, 2024
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Session One: Speaker: Dr. Rong Fan (Yale University) Talk Title: Spatial omics: current technology landscape and future prospective Session Two: Speaker: Dr. Travis Lee (Salk Institute for Biological Studies) Talk Title: Spatial Omics in Plants: The How, When, Where, and Why Speaker: Alex Monell (University of California, San Diego) Talk Title: Spatial Transcriptomics in Plants: Computational Methods for Data Analysis |
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SynBio Hackathon - August 14-15, 2024
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Speaker: Alex Borowsky, Stanford University Section Title: Introduction Speaker: Nicola J Patron, University of Cambridge Section Title: Synthetic Circuits: The Basics Speaker: Sarah Guizhou, Earlham Institute, Norwich Section Title: Synthetic Circuits Design |
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2023 Workshop Videos
scSeq Techniques in Plant Biology: Part 2 - November 3, 2023
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Speaker: Dr. Irene Papatheodorou (EMBL-EBI, UK) Talk Title: From Raw Data to Count Matrix - An Introduction to Standardised Analysis Pipelines in Single Cell Expression Atlas Moderator: Dr. Rachel Shahan (University of California, Los Angeles, USA) Speaker: Dr. Hongyu Chen (Zhejiang University, China) Talk Title: PlantscRNADB: How to Facilitate Single-Cell Research in Plants? Moderator: Dr. Kevin Cox, Jr (Donald Danforth Plant Science Center, USA) Speaker: Dr. Che-Wei Hsu (Duke University, USA) Talk Title: Non-Arbitrary Alternatives of Basic Quality Control Scheme for sc/snRNA-seq Analysis: COPILOT Moderator: Dr. Rachel Shahan (University of California, Los Angeles, USA) Speaker: Dr. Benjamin Cole (Joint Genome Institute, USA) Talk Title: Creating and Reading Metadata Moderator: Dr. Rachel Shahan (University of California, Los Angeles, USA) Speaker: Andrew Farmer (NCGR, USA) Talk Title: Single Nucleus Gene Expression + Chromatin Accessibility: From Unpaired to Paired Multimodal Measurements Moderator: Dr. Kevin Cox, Jr (Donald Danforth Plant Science Center, USA) |
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Broadening Participation in Scientific Research - June 22, 2023
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Speaker: Dr. Eshchar Mizrachi (U of Pretoria, South Africa) Talk Title: Ecocultural Justice: Addressing Inequality of Access or Connection to Biodiversity in South Africa and Africa Moderator: Dr. Rose Marks (Michigan State University, USA) Speaker: Dr. Jean-Baka Domelevo Entfellner (ILRI, Kenya) Talk Title: Communities of Practice in Genomics & Bioinformatics in Africa: Enabling the Next Generation Moderator: Dr. Rose Marks (Michigan State University, USA) Speaker: Dr. Bernice Waweru (John Innes Centre, UK) Talk Title: Underutilized (‘Forgotten’) Crop Genomic Resources: From Africa to the World Moderator: Dr. Rose Marks (Michigan State University, USA) Speaker: Jack Langworthy (Maua Mazuri, Tanzania) Talk Title: The Impact and Strategy for Superior Plant Genetics in Emerging Markets Moderator: William Dwyer (Carnegie Institution for Science, USA) Speaker: Dr. Liz Carlisle (UC Santa Barbara, USA) Talk Title: Healing Grounds: Climate, Justice, and the Deep Roots of Regenerative Farming Moderator: William Dwyer (Carnegie Institution for Science, USA) |
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scSeq Techniques in Plant Biology: Part 1 - April 14, 2023
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Speaker: Dr. Gergo Palfalvi (Max Planck Institute, Germany) Talk Title: Nuclei Isolation from Diverse Plant Species Moderator: Dr. Marc Libault (University of Nebraska-Lincoln, USA) Speaker: Dr. Trevor Nolan (Duke University, USA) Talk Title: scRNA-Seq in Plants Experimental Design and Considerations for Doing Single-Cell in Your Lab Moderator: Dr. Marc Libault (University of Nebraska-Lincoln, USA) Speaker: Dr. Joseph Swift (Salk Institute, USA) Talk Title: Optimizing Multiome Techniques for Plants Moderator: Dr. Gergo Palfalvi (Max Planck Institute for Plant Breeding Research, Germany) Speaker: Dr. Bertrand Yeung (Curio Bioscences, USA) Talk Title: Whole Transcriptome High-Resolution Spatial Sequencing Moderator: Dr. Kevin Cox, Jr (Donald Danforth Plant Science Center, USA) Speaker: Sandra Thibivilliers (UNL, USA) Talk Title: Good Practices to Enable Unified sNucRNA-seq and sNucATAC-seq Library Construction Moderator: Dr. Gergo Palfalvi (Max Planck Institute for Plant Breeding Research, Germany) Speaker: Dr. Hilde Nelissen (VIB/Ghent University, Belgium) Talk Title: Targeted Spatial Transcriptomics Moderator: Dr. Kevin Cox, Jr (Donald Danforth Plant Science Center, USA) |
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Joanne Kimutai Interview - PCA-JR Biotek Media Prize Winner - March 2023
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Interview with Joanne Josephine C. Kimutai a PhD candidate at the University of Ghana. Joanne discusses her background, career path, research, and inspiration and challenges she has experienced as a scientist with members of the PCA Outreach Committee. Joanne participated in the 2022 JR Biotek-PCA Mentoring Program and won first prize for best talk at the program's closing ceremony.
Moderators: PCA Outreach Commitee: Dr. Kevin Cox Dr. Terry Jackson Elena Lazarus |
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2022 Workshop Videos
2nd PCA Symposium - December 12 & 13, 2022
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Speaker: Tran Chau (Virginia Polytechnic Institute, USA)
Talk Title: Discovery of conserved marker genes for cross-species cell type assignment by machine learning Moderator: Dr. Kaisa Kajala (Utrecht University, The Netherlands) Speaker: Dr. Ying Zhu (Genentech, USA)
Talk Title: Technology advances in single-cell and spatial proteomics for plant biology Moderator: Dr. Devang Mehta (Katholieke Universiteit Leuven, Belgium) Speaker: Alexander Borowsky (University of California, Riverside, USA)
Talk Title: Gene network discovery and engineering to enhance rice root resilience Moderator: Dr. Kaisa Kajala (Utrecht University, The Netherlands) Speaker: Dr. Tatsuya Nobori (Salk Institute for Biological Studies, USA)
Talk Title: PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue Moderator: Dr. Benjamin Cole (Joint Genome Institute, USA) Speaker: Dr. Anshul Kundaje (Stanford University, USA)
Talk Title: Deep learning for genomic discovery Moderator: Dr. Benjamin Cole (Joint Genome Institute, USA) Speaker: Dr. Dušan Veličković (Pacific Northwest National Laboratory, USA)
Talk Title: In situ spatial metabolomics for revealing root-microbe molecular interactions down to the cellular scale Moderator: Dr. Benjamin Cole (Joint Genome Institute, USA) Speaker: Dr. Christopher Anderton (Pacific Northwest National Laboratory, USA)
Talk Title: Towards revealing the metabolome within plant tissue at the single cell level with spatially resolved mass spectrometry and mass spectrometry imaging approaches Moderator: Dr. Margaret Frank (Cornell University, USA) Speaker: Itzel Meneses (Universidad Nacional Autónoma de México, México)
Talk Title: Systematic modification of a FRET biosensor based on a intrinsically disordered protein for tracking the effects of osmotic stress in Arabidopsis Moderator: Dr. Margaret Frank (Cornell University, USA) Speaker: Noé Perron (University of Florida, USA)
Talk Title: A single nuclei transcriptomic study of the C3 to CAM transition in the ice plant provides insight into the key regulators of CAM induction Moderator: Dr. Christopher Anderton (Pacific Northwest National Laboratory, USA) |
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Multiplex Microscopy Symposium - May 19, 2022
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Speaker: Dr. Jiang He (Vizgen)
Talk Title: In Situ Single-Cell Transcriptomic Imaging with Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) Moderator: Dr. Kun Huang (Dana-Farber Cancer Institute) Speaker: Dr. Regan Baird (Visiopharm)
Talk Title: Multiplex Analysis Workflow Moderator: Dr. Kirk Czymmek (Donald Danforth Plant Science Center) |
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2021 Workshop Videos
1st PCA Symposium - December 9 & 10, 2021
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Speaker: Dr. Yvon Jaillais (ENS Lyon, France)
Talk Title: Anionic phospholipids across scales: from plasma membrane nanodomains to plant development Moderator: Dr. Shao-shan Carol Huang (New York University, USA) Speaker: Dr. Hilde Nelissen (VIB-Ghent University, Belgium)
Talk Title: An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells Moderator: Dr. Shao-shan Carol Huang (New York University, USA) Speaker: Dr. Mathew Lewsey (La Trobe University, Australia)
Talk Title: Gene regulatory dynamics of germinating from bulk tissue to single-cell resolution Moderator: Dr. Samuel Leiboff (Oregon State University, USA) Speaker: Dr. Camilla Ferrari (VIB-Ghent University, Belgium)
Talk Title: Identification of cell-type specific gene regulatory networks in plants using MINI-EX, a Motif-Informed Network Inference method based on single-cell EXpression data Moderator: Dr. Kaisa Kajala (Utrecht University, The Netherlands) Speaker: Dr. Michael Taylor (Pacific Northwest National Laboratory, USA)
Talk Title: Development of targeted single cell analysis and metabolic imaging of plants using high spatial resolution laser ablation electrospray ionization mass spectrometry Moderator: Dr. Marc Libault (University of Nebraska-Lincoln, USA) |
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Spatial Metabolomics Workshop - October 19, 2021
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Speaker: Dr. Theodore Alexandrov (EMBL)
Talk Title: METASPACE and SpaceM, tools for spatial single-cell metabolomics Speaker: Dr. Hua Tian (Pennsylvania State University)
Talk Title: Successive high-resolution (H2O)n-GCIB and C60-SIMS imaging integrates spatial omics (metabolites, lipids and proteins) in single cells on frozen-hydrated tissues Speaker: Dr. Young-Jin Lee (Iowa State University)
Talk Title: High-spatial resolution mass spectrometry imaging of plant metabolites with matrix-assisted laser desorption ionization |
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Spatial Proteomics Workshop - April 8, 2021
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Speaker: Dr. Claire McWhite (Princeton University)
Talk Title: Mapping conserved protein complexes across plant species Speaker: Dr. Nikolai Slavov (Northeastern University)
Talk Title: Mapping the transcriptome and proteome of tissues in 3D at single-cell resolution Speaker: Dr. Ryan Kelly (Brigham Young University)
Talk Title: In-depth and high-spatial-resolution proteome profiling of plant tissues Speaker: Dr. Julia Mergner (Technical University of Munich)
Talk Title: Protein expression profiling in Arabidopsis tissues |
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Single Cell Sequencing Workshop - February 23, 2021
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Speaker: Dr. Mary Ghering (Massachusetts Institute of Technology)
Talk Title: Insights into endosperm development and gene imprinting at single nucleus resolution Speaker: Dr. John Marioni (EMBL-European Bioinformatics Institute)
Talk Title: Computational challenges in single cell genomics |
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2020 Workshop Videos
1st PCA Workshop: Session 1 - May 15, 2020
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Speakers: Dr. Seung Yon Rhee & Dr. David Ehrhardt (Carnegie Institution for Science)
Talk Title: Session 1 Introduction - Vision for Plant Cell Atlas Speaker: Dr. Liwen Jiang (The Chinese University of Hong Kong)
Talk Title: Plant Cell Atlas - Organelle Biosynthesis Speaker: Dr. Martin Jonikas (Princeton University)
Talk Title: Protein localizations and protein-protein interactions have transformed our understanding of the pyrenoid Session 1 Q&A: Vision for Plant Cell Atlas
Speakers: Dr. Dominique Bergmann, Dr. Uta Paszkowski, Dr. Liwen Jiang, Dr. Martin Jonikas Moderators: Dr. Sury Jha, Dr. Kangmei Zhao, Dr. Heather Meyer, and Dr. Jason Thomas |
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1st PCA Workshop: Session 2 - May 22, 2020
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Speakers: Dr. Zhiyong Wang (Carnegie Institution for Science) and Dr. Ken Birnbaum (New York University)
Talk Title: Session 2 Introduction - Tools and Techniques for PCA Speaker: Dr. Tess Branon (University of California, Berkeley)
Talk Title: TurboID - A new proximity labeling technology for proteomic mapping in plants Speaker: Dr. Becky Bart (Donald Danforth Plant Science Center)
Talk Title: Tools and techniques for developing the Plant Cell Atlas - Non-model system edition Speaker: Dr. Alexander Jones (Sainsbury Laboratory, Cambridge University)
Talk Title: The sonata from the symphony - hormone dynamics resulting from many cellular activities Session 2 Q&A: Tools and Techniques for PCA
Speakers: Dr. Alexander Jones, Dr. Tess Branon, Dr. Markita Landry, Dr. Becky Bart Moderators: Dr. Sury Jha, Dr. Renate Weizbauer, Dr. Jason Thomas, and Emily Fryer |
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1st PCA Workshop: Session 3 - June 2, 2020
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Speaker: Dr. Heather Meyer & Dr. Sury Jha (Carnegie Institution for Science)
Talk Title: Session 3 Introduction - Broader Impacts, Infrastructure, and Community Building Speaker: Dr. Nicholas Provart (University of Toronto)
Talk Title: Visualizing the Plant Cell Atlas Speaker: Dr. George Bassel (University of Warwick)
Talk Title: Tissue modeling & multiplex data integration Speaker: Dr. Amy Marshall-Colón (University of Illinois Urbana-Champaign)
Talk Title: Plant Cell Atlas Workshop: Crop Engineering Speaker: Dr. Drew Endy (Stanford University)
Talk Topic: Synthetic Biology and Bio-based Economy Session 3 Q&A: Broader Impacts, Infrastructure, and Community Building
Speakers: Dr. Nicholas Provart, Dr. George Bassel, Dr. Amy Marshall-Colón, Dr. Drew Endy Moderators: Dr. Renate Weizbauer, Dr. Jason Thomas, Emily Fryer, and Dr. Kangmei Zhao |
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