PCA Videos

May 4, 2026

Speaker: Dr. Dong Xu, Health Informatics Institute, Morsani College of Medicine, University of South Florida
Talk Title: Deep-Learning Methods for Single-cell Data Analyses

May 11, 2026

Speaker: Dr. Romain Lopez, Assistant Professor of Computer Science and Biology at New York University
Talk Title: Multimodal pooled genetic screens integrating transcriptomics and image-based phenotypes

Speaker: Benjamin Cole, Joint Genome Institute
Part 1

Speaker: Andrew Farmer, National Center for Genome Resources
Part 2

Speaker: Michael Passalacqua, Cold Spring Harbor Laboratory
Part 3

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

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

Date: April 29, 2026
Workshop Title: Introduction to 2D and 3D Segmentation with MorphoGraphX
Host: Ivan Radin

Led by: Anne-Lise Routier, Amélie Bauer, and Daniel Kierzkowski.

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

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

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

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)

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)

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)

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

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)

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)

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)

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

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

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

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

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

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