PLANT CELL ATLAS
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Introduction to Plant Cell Atlas

A ~20 minute presentation by Dr. Sue Rhee on the goals and vision of the Plant Cell Atlas initiative.

2023 Workshop Videos

Single Cell Sequencing Techniques in Plant Biology - Part 2 - November 30, 2022
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: 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. 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. 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. 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: 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)
 The Missing Link: Broadening Participation and Embracing Biodiversity in Scientific Research - June 22, 2023
​Speaker: Dr. Eshchar Mizrachi (FABI-University 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. Liz Carlisle (University of California, 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: 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. 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: 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: 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)
Single Cell Sequencing Techniques in Plant Biology - Part 1 - April 14, 2023
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. Gergo Palfalvi (Max Planck Institute, Germany)
Talk Title: Nuclei Isolation from Diverse Plant Species
Moderator: Dr. Marc Libault​ (University of Nebraska-Lincoln, 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. 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: Dr. Hilde Nelissen (VIB/Ghent University, Belgium)
Talk Title: Targeted Spatial Transcriptomics
Moderator: Dr. Kevin Cox, Jr (Donald Danforth Plant Science Center, USA)

2022 Workshop Videos

2nd PCA Symposium - December 12 & 13, 2022
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)
Multiplex Microscopy Symposium - May 19, 2022
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)

2021 Workshop Videos

1st PCA Symposium - December 9 & 10, 2021
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)
Spatial Metabolomics Workshop - October 19, 2021
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
Spatial Proteomics Workshop - April 8, 2021
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
Single Cell Sequencing Workshop - February 23, 2021
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

2020 Workshop Videos

1st PCA Workshop: Session 1 - May 15, 2020
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
1st PCA Workshop: Session 2 - May 22, 2020
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
1st PCA Workshop: Session 3 - June 2, 2020
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
MICHIGAN STATE UNIVERSITY LAND ACKNOWLEDGEMENT
“The Plant Cell Atlas operates predominantly out of Michigan State University. We acknowledge that Michigan State University occupies the ancestral, traditional, and contemporary Lands of the Anishinaabeg – the Three Fires Confederacy of Ojibwe, Odawa, and Potawatomi peoples. We affirm Indigenous sovereignty and hold Michigan State University accountable to the needs of American Indian and Indigenous peoples.”

For questions about the PCA Initiative please contact us at [email protected].

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  • Home
  • About
    • Annual Report
    • Newsletter
    • People
    • Motivation
    • Goals
    • Milestones
    • Affilations
    • News >
      • Breaking News
      • Past News
    • Code of Conduct
    • Bylaws
    • Contact
  • Resources
    • Publications >
      • 2022 Plant Physiology Focus Issue
    • Tools and Repositories
    • PCA Videos
  • Events
    • Upcoming Events >
      • Spatial Metabolomics Workshop - March 2025
    • Previous Events
  • Opportunities
    • Job Posts
    • Fellowships
  • Outreach
    • JR Biotek-PCA Best Talk Winner
    • PCA Art Exhibit >
      • About
      • Plant Biotechnology
      • Black Plant Scientists
      • Bowie State University
      • Howard University
      • Morgan State University
    • Futurum Brochure
  • Blog