3 Works

Dynamics of Drosophila endoderm specification

Shannon Keenan
During early Drosophila embryogenesis, a network of gene regulatory interactions orchestrates terminal patterning, playing a critical role in the subsequent formation of the gut. We utilized CRISPR gene editing at endogenous loci to create live reporters of transcription and light-sheet microscopy to monitor the individual components of posterior patterning network across 90 minutes prior to gastrulation. We developed a computational pipeline for fusing imaging datasets of the individual components into a common multivariable trajectory. This...

Data from: A global genetic interaction network maps a wiring diagram of cellular function

Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda Van Leeuwen, Nydia Van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li … & Charles Boone
INTRODUCTION: Genetic interactions occur when mutations in two or more genes combine to generate an unexpected phenotype. An extreme negative or synthetic lethal genetic interaction occurs when two mutations, neither lethal individually, combine to cause cell death. Conversely, positive genetic interactions occur when two mutations produce a phenotype that is less severe than expected. Genetic interactions identify functional relationships between genes and can be harnessed for biological discovery and therapeutic target identification. They may also...

Data from: Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

Pengcheng Zhou, Shanna L. Resendez, Jose Rodriguez-Romaguera, Jessica C. Jimenez, Shay Q. Neufeld, Andrea Giovannucci, Johannes Friedrich, Eftychios A Pnevmatikakis, Garret D. Stuber, Rene Hen, Mazen A. Kheirbek, Bernardo L. Sabatini, Robert E. Kass & Liam Paninski
In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We...

Registration Year

  • 2021
    1
  • 2018
    1
  • 2016
    1

Resource Types

  • Dataset
    2
  • Image
    1

Affiliations

  • Simons Foundation
    3
  • Princeton University
    2
  • Howard Hughes Medical Institute
    1
  • Columbia University
    1
  • University of North Carolina
    1
  • University of Minnesota
    1
  • Heidelberg University
    1
  • University of Toronto
    1
  • Imperial College London
    1
  • University College London Hospitals NHS Foundation Trust
    1