Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

NeuriteTracker is a computer vision approach used to analyze neuronal morphodynamics and to examine spatiotemporal Rho GTPase signaling networks regulating neurite outgrowth.

[1]  François Fleuret,et al.  Machine learning-based tools to model and to remove the off-target effect , 2017, Pattern Analysis and Applications.

[2]  Monilola A. Olayioye,et al.  Rho regulation: DLC proteins in space and time. , 2015, Cellular signalling.

[3]  G. von Dassow,et al.  Single cell pattern formation and transient cytoskeletal arrays. , 2014, Current opinion in cell biology.

[4]  Jacco van Rheenen,et al.  A Versatile Toolkit to Produce Sensitive FRET Biosensors to Visualize Signaling in Time and Space , 2013, Science Signaling.

[5]  Stephen T. C. Wong,et al.  A Screen for Morphological Complexity Identifies Regulators of Switch-like Transitions between Discrete Cell Shapes , 2013, Nature Cell Biology.

[6]  P. Scheiffele,et al.  Growth Cone MKK7 mRNA Targeting Regulates MAP1b-Dependent Microtubule Bundling to Control Neurite Elongation , 2012, PLoS biology.

[7]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[8]  Tobias Meyer,et al.  Supplemental Experimental Procedures A Two-Dimensional ERK-AKT Signaling Code for an NGF-Triggered Cell-Fate Decision , 2011 .

[9]  Wenyu Bu,et al.  mDia1 and WAVE2 Proteins Interact Directly with IRSp53 in Filopodia and Are Involved in Filopodium Formation , 2011, The Journal of Biological Chemistry.

[10]  Bernd Rinn,et al.  openBIS: a flexible framework for managing and analyzing complex data in biology research , 2011, BMC Bioinformatics.

[11]  H. Higashida,et al.  Ect2, an Ortholog of Drosophila’sPebble, Negatively Regulates Neurite Outgrowth in Neuroblastoma × Glioma Hybrid NG108-15 Cells , 2011, Cellular and Molecular Neurobiology.

[12]  Alexander Borst,et al.  One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application , 2010, PLoS Comput. Biol..

[13]  Olivier Pertz,et al.  Spatio-temporal Rho GTPase signaling – where are we now? , 2010, Journal of Cell Science.

[14]  R. Hindges,et al.  Rac1 Regulates Neuronal Polarization through the WAVE Complex , 2010, The Journal of Neuroscience.

[15]  A. Koleske,et al.  Regulation of cell migration and morphogenesis by Abl-family kinases: emerging mechanisms and physiological contexts , 2009, Journal of Cell Science.

[16]  C. Der,et al.  Role of DLC-1, a tumor suppressor protein with RhoGAP activity, in regulation of the cytoskeleton and cell motility , 2009, Cancer and Metastasis Reviews.

[17]  Laurent D. Cohen,et al.  Fast Object Segmentation by Growing Minimal Paths from a Single Point on 2D or 3D Images , 2009, Journal of Mathematical Imaging and Vision.

[18]  Jean-Marc Odobez,et al.  Tracking the Visual Focus of Attention for a Varying Number of Wandering People , 2008, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[19]  T. Holak,et al.  Lifeact: a versatile marker to visualize F-actin , 2008, Nature Methods.

[20]  Wei Wang,et al.  Spatial mapping of the neurite and soma proteomes reveals a functional Cdc42/Rac regulatory network , 2008, Proceedings of the National Academy of Sciences.

[21]  C. Bakal,et al.  Quantitative Morphological Signatures Define Local Signaling Networks Regulating Cell Morphology , 2007, Science.

[22]  Q. Feng,et al.  Identification of a DOCK180-related Guanine Nucleotide Exchange Factor That Is Capable of Mediating a Positive Feedback Activation of Cdc42* , 2006, Journal of Biological Chemistry.

[23]  E. Koay,et al.  pH dependent high transfection efficiency of mouse neuroblastomas using TransFectin , 2006, Journal of Neuroscience Methods.

[24]  Nir Hacohen,et al.  Minimizing the risk of reporting false positives in large-scale RNAi screens , 2006, Nature Methods.

[25]  F. Gertler,et al.  Nervous Rac: DOCK7 Regulation of Axon Formation , 2006, Neuron.

[26]  P. Hordijk,et al.  Jcb: Article Introduction , 2002 .

[27]  C. Marshall,et al.  Cdc42–MRCK and Rho–ROCK signalling cooperate in myosin phosphorylation and cell invasion , 2005, Nature Cell Biology.

[28]  C. Der,et al.  GEF means go: turning on RHO GTPases with guanine nucleotide-exchange factors , 2005, Nature Reviews Molecular Cell Biology.

[29]  Jiri Matas,et al.  Robust wide-baseline stereo from maximally stable extremal regions , 2004, Image Vis. Comput..

[30]  J. Steeves,et al.  Suppression of Rho-kinase activity promotes axonal growth on inhibitory CNS substrates , 2003, Molecular and Cellular Neuroscience.

[31]  Carlos G. Dotti,et al.  Breaking the neuronal sphere: regulation of the actin cytoskeleton in neuritogenesis , 2002, Nature Reviews Neuroscience.

[32]  A. Hall,et al.  Guanine nucleotide exchange factors for Rho GTPases: turning on the switch. , 2002, Genes & development.

[33]  John G. Parnavelas,et al.  Modes of neuronal migration in the developing cerebral cortex , 2002, Nature Reviews Neuroscience.

[34]  W. Arthur,et al.  RhoA inactivation by p190RhoGAP regulates cell spreading and migration by promoting membrane protrusion and polarity. , 2001, Molecular biology of the cell.

[35]  T. Stossel,et al.  The Rac1- and RhoG-specific GEF domain of Trio targets filamin to remodel cytoskeletal actin , 2000, Nature Cell Biology.

[36]  T. Takenawa,et al.  Essential Role of Neural Wiskott-Aldrich Syndrome Protein in Neurite Extension in PC12 Cells and Rat Hippocampal Primary Culture Cells* , 2000, The Journal of Biological Chemistry.

[37]  Alex M. Andrew,et al.  Level Set Methods and Fast Marching Methods: Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science (2nd edition) , 2000 .

[38]  T. Leung,et al.  The Myotonic Dystrophy Kinase-related Cdc42-binding Kinase Is Involved in the Regulation of Neurite Outgrowth in PC12 Cells* , 1999, The Journal of Biological Chemistry.

[39]  T. Pollard,et al.  Scar, a WASp-related protein, activates nucleation of actin filaments by the Arp2/3 complex. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[40]  S. Narumiya,et al.  Molecular Dissection of the Rho-associated Protein Kinase (p160ROCK)-regulated Neurite Remodeling in Neuroblastoma N1E-115 Cells , 1998, The Journal of cell biology.

[41]  L. Lim,et al.  Myotonic Dystrophy Kinase-Related Cdc42-Binding Kinase Acts as a Cdc42 Effector in Promoting Cytoskeletal Reorganization , 1998, Molecular and Cellular Biology.

[42]  Yoshiharu Matsuura,et al.  Phosphorylation and Activation of Myosin by Rho-associated Kinase (Rho-kinase)* , 1996, The Journal of Biological Chemistry.

[43]  T. Yamamoto,et al.  Rho‐associated kinase, a novel serine/threonine kinase, as a putative target for small GTP binding protein Rho. , 1996, The EMBO journal.

[44]  C. Marshall,et al.  rho family GTPase activating proteins p190, bcr and rhoGAP show distinct specificities in vitro and in vivo. , 1993, The EMBO journal.

[45]  L. Van Aelst,et al.  The role of the Rho GTPases in neuronal development. , 2005, Genes & development.

[46]  Yi Zheng,et al.  Rho GTPase-activating proteins in cell regulation. , 2003, Trends in cell biology.