Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies

[1]  J. Fernandez-Checa,et al.  Intracellular Cholesterol Trafficking and Impact in Neurodegeneration , 2017, Front. Mol. Neurosci..

[2]  R. Zoncu,et al.  Emerging Roles for the Lysosome in Lipid Metabolism. , 2017, Trends in cell biology.

[3]  Raquel Hontecillas,et al.  Agents and networks to model the dynamic interactions of intracellular transport , 2017, Cellular logistics.

[4]  M. Lucas,et al.  Retromer , 2017, Current Biology.

[5]  S. Pfeffer.  Rab GTPases: master regulators that establish the secretory and endocytic pathways , 2017, Molecular biology of the cell.

[6]  Kyoungtae Kim,et al.  Traffic from the endosome towards trans-Golgi network. , 2017, European journal of cell biology.

[7]  A. Hamacher-Brady,et al.  Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity , 2017, PloS one.

[8]  M. Rao,et al.  Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae , 2016, Scientific Reports.

[9]  Natalia Gomez-Navarro,et al.  Protein sorting at the ER–Golgi interface , 2016, The Journal of cell biology.

[10]  K. Sandhoff.  Neuronal sphingolipidoses: Membrane lipids and sphingolipid activator proteins regulate lysosomal sphingolipid catabolism. , 2016, Biochimie.

[11]  O. Bakke,et al.  Bidirectional traffic between the Golgi and the endosomes – machineries and regulation , 2016, Journal of Cell Science.

[12]  I. Cebrian,et al.  Rab22a controls MHC‐I intracellular trafficking and antigen cross‐presentation by dendritic cells , 2016, EMBO reports.

[13]  M. Thattai,et al.  Stacking the odds for Golgi cisternal maturation , 2016, eLife.

[14]  Tim Angus,et al.  Modelling the Structure and Dynamics of Biological Pathways , 2016, PLoS biology.

[15]  Kyoungtae Kim.  Cargo trafficking from the trans‐Golgi network towards the endosome , 2016, Biology of the cell.

[16]  M. Betenbaugh,et al.  Cellular traffic cops: the interplay between lipids and proteins regulates vesicular formation, trafficking, and signaling in mammalian cells. , 2015, Current opinion in biotechnology.

[17]  G. Schwarzmann,et al.  Membrane lipids regulate ganglioside GM2 catabolism and GM2 activator protein activity[S] , 2015, Journal of Lipid Research.

[18]  A. Hamacher-Brady,et al.  Autophagy capacity and sub-mitochondrial heterogeneity shape Bnip3-induced mitophagy regulation of apoptosis , 2015, Cell Communication and Signaling.

[19]  S. Grinstein,et al.  The vacuolar-type H+-ATPase at a glance – more than a proton pump , 2014, Journal of Cell Science.

[20]  J. Gunawardena.  Beware the tail that wags the dog: informal and formal models in biology , 2014, Molecular biology of the cell.

[21]  Marino Zerial,et al.  Rab Proteins and the Compartmentalization of the Endosomal System , 2014 .

[22]  Yongguo Mei,et al.  ENISI MSM: A novel multi-scale modeling platform for computational immunology , 2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[23]  A. Hamacher-Brady,et al.  Agent-based modeling of autophagy reveals emergent regulatory behavior of spatio-temporal autophagy dynamics , 2014, Cell Communication and Signaling.

[24]  L. Johannes,et al.  Rab7 Is Functionally Required for Selective Cargo Sorting at the Early Endosome , 2014, Traffic.

[25]  F. Barr.  Rab GTPases and membrane identity: Causal or inconsequential? , 2013, The Journal of cell biology.

[26]  W. Sundquist,et al.  Membrane fission reactions of the mammalian ESCRT pathway. , 2013, Annual review of biochemistry.

[27]  Michael J. North,et al.  Complex adaptive systems modeling with Repast Simphony , 2013, Complex Adapt. Syst. Model..

[28]  Heinz Koeppl,et al.  Spatial Modeling of Vesicle Transport and the Cytoskeleton: The Challenge of Hitting the Right Road , 2012, PloS one.

[29]  Yoan Diekmann,et al.  Thousands of Rab GTPases for the Cell Biologist , 2011, PLoS Comput. Biol..

[30]  Matthias Reuss,et al.  Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants , 2011, BMC Systems Biology.

[31]  Gordon B Mills,et al.  Rab GTPases implicated in inherited and acquired disorders. , 2011, Seminars in cell & developmental biology.

[32]  L. Mayorga,et al.  Modeling Fusion/Fission‐Dependent Intracellular Transport of Fluid Phase Markers , 2010, Traffic.

[33]  K. Sandhoff,et al.  Lysosomal degradation of membrane lipids , 2010, FEBS letters.

[34]  J. Bonifacino,et al.  Sorting of lysosomal proteins. , 2009, Biochimica et biophysica acta.

[35]  Andreas Deutsch,et al.  Membrane identity and GTPase cascades regulated by toggle and cut-out switches , 2008, Molecular systems biology.

[36]  P. Cullen.  Endosomal sorting and signalling: an emerging role for sorting nexins , 2008, Nature Reviews Molecular Cell Biology.

[37]  Robert D. Phair,et al.  Transport through the Golgi Apparatus by Rapid Partitioning within a Two-Phase Membrane System , 2008, Cell.

[38]  C. Ungermann,et al.  Rab cascades and tethering factors in the endomembrane system , 2007, FEBS letters.

[39]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[40]  Helmut Grubmüller,et al.  Molecular Anatomy of a Trafficking Organelle , 2006, Cell.

[41]  Javier G. Magadán,et al.  Rab22a Regulates the Sorting of Transferrin to Recycling Endosomes , 2006, Molecular and Cellular Biology.

[42]  Y. Kalaidzidis,et al.  Rab Conversion as a Mechanism of Progression from Early to Late Endosomes , 2005, Cell.

[43]  Yukiko Matsuoka,et al.  Using process diagrams for the graphical representation of biological networks , 2005, Nature Biotechnology.

[44]  Javier G. Magadán,et al.  Overexpression of Rab22a hampers the transport between endosomes and the Golgi apparatus. , 2005, Experimental cell research.

[45]  Tom A. Rapoport,et al.  Generation of nonidentical compartments in vesicular transport systems , 2005, The Journal of cell biology.

[46]  R. Weigert,et al.  Rab22a regulates the recycling of membrane proteins internalized independently of clathrin. , 2004, Molecular biology of the cell.

[47]  Jean Gruenberg,et al.  The biogenesis of multivesicular endosomes , 2004, Nature Reviews Molecular Cell Biology.

[48]  J. Bonifacino,et al.  The Mechanisms of Vesicle Budding and Fusion , 2004, Cell.

[49]  G. Apodaca,et al.  Endocytic Traffic in Polarized Epithelial Cells: Role of the Actin and Microtubule Cytoskeleton , 2001, Traffic.

[50]  B. Deurs,et al.  Rab7: a key to lysosome biogenesis. , 2000, Molecular biology of the cell.

[51]  S. Kornfeld,et al.  Mannose 6-phosphate receptors and lysosomal enzyme targeting. , 1989, The Journal of biological chemistry.