Agent-based modeling of autophagy reveals emergent regulatory behavior of spatio-temporal autophagy dynamics

GA: A Package for Genetic Algorithms inR

(2015) Luca Scrucca   Journal of Statistical Software

RMarriesNetLogo: Introduction to theRNetLogoPackage

(2015) Jan C. Thiele   Journal of Statistical Software

Does bafilomycin A1block the fusion of autophagosomes with lysosomes?

(2014) Daniel J. Klionsky et al.   Autophagy

Lysosome Transport as a Function of Lysosome Diameter

(2014) Debjyoti Bandyopadhyay et al.   PLoS One

The protective roles of autophagy in ischemic preconditioning

(2013) Wen-jun Yan et al.   ACTA PHARMACOLOGICA SINICA

Live imaging and single-cell analysis reveal differential dynamics of autophagy and apoptosis

(2013) Yangqing Xu et al.   Autophagy

Activation of lysosomal function in the course of autophagy via mTORC1 suppression and autophagosome-lysosome fusion

(2013) Jing Zhou et al.   CELL RESEARCH

Suppression of Lysosome Function Induces Autophagy via a Feedback Down-regulation of MTOR Complex 1 (MTORC1) Activity

(2013) Min Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Microtubule-based transport - basic mechanisms, traffic rules and role in neurological pathogenesis

(2013) M. A. M. Franker et al.   JOURNAL OF CELL SCIENCE

Autophagy variation within a cell population determines cell fate through selective degradation of Fap-1

(2013) Jacob M. Gump et al.   NATURE CELL BIOLOGY

Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks

(2013) Pinkesh K. Patel et al.   PLoS Computational Biology

Interpretation of bafilomycin, pH neutralizing or protease inhibitor treatments in autophagic flux experiments

(2012) Gábor Juhász   Autophagy

Guidelines for the use and interpretation of assays for monitoring autophagy

(2012) Daniel J. Klionsky et al.   Autophagy

Computational model for autophagic vesicle dynamics in single cells

(2012) Katie R. Martin et al.   Autophagy

Leucyl-tRNA Synthetase Is an Intracellular Leucine Sensor for the mTORC1-Signaling Pathway

(2012) Jung Min Han et al.   CELL

A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB

(2012) Carmine Settembre et al.   EMBO JOURNAL

Modulation of Serines 17 and 24 in the LC3-interacting Region of Bnip3 Determines Pro-survival MitophagyversusApoptosis

(2012) Yanyan Zhu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stoichiometry of the CD95 Death-Inducing Signaling Complex: Experimental and Modeling Evidence for a Death Effector Domain Chain Model

(2012) Kolja Schleich et al.   MOLECULAR CELL

Leucyl-tRNA Synthetase Controls TORC1 via the EGO Complex

(2012) Grégory Bonfils et al.   MOLECULAR CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Autophagy modulation as a potential therapeutic target for diverse diseases

(2012) David C. Rubinsztein et al.   NATURE REVIEWS DRUG DISCOVERY

RNETLOGO: an R package for running and exploring individual-based models implemented in NETLOGO

(2012) Jan C. Thiele et al.   Methods in Ecology and Evolution

Autophagy Regulation and Integration with Cell Signaling

(2011) Anne Hamacher-Brady   ANTIOXIDANTS & REDOX SIGNALING

Autophagy receptors in developmental clearance of mitochondria

(2011) Ivana Novak et al.   Autophagy

Regulation of autophagy by lysosomal positioning

(2011) Viktor I. Korolchuk et al.   Autophagy

Selective autophagy mediated by autophagic adapter proteins

(2011) Terje Johansen et al.   Autophagy

Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy

(2011) Phillip Hundeshagen et al.   BMC BIOLOGY

Principles and Current Strategies for Targeting Autophagy for Cancer Treatment

(2011) R. K. Amaravadi et al.   CLINICAL CANCER RESEARCH

Lysosomal positioning coordinates cellular nutrient responses

(2011) Viktor I. Korolchuk et al.   NATURE CELL BIOLOGY

Origins of regulated cell-to-cell variability

(2011) Berend Snijder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Spinster is required for autophagic lysosome reformation and mTOR reactivation following starvation

(2011) Y. Rong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mTORC1 Senses Lysosomal Amino Acids Through an Inside-Out Mechanism That Requires the Vacuolar H+-ATPase

(2011) R. Zoncu et al.   SCIENCE

p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both

(2010) Derek Narendra et al.   Autophagy

Termination of autophagy and reformation of lysosomes regulated by mTOR

(2010) Li Yu et al.   NATURE

Autophagy Suppresses Tumorigenesis through Elimination of p62

(2009) Robin Mathew et al.   CELL

mTOR signaling at a glance

(2009) M. Laplante et al.   JOURNAL OF CELL SCIENCE

Ordered Organelle Degradation during Starvation-induced Autophagy

(2008) Anders Riis Kristensen et al.   MOLECULAR & CELLULAR PROTEOMICS

Autophagy fights disease through cellular self-digestion

(2008) Noboru Mizushima et al.   NATURE

The Itinerary of Autophagosomes: From Peripheral Formation to Kiss-and-Run Fusion with Lysosomes

(2008) Luca Jahreiss et al.   TRAFFIC