The big and intricate dreams of little organelles: Embracing complexity in the study of membrane traffic. (Q39345932)

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21 March 2020

review article

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title

The big and intricate dreams of little organelles: Embracing complexity in the study of membrane traffic (English)

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21 March 2020

1

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21 March 2020

Roberto J. Botelho

2

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21 March 2020

Costin Antonescu

3

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21 March 2020

author name string

Allen P Liu

1

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11 September 2017

Roberto J Botelho

2

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11 September 2017

Costin N Antonescu

3

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11 September 2017

4 July 2017

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21 March 2020

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21 March 2020

volume

18

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21 March 2020

issue

9

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21 March 2020

page(s)

567-579

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28574194%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

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Role of Rab GTPases in membrane traffic and cell physiology

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Role of endosomes and lysosomes in human disease.

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Reciprocal regulation of endocytosis and metabolism

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On the move: endocytic trafficking in cell migration.

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Complexity and the reductionism-holism debate in systems biology

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George Emil Palade: charismatic virtuoso of cell biology.

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A Feeling for the Cell: Christian de Duve (1917â€“2013)

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Identification of 23 complementation groups required for post-translational events in the yeast secretory pathway

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The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions

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Mass spectrometry-based proteomics in cell biology

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Proteomics of organelles and large cellular structures

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A mammalian organelle map by protein correlation profiling

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A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

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Global analysis of protein localization in budding yeast

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Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling

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A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

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Multiplex detection of homo- and heterodimerization of g protein-coupled receptors by proximity biotinylation

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Imaging LDL receptor oligomerization during endocytosis using a co-internalization assay

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Promiscuous protein biotinylation by Escherichia coli biotin protein ligase

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Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.

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Directed evolution of APEX2 for electron microscopy and proximity labeling.

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EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions.

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Proteomic analysis of proteins surrounding occludin and claudin-4 reveals their proximity to signaling and trafficking networks

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Proximity Labeling Reveals Molecular Determinants of FGFR4 Endosomal Transport

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Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.

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Proteomics of Primary Cilia by Proximity Labeling

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An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells

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High-content screening microscopy identifies novel proteins with a putative role in secretory membrane traffic

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Population context determines cell-to-cell variability in endocytosis and virus infection

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A human genome-wide screen for regulators of clathrin-coated vesicle formation reveals an unexpected role for the V-ATPase

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Image-based genome-wide siRNA screen identifies selective autophagy factors

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Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis.

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High-throughput screens in mammalian cells using the CRISPR-Cas9 system

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Proteome-scale Binary Interactomics in Human Cells

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Phosphoinositides in cell regulation and membrane dynamics

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Phosphoinositides: tiny lipids with giant impact on cell regulation

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Essential role of phosphoinositide metabolism in synaptic vesicle recycling

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Two synaptojanin 1 isoforms are recruited to clathrin-coated pits at different stages

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Phosphatidylinositol-(4,5)-bisphosphate regulates clathrin-coated pit initiation, stabilization, and size

21 January 2018

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EEA1 links PI(3)K function to Rab5 regulation of endosome fusion

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LYCAT, a homologue of C. elegans acl-8, acl-9, and acl-10, determines the fatty acid composition of phosphatidylinositol in mice

21 January 2018

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The acyltransferase LYCAT controls specific phosphoinositides and related membrane traffic.

21 January 2018

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Lysophosphatidylinositol-acyltransferase-1 (LPIAT1) is required to maintain physiological levels of PtdIns and PtdInsP(2) in the mouse

21 January 2018

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LPIAT1 regulates arachidonic acid content in phosphatidylinositol and is required for cortical lamination in mice

21 January 2018

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Diacylglycerol kinase epsilon is selective for both acyl chains of phosphatidic acid or diacylglycerol

21 January 2018

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p53 mutations change phosphatidylinositol acyl chain composition

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The impact of chronic stress on the rat brain lipidome

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Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour

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Determination of site-specific glycan heterogeneity on glycoproteins.

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Complex N-glycan number and degree of branching cooperate to regulate cell proliferation and differentiation.

21 January 2018

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Molecular mechanism and physiological functions of clathrin-mediated endocytosis

21 January 2018

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Regulated portals of entry into the cell

21 January 2018

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TTP specifically regulates the internalization of the transferrin receptor

21 January 2018

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Activation of the epidermal growth factor (EGF) receptor induces formation of EGF receptor- and Grb2-containing clathrin-coated pits

21 January 2018

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Phosphatidic acid plays a regulatory role in clathrin-mediated endocytosis

21 January 2018

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Tyrosine phosphorylation of Eps15 is required for ligand-regulated, but not constitutive, endocytosis

21 January 2018

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Clathrin-mediated endocytosis in AP-2-depleted cells

21 January 2018

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Differential requirements for AP-2 in clathrin-mediated endocytosis

21 January 2018

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Analysis of clathrin-mediated endocytosis of epidermal growth factor receptor by RNA interference

21 January 2018

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TRAIL-death receptor endocytosis and apoptosis are selectively regulated by dynamin-1 activation.

21 January 2018

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A high precision survey of the molecular dynamics of mammalian clathrin-mediated endocytosis

21 January 2018

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Global and local regulation of clathrin-coated pit dynamics detected on patterned substrates.

21 January 2018

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Cargo- and adaptor-specific mechanisms regulate clathrin-mediated endocytosis.

21 January 2018

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Endocytic accessory proteins are functionally distinguished by their differential effects on the maturation of clathrin-coated pits

21 January 2018

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Local clustering of transferrin receptors promotes clathrin-coated pit initiation.

21 January 2018

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Measuring the hierarchy of molecular events during clathrin-mediated endocytosis

21 January 2018

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Hotspots organize clathrin-mediated endocytosis by efficient recruitment and retention of nucleating resources.

21 January 2018

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Cargo and dynamin regulate clathrin-coated pit maturation.

21 January 2018

1 reference

Advances in analysis of low signal-to-noise images link dynamin and AP2 to the functions of an endocytic checkpoint

21 January 2018

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Cargo regulates clathrin-coated pit dynamics

21 January 2018

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Stochastic model of clathrin-coated pit assembly

21 January 2018

1 reference

Identification of molecular heterogeneity in SNX27-retromer-mediated endosome-to-plasma-membrane recycling

21 January 2018

1 reference

Organelles - understanding noise and heterogeneity in cell biology at an intermediate scale

21 January 2018

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Heterogeneity of lysosomes in human fibroblasts

21 January 2018

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The position of lysosomes within the cell determines their luminal pH

21 January 2018

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Radial extension of macrophage tubular lysosomes supported by kinesin

21 January 2018

1 reference

Rab7 and Arl8 GTPases are necessary for lysosome tubulation in macrophages

21 January 2018

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mTOR controls lysosome tubulation and antigen presentation in macrophages and dendritic cells

21 January 2018

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Analytical subcellular fractionation of alveolar macrophages from normal and BCG-vaccinated rabbits with particular reference to heterogeneity of hydrolase-containing granules

21 January 2018

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BORC, a multisubunit complex that regulates lysosome positioning.

21 January 2018

1 reference

Probabilistic density maps to study global endomembrane organization

21 January 2018

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Control of Transcript Variability in Single Mammalian Cells.

21 January 2018

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Intrinsic noise in gene regulatory networks

21 January 2018

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Nature, nurture, or chance: stochastic gene expression and its consequences

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Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.

21 January 2018

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Spatial partitioning improves the reliability of biochemical signaling

21 January 2018

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Passive Noise Filtering by Cellular Compartmentalization.

21 January 2018

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Scaling factors: transcription factors regulating subcellular domains

21 January 2018

1 reference

The molecular machinery for lysosome biogenesis

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The delivery of endocytosed cargo to lysosomes

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Lysosome: regulator of lipid degradation pathways

21 January 2018

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Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways.

21 January 2018

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Lysosomes: fusion and function

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Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB.

21 January 2018

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Lysosomal adaptation: how the lysosome responds to external cues

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Lysosomal signaling in control of degradation pathways

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Rag GTPases mediate amino acid-dependent recruitment of TFEB and MITF to lysosomes

21 January 2018

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TFEB links autophagy to lysosomal biogenesis

21 January 2018

1 reference

Novel roles for the MiTF/TFE family of transcription factors in organelle biogenesis, nutrient sensing, and energy homeostasis

21 January 2018

1 reference

TFEB and TFE3: Linking Lysosomes to Cellular Adaptation to Stress

21 January 2018

1 reference

The MITF family of transcription factors: Role in endolysosomal biogenesis, Wnt signaling, and oncogenesis.

21 January 2018

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mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase

21 January 2018

1 reference

Amino acids and mTORC1: from lysosomes to disease

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Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids

21 January 2018

1 reference

Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway

21 January 2018

1 reference

Regulation of TFEB and V-ATPases by mTORC1.

21 January 2018

1 reference

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

21 January 2018

1 reference

The nutrient-responsive transcription factor TFE3 promotes autophagy, lysosomal biogenesis, and clearance of cellular debris

21 January 2018

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TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop

21 January 2018

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MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability

21 January 2018

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PGC-1α rescues Huntington's disease proteotoxicity by preventing oxidative stress and promoting TFEB function.

21 January 2018

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MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5

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TFEB and TFE3 are novel components of the integrated stress response

21 January 2018

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Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes

21 January 2018

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TFEB and TFE3 cooperate in the regulation of the innate immune response in activated macrophages

21 January 2018

1 reference

Phagocytosis Enhances Lysosomal and Bactericidal Properties by Activating the Transcription Factor TFEB.

21 January 2018

1 reference

A RANKL-PKCβ-TFEB signaling cascade is necessary for lysosomal biogenesis in osteoclasts

21 January 2018

1 reference

Protein kinase C controls lysosome biogenesis independently of mTORC1.

21 January 2018

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Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism

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Regulation of acinar cell function in the pancreas.

21 January 2018

1 reference

A systems biology approach identifies a regulatory network in parotid acinar cell terminal differentiation

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MIST1 and PTF1 Collaborate in Feed-forward Regulatory Loops that Maintain the Pancreatic Acinar Phenotype in Adult Mice.

21 January 2018

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The bHLH transcription factor Mist1 is required to maintain exocrine pancreas cell organization and acinar cell identity

21 January 2018

1 reference

XBP1 controls maturation of gastric zymogenic cells by induction of MIST1 and expansion of the rough endoplasmic reticulum

21 January 2018

1 reference

MIST1 Links Secretion and Stress as Both Target and Regulator of the UPR.

21 January 2018

1 reference

XBP-1 is required for biogenesis of cellular secretory machinery of exocrine glands

21 January 2018

1 reference

Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A.

21 January 2018

1 reference

The maturation of mucus-secreting gastric epithelial progenitors into digestive-enzyme secreting zymogenic cells requires Mist1

21 January 2018

1 reference

Inhibition of Mist1 homodimer formation induces pancreatic acinar-to-ductal metaplasia

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Mist1 is necessary for the establishment of granule organization in serous exocrine cells of the gastrointestinal tract.

21 January 2018

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Induced Mist1 expression promotes remodeling of mouse pancreatic acinar cells

21 January 2018

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MIST1 regulates the pancreatic acinar cell expression of Atp2c2, the gene encoding secretory pathway calcium ATPase 2.

21 January 2018

1 reference

Aberrant localization of intracellular organelles, Ca2+ signaling, and exocytosis in Mist1 null mice

21 January 2018

1 reference

RAB26 and RAB3D are direct transcriptional targets of MIST1 that regulate exocrine granule maturation

21 January 2018

1 reference

RAB26 coordinates lysosome traffic and mitochondrial localization

21 January 2018

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Systems biology of the autophagy-lysosomal pathway

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Complexity in biology. Exceeding the limits of reductionism and determinism using complexity theory

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Computational Modeling, Formal Analysis, and Tools for Systems Biology

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The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch

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Metabolic stability and epigenesis in randomly constructed genetic nets

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Logic-based models in systems biology: a predictive and parameter-free network analysis method.

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Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling

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Phosphorylation site dynamics of early T-cell receptor signaling

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Formal agent-based modelling of intracellular chemical interactions.

21 January 2018

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Systems biology and physical biology of clathrin-mediated endocytosis.

21 January 2018

1 reference

Actin dynamics counteract membrane tension during clathrin-mediated endocytosis

21 January 2018

1 reference

Cell spreading area regulates clathrin-coated pit dynamics on micropatterned substrate.

21 January 2018

1 reference

Design principles for robust vesiculation in clathrin-mediated endocytosis

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1 reference

Clathrin polymerization exhibits high mechano-geometric sensitivity.

21 January 2018

1 reference

Multiscale computational models in physical systems biology of intracellular trafficking

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21 January 2018

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Regulation of endocytosis, exocytosis, and shape by membrane tension

21 January 2018

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Getting membrane flow and the cytoskeleton to cooperate in moving cells

21 January 2018

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Temporary increase in plasma membrane tension coordinates the activation of exocytosis and contraction during cell spreading.

21 January 2018

1 reference

Cells respond to mechanical stress by rapid disassembly of caveolae

21 January 2018

1 reference

Membrane tension maintains cell polarity by confining signals to the leading edge during neutrophil migration

21 January 2018

1 reference

Real-time analysis of clathrin-mediated endocytosis during cell migration

21 January 2018

1 reference

Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edges of motile cells and on protrusions of immobile cells

21 January 2018

1 reference

Deciphering dynamics of clathrin-mediated endocytosis in a living organism

21 January 2018

1 reference

ESCRT machinery is required for plasma membrane repair.

21 January 2018

1 reference

ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death.

21 January 2018

1 reference

Nuclear envelope rupture and repair during cancer cell migration.

21 January 2018

1 reference

Endosomal recycling controls plasma membrane area during mitosis

21 January 2018

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Clathrin-mediated endocytosis is inhibited during mitosis

21 January 2018

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Clathrin-mediated endocytosis persists during unperturbed mitosis.

21 January 2018

1 reference

An unmet actin requirement explains the mitotic inhibition of clathrin-mediated endocytosis.

21 January 2018

1 reference

Integrating molecular and network biology to decode endocytosis

21 January 2018

1 reference

Clathrin-mediated endocytic proteins are involved in regulating mitotic progression and completion.

21 January 2018

1 reference

Rab35 GTPase couples cell division with initiation of epithelial apico-basal polarity and lumen opening

21 January 2018

1 reference

Quantitative Proteomic Comparison of Rat Mitochondria from Muscle, Heart, and Liver

21 January 2018

1 reference

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway

21 January 2018

1 reference

Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis

21 January 2018

1 reference

TFEB regulates autophagy: An integrated coordination of cellular degradation and recycling processes

21 January 2018

1 reference

Lipidomics: coming to grips with lipid diversity

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1111/TRA.12497

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28574194%20AND%20SRC:MED&resulttype=core&format=json

21 March 2020

1 reference