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

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

(2017) Amy Y. Chang et al.   JOURNAL OF CELL SCIENCE

The acyltransferase LYCAT controls specific phosphoinositides and related membrane traffic

(2017) Leslie N. Bone et al.   MOLECULAR BIOLOGY OF THE CELL

Design principles for robust vesiculation in clathrin-mediated endocytosis

(2017) Julian E. Hassinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Carlos R. Reis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Clathrin polymerization exhibits high mechano-geometric sensitivity

(2017) Ehsan Irajizad et al.   Soft Matter

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

(2017) Rezarta Islamaj Doğan et al.   Database-The Journal of Biological Databases and Curation

TFEB and TFE3: Linking Lysosomes to Cellular Adaptation to Stress

(2016) Nina Raben et al.   Annual Review of Cell and Developmental Biology

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

(2016) Nunzia Pastore et al.   Autophagy

Passive Noise Filtering by Cellular Compartmentalization

(2016) Thomas Stoeger et al.   CELL

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

(2016) Matthew A. Gray et al.   CURRENT BIOLOGY

Lysosomal signaling in control of degradation pathways

(2016) Lukas A Huber et al.   CURRENT OPINION IN CELL BIOLOGY

TFEB and TFE3 are novel components of the integrated stress response

(2016) J. A. Martina et al.   EMBO JOURNAL

The position of lysosomes within the cell determines their luminal pH

(2016) Danielle E. Johnson et al.   JOURNAL OF CELL BIOLOGY

Deciphering dynamics of clathrin-mediated endocytosis in a living organism

(2016) Joshua P. Ferguson et al.   JOURNAL OF CELL BIOLOGY

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

(2016) Bethany E. Perez White et al.   JOURNAL OF CELL SCIENCE

Proximity Labeling Reveals Molecular Determinants of FGFR4 Endosomal Transport

(2016) Ellen Margrethe Haugsten et al.   JOURNAL OF PROTEOME RESEARCH

Proteome-scale Binary Interactomics in Human Cells

(2016) Sam Lievens et al.   MOLECULAR & CELLULAR PROTEOMICS

MIST1 Links Secretion and Stress as both Target and Regulator of the Unfolded Protein Response

(2016) David A. Hess et al.   MOLECULAR AND CELLULAR BIOLOGY

MIST1 and PTF1 Collaborate in Feed-Forward Regulatory Loops That Maintain the Pancreatic Acinar Phenotype in Adult Mice

(2016) Mei Jiang et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2016) Chinh Q. Hoang et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2016) Amra Saric et al.   MOLECULAR BIOLOGY OF THE CELL

Protein kinase C controls lysosome biogenesis independently of mTORC1

(2016) Yang Li et al.   NATURE CELL BIOLOGY

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

(2016) Mireille Ouimet et al.   NATURE IMMUNOLOGY

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

(2016) M. Raab et al.   SCIENCE

Nuclear envelope rupture and repair during cancer cell migration

(2016) C. M. Denais et al.   SCIENCE

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

(2016) Kerstin Klinkert et al.   Nature Communications

Computational Modeling, Formal Analysis, and Tools for Systems Biology

(2016) Ezio Bartocci et al.   PLoS Computational Biology

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

On the move: endocytic trafficking in cell migration

(2015) Tanja Maritzen et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Proteomics of Primary Cilia by Proximity Labeling

(2015) David U. Mick et al.   DEVELOPMENTAL CELL

BORC, a Multisubunit Complex that Regulates Lysosome Positioning

(2015) Jing Pu et al.   DEVELOPMENTAL CELL

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

(2015) Jingyu Peng et al.   FEBS Journal

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

(2015) Xinyu Tan et al.   Integrative Biology

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

(2015) Catherine L. Nezich et al.   JOURNAL OF CELL BIOLOGY

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

(2015) Comert Kural et al.   MOLECULAR BIOLOGY OF THE CELL

The impact of chronic stress on the rat brain lipidome

(2015) T G Oliveira et al.   MOLECULAR PSYCHIATRY

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

(2015) Mathieu Frechin et al.   NATURE

Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB

(2015) Diego L. Medina et al.   NATURE CELL BIOLOGY

Mapping proteins with spatial proteomics

(2015) Vivien Marx   NATURE METHODS

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

(2015) Diego Ploper et al.   PHARMACOLOGICAL RESEARCH

A Systems Biology Approach Identifies a Regulatory Network in Parotid Acinar Cell Terminal Differentiation

(2015) Melissa A. Metzler et al.   PLoS One

P53 Mutations Change Phosphatidylinositol Acyl Chain Composition

(2015) Adam Naguib et al.   Cell Reports

Proteomic Analysis of Proteins Surrounding Occludin and Claudin-4 Reveals Their Proximity to Signaling and Trafficking Networks

(2015) Karin Fredriksson et al.   PLoS One

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking

(2014) Prisca Liberali et al.   CELL

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

(2014) Christoph S Börlin et al.   Cell Communication and Signaling

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

(2014) José A. Martina et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Multiscale computational models in physical systems biology of intracellular trafficking

(2014) Richard W. Tourdot et al.   IET Systems Biology

Innate Host Defense Requires TFEB-Mediated Transcription of Cytoprotective and Antimicrobial Genes

(2014) Orane Visvikis et al.   IMMUNITY

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

(2014) I. J. McGough et al.   JOURNAL OF CELL SCIENCE

RAB26 coordinates lysosome traffic and mitochondrial localization

(2014) R. U. Jin et al.   JOURNAL OF CELL SCIENCE

Proteomic Mapping of the Human Mitochondrial Intermembrane Space in Live Cells via Ratiometric APEX Tagging

(2014) Victoria Hung et al.   MOLECULAR CELL

Directed evolution of APEX2 for electron microscopy and proximity labeling

(2014) Stephanie S Lam et al.   NATURE METHODS

Multiplex Detection of Homo- and Heterodimerization of G Protein-Coupled Receptors by Proximity Biotinylation

(2014) Elisabeth Steel et al.   PLoS One

Phosphorylation Site Dynamics of Early T-cell Receptor Signaling

(2014) Lily A. Chylek et al.   PLoS One

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

(2014) C. C. Williams et al.   SCIENCE

ESCRT Machinery Is Required for Plasma Membrane Repair

(2014) A. J. Jimenez et al.   SCIENCE

The Nutrient-Responsive Transcription Factor TFE3 Promotes Autophagy, Lysosomal Biogenesis, and Clearance of Cellular Debris

(2014) J. A. Martina et al.   Science Signaling

Lysosome: regulator of lipid degradation pathways

(2014) Carmine Settembre et al.   TRENDS IN CELL BIOLOGY

Reciprocal Regulation of Endocytosis and Metabolism

(2014) C. N. Antonescu et al.   Cold Spring Harbor Perspectives in Biology

Role of Endosomes and Lysosomes in Human Disease

(2014) F. R. Maxfield   Cold Spring Harbor Perspectives in Biology

Lysosomal Adaptation: How the Lysosome Responds to External Cues

(2014) C. Settembre et al.   Cold Spring Harbor Perspectives in Biology

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

(2014) Satdip Kaur et al.   eLife

Advances in Analysis of Low Signal-to-Noise Images Link Dynamin and AP2 to the Functions of an Endocytic Checkpoint

(2013) François Aguet et al.   DEVELOPMENTAL CELL

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

(2013) M. Ferron et al.   GENES & DEVELOPMENT

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

(2013) Jose A. Martina et al.   JOURNAL OF CELL BIOLOGY

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

(2013) Carmine Settembre et al.   NATURE CELL BIOLOGY

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

(2013) Eyleen J. O’Rourke et al.   NATURE CELL BIOLOGY

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

(2013) Qiong Yang et al.   NATURE CELL BIOLOGY

Phosphoinositides: Tiny Lipids With Giant Impact on Cell Regulation

(2013) Tamas Balla   PHYSIOLOGICAL REVIEWS

Lysophosphatidylinositol-Acyltransferase-1 (LPIAT1) Is Required to Maintain Physiological Levels of PtdIns and PtdInsP2 in the Mouse

(2013) Karen E. Anderson et al.   PLoS One

Spatial partitioning improves the reliability of biochemical signaling

(2013) A. Mugler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

(2013) H.-W. Rhee et al.   SCIENCE

Clathrin-Mediated Endocytosis Persists during Unperturbed Mitosis

(2013) Silvia K. Tacheva-Grigorova et al.   Cell Reports

A Feeling for the Cell: Christian de Duve (1917–2013)

(2013) Fred Opperdoes   PLOS BIOLOGY

Stochastic Model of Clathrin-Coated Pit Assembly

(2012) Anand Banerjee et al.   BIOPHYSICAL JOURNAL

Membrane Tension Maintains Cell Polarity by Confining Signals to the Leading Edge during Neutrophil Migration

(2012) Andrew R. Houk et al.   CELL

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

Induced Mist1 Expression Promotes Remodeling of Mouse Pancreatic Acinar Cells

(2012) Daniel Direnzo et al.   GASTROENTEROLOGY

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

(2012) Michelle L. Wynn et al.   Integrative Biology

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

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

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

(2012) Hyeon-Cheol Lee et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2012) Patrycja Kozik et al.   NATURE CELL BIOLOGY

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

(2012) Jeremy C. Simpson et al.   NATURE CELL BIOLOGY

Determination of site-specific glycan heterogeneity on glycoproteins

(2012) Daniel Kolarich et al.   Nature Protocols

Clathrin-mediated endocytosis is inhibited during mitosis

(2012) A. B. Fielding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PGC-1  Rescues Huntington's Disease Proteotoxicity by Preventing Oxidative Stress and Promoting TFEB Function

(2012) T. Tsunemi et al.   Science Translational Medicine

Rab7 and Arl8 GTPases are Necessary for Lysosome Tubulation in Macrophages

(2012) Amra Mrakovic et al.   TRAFFIC

Clathrin-Mediated Endocytic Proteins are Involved in Regulating Mitotic Progression and Completion

(2012) Charlotte M. Smith et al.   TRAFFIC

Amino acids and mTORC1: from lysosomes to disease

(2012) Alejo Efeyan et al.   TRENDS IN MOLECULAR MEDICINE

Complexity and the reductionism-holism debate in systems biology

(2012) Fulvio Mazzocchi   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Imaging LDL Receptor Oligomerization during Endocytosis Using a Co-internalization Assay

(2011) Peng Zou et al.   ACS Chemical Biology

Systems biology of the autophagy-lysosomal pathway

(2011) Anil G. Jegga et al.   Autophagy

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

(2011) Carmine Settembre et al.   Autophagy

Scaling factors: Transcription factors regulating subcellular domains

(2011) Jason C. Mills et al.   BIOESSAYS

Cells Respond to Mechanical Stress by Rapid Disassembly of Caveolae

(2011) Bidisha Sinha et al.   CELL

Regulation of TFEB and V-ATPases by mTORC1

(2011) Samuel Peña-Llopis et al.   EMBO JOURNAL

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

(2011) Michela Palmieri et al.   HUMAN MOLECULAR GENETICS

Systems biology and physical biology of clathrin-mediated endocytosis

(2011) Vyas Ramanan et al.   Integrative Biology

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

(2011) Rieko Imae et al.   JOURNAL OF LIPID RESEARCH

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

(2011) Costin N. Antonescu et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2011) Anthony Orvedahl et al.   NATURE

Actin dynamics counteract membrane tension during clathrin-mediated endocytosis

(2011) Steeve Boulant et al.   NATURE CELL BIOLOGY

Origins of regulated cell-to-cell variability

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

Molecular mechanism and physiological functions of clathrin-mediated endocytosis

(2011) Harvey T. McMahon et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Role of Rab GTPases in Membrane Traffic and Cell Physiology

(2011) Alex H. Hutagalung et al.   PHYSIOLOGICAL REVIEWS

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

(2011) N. C. Gauthier 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

TFEB Links Autophagy to Lysosomal Biogenesis

(2011) C. Settembre et al.   SCIENCE

Hotspots Organize Clathrin-Mediated Endocytosis by Efficient Recruitment and Retention of Nucleating Resources

(2011) Daniel Nunez et al.   TRAFFIC

Measuring the Hierarchy of Molecular Events During Clathrin-Mediated Endocytosis

(2011) Dinah Loerke et al.   TRAFFIC

A High Precision Survey of the Molecular Dynamics of Mammalian Clathrin-Mediated Endocytosis

(2011) Marcus J. Taylor et al.   PLOS BIOLOGY

Ragulator-Rag Complex Targets mTORC1 to the Lysosomal Surface and Is Necessary for Its Activation by Amino Acids

(2010) Yasemin Sancak et al.   CELL

Regulation of acinar cell function in the pancreas

(2010) John A Williams   CURRENT OPINION IN GASTROENTEROLOGY

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

(2010) Victoria C. Garside et al.   EXPERIMENTAL CELL RESEARCH

XBP1 Controls Maturation of Gastric Zymogenic Cells by Induction of MIST1 and Expansion of the Rough Endoplasmic Reticulum

(2010) Won Jae Huh et al.   GASTROENTEROLOGY

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

(2010) Marcel Mettlen et al.   JOURNAL OF CELL BIOLOGY

Mass spectrometry–based proteomics in cell biology

(2010) Tobias C. Walther et al.   JOURNAL OF CELL BIOLOGY

Local clustering of transferrin receptors promotes clathrin-coated pit initiation

(2010) Allen P. Liu et al.   JOURNAL OF CELL BIOLOGY

Phosphatidic Acid Plays a Regulatory Role in Clathrin-mediated Endocytosis

(2010) Costin N. Antonescu et al.   MOLECULAR BIOLOGY OF THE CELL

The endocytic matrix

(2010) Giorgio Scita et al.   NATURE

Probabilistic density maps to study global endomembrane organization

(2010) Kristine Schauer et al.   NATURE METHODS

Lipidomics: coming to grips with lipid diversity

(2010) Andrej Shevchenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The delivery of endocytosed cargo to lysosomes: Figure 1

(2009) J. Paul Luzio et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Global and Local Regulation of Clathrin-Coated Pit Dynamics Detected on Patterned Substrates

(2009) Allen P. Liu et al.   BIOPHYSICAL JOURNAL

Diacylglycerol Kinase ϵ Is Selective for Both Acyl Chains of Phosphatidic Acid or Diacylglycerol

(2009) Michael Lung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage

(2009) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

RAB26 and RAB3D Are Direct Transcriptional Targets of MIST1 That Regulate Exocrine Granule Maturation

(2009) X. Tian et al.   MOLECULAR AND CELLULAR BIOLOGY

Endocytic Accessory Proteins Are Functionally Distinguished by Their Differential Effects on the Maturation of Clathrin-coated Pits

(2009) Marcel Mettlen et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2009) Berend Snijder et al.   NATURE

Cargo and Dynamin Regulate Clathrin-Coated Pit Maturation

(2009) Dinah Loerke et al.   PLOS BIOLOGY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

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

(2008) Fulvio Mazzocchi   EMBO REPORTS

Promiscuous protein biotinylation by Escherichia coli biotin protein ligase

(2004) Eunjoo Choi-Rhee et al.   PROTEIN SCIENCE