A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits

Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates

(2020) Akinori Yamasaki et al.   MOLECULAR CELL

Selective autophagy degrades nuclear pore complexes

(2020) Chia-Wei Lee et al.   NATURE CELL BIOLOGY

Endoplasmic reticulum contact sites regulate the dynamics of membraneless organelles

(2020) Jason E. Lee et al.   SCIENCE

Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake

(2020) Arjen J. Jakobi et al.   Nature Communications

Atg2 mediates direct lipid transfer between membranes for autophagosome formation

(2019) Takuo Osawa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates

(2019) Eleonora Turco et al.   MOLECULAR CELL

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

YeastSpotter: Accurate and parameter-free web segmentation for microscopy images of yeast cells

(2019) Alex X Lu et al.   BIOINFORMATICS

ATG2 transports lipids to promote autophagosome biogenesis

(2019) Diana P. Valverde et al.   JOURNAL OF CELL BIOLOGY

Selective Autophagy: ATG8 Family Proteins, LIR Motifs and Cargo Receptors

(2019) Terje Johansen et al.   JOURNAL OF MOLECULAR BIOLOGY

Atg11 tethers Atg9 vesicles to initiate selective autophagy

(2019) Nena Matscheko et al.   PLOS BIOLOGY

The autophagic membrane tether ATG2A transfers lipids between membranes

(2019) Shintaro Maeda et al.   eLife

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway

(2019) Vladimir Kirkin et al.   MOLECULAR CELL

Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery

(2019) Pengwei Wang et al.   Nature Communications

Local Fatty Acid Channeling into Phospholipid Synthesis Drives Phagophore Expansion during Autophagy

(2019) Maximilian Schütter et al.   CELL

Regulation of Clathrin-Mediated Endocytosis

(2018) Marcel Mettlen et al.   Annual Review of Biochemistry

Relationship of Sequence and Phase Separation in Protein Low-Complexity Regions

(2018) Erik W. Martin et al.   BIOCHEMISTRY

Polyubiquitin chain-induced p62 phase separation drives autophagic cargo segregation

(2018) Daxiao Sun et al.   CELL RESEARCH

p62 filaments capture and present ubiquitinated cargos for autophagy

(2018) Gabriele Zaffagnini et al.   EMBO JOURNAL

Cargo recognition and degradation by selective autophagy

(2018) Damián Gatica et al.   NATURE CELL BIOLOGY

Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins

(2018) Jianchao Li et al.   Nature Chemical Biology

Mechanism and medical implications of mammalian autophagy

(2018) Ivan Dikic et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins

(2017) Miroslava Schaffer et al.   JOURNAL OF STRUCTURAL BIOLOGY

Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging

(2017) Wim J.H. Hagen et al.   JOURNAL OF STRUCTURAL BIOLOGY

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Switch-like Arp2/3 activation upon WASP and WIP recruitment to an apparent threshold level by multivalent linker proteins in vivo

(2017) Yidi Sun et al.   eLife

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

(2017) Tyler S Harmon et al.   eLife

Recent developments in the CCP-EM software suite

(2017) Tom Burnley et al.   Acta Crystallographica Section D-Structural Biology

Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy

(2016) Jan Arnold et al.   BIOPHYSICAL JOURNAL

Clathrin-mediated endocytosis in budding yeast at a glance

(2016) Rebecca Lu et al.   JOURNAL OF CELL SCIENCE

An overview of macroautophagy in yeast

(2016) Xin Wen et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanisms of Selective Autophagy

(2016) Gabriele Zaffagnini et al.   JOURNAL OF MOLECULAR BIOLOGY

Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole

(2016) Raffaela Torggler et al.   MOLECULAR CELL

Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery

(2016) Fiorenza Fumagalli et al.   NATURE CELL BIOLOGY

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Mechanistic insights into selective autophagy pathways: lessons from yeast

(2016) Jean-Claude Farré et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanisms of Autophagy

(2015) Nobuo N. Noda et al.   Annual Review of Biophysics

Analysis of the native conformation of the LIR/AIM motif in the Atg8/LC3/GABARAP-binding proteins

(2015) Hana Popelka et al.   Autophagy

LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences

(2015) Ioannis Kirmitzoglou et al.   BIOINFORMATICS

Actin and Endocytosis in Budding Yeast

(2015) Bruce L. Goode et al.   GENETICS

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

A Pan1/End3/Sla1 complex links Arp2/3-mediated actin assembly to sites of clathrin-mediated endocytosis

(2015) Yidi Sun et al.   MOLECULAR BIOLOGY OF THE CELL

Receptor-Bound Targets of Selective Autophagy Use a Scaffold Protein to Activate the Atg1 Kinase

(2015) Roarke A. Kamber et al.   MOLECULAR CELL

Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus

(2015) Keisuke Mochida et al.   NATURE

Actin and Endocytosis in Budding Yeast

(2015) Bruce L. Goode et al.   GENETICS

iLIR

(2014) Ioanna Kalvari et al.   Autophagy

Autophagic Clearance of PolyQ Proteins Mediated by Ubiquitin-Atg8 Adaptors of the Conserved CUET Protein Family

(2014) Kefeng Lu et al.   CELL

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantification of cytosolic interactions identifies Ede1 oligomers as key organizers of endocytosis

(2014) D. Boeke et al.   Molecular Systems Biology

Endocytic Accessory Factors and Regulation of Clathrin-Mediated Endocytosis

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

Molecular Structure, Function, and Dynamics of Clathrin-Mediated Membrane Traffic

(2014) T. Kirchhausen et al.   Cold Spring Harbor Perspectives in Biology

A current perspective of autophagosome biogenesis

(2013) Shusaku T Shibutani et al.   CELL RESEARCH

Plasma Membrane Reshaping during Endocytosis Is Revealed by Time-Resolved Electron Tomography

(2012) Wanda Kukulski et al.   CELL

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Autophagy modulates dynamics of connexins at the plasma membrane in a ubiquitin-dependent manner

(2012) Eloy Bejarano et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

The Role of Atg Proteins in Autophagosome Formation

(2011) Noboru Mizushima et al.   Annual Review of Cell and Developmental Biology

PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis

(2011) Thomas Hrabe et al.   JOURNAL OF STRUCTURAL BIOLOGY

Analysis of yeast endocytic site formation and maturation through a regulatory transition point

(2011) Susheela Y. Carroll et al.   MOLECULAR BIOLOGY OF THE CELL

Lessons from yeast for clathrin-mediated endocytosis

(2011) Douglas R. Boettner et al.   NATURE CELL BIOLOGY

Clathrin-mediated endocytosis in budding yeast

(2011) Jasper Weinberg et al.   TRENDS IN CELL BIOLOGY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Atg8-family interacting motif crucial for selective autophagy

(2010) Nobuo N. Noda et al.   FEBS LETTERS

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Micromachining tools and correlative approaches for cellular cryo-electron tomography

(2010) Alexander Rigort et al.   JOURNAL OF STRUCTURAL BIOLOGY

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

Mutation at the cargo-receptor binding site of Atg8 also affects its general autophagy regulation function

(2009) Kung-Hsien Ho et al.   Autophagy

Dynamics and diversity in autophagy mechanisms: lessons from yeast

(2009) Hitoshi Nakatogawa et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Function of Yeast Epsin and Ede1 Ubiquitin-Binding Domains During Receptor Internalization

(2009) Michael R. Dores et al.   TRAFFIC

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

(2008) Thouis R Jones et al.   BMC BIOINFORMATICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY