Genetically encoded multimeric tags for subcellular protein localization in cryo-EM

Convolutional networks for supervised mining of molecular patterns within cellular context

(2023) Irene de Teresa-Trueba et al.   NATURE METHODS

Molecular mechanisms of stress-induced reactivation in mumps virus condensates

(2023) Xiaojie Zhang et al.   CELL

In situ architecture of the ER–mitochondria encounter structure

(2023) Michael R. Wozny et al.   NATURE

Genetically encoded barcodes for correlative volume electron microscopy

(2023) Felix Sigmund et al.   NATURE BIOTECHNOLOGY

TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining

(2023) Gavin Rice et al.   NATURE METHODS

Seipin localizes at endoplasmic-reticulum-mitochondria contact sites to control mitochondrial calcium import and metabolism in adipocytes

(2022) Yoann Combot et al.   Cell Reports

In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains

(2022) Hugo van den Hoek et al.   SCIENCE

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

(2022) Shyamal Mosalaganti et al.   SCIENCE

A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0

(2022) Jasenko Zivanov et al.   eLife

DNA origami signposts for identifying proteins on cell membranes by electron cryotomography

(2021) Emma Silvester et al.   CELL

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells

(2021) Dimitry Tegunov et al.   NATURE METHODS

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism

(2021) Robert J Nichols et al.   eLife

CellProfiler 4: improvements in speed, utility and usability

(2021) David R. Stirling et al.   BMC BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Large-scale computational discovery and analysis of virus-derived microbial nanocompartments

(2021) Michael P. Andreas et al.   Nature Communications

New tools for automated cryo-EM single-particle analysis in RELION-4.0

(2021) Dari Kimanius et al.   BIOCHEMICAL JOURNAL

Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms

(2021) Emmanuel Moebel et al.   NATURE METHODS

Nuclear pores dilate and constrict in cellulo

(2021) Christian E. Zimmerli et al.   SCIENCE

A modular platform for automated cryo-FIB workflows

(2021) Sven Klumpe et al.   eLife

Design and Characterization of an Icosahedral Protein Cage Formed by a Double-Fusion Protein Containing Three Distinct Symmetry Elements

(2020) Kevin A. Cannon et al.   ACS Synthetic Biology

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

(2020) Jordina Guillén-Boixet et al.   CELL

Structure of a robust bacterial protein cage and its application as a versatile biocatalytic platform through enzyme encapsulation

(2020) Nikola Lončar et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

(2020) Peter D. Dahlberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In-cell architecture of an actively transcribing-translating expressome

(2020) Francis J. O’Reilly et al.   SCIENCE

Advances in encapsulin nanocompartment biology and engineering

(2020) Jesse A. Jones et al.   BIOTECHNOLOGY AND BIOENGINEERING

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

Reversible association with motor proteins (RAMP): A streptavidin-based method to manipulate organelle positioning

(2019) Carlos M. Guardia et al.   PLOS BIOLOGY

Seipin Facilitates Triglyceride Flow to Lipid Droplet and Counteracts Droplet Ripening via Endoplasmic Reticulum Contact

(2019) Veijo T. Salo et al.   DEVELOPMENTAL CELL

The amazing HK97 fold: versatile results of modest differences

(2019) Robert L Duda et al.   Current Opinion in Virology

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

An efficient auxin-inducible degron system with low basal degradation in human cells

(2019) Shiqian Li et al.   NATURE METHODS

Nuclear pores as versatile reference standards for quantitative superresolution microscopy

(2019) Jervis Vermal Thevathasan et al.   NATURE METHODS

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

A complete data processing workflow for cryo-ET and subtomogram averaging

(2019) Muyuan Chen et al.   NATURE METHODS

Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies

(2019) Mauricio Toro-Nahuelpan et al.   NATURE METHODS

LDAF1 and Seipin Form a Lipid Droplet Assembly Complex

(2019) Jeeyun Chung et al.   DEVELOPMENTAL CELL

The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria

(2019) John C. Tracey et al.   Scientific Reports

mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding

(2018) M. Delarue et al.   CELL

Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging

(2018) Antonio Z Politi et al.   Nature Protocols

Bacterial encapsulins as orthogonal compartments for mammalian cell engineering

(2018) Felix Sigmund et al.   Nature Communications

FerriTag is a new genetically-encoded inducible tag for correlative light-electron microscopy

(2018) Nicholas I. Clarke et al.   Nature Communications

Experimental and computational framework for a dynamic protein atlas of human cell division

(2018) Yin Cai et al.   NATURE

Conditional control of fluorescent protein degradation by an auxin-dependent nanobody

(2018) Katrin Daniel et al.   Nature Communications

Cryo–electron microscopy structure of the lipid droplet–formation protein seipin

(2018) Xuewu Sui et al.   JOURNAL OF CELL BIOLOGY

emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging

(2018) Benjamin A. Himes et al.   NATURE METHODS

Automated tilt series alignment and tomographic reconstruction in IMOD

(2017) David N. Mastronarde 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

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

eC-CLEM: flexible multidimensional registration software for correlative microscopies

(2017) Perrine Paul-Gilloteaux et al.   NATURE METHODS

Widespread distribution of encapsulin nanocompartments reveals functional diversity

(2017) Tobias W. Giessen et al.   Nature Microbiology

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

(2016) Jan Arnold et al.   BIOPHYSICAL JOURNAL

Seipin regulates ER–lipid droplet contacts and cargo delivery

(2016) Veijo T Salo et al.   EMBO JOURNAL

Design of a hyperstable 60-subunit protein icosahedron

(2016) Yang Hsia et al.   NATURE

Ki-67 acts as a biological surfactant to disperse mitotic chromosomes

(2016) Sara Cuylen et al.   NATURE

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments

(2016) Didi He et al.   eLife

Seipin is required for converting nascent to mature lipid droplets

(2016) Huajin Wang et al.   eLife

Designing and defining dynamic protein cage nanoassemblies in solution

(2016) Y.-T. Lai et al.   Science Advances

Packaging guest proteins into the encapsulin nanocompartment fromRhodococcus erythropolisN771

(2014) Akio Tamura et al.   BIOTECHNOLOGY AND BIOENGINEERING

ER Contact Sites Define the Position and Timing of Endosome Fission

(2014) Ashley A. Rowland et al.   CELL

Robust membrane detection based on tensor voting for electron tomography

(2014) Antonio Martinez-Sanchez et al.   JOURNAL OF STRUCTURAL BIOLOGY

Assemblyin vitroofRhodococcus jostii RHA1 encapsulin and peroxidase DypB to form a nanocompartment

(2013) Rahman Rahmanpour et al.   FEBS Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Permeability of Reconstituted Nuclear Pores Provides Direct Evidence for the Selective Phase Model

(2012) Bastian B. Hülsmann et al.   CELL

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

(2012) Johannes Schindelin et al.   NATURE METHODS

A Ferritin-Based Label for Cellular Electron Cryotomography

(2011) Qing Wang et al.   STRUCTURE

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Rapid Inactivation of Proteins by Rapamycin-Induced Rerouting to Mitochondria

(2010) Margaret S. Robinson et al.   DEVELOPMENTAL CELL

Live-cell imaging RNAi screen identifies PP2A–B55α and importin-β1 as key mitotic exit regulators in human cells

(2010) Michael H. A. Schmitz et al.   NATURE CELL BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Live Cell Multicolor Imaging of Lipid Droplets with a New Dye, LD540

(2009) Johanna Spandl et al.   TRAFFIC

Structural basis of enzyme encapsulation into a bacterial nanocompartment

(2008) Markus Sutter et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY