Computational Screening of Biological Phase-separating Proteins

Proteome-scale analysis of phase-separated proteins in immunofluorescence images

(2020) Chunyu Yu et al.   BRIEFINGS IN BIOINFORMATICS

Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation

(2019) Brian Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of transcriptional enhancers and chromosome topology in gene regulation

(2019) Moe Yokoshi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

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

(2019) Simon Alberti et al.   CELL

Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates

(2019) Gabriele Orlando et al.   BIOINFORMATICS

Liquid–Liquid Phase Separation in Disease

(2019) Simon Alberti et al.   Annual Review of Genetics

LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro

(2019) Qian Li et al.   NUCLEIC ACIDS RESEARCH

Phospho-dependent phase separation of FMRP and CAPRIN1 recapitulates regulation of translation and deadenylation

(2019) Tae Hun Kim et al.   SCIENCE

First-generation predictors of biological protein phase separation

(2019) Robert M Vernon et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PhaSepDB: a database of liquid–liquid phase separation related proteins

(2019) Kaiqiang You et al.   NUCLEIC ACIDS RESEARCH

The functional landscape of the human phosphoproteome

(2019) David Ochoa et al.   NATURE BIOTECHNOLOGY

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

Tau protein liquid–liquid phase separation can initiate tau aggregation

(2018) Susanne Wegmann et al.   EMBO JOURNAL

Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior

(2018) Titus Franzmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A User’s Guide for Phase Separation Assays with Purified Proteins

(2018) Simon Alberti et al.   JOURNAL OF MOLECULAR BIOLOGY

Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks

(2018) Michael P. Hughes et al.   SCIENCE

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

Citrullination of RGG Motifs in FET Proteins by PAD4 Regulates Protein Aggregation and ALS Susceptibility

(2018) Chizu Tanikawa et al.   Cell Reports

Intrinsically Disordered Regions Can Contribute Promiscuous Interactions to RNP Granule Assembly

(2018) David S.W. Protter et al.   Cell Reports

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

(2018) Robert McCoy Vernon et al.   eLife

Friend or foe — post-translational modifications as regulators of phase separation and RNP granule dynamics

(2018) Mario Hofweber et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Acetylation of intrinsically disordered regions regulates phase separation

(2018) Makoto Saito et al.   Nature Chemical Biology

Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs

(2017) Yuan Lin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phase separation of BuGZ promotes Aurora A activation and spindle assembly

(2017) Jeffrey B. Woodruff   JOURNAL OF CELL BIOLOGY

Aurora A activation in mitosis promoted by BuGZ

(2017) Yuejia Huang et al.   JOURNAL OF CELL BIOLOGY

Stress-specific differences in assembly and composition of stress granules and related foci

(2017) Anaïs Aulas et al.   JOURNAL OF CELL SCIENCE

P-Body Purification Reveals the Condensation of Repressed mRNA Regulons

(2017) Arnaud Hubstenberger et al.   MOLECULAR CELL

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

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

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

(2017) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding

(2017) Bagdeser A. Ozdilek et al.   NUCLEIC ACIDS RESEARCH

Prediction of protein disorder based on IUPred

(2017) Zsuzsanna Dosztányi   PROTEIN SCIENCE

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau

(2017) Susmitha Ambadipudi et al.   Nature Communications

RNA stores tau reversibly in complex coacervates

(2017) Xuemei Zhang et al.   PLOS BIOLOGY

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

(2017) Tyler S Harmon et al.   eLife

Prion-like domains as epigenetic regulators, scaffolds for subcellular organization, and drivers of neurodegenerative disease

(2016) Zachary M. March et al.   BRAIN RESEARCH

ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure

(2016) Saumya Jain et al.   CELL

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

(2016) Benedetta Bolognesi et al.   Cell Reports

Biochemical Properties and Biological Functions of FET Proteins

(2015) Jacob C. Schwartz et al.   Annual Review of Biochemistry

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Relating sequence encoded information to form and function of intrinsically disordered proteins

(2015) Rahul K Das et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

(2014) A. K. Lancaster et al.   BIOINFORMATICS

Quantifying mRNA targeting to P-bodies in living human cells reveals their dual role in mRNA decay and storage

(2014) Adva Aizer et al.   JOURNAL OF CELL SCIENCE

A Million Peptide Motifs for the Molecular Biologist

(2014) Peter Tompa et al.   MOLECULAR CELL

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling

(2013) Frank Wippich et al.   CELL

Describing intrinsically disordered proteins at atomic resolution by NMR

(2013) Malene Ringkjøbing Jensen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

From Sequence and Forces to Structure, Function, and Evolution of Intrinsically Disordered Proteins

(2013) Julie D. Forman-Kay et al.   STRUCTURE

Differential Roles of PML Isoforms

(2013) Sébastien Nisole et al.   Frontiers in Oncology

Energy Component Analysis of π Interactions

(2012) C. David Sherrill   ACCOUNTS OF CHEMICAL RESEARCH

MobiDB: a comprehensive database of intrinsic protein disorder annotations

(2012) T. Di Domenico et al.   BIOINFORMATICS

The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease

(2012) Oliver D. King et al.   BRAIN RESEARCH

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

D2P2: database of disordered protein predictions

(2012) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

ESpritz: accurate and fast prediction of protein disorder

(2011) Ian Walsh et al.   BIOINFORMATICS

Identifying the amylome, proteins capable of forming amyloid-like fibrils

(2010) Lukasz Goldschmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE