Predicting protein condensate formation using machine learning

m6A-binding YTHDF proteins promote stress granule formation

(2020) Ye Fu et al.   Nature Chemical Biology

RNA Binding Antagonizes Neurotoxic Phase Transitions of TDP-43

(2019) Jacob R. Mann et al.   NEURON

Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications

(2019) Roland Hermann Alfons Winter et al.   CHEMISTRY-A EUROPEAN JOURNAL

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain

(2019) Anastasia C. Murthy et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates

(2019) Marina Garcia-Jove Navarro et al.   Nature Communications

Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors

(2019) Fabio Pessina et al.   NATURE CELL BIOLOGY

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

(2019) Qian Li et al.   NUCLEIC ACIDS RESEARCH

CPEB3 inhibits translation of mRNA targets by localizing them to P bodies

(2019) Lenzie Ford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phase Separation as a Melting Pot for DNA Repeats

(2019) Amanda C. Hall et al.   TRENDS IN GENETICS

First-generation predictors of biological protein phase separation

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

Properties of Stress Granule and P-Body Proteomes

(2019) Ji-Young Youn et al.   MOLECULAR CELL

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

(2019) Kaiqiang You et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Erik W. Martin et al.   BIOCHEMISTRY

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

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

(2018) Jie Wang et al.   CELL

RGG/RG Motif Regions in RNA Binding and Phase Separation

(2018) P. Andrew Chong et al.   JOURNAL OF MOLECULAR BIOLOGY

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Michael P. Hughes et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Protein Phase Separation: A New Phase in Cell Biology

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

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

(2018) Robert McCoy Vernon et al.   eLife

Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

(2018) Katrina Meyer et al.   CELL

The molecular language of membraneless organelles

(2018) Edward Gomes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly?

(2018) Aishwarya Gurumurthy et al.   BIOESSAYS

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Liquid and Hydrogel Phases of PrPC Linked to Conformation Shifts and Triggered by Alzheimer’s Amyloid-β Oligomers

(2018) Mikhail A. Kostylev et al.   MOLECULAR CELL

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

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

Biomolecular condensates: organizers of cellular biochemistry

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

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein

(2016) Chi W. Pak et al.   MOLECULAR CELL

ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain

(2016) Alexander E. Conicella et al.   STRUCTURE

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

(2016) Benedetta Bolognesi et al.   Cell Reports

Distinct stages in stress granule assembly and disassembly

(2016) Joshua R Wheeler et al.   eLife

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

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

(2015) Avinash Patel et al.   CELL

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

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

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

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

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

TARDBPandFUSMutations Associated with Amyotrophic Lateral Sclerosis: Summary and Update

(2013) Serena Lattante et al.   HUMAN MUTATION

Phase transitions and size scaling of membrane-less organelles

(2013) Clifford P. Brangwynne   JOURNAL OF CELL BIOLOGY

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

(2012) Vladimir Vacic et al.   PLoS Computational Biology

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

(2008) Ina Poser et al.   NATURE METHODS