Identifying molecular features that are associated with biological function of intrinsically disordered protein regions

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Condensation of Ded1p Promotes a Translational Switch from Housekeeping to Stress Protein Production

(2020) Christiane Iserman et al.   CELL

Computational Prediction of MoRFs, Short Disorder-to-order Transitioning Protein Binding Regions

(2019) Akila Katuwawala et al.   Computational and Structural Biotechnology Journal

Proteome-wide signatures of function in highly diverged intrinsically disordered regions

(2019) Taraneh Zarin et al.   eLife

First-generation predictors of biological protein phase separation

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

RGG/RG Motif Regions in RNA Binding and Phase Separation

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

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

(2018) Robert McCoy Vernon et al.   eLife

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries

(2018) Benjamin Dubreuil et al.   NUCLEIC ACIDS RESEARCH

Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain

(2018) Alexander S. Krois et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selection maintains signaling function of a highly diverged intrinsically disordered region

(2017) Taraneh Zarin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsically Disordered Proteome of Human Membrane-Less Organelles

(2017) April L. Darling et al.   PROTEOMICS

The Tail That Wags the Dog: How the Disordered C-Terminal Domain Controls the Transcriptional Activities of the p53 Tumor-Suppressor Protein

(2016) Oleg Laptenko et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Role of Charge in Protein Targeting Evolution

(2016) Sriram G. Garg et al.   TRENDS IN CELL BIOLOGY

Characterization of Fluorescent Proteins for Three- and Four-Color Live-Cell Imaging in S. cerevisiae

(2016) Ryo Higuchi-Sanabria et al.   PLoS One

Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress

(2015) Edward W.J. Wallace et al.   CELL

MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites

(2015) Yoshinori Fukasawa et al.   MOLECULAR & CELLULAR PROTEOMICS

Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity

(2015) Rita Gemayel et al.   MOLECULAR CELL

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

(2014) Alex N. Nguyen Ba et al.   PLoS Computational Biology

A novel single-cell screening platform reveals proteome plasticity during yeast stress responses

(2013) Michal Breker et al.   JOURNAL OF CELL BIOLOGY

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

LoQAtE—Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast

(2013) Michal Breker et al.   NUCLEIC ACIDS RESEARCH

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

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

Computational prediction of N-linked glycosylation incorporating structural properties and patterns

(2012) Gwo-Yu Chuang et al.   BIOINFORMATICS

Predicting kinase substrates using conservation of local motif density

(2012) Andy C. W. Lai et al.   BIOINFORMATICS

Global analysis of yeast mRNPs

(2012) Sarah F Mitchell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global Gene Deletion Analysis Exploring Yeast Filamentous Growth

(2012) O. Ryan et al.   SCIENCE

Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions

(2012) A. N. Nguyen Ba et al.   Science Signaling

Disease mutations in disordered regions—exception to the rule?

(2011) Vladimir Vacic et al.   Molecular BioSystems

Attributes of short linear motifs

(2011) Norman E. Davey et al.   Molecular BioSystems

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

A quantitative literature-curated gold standard for kinase-substrate pairs

(2011) Sara Sharifpoor et al.   GENOME BIOLOGY

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Global Analysis of the Mitochondrial N-Proteome Identifies a Processing Peptidase Critical for Protein Stability

(2009) F.-Nora Vögtle et al.   CELL

Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation

(2009) R. Narayanaswamy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Predicting PDZ domain–peptide interactions from primary sequences

(2008) Jiunn R Chen et al.   NATURE BIOTECHNOLOGY