A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling

Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics

(2020) Susan Y. Chen et al.   Cell Systems

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

(2019) Alex X Lu et al.   BIOINFORMATICS

Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships

(2019) Christopher M. Jakobson et al.   Cell Systems

Entropy and Information within Intrinsically Disordered Protein Regions

(2019) Iva Pritišanac et al.   Entropy

Predicting microbial growth in a mixed culture from growth curve data

(2019) Yoav Ram et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis

(2019) Cerys S. Manning et al.   Nature Communications

Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads

(2019) Huy Quoc Nguyen et al.   eLife

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

(2019) Taraneh Zarin et al.   eLife

Dynamic Ligand Discrimination in the Notch Signaling Pathway

(2018) Nagarajan Nandagopal et al.   CELL

PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants

(2018) Izabella Krystkowiak et al.   NUCLEIC ACIDS RESEARCH

15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins

(2018) Sandeep Chhabra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins

(2018) Mohanalakshmi Narasumani et al.   PLoS Computational Biology

The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins

(2018) Yixun Li et al.   BMC BIOINFORMATICS

Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation

(2018) Neel H. Shah et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

A Noisy Analog-to-Digital Converter Connects Cytosolic Calcium Bursts to Transcription Factor Nuclear Localization Pulses in Yeast

(2018) Ian S. Hsu et al.   G3-Genes Genomes Genetics

Sexual pheromone modulates the frequency of cytosolic Ca2+ bursts in Saccharomyces cerevisiae

(2017) Natalia Carbó et al.   MOLECULAR BIOLOGY OF THE CELL

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

Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes

(2017) Nick E. Phillips et al.   PLoS Computational Biology

Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans

(2017) Eve W. L. Chow et al.   PLoS Genetics

Conservation and Divergence of p53 Oscillation Dynamics across Species

(2017) Jacob Stewart-Ornstein et al.   Cell Systems

Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast

(2016) K. Chatfield-Reed et al.   GENETICS

Evolution of protein phosphorylation across 18 fungal species

(2016) R. A. Studer et al.   SCIENCE

Inferring time derivatives including cell growth rates using Gaussian processes

(2016) Peter S. Swain et al.   Nature Communications

Short linear motifs – ex nihilo evolution of protein regulation

(2015) Norman E. Davey et al.   Cell Communication and Signaling

Combinatorial gene regulation by modulation of relative pulse timing

(2015) Yihan Lin et al.   NATURE

Limits on information transduction through amplitude and frequency regulation of transcription factor activity

(2015) Anders S Hansen et al.   eLife

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

(2014) David T. Jones et al.   BIOINFORMATICS

Calcineurin-Crz1 Signaling in Lower Eukaryotes

(2014) S. Thewes   EUKARYOTIC CELL

The Calcineurin Signaling Network Evolves via Conserved Kinase-Phosphatase Modules that Transcend Substrate Identity

(2014) Aaron Goldman et al.   MOLECULAR CELL

Accurate information transmission through dynamic biochemical signaling networks

(2014) J. Selimkhanov et al.   SCIENCE

Turnover of protein phosphorylation evolving under stabilizing selection

(2014) Christian R. Landry et al.   Frontiers in Genetics

Evolution and functional cross-talk of protein post-translational modifications

(2013) Pedro Beltrao et al.   Molecular Systems Biology

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

The Yeast Transcription Factor Crz1 Is Activated by Light in a Ca2+/Calcineurin-Dependent and PKA-Independent Manner

(2013) Kristofer Bodvard et al.   PLoS One

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin

(2013) Simina Grigoriu et al.   PLOS BIOLOGY

Dynamic Response Diversity of NFAT Isoforms in Individual Living Cells

(2012) Nissan Yissachar et al.   MOLECULAR CELL

Frequency-Modulated Pulses of ERK Activity Transmit Quantitative Proliferation Signals

(2012) John G. Albeck et al.   MOLECULAR CELL

D2P2: database of disordered protein predictions

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

The Crz1/Sp1 Transcription Factor of Cryptococcus neoformans Is Activated by Calcineurin and Regulates Cell Wall Integrity

(2012) Sophie Lev et al.   PLoS One

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial aspects of intracellular information processing

(2010) Ali Kinkhabwala et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Interaction of calcineurin with substrates and targeting proteins

(2010) Huiming Li et al.   TRENDS IN CELL BIOLOGY

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

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

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators

(2009) Lin Tian et al.   NATURE METHODS

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome

(2008) David K Breslow et al.   NATURE METHODS