Memorizing environmental signals through feedback and feedforward loops

Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression

(2020) Supriya Sen et al.   Cell Systems

A protein kinase A–regulated network encodes short- and long-lived cellular memories

(2020) Yanfei Jiang et al.   Science Signaling

Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction

(2020) Frédérique Kok et al.   Molecular Systems Biology

It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology

(2020) Niklas Korsbo et al.   PLoS Computational Biology

Cell-cycle-gated feedback control mediates desensitization to interferon stimulation

(2020) Anusorn Mudla et al.   eLife

GPCR Signaling Regulation: The Role of GRKs and Arrestins

(2019) Vsevolod V. Gurevich et al.   Frontiers in Pharmacology

Feedback inhibition of cAMP effector signaling by a chaperone-assisted ubiquitin system

(2019) Laura Rinaldi et al.   Nature Communications

Techniques for Studying Decoding of Single Cell Dynamics

(2019) Stevan Jeknić et al.   Frontiers in Immunology

Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae

(2019) Alan K. Itakura et al.   MOLECULAR CELL

A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program

(2019) Anupam K. Chakravarty et al.   MOLECULAR CELL

Phase separation of a yeast prion protein promotes cellular fitness

(2018) Titus M. Franzmann et al.   SCIENCE

A semi-synthetic regulon enables rapid growth of yeast on xylose

(2018) Venkatesh Endalur Gopinarayanan et al.   Nature Communications

A kinase-dependent feedforward loop affects CREBB stability and long term memory formation

(2018) Pei-Tseng Lee et al.   eLife

Modeling Cell-to-Cell Communication Networks Using Response-Time Distributions

(2018) Kevin Thurley et al.   Cell Systems

Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli

(2018) Elliot Dine et al.   Cell Systems

Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation

(2018) Ruby Yu et al.   NATURE

Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability

(2018) Nahid Iglesias et al.   NATURE

Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia coli cells

(2018) Sander K. Govers et al.   PLOS BIOLOGY

Correction: Context-dependent deposition and regulation of mRNAs in P-bodies

(2018) Congwei Wang et al.   eLife

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

(2018) Minhee Park et al.   CELL

Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources

(2018) Bram Cerulus et al.   eLife

Increased heme synthesis in yeast induces a metabolic switch from fermentation to respiration even under conditions of glucose repression

(2017) Tiantian Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

STAT2 is an essential adaptor in USP18-mediated suppression of type I interferon signaling

(2017) Kei-ichiro Arimoto et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STAT2 is an essential adaptor in USP18-mediated suppression of type I interferon signaling

(2017) Kei-ichiro Arimoto et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Yeast Short-Lived Actin-Associated Protein Forms a Metastable Prion in Response to Thermal Stress

(2017) Tatiana A. Chernova et al.   Cell Reports

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination

(2017) Fuqing Wu et al.   eLife

Linear models of activation cascades: analytical solutions and coarse-graining of delayed signal transduction

(2016) Mariano Beguerisse-Díaz et al.   Journal of the Royal Society Interface

Dynamic control of gene regulatory logic by seemingly redundant transcription factors

(2016) Zohreh AkhavanAghdam et al.   eLife

The interplay of histone modifications - writers that read

(2015) T. Zhang et al.   EMBO REPORTS

cis Determinants of Promoter Threshold and Activation Timescale

(2015) Anders S. Hansen et al.   Cell Reports

Interferon-Stimulated Genes: A Complex Web of Host Defenses

(2014) William M. Schneider et al.   Annual Review of Immunology

A Brief History of G-Protein Coupled Receptors (Nobel Lecture)

(2013) Robert J. Lefkowitz   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Super-Assembly of Whi3 Encodes Memory of Deceptive Encounters by Single Cells during Yeast Courtship

(2013) Fabrice Caudron et al.   CELL

IFNβ-dependent increases in STAT1, STAT2, and IRF9 mediate resistance to viruses and DNA damage

(2013) HyeonJoo Cheon et al.   EMBO JOURNAL

P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA Degradation

(2012) C. J. Decker et al.   Cold Spring Harbor Perspectives in Biology

Decision Making in Living Cells: Lessons from a Simple System

(2011) Ido Golding   Annual Review of Biophysics

Mechanisms for the Inheritance of Chromatin States

(2011) Danesh Moazed   CELL

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

(2011) L. T. MacNeil et al.   GENOME RESEARCH

Signal-dependent dynamics of transcription factor translocation controls gene expression

(2011) Nan Hao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Making Cellular Memories

(2010) Devin R. Burrill et al.   CELL

Bistable switches control memory and plasticity in cellular differentiation

(2009) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positive feedback in cellular control systems

(2008) Alexander Y. Mitrophanov et al.   BIOESSAYS

Multistable Decision Switches for Flexible Control of Epigenetic Differentiation

(2008) Raúl Guantes et al.   PLoS Computational Biology