Signalling dynamics, cell decisions, and homeostatic control in health and disease

The distribution of cellular turnover in the human body

(2021) Ron Sender et al.   NATURE MEDICINE

A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch

(2021) Hélène Duplus-Bottin et al.   eLife

CODEX, a neural network approach to explore signaling dynamics landscapes

(2021) Marc‐Antoine Jacques et al.   Molecular Systems Biology

Quantifying single-cell ERK dynamics in colorectal cancer organoids reveals EGFR as an amplifier of oncogenic MAPK pathway signalling

(2021) Bas Ponsioen et al.   NATURE CELL BIOLOGY

Single-Cell Biochemical Multiplexing by Multidimensional Phasor Demixing and Spectral Fluorescence Lifetime Imaging Microscopy

(2021) Kalina T. Haas et al.   Frontiers in Physics

A structural model of a Ras–Raf signalosome

(2021) Venkatesh P. Mysore et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cracking the context-specific PI3K signaling code

(2020) Ralitsa R. Madsen et al.   Science Signaling

Pulsatile MAPK Signaling Modulates p53 Activity to Control Cell Fate Decisions at the G2 Checkpoint for DNA Damage

(2020) Siddharth De et al.   Cell Reports

Temporal integration of mitogen history in mother cells controls proliferation of daughter cells

(2020) Mingwei Min et al.   SCIENCE

A Live-Cell Screen for Altered Erk Dynamics Reveals Principles of Proliferative Control

(2020) Alexander G. Goglia et al.   Cell Systems

An in vivo KRAS allelic series reveals distinct phenotypes of common oncogenic variants

(2020) Maria Paz Zafra et al.   Cancer Discovery

Systems-Level Properties of EGFR-RAS-ERK Signaling Amplify Local Signals to Generate Dynamic Gene Expression Heterogeneity

(2020) Alexander E. Davies et al.   Cell Systems

Seeing around corners: Cells solve mazes and respond at a distance using attractant breakdown

(2020) Luke Tweedy et al.   SCIENCE

MAPK activity dynamics regulate non-cell autonomous effects of oncogene expression

(2020) Timothy J Aikin et al.   eLife

CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images

(2020) Tao Hu et al.   BIOINFORMATICS

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

Tissue-specificity in cancer: The rule, not the exception

(2019) Kevin M. Haigis et al.   SCIENCE

Nuclear ERK: Mechanism of Translocation, Substrates, and Role in Cancer

(2019) Galia Maik-Rachline et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Fast single-cell biochemistry: theory, open source microscopy and applications

(2019) Andrew L Trinh et al.   Methods and Applications in Fluorescence

Mining single-cell time-series datasets with Time Course Inspector

(2019) Maciej Dobrzyński et al.   BIOINFORMATICS

Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling

(2019) Yannick Blum et al.   Molecular Systems Biology

CLIJ: GPU-accelerated image processing for everyone

(2019) Robert Haase et al.   NATURE METHODS

A Comparative Analysis of Individual RAS Mutations in Cancer Biology

(2019) Carmen Muñoz-Maldonado et al.   Frontiers in Oncology

Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation

(2018) Katharina F. Sonnen et al.   CELL

Dynamic Ligand Discrimination in the Notch Signaling Pathway

(2018) Nagarajan Nandagopal et al.   CELL

Integrated Platform for Monitoring Single-cell MAPK Kinetics in Computer-controlled Temporal Stimulations

(2018) Hyunryul Ryu et al.   Scientific Reports

Aging and the rise of somatic cancer-associated mutations in normal tissues

(2018) Rosa Ana Risques et al.   PLoS Genetics

Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks

(2018) Eric C. Greenwald et al.   CHEMICAL REVIEWS

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control

(2017) Maxwell Z. Wilson et al.   MOLECULAR CELL

An immediate–late gene expression module decodes ERK signal duration

(2017) Florian Uhlitz et al.   Molecular Systems Biology

A new online tool for visualization of volumetric data

(2017) Marcus Fantham et al.   Nature Photonics

Linear Integration of ERK Activity Predominates over Persistence Detection in Fra-1 Regulation

(2017) Taryn E. Gillies et al.   Cell Systems

Cell-to-Cell Variation in p53 Dynamics Leads to Fractional Killing

(2016) Andrew L. Paek et al.   CELL

Frequency modulation of ERK activation dynamics rewires cell fate

(2016) H. Ryu et al.   Molecular Systems Biology

A single dividing cell population with imbalanced fate drives oesophageal tumour growth

(2016) Julia Frede et al.   NATURE CELL BIOLOGY

Variation in KRAS driver substitution distributions between tumor types is determined by both mutation and natural selection

(2016) Sheli L. Ostrow et al.   Scientific Reports

Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway

(2016) Kazunari Iwamoto et al.   PLoS Computational Biology

Orchestration of ErbB3 signaling through heterointeractions and homointeractions

(2015) Meghan McCabe Pryor et al.   MOLECULAR BIOLOGY OF THE CELL

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features

(2015) Hirenkumar K. Makadia et al.   PLoS Computational Biology

Differentiation imbalance in single oesophageal progenitor cells causes clonal immortalization and field change

(2014) Maria P. Alcolea et al.   NATURE CELL BIOLOGY

Tumor heterogeneity and plasticity as elusive drivers for resistance to MAPK pathway inhibition in melanoma

(2014) A Roesch   ONCOGENE

Visualizing and Manipulating Temporal Signaling Dynamics with Fluorescence-Based Tools

(2014) D. P. Doupe et al.   Science Signaling

Cross Talk and Interference Enhance Information Capacity of a Signaling Pathway

(2013) Sahand Hormoz   BIOPHYSICAL JOURNAL

Encoding and Decoding Cellular Information through Signaling Dynamics

(2013) Jeremy E. Purvis et al.   CELL

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Frequency-Modulated Pulses of ERK Activity Transmit Quantitative Proliferation Signals

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

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

Two Phases of Mitogenic Signaling Unveil Roles for p53 and EGR1 in Elimination of Inconsistent Growth Signals

(2011) Yaara Zwang et al.   MOLECULAR CELL

Stimulus-dependent dynamics of p53 in single cells

(2011) E. Batchelor et al.   Molecular Systems Biology

High-resolution dose-response screening using droplet-based microfluidics

(2011) O. J. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Basal Dynamics of p53 Reveal Transcriptionally Attenuated Pulses in Cycling Cells

(2010) Alexander Loewer et al.   CELL

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

Dynamics and Variability of ERK2 Response to EGF in Individual Living Cells

(2009) Cellina Cohen-Saidon et al.   MOLECULAR CELL

Rapid and sustained nuclear–cytoplasmic ERK oscillations induced by epidermal growth factor

(2009) Harish Shankaran et al.   Molecular Systems Biology

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

The epidermal growth factor receptor family: Biology driving targeted therapeutics

(2008) M. J. Wieduwilt et al.   CELLULAR AND MOLECULAR LIFE SCIENCES