Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance

Prospective identification of hematopoietic lineage choice by deep learning

(2017) Felix Buggenthin et al.   NATURE METHODS

Time series modeling of live-cell shape dynamics for image-based phenotypic profiling

(2016) Simon Gordonov et al.   Integrative Biology

Automated mapping of phenotype space with single-cell data

(2016) Nikolay Samusik et al.   NATURE METHODS

Broken detailed balance at mesoscopic scales in active biological systems

(2016) Christopher Battle et al.   SCIENCE

Satellite Cell Heterogeneity in Skeletal Muscle Homeostasis

(2016) Matthew T. Tierney et al.   TRENDS IN CELL BIOLOGY

Migration Phenotype of Brain-Cancer Cells Predicts Patient Outcomes

(2016) Chris L. Smith et al.   Cell Reports

A generic methodological framework for studying single cell motility in high-throughput time-lapse data

(2015) Alice Schoenauer Sebag et al.   BIOINFORMATICS

Differential Requirements for eIF4E Dose in Normal Development and Cancer

(2015) Morgan L. Truitt et al.   CELL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Joint modeling of cell and nuclear shape variation

(2015) Gregory R. Johnson et al.   MOLECULAR BIOLOGY OF THE CELL

Apolar and polar transitions drive the conversion between amoeboid and mesenchymal shapes in melanoma cells

(2015) Sam Cooper et al.   MOLECULAR BIOLOGY OF THE CELL

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Somatic stem cell heterogeneity: diversity in the blood, skin and intestinal stem cell compartments

(2015) Margaret A. Goodell et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

(2015) Malika Charrad et al.   Journal of Statistical Software

Cell-State-Specific Metabolic Dependency in Hematopoiesis and Leukemogenesis

(2014) Ying-Hua Wang et al.   CELL

Early forming label-retaining muscle stem cells require p27kip1 for maintenance of the primitive state

(2014) J. V. Chakkalakal et al.   DEVELOPMENT

Wnt7a stimulates myogenic stem cell motility and engraftment resulting in improved muscle strength

(2014) C. Florian Bentzinger et al.   JOURNAL OF CELL BIOLOGY

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

mTORC1 controls the adaptive transition of quiescent stem cells from G0 to GAlert

(2014) Joseph T. Rodgers et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Quantitative and unbiased analysis of directional persistence in cell migration

(2014) Roman Gorelik et al.   Nature Protocols

Remodelling the extracellular matrix in development and disease

(2014) Caroline Bonnans et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Plasticity in the Macromolecular-Scale Causal Networks of Cell Migration

(2014) John G. Lock et al.   PLoS One

The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity

(2013) Bradley R. Parry et al.   CELL

Tumour heterogeneity and cancer cell plasticity

(2013) Corbin E. Meacham et al.   NATURE

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes

(2013) Zheng Yin et al.   NATURE CELL BIOLOGY

Automated Cell Tracking and Analysis in Phase-Contrast Videos (iTrack4U): Development of Java Software Based on Combined Mean-Shift Processes

(2013) Fabrice P. Cordelières et al.   PLoS One

c-MET Regulates Myoblast Motility and Myocyte Fusion during Adult Skeletal Muscle Regeneration

(2013) Micah T. Webster et al.   PLoS One

Time-coordinated prevalence of extracellular HGF, FGF2 and TGF-β3 in crush-injured skeletal muscle

(2012) Mai-Khoi Q. DO et al.   ANIMAL SCIENCE JOURNAL

Tissue-Specific Stem Cells: Lessons from the Skeletal Muscle Satellite Cell

(2012) Andrew S. Brack et al.   Cell Stem Cell

Hematopoietic Stem Cell Heterogeneity Takes Center Stage

(2012) Michael R. Copley et al.   Cell Stem Cell

PhenoRipper: software for rapidly profiling microscopy images

(2012) Satwik Rajaram et al.   NATURE METHODS

Revisiting detrended fluctuation analysis

(2012) R. M. Bryce et al.   Scientific Reports

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?

(2011) Sui Huang   BIOESSAYS

Satellite cells, the engines of muscle repair

(2011) Yu Xin Wang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Sprouty1 Regulates Reversible Quiescence of a Self-Renewing Adult Muscle Stem Cell Pool during Regeneration

(2010) Kelly L. Shea et al.   Cell Stem Cell

Epithelial and mesenchymal phenotypic switchings modulate cell motility in metastasis

(2010) Alan Wells   Frontiers in Bioscience-Landmark

Environmental context explains Lévy and Brownian movement patterns of marine predators

(2010) Nicolas E. Humphries et al.   NATURE

Computational prediction of neural progenitor cell fates

(2010) Andrew R Cohen et al.   NATURE METHODS

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging

(2010) Michael Held et al.   NATURE METHODS

Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning

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

3D Timelapse Analysis of Muscle Satellite Cell Motility

(2009) Ashley L. Siegel et al.   STEM CELLS

CellTrack: an open-source software for cell tracking and motility analysis

(2008) A. Sacan et al.   BIOINFORMATICS

Stem Cell Trafficking in Tissue Development, Growth, and Disease

(2008) Diana J. Laird et al.   CELL

Regulation of Myoblast Motility and Fusion by the CXCR4-associated Sialomucin, CD164

(2008) Gyu-Un Bae et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanism of shape determination in motile cells

(2008) Kinneret Keren et al.   NATURE

Robust single-particle tracking in live-cell time-lapse sequences

(2008) Khuloud Jaqaman et al.   NATURE METHODS

Lévy flights and superdiffusion in the context of biological encounters and random searches

(2008) G.M. Viswanathan et al.   Physics of Life Reviews