Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome

Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy

(2016) Madhusudhanan Sukumar et al.   Cell Metabolism

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia

(2016) Sheng Li et al.   NATURE MEDICINE

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

(2016) Florian Schmidt et al.   NUCLEIC ACIDS RESEARCH

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Energy metabolism in the acquisition and maintenance of stemness

(2016) Clifford D.L. Folmes et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development

(2016) Jinmiao Chen et al.   Nature Communications

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process

(2016) Angélique Richard et al.   PLOS BIOLOGY

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Global variability in gene expression and alternative splicing is modulated by mitochondrial content

(2015) Raul Guantes et al.   GENOME RESEARCH

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

Comparing the performance of biomedical clustering methods

(2015) Christian Wiwie et al.   NATURE METHODS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance

(2015) D. T. Miyamoto et al.   SCIENCE

Connecting Mitochondria, Metabolism, and Stem Cell Fate

(2015) Anaïs Wanet et al.   STEM CELLS AND DEVELOPMENT

Increased signaling entropy in cancer requires the scale-free property of protein interaction networks

(2015) Andrew E. Teschendorff et al.   Scientific Reports

Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis

(2015) Cristina Pina et al.   Cell Reports

Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer

(2015) Christopher R. S. Banerji et al.   PLoS Computational Biology

Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data

(2014) Andrew E. Teschendorff et al.   METHODS

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein 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

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical Mechanics of Pluripotency

(2013) Ben D. MacArthur et al.   CELL

Network link prediction by global silencing of indirect correlations

(2013) Baruch Barzel et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cellular network entropy as the energy potential in Waddington's differentiation landscape

(2013) Christopher R. S. Banerji et al.   Scientific Reports

Inferring rules of lineage commitment in haematopoiesis

(2012) Cristina Pina et al.   NATURE CELL BIOLOGY

Mitochondrial Variability as a Source of Extrinsic Cellular Noise

(2012) Iain G. Johnston et al.   PLoS Computational Biology

A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers

(2012) Nathan P Palmer et al.   GENOME BIOLOGY

Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Endothelial cell plasticity: how to become and remain a lymphatic endothelial cell

(2010) G. Oliver et al.   DEVELOPMENT

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Connecting Variability in Global Transcription Rate to Mitochondrial Variability

(2010) Ricardo Pires das Neves et al.   PLOS BIOLOGY

An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer

(2009) Andrew E. Teschendorff et al.   PLoS One

Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

(2009) Tibor Kalmar et al.   PLOS BIOLOGY

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'

(2008) Alexandre Kuhn et al.   BMC BIOINFORMATICS

Mitochondrial Metabolism Modulates Differentiation and Teratoma Formation Capacity in Mouse Embryonic Stem Cells

(2008) Stefan M. Schieke et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Entropy rate of diffusion processes on complex networks

(2008) Jesús Gómez-Gardeñes et al.   PHYSICAL REVIEW E