Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning

Hallmarks of Cancer: New Dimensions

(2022) Douglas Hanahan   Cancer Discovery

2-Hydroxyglutarate destabilizes chromatin regulatory landscape and lineage fidelity to promote cellular heterogeneity

(2022) Meena Kusi et al.   Cell Reports

Multiscale PHATE identifies multimodal signatures of COVID-19

(2022) Manik Kuchroo et al.   NATURE BIOTECHNOLOGY

Functional antagonism of chromatin modulators regulates epithelial-mesenchymal transition

(2021) Michela Serresi et al.   Science Advances

Computational principles and challenges in single-cell data integration

(2021) Ricard Argelaguet et al.   NATURE BIOTECHNOLOGY

Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states

(2021) Kamen P. Simeonov et al.   CANCER CELL

Cycling cancer persister cells arise from lineages with distinct programs

(2021) Yaara Oren et al.   NATURE

Tumor Immunology and Tumor Evolution: Intertwined Histories

(2020) Jérôme Galon et al.   IMMUNITY

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Proline Metabolism in Tumor Growth and Metastatic Progression

(2020) Cristina D'Aniello et al.   Frontiers in Oncology

Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma

(2020) Lindsay M. LaFave et al.   CANCER CELL

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

(2020) Nemanja Despot Marjanovic et al.   CANCER CELL

How Tumor Cell Dedifferentiation Drives Immune Evasion And Resistance to Immunotherapy

(2020) Jinyang Li et al.   CANCER RESEARCH

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

CD44 regulates epigenetic plasticity by mediating iron endocytosis

(2020) Sebastian Müller et al.   Nature Chemistry

Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment

(2020) Mélanie A. Eckersley-Maslin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition

(2020) Bryan Ngo et al.   Cancer Discovery

Continuum of Gene-Expression Profiles Provides Spatial Division of Labor within a Differentiated Cell Type

(2019) Miri Adler et al.   Cell Systems

Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells

(2019) Cornelia Kröger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breast cancer cells rely on environmental pyruvate to shape the metastatic niche

(2019) Ilaria Elia et al.   NATURE

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

A Niche-Dependent Myeloid Transcriptome Signature Defines Dormant Myeloma Cells

(2019) Weng Hua Khoo et al.   BLOOD

Wild type- and mutant p53 proteins in mitochondrial dysfunction: emerging insights in cancer disease

(2019) Giovanni Blandino et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

The pan-therapeutic resistance of disseminated tumor cells: Role of phenotypic plasticity and the metastatic microenvironment

(2019) Bo Ma et al.   SEMINARS IN CANCER BIOLOGY

Chemical biology approaches targeting the actin cytoskeleton through phenotypic screening

(2019) Nicole S Bryce et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Targeting tumor phenotypic plasticity and metabolic remodeling in adaptive cross-drug tolerance

(2019) Aaron Goldman et al.   Science Signaling

Clinical Evolution of Epithelial-Mesenchymal Transition in Human Carcinomas

(2019) Tony Navas et al.   CANCER RESEARCH

Exploring single-cell data with deep multitasking neural networks

(2019) Matthew Amodio et al.   NATURE METHODS

The great escape: tumour cell plasticity in resistance to targeted therapy

(2019) Soufiane Boumahdi et al.   NATURE REVIEWS DRUG DISCOVERY

Metabolic functions of the tumor suppressor p53: Implications in normal physiology, metabolic disorders, and cancer

(2019) Matthieu Lacroix et al.   Molecular Metabolism

High-Content Imaging of Unbiased Chemical Perturbations Reveals that the Phenotypic Plasticity of the Actin Cytoskeleton Is Constrained

(2019) Nicole S. Bryce et al.   Cell Systems

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Toward Minimal Residual Disease-Directed Therapy in Melanoma

(2018) Florian Rambow et al.   CELL

The Kraken Wakes: induced EMT as a driver of tumour aggression and poor outcome

(2018) Andrew D. Redfern et al.   CLINICAL & EXPERIMENTAL METASTASIS

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Identification of the tumour transition states occurring during EMT

(2018) Ievgenia Pastushenko et al.   NATURE

IL-1β inflammatory response driven by primary breast cancer prevents metastasis-initiating cell colonization

(2018) Zafira Castaño et al.   NATURE CELL BIOLOGY

Hybrid epithelial/mesenchymal phenotypes promote metastasis and therapy resistance across carcinomas

(2018) Mohit Kumar Jolly et al.   PHARMACOLOGY & THERAPEUTICS

Tumor cell escape from therapy-induced senescence

(2018) Tareq Saleh et al.   BIOCHEMICAL PHARMACOLOGY

Mesenchymal–epithelial transition in development and reprogramming

(2018) Duanqing Pei et al.   NATURE CELL BIOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Tumour microenvironment and metabolic plasticity in cancer and cancer stem cells: Perspectives on metabolic and immune regulatory signatures in chemoresistant ovarian cancer stem cells

(2018) Nuzhat Ahmed et al.   SEMINARS IN CANCER BIOLOGY

Hysteresis control of epithelial-mesenchymal transition dynamics conveys a distinct program with enhanced metastatic ability

(2018) Toni Celià-Terrassa et al.   Nature Communications

VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder

(2018) Dongfang Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Senescence-associated reprogramming promotes cancer stemness

(2017) Maja Milanovic et al.   NATURE

A stemness-related ZEB1–MSRB3 axis governs cellular pliancy and breast cancer genome stability

(2017) Anne-Pierre Morel et al.   NATURE MEDICINE

EMT, CSCs, and drug resistance: the mechanistic link and clinical implications

(2017) Tsukasa Shibue et al.   Nature Reviews Clinical Oncology

Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance

(2017) Yapeng Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrin-β4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells

(2017) Brian Bierie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

The immune checkpoint ligand PD-L1 is upregulated in EMT-activated human breast cancer cells by a mechanism involving ZEB-1 and miR-200

(2017) Muhammad Zaeem Noman et al.   OncoImmunology

EMT: 2016

(2016) M. Angela Nieto et al.   CELL

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data

(2016) Walid M. Abdelmoula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability

(2016) D. R. Pattabiraman et al.   SCIENCE

Breast Cancer-Derived Lung Metastases Show Increased Pyruvate Carboxylase-Dependent Anaplerosis

(2016) Stefan Christen et al.   Cell Reports

Non-monotonic cellular responses to heterogeneity in talin protein expression-level

(2015) Alexa Kiss et al.   Integrative Biology

Reactivation of multipotency by oncogenic PIK3CA induces breast tumour heterogeneity

(2015) Alexandra Van Keymeulen et al.   NATURE

PIK3CAH1047R induces multipotency and multi-lineage mammary tumours

(2015) Shany Koren et al.   NATURE

Exploration versus exploitation in space, mind, and society

(2015) Thomas T. Hills et al.   TRENDS IN COGNITIVE SCIENCES

Evolutionary Determinants of Cancer

(2015) M. Greaves   Cancer Discovery

Stem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation

(2015) Johanna M. Schmidt et al.   Cell Reports

Geometry of the Gene Expression Space of Individual Cells

(2015) Yael Korem et al.   PLoS Computational Biology

Disentangling Membrane Dynamics and Cell Migration; Differential Influences of F-actin and Cell-Matrix Adhesions

(2015) Jacob M. Kowalewski et al.   PLoS One

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Evolution of the Cancer Stem Cell Model

(2014) Antonija Kreso et al.   Cell Stem Cell

Noise Genetics: Inferring Protein Function by Correlating Phenotype with Protein Levels and Localization in Individual Human Cells

(2014) Shlomit Farkash-Amar et al.   PLoS Genetics

Poised Chromatin at the ZEB1 Promoter Enables Breast Cancer Cell Plasticity and Enhances Tumorigenicity

(2013) Christine L. Chaffer et al.   CELL

The epigenetics of epithelial-mesenchymal plasticity in cancer

(2013) Wai Leong Tam et al.   NATURE MEDICINE

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

Accessories to the Crime: Functions of Cells Recruited to the Tumor Microenvironment

(2012) Douglas Hanahan et al.   CANCER CELL

Metastatic Colonization Requires the Repression of the Epithelial-Mesenchymal Transition Inducer Prrx1

(2012) Oscar H. Ocaña et al.   CANCER CELL

Intratumor Heterogeneity: Evolution through Space and Time

(2012) C. Swanton   CANCER RESEARCH

Intestinal Tumorigenesis Initiated by Dedifferentiation and Acquisition of Stem-Cell-like Properties

(2012) Sarah Schwitalla et al.   CELL

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

(2012) Sohrab P. Shah et al.   NATURE

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

Intratumor Heterogeneity: Seeing the Wood for the Trees

(2012) T. A. Yap et al.   Science Translational Medicine

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

(2011) Sui Huang   BIOESSAYS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Normal and neoplastic nonstem cells can spontaneously convert to a stem-like state

(2011) C. L. Chaffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium

(2011) Reo Maruyama et al.   PLoS Genetics

A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth

(2010) Alexander Roesch et al.   CELL

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

Epithelial-Mesenchymal Transitions in Development and Disease

(2009) Jean Paul Thiery et al.   CELL

The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem Cells

(2008) Sendurai A. Mani et al.   CELL

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Polycomb Complex 2 Is Required for E-cadherin Repression by the Snail1 Transcription Factor

(2008) N. Herranz et al.   MOLECULAR AND CELLULAR BIOLOGY