The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile

Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing

(2020) Ryan T. Davis et al.   NATURE CELL BIOLOGY

Intratumor Heterogeneity: The Rosetta Stone of Therapy Resistance

(2020) Andriy Marusyk et al.   CANCER CELL

Targeting triple-negative breast cancers with the Smac-mimetic birinapant

(2020) Najoua Lalaoui et al.   CELL DEATH AND DIFFERENTIATION

Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases

(2020) Zheng Hu et al.   NATURE GENETICS

Multi-color clonal tracking reveals intra-stage proliferative heterogeneity during mammary tumor progression

(2020) Stefanie Tiede et al.   ONCOGENE

Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer

(2019) D. Merino et al.   Nature Communications

Spatiotemporal regulation of clonogenicity in colorectal cancer xenografts

(2019) Maartje van der Heijden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments

(2019) Michalina Janiszewska et al.   NATURE CELL BIOLOGY

Inhibition of tumour necrosis factor alpha in the R6/2 mouse model of Huntington’s disease by etanercept treatment

(2019) Jeffrey Pido-Lopez et al.   Scientific Reports

The TNF Paradox in Cancer Progression and Immunotherapy

(2019) Anne Montfort et al.   Frontiers in Immunology

The Complexities of Metastasis

(2019) San Juan et al.   Cancers

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

(2018) Anna K. Casasent et al.   CELL

Shared-nearest-neighbor-based clustering by fast search and find of density peaks

(2018) Rui Liu et al.   INFORMATION SCIENCES

A Spatio-Temporal Model and Inference Tools for Longitudinal Count Data on Multicolor Cell Growth

(2018) PuXue Qiao et al.  

Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer

(2018) Marni B. Siegel et al.   JOURNAL OF CLINICAL INVESTIGATION

Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity

(2018) Quy H. Nguyen et al.   Nature Communications

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer

(2018) Gloria V. Echeverria et al.   Nature Communications

Cellular Barcoding Identifies Clonal Substitution as a Hallmark of Local Recurrence in a Surgical Model of Head and Neck Squamous Cell Carcinoma

(2018) Vincent Roh et al.   Cell Reports

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Optical Barcoding for Single-Clone Tracking to Study Tumor Heterogeneity

(2017) Malte Mohme et al.   MOLECULAR THERAPY

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters

(2016) Kevin J. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Semisupervised Clustering by Iterative Partition and Regression with Neuroscience Applications

(2016) Guoqi Qian et al.   Computational Intelligence and Neuroscience

PDK1-Dependent Metabolic Reprogramming Dictates Metastatic Potential in Breast Cancer

(2015) Fanny Dupuy et al.   Cell Metabolism

Tumor necrosis factor, tumor necrosis factor inhibition, and cancer risk

(2015) Hervé Lebrec et al.   CURRENT MEDICAL RESEARCH AND OPINION

Emerging roles for IL-11 signaling in cancer development and progression: Focus on breast cancer

(2015) Cameron N. Johnstone et al.   CYTOKINE & GROWTH FACTOR REVIEWS

A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis

(2015) Elvin Wagenblast et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis

(2014) Nicola Aceto et al.   CELL

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity

(2014) Andriy Marusyk et al.   NATURE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts

(2014) Long V. Nguyen et al.   Nature Communications

In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

(2014) Daniela Malide et al.   Jove-Journal of Visualized Experiments

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization

(2013) Jean Ollion et al.   BIOINFORMATICS

Analysis of pattern, time and risk factors influencing recurrence in triple-negative breast cancer patients

(2013) Katarzyna Pogoda et al.   MEDICAL ONCOLOGY

Selection and adaptation during metastatic cancer progression

(2013) Christoph A. Klein   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Measurement of Cancer Cell Growth Heterogeneity through Lentiviral Barcoding Identifies Clonal Dominance as a Characteristic of In Vivo Tumor Engraftment

(2013) Olivier Nolan-Stevaux et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Clinical Significance and Molecular Characteristics of Circulating Tumor Cells and Circulating Tumor Microemboli in Patients With Small-Cell Lung Cancer

(2012) Jian-Mei Hou et al.   JOURNAL OF CLINICAL ONCOLOGY

OMERO: flexible, model-driven data management for experimental biology

(2012) Chris Allan et al.   NATURE METHODS

RGB marking with lentiviral vectors for multicolor clonal cell tracking

(2012) Kristoffer Weber et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

RGB marking facilitates multicolor clonal cell tracking

(2011) Kristoffer Weber et al.   NATURE MEDICINE

Rapid Extravasation and Establishment of Breast Cancer Micrometastases in the Liver Microenvironment

(2010) Michelle D. Martin et al.   MOLECULAR CANCER RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Tumor Self-Seeding by Circulating Cancer Cells

(2009) Mi-Young Kim et al.   CELL

Response to Neoadjuvant Therapy and Long-Term Survival in Patients With Triple-Negative Breast Cancer

(2008) Cornelia Liedtke et al.   JOURNAL OF CLINICAL ONCOLOGY

A Multicolor Panel of Novel Lentiviral “Gene Ontology” (LeGO) Vectors for Functional Gene Analysis

(2008) Kristoffer Weber et al.   MOLECULAR THERAPY