Pheno-seq – linking visual features and gene expression in 3D cell culture systems

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Self-organization and symmetry breaking in intestinal organoid development

(2019) Denise Serra et al.   NATURE

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity

(2018) Norman Sachs et al.   CELL

Human Pancreatic Tumor Organoids Reveal Loss of Stem Cell Niche Factor Dependence during Disease Progression

(2018) Takashi Seino et al.   Cell Stem Cell

A practical solution for preserving single cells for RNA sequencing

(2018) Moustafa Attar et al.   Scientific Reports

Automated brightfield morphometry of 3D organoid populations by OrganoSeg

(2018) Michael A. Borten et al.   Scientific Reports

Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer

(2017) Klara M. Giessler et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Expansion of patient-derived circulating tumor cells from liquid biopsies using a CTC microfluidic culture device

(2017) Bee Luan Khoo et al.   Nature Protocols

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer

(2017) Ruli Gao et al.   Nature Communications

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

(2017) Karsten Bach et al.   Nature Communications

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

(2016) Charles Girardot et al.   BMC BIOINFORMATICS

Intratumoral Heterogeneity of the Epigenome

(2016) Tali Mazor et al.   CANCER CELL

Organoids as an in vitro model of human development and disease

(2016) Aliya Fatehullah et al.   NATURE CELL BIOLOGY

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

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

(2016) P. L. Stahl et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

Targeting Notch, Hedgehog and Wnt pathways in cancer stem cells: clinical update

(2015) Naoko Takebe et al.   Nature Reviews Clinical Oncology

Epithelial–Mesenchymal Plasticity: A Central Regulator of Cancer Progression

(2015) Xin Ye et al.   TRENDS IN CELL BIOLOGY

Spherical Cancer Models in Tumor Biology

(2015) Louis-Bastien Weiswald et al.   NEOPLASIA

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

(2014) Sameer S. Bajikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) A. P. Patel et al.   SCIENCE

Prox1 Promotes Expansion of the Colorectal Cancer Stem Cell Population to Fuel Tumor Growth and Ischemia Resistance

(2014) Zoltán Wiener et al.   Cell Reports

PROX1 Promotes Metabolic Adaptation and Fuels Outgrowth of Wnt high Metastatic Colon Cancer Cells

(2014) Simone Ragusa et al.   Cell Reports

Epithelial-mesenchymal plasticity in carcinoma metastasis

(2013) J. H. Tsai et al.   GENES & DEVELOPMENT

Tumour heterogeneity in the clinic

(2013) Philippe L. Bedard et al.   NATURE

Influence of tumour micro-environment heterogeneity on therapeutic response

(2013) Melissa R. Junttila et al.   NATURE

Distinct Types of Tumor-Initiating Cells Form Human Colon Cancer Tumors and Metastases

(2011) Sebastian M. Dieter et al.   Cell Stem Cell

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Cytogenetic and cDNA Microarray Expression Analysis of MCF10 Human Breast Cancer Progression Cell Lines

(2009) N. V. Marella et al.   CANCER RESEARCH