Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

(2021) Jeffrey J. Quinn et al.   SCIENCE

Global computational alignment of tumor and cell line transcriptional profiles

(2021) Allison Warren et al.   Nature Communications

Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing

(2021) Yael C. Cohen et al.   NATURE MEDICINE

bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses

(2021) Luis García-Jimeno et al.   BIOINFORMATICS

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient

(2020) Hye Won Lee et al.   Genome Medicine

DREIMT: a drug repositioning database and prioritization tool for immunomodulation

(2020) Kevin Troulé et al.   BIOINFORMATICS

Targeting Epidermal Growth Factor Receptor (EGFR) and Human Epidermal Growth Factor Receptor 2 (HER2) Expressing Bladder Cancer Using Combination Photoimmunotherapy (PIT)

(2019) Mohammad R. Siddiqui et al.   Scientific Reports

Resolving genetic heterogeneity in cancer

(2019) Samra Turajlic et al.   NATURE REVIEWS GENETICS

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges

(2019) Mario L. Suvà et al.   MOLECULAR CELL

A Pharmacogenomic Landscape in Human Liver Cancers

(2019) Zhixin Qiu et al.   CANCER CELL

In Silico Drug Prescription for Targeting Cancer Patient Heterogeneity and Prediction of Clinical Outcome

(2019) Elena Piñeiro-Yáñez et al.   Cancers

Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor-resistant HER2-positive breast cancer

(2019) Qingfei Wang et al.   Nature Communications

Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors

(2019) Anchal Sharma et al.   Cell Reports

Encorafenib plus binimetinib versus vemurafenib or encorafenib in patients with BRAF -mutant melanoma (COLUMBUS): a multicentre, open-label, randomised phase 3 trial

(2018) Reinhard Dummer et al.   LANCET ONCOLOGY

Concomitant attenuation of HMG-CoA reductase expression potentiates the cancer cell growth-inhibitory effect of statins and expands their efficacy in tumor cells with epithelial characteristics

(2018) Takuro Ishikawa et al.   Oncotarget

Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations

(2018) Yu-Jui Ho et al.   GENOME RESEARCH

Clonal heterogeneity influences drug responsiveness in renal cancer assessed by ex vivo drug testing of multiple patient-derived cancer cells

(2018) Khalid Saeed et al.   INTERNATIONAL JOURNAL OF CANCER

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Identification of the tumour transition states occurring during EMT

(2018) Ievgenia Pastushenko et al.   NATURE

Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics

(2018) Xiaodun Li et al.   Nature Communications

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

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

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

An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules

(2013) Amrita Basu et al.   CELL

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Proteomic Profiling Identifies Dysregulated Pathways in Small Cell Lung Cancer and Novel Therapeutic Targets Including PARP1

(2012) Lauren Averett Byers et al.   Cancer Discovery

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Bortezomib as the First Proteasome Inhibitor Anticancer Drug: Current Status and Future Perspectives

(2011) D. Chen et al.   CURRENT CANCER DRUG TARGETS

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA