Spatially confined sub-tumor microenvironments in pancreatic cancer

Intratumoral heterogeneity in cancer progression and response to immunotherapy

(2021) Ilio Vitale et al.   NATURE MEDICINE

Self-organization in cancer: Implications for histopathology, cancer cell biology, and metastasis

(2021) Senthil K. Muthuswamy   CANCER CELL

Genomic Features and Classification of Homologous Recombination Deficient Pancreatic Ductal Adenocarcinoma

(2021) Talia Golan et al.   GASTROENTEROLOGY

Current advances and outlooks in immunotherapy for pancreatic ductal adenocarcinoma

(2020) Jia-qiao Fan et al.   Molecular Cancer

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

(2020) Michelle Chan-Seng-Yue et al.   NATURE GENETICS

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

GATA6 Expression Distinguishes Classical and Basal-like Subtypes in Advanced Pancreatic Cancer

(2020) Grainne M. O'Kane et al.   CLINICAL CANCER RESEARCH

The tumour microenvironment in pancreatic cancer — clinical challenges and opportunities

(2020) Won Jin Ho et al.   Nature Reviews Clinical Oncology

Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer

(2020) Yann Kieffer et al.   Cancer Discovery

Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation

(2020) Tim DD Somerville et al.   eLife

Three distinct stroma types in human pancreatic cancer identified by image analysis of fibroblast subpopulations and collagen

(2020) Yurina Ogawa et al.   CLINICAL CANCER RESEARCH

Deconstructing tumor heterogeneity: the stromal perspective

(2020) Renee E. Vickman et al.   Oncotarget

Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes

(2019) Hans Carlo Maurer et al.   GUT

The Proteogenomic Landscape of Curable Prostate Cancer

(2019) Ankit Sinha et al.   CANCER CELL

Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases

(2019) Ashton A. Connor et al.   CANCER CELL

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

(2019) Matteo Ligorio et al.   CELL

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

(2019) Ela Elyada et al.   Cancer Discovery

Single-cell RNA sequencing reveals stromal evolution into LRRC15+ myofibroblasts as a determinant of patient response to cancer immunotherapy

(2019) Claudia X Dominguez et al.   Cancer Discovery

From single cells to tissue self-organization

(2018) Aline Xavier da Silveira dos Santos et al.   FEBS Journal

Stratification of Pancreatic Ductal Adenocarcinomas Based on Tumor and Microenvironment Features

(2018) Francesco Puleo et al.   GASTROENTEROLOGY

The Role of Fibroblasts in Pancreatic Cancer: Extracellular Matrix Versus Paracrine Factors

(2017) Louisa Bolm et al.   Translational Oncology

Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma

(2017) Ashton A. Connor et al.   JAMA Oncology

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors

(2016) Edyta E. Wojtowicz et al.   Cell Stem Cell

Genomic analyses identify molecular subtypes of pancreatic cancer

(2016) Peter Bailey et al.   NATURE

Analyzing and interpreting genome data at the network level with ConsensusPathDB

(2016) Ralf Herwig et al.   Nature Protocols

Evaluation of Pancreatic Cancer Clinical Trials and Benchmarks for Clinically Meaningful Future Trials

(2016) Lola Rahib et al.   JAMA Oncology

Depletion of Carcinoma-Associated Fibroblasts and Fibrosis Induces Immunosuppression and Accelerates Pancreas Cancer with Reduced Survival

(2015) Berna C. Özdemir et al.   CANCER CELL

Organoid Models of Human and Mouse Ductal Pancreatic Cancer

(2015) Sylvia F. Boj et al.   CELL

Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma

(2015) Richard A Moffitt et al.   NATURE GENETICS

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

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

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

α-Smooth muscle actin expression and desmoplastic stromal reaction in pancreatic cancer: results from the CONKO-001 study

(2014) M Sinn et al.   BRITISH JOURNAL OF CANCER

Stromal Elements Act to Restrain, Rather Than Support, Pancreatic Ductal Adenocarcinoma

(2014) Andrew D. Rhim et al.   CANCER CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Reciprocal control of cell proliferation and migration

(2010) Alina De Donatis et al.   Cell Communication and Signaling

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

The Activated Stroma Index Is a Novel and Independent Prognostic Marker in Pancreatic Ductal Adenocarcinoma

(2008) Mert Erkan et al.   Clinical Gastroenterology and Hepatology