Comprehensive analysis of spatial architecture in primary liver cancer

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

(2021) Alma Andersson et al.   Nature Communications

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Intratumoral heterogeneity and clonal evolution in liver cancer

(2020) Bojan Losic et al.   Nature Communications

Trajectory and Functional Analysis of PD‐1 high CD4 + CD8 + T Cells in Hepatocellular Carcinoma by Single‐Cell Cytometry and Transcriptome Sequencing

(2020) Bo Zheng et al.   Advanced Science

scCancer: a package for automated processing of single-cell RNA-seq data in cancer

(2020) Wenbo Guo et al.   BRIEFINGS IN BIOINFORMATICS

Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma

(2020) Ankur Sharma et al.   CELL

Roles of EphA1/A2 and ephrin-A1 in cancer

(2019) Katsuaki Ieguchi et al.   CANCER SCIENCE

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

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

Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling

(2019) Yashwanth Subbannayya et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

SORLA regulates endosomal trafficking and oncogenic fitness of HER2

(2019) Mika Pietilä et al.   Nature Communications

Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas

(2019) Xiaofan Ding et al.   GASTROENTEROLOGY

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Emerging insights of tumor heterogeneity and drug resistance mechanisms in lung cancer targeted therapy

(2019) Zuan-Fu Lim et al.   Journal of Hematology & Oncology

Redefinition of tumor capsule: Rho-dependent clustering of cancer-associated fibroblasts in favor of tensional homeostasis

(2019) Ramin Rahmanzade   MEDICAL HYPOTHESES

Tumour evolution in hepatocellular carcinoma

(2019) Amanda J. Craig et al.   Nature Reviews Gastroenterology & Hepatology

CD10 + GPR77 + Cancer-Associated Fibroblasts Promote Cancer Formation and Chemoresistance by Sustaining Cancer Stemness

(2018) Shicheng Su et al.   CELL

Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma

(2018) Hongping Zheng et al.   HEPATOLOGY

Fibroblast heterogeneity: implications for human disease

(2018) Magnus D. Lynch et al.   JOURNAL OF CLINICAL INVESTIGATION

Immune Cell Infiltration and Tertiary Lymphoid Structures as Determinants of Antitumor Immunity

(2018) Victor H. Engelhard et al.   JOURNAL OF IMMUNOLOGY

Pembrolizumab in patients with advanced hepatocellular carcinoma previously treated with sorafenib (KEYNOTE-224): a non-randomised, open-label phase 2 trial

(2018) Andrew X Zhu et al.   LANCET ONCOLOGY

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

(2018) Emelie Berglund et al.   Nature Communications

Cell Cycle-Associated CXCR4 Expression in Germinal Center B Cells and Its Implications on Affinity Maturation

(2018) Tom S. Weber   Frontiers in Immunology

HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas

(2018) Qiuyu Lian et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Cancer stem cells (CSCs) in cancer progression and therapy

(2018) Masoud Najafi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Tumour heterogeneity and metastasis at single-cell resolution

(2018) Devon A. Lawson et al.   NATURE CELL BIOLOGY

Liver Cancer Cell of Origin, Molecular Class, and Effects on Patient Prognosis

(2017) Daniela Sia et al.   GASTROENTEROLOGY

Targeting the T cell receptor β-chain constant region for immunotherapy of T cell malignancies

(2017) Paul M Maciocia et al.   NATURE MEDICINE

Tumour heterogeneity and resistance to cancer therapies

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

Endothelial LRP1 regulates metabolic responses by acting as a co-activator of PPARγ

(2017) Hua Mao et al.   Nature Communications

Cancer Stem cells and their cellular origins in primary liver and biliary tract cancers

(2016) Tsunekazu Oikawa   HEPATOLOGY

Tertiary lymphoid structures, drivers of the anti-tumor responses in human cancers

(2016) Marie-Caroline Dieu-Nosjean et al.   IMMUNOLOGICAL REVIEWS

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

(2016) P. L. Stahl et al.   SCIENCE

Tissue-specific and convergent metabolic transformation of cancer correlates with metastatic potential and patient survival

(2016) Edoardo Gaude et al.   Nature Communications

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Current concepts of immune based treatments for patients with HCC: from basic science to novel treatment approaches

(2015) Tim F Greten et al.   GUT

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Early Growth Response Genes Regulate B Cell Development, Proliferation, and Immune Response

(2014) M. Gururajan et al.   JOURNAL OF IMMUNOLOGY

Vascular Endothelial Growth Factor-B in Physiology and Disease

(2014) Maija Bry et al.   PHYSIOLOGICAL REVIEWS

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

(2014) A. P. Patel et al.   SCIENCE

Role of Tertiary Lymphoid Structures (TLS) in Anti-Tumor Immunity: Potential Tumor-Induced Cytokines/Chemokines that Regulate TLS Formation in Epithelial-Derived Cancers

(2014) Erica Pimenta et al.   Cancers

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Microenvironmental regulation of tumor progression and metastasis

(2013) Daniela F Quail et al.   NATURE MEDICINE

The EphB4 Receptor Tyrosine Kinase Promotes Lung Cancer Growth: A Potential Novel Therapeutic Target

(2013) Benjamin D. Ferguson et al.   PLoS One

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

A Unique Metastasis Gene Signature Enables Prediction of Tumor Relapse in Early-Stage Hepatocellular Carcinoma Patients

(2010) S. Roessler et al.   CANCER RESEARCH

Sorafenib in Advanced Hepatocellular Carcinoma

(2008) Josep M. Llovet et al.   NEW ENGLAND JOURNAL OF MEDICINE