Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels tumour heterogeneity plus M2-like tumour-associated macrophage infiltration and aggressiveness in TNBC

Immune Landscape of Invasive Ductal Carcinoma Tumor Microenvironment Identifies a Prognostic and Immunotherapeutically Relevant Gene Signature

(2019) Xuanwen Bao et al.   Frontiers in Oncology

A novel epigenetic signature for overall survival prediction in patients with breast cancer

(2019) Xuanwen Bao et al.   Journal of Translational Medicine

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Anti-PD-1 and Anti-CTLA-4 Therapies in Cancer: Mechanisms of Action, Efficacy, and Limitations

(2018) Judith A. Seidel et al.   Frontiers in Oncology

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq

(2018) Mihriban Karaayvaz et al.   Nature Communications

Macrophage Polarization: Anti-Cancer Strategies to Target Tumor-Associated Macrophage in Breast Cancer

(2017) Muhammad Tariq et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

Infiltrating macrophages increase RCC epithelial mesenchymal transition (EMT) and stem cell-like populations via AKT and mTOR signaling

(2016) Zhao Yang et al.   Oncotarget

Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

(2016) Katherine A. Hoadley et al.   PLOS MEDICINE

Classifying Cancers Based on T-cell Infiltration and PD-L1

(2015) Michele W.L. Teng et al.   CANCER RESEARCH

Molecular characteristics of recurrent triple-negative breast cancer

(2015) CHUNG-HSIN TSAI et al.   Molecular Medicine Reports

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

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

Prognostic Value of Tumor-Associated Macrophages According to Histologic Locations and Hormone Receptor Status in Breast Cancer

(2015) Jae Moon Gwak et al.   PLoS One

A Positive Feedback Loop between Mesenchymal-like Cancer Cells and Macrophages Is Essential to Breast Cancer Metastasis

(2014) Shicheng Su et al.   CANCER CELL

CSF1/CSF1R Blockade Reprograms Tumor-Infiltrating Macrophages and Improves Response to T-cell Checkpoint Immunotherapy in Pancreatic Cancer Models

(2014) Y. Zhu et al.   CANCER RESEARCH

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

(2014) S. D. Brown et al.   GENOME RESEARCH

Tumor-Associated Macrophages: From Mechanisms to Therapy

(2014) Roy Noy et al.   IMMUNITY

CSF1R inhibition delays cervical and mammary tumor growth in murine models by attenuating the turnover of tumor-associated macrophages and enhancing infiltration by CD8+T cells

(2014) Debbie C Strachan et al.   OncoImmunology

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Gestational diabetes mellitus epigenetically affects genes predominantly involved in metabolic diseases

(2013) Stephanie-May Ruchat et al.   Epigenetics

Prognostic and Predictive Value of Tumor-Infiltrating Lymphocytes in a Phase III Randomized Adjuvant Breast Cancer Trial in Node-Positive Breast Cancer Comparing the Addition of Docetaxel to Doxorubicin With Doxorubicin-Based Chemotherapy: BIG 02-98

(2013) Sherene Loi et al.   JOURNAL OF CLINICAL ONCOLOGY

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

(2012) Sohrab P. Shah et al.   NATURE

Mutations in ABCD4 cause a new inborn error of vitamin B12 metabolism

(2012) David Coelho et al.   NATURE GENETICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Role of tumor-associated macrophages in the progression of hepatocellular carcinoma

(2011) Ken Shirabe et al.   SURGERY TODAY

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

Triple-Negative Breast Cancer

(2010) William D. Foulkes et al.   NEW ENGLAND JOURNAL OF MEDICINE

Association of genetic variants with the metabolic syndrome in 20,806 white women: The women's health genome study

(2009) Alessandra C. Goulart et al.   AMERICAN HEART JOURNAL

Significantly higher levels of vascular endothelial growth factor (VEGF) and shorter survival times for patients with primary operable triple-negative breast cancer

(2009) B. K. Linderholm et al.   ANNALS OF ONCOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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

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