A Robust Immuno-Prognostic Model of Non-Muscle-Invasive Bladder Cancer Indicates Dynamic Interaction in Tumor Immune Microenvironment Contributes to Cancer Progression

European Association of Urology (EAU) Prognostic Factor Risk Groups for Non–muscle-invasive Bladder Cancer (NMIBC) Incorporating the WHO 2004/2016 and WHO 1973 Classification Systems for Grade: An Update from the EAU NMIBC Guidelines Panel

(2021) Richard J. Sylvester et al.   EUROPEAN UROLOGY

Dysregulation of the Immune Microenvironment Contributes to Malignant Progression and Has Prognostic Value in Bladder Cancer

(2021) Zongtai Zheng et al.   Frontiers in Oncology

Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2021) Hyuna Sung et al.   CA-A CANCER JOURNAL FOR CLINICIANS

An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer

(2021) Sia Viborg Lindskrog et al.   Nature Communications

Powerful p-value combination methods to detect incomplete association

(2021) Sora Yoon et al.   Scientific Reports

A survey of gene expression meta-analysis: methods and applications

(2020) Daniel Toro-Domínguez et al.   BRIEFINGS IN BIOINFORMATICS

Greater utility of molecular subtype rather than epithelial‐to‐mesenchymal transition ( EMT ) markers for prognosis in high‐risk non‐muscle‐invasive ( HGT1 ) bladder cancer

(2020) Edward C Ottley et al.   Journal of Pathology Clinical Research

Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade

(2020) Robert J. Motzer et al.   CANCER CELL

Bladder Cancer

(2020) Andrew T. Lenis et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The Gene Ontology resource: enriching a GOld mine

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Stromal lymphocyte infiltration is associated with tumour invasion depth but is not prognostic in high-grade T1 bladder cancer

(2019) Mathieu Rouanne et al.   EUROPEAN JOURNAL OF CANCER

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

(2019) Francesca Finotello et al.   Genome Medicine

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

(2019) Gregor Sturm et al.   BIOINFORMATICS

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

The role of collagen in cancer: from bench to bedside

(2019) Shuaishuai Xu et al.   Journal of Translational Medicine

Normalization Methods for the Analysis of Unbalanced Transcriptome Data: A Review

(2019) Xueyan Liu et al.   Frontiers in Bioengineering and Biotechnology

Pan-cancer adaptive immune resistance as defined by the Tumor Inflammation Signature (TIS): results from The Cancer Genome Atlas (TCGA)

(2018) Patrick Danaher et al.   Journal for ImmunoTherapy of Cancer

ArrayExpress update – from bulk to single-cell expression data

(2018) Awais Athar et al.   NUCLEIC ACIDS RESEARCH

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

(2017) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

(2017) Julien Racle et al.   eLife

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Diagnosis and Treatment of Non-Muscle Invasive Bladder Cancer: AUA/SUO Guideline

(2016) Sam S. Chang et al.   JOURNAL OF UROLOGY

Normalization and integration of large-scale metabolomics data using support vector regression

(2016) Xiaotao Shen et al.   Metabolomics

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

(2015) Peipei Li et al.   BMC BIOINFORMATICS

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

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

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

The Evaluation of the Risk Factors for Non-Muscle Invasive Bladder Cancer (NMIBC) Recurrence after Transurethral Resection (TURBt) in Chinese Population

(2015) Shenghua Liu et al.   PLoS One

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris

(2013) Marie Mooney et al.   PLoS One

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

pROC: an open-source package for R and S+ to analyze and compare ROC curves

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Long-term Cancer-specific Survival in Patients with High-risk, Non–muscle-invasive Bladder Cancer and Tumour Progression: A Systematic Review

(2011) Sven van den Bosch et al.   EUROPEAN UROLOGY

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE