The prognostic landscape of genes and infiltrating immune cells across human cancers

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

An InteractiveJavaStatistical Image Segmentation System:GemIdent

(2015) Susan Holmes et al.   Journal of Statistical Software

Colorectal Cancer Stem Cells: From the Crypt to the Clinic

(2014) Ann Zeuner et al.   Cell Stem Cell

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

(2014) Yuan Yuan et al.   NATURE BIOTECHNOLOGY

TCGA-Assembler: open-source software for retrieving and processing TCGA data

(2014) Yitan Zhu et al.   NATURE METHODS

CD161 Defines a Transcriptional and Functional Phenotype across Distinct Human T Cell Lineages

(2014) Joannah R. Fergusson et al.   Cell Reports

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

Regulatory T cells, dendritic cells and neutrophils in patients with renal cell carcinoma

(2013) Ivo Minárik et al.   IMMUNOLOGY LETTERS

Neutralizing Tumor-Promoting Chronic Inflammation: A Magic Bullet?

(2013) L. M. Coussens et al.   SCIENCE

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

(2013) Alayne L Brunner et al.   GENOME BIOLOGY

Tumor-associated neutrophils: friend or foe?

(2012) Z. G. Fridlender et al.   CARCINOGENESIS

A single-sample microarray normalization method to facilitate personalized-medicine workflows

(2012) Stephen R. Piccolo et al.   GENOMICS

The Forkhead Transcription Factor FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism

(2012) X. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Tumor Immunotherapy Directed at PD-1

(2012) Antoni Ribas   NEW ENGLAND JOURNAL OF MEDICINE

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer

(2012) Suzanne L. Topalian et al.   NEW ENGLAND JOURNAL OF MEDICINE

Leukemia Gene Atlas – A Public Platform for Integrative Exploration of Genome-Wide Molecular Data

(2012) Katja Hebestreit et al.   PLoS One

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment

(2011) A. A. Alizadeh et al.   BLOOD

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Optimally weighted Z-test is a powerful method for combining probabilities in meta-analysis

(2011) D. V. ZAYKIN   JOURNAL OF EVOLUTIONARY BIOLOGY

Gene expression deconvolution in linear space

(2011) Yi Zhong et al.   NATURE METHODS

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

(2010) Aaron M Newman et al.   BMC BIOINFORMATICS

Association of a Leukemic Stem Cell Gene Expression Signature With Clinical Outcomes in Acute Myeloid Leukemia

(2010) Andrew J. Gentles   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Gene Expression-Based Prognostic Signatures in Lung Cancer: Ready for Clinical Use?

(2010) J. Subramanian et al.   JNCI-Journal of the National Cancer Institute

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Ten Years On — The Human Genome and Medicine

(2010) Harold Varmus   NEW ENGLAND JOURNAL OF MEDICINE

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Why Most Gene Expression Signatures of Tumors Have Not Been Useful in the Clinic

(2010) S. Koscielny   Science Translational Medicine

PrognoScan: a new database for meta-analysis of the prognostic value of genes

(2009) Hideaki Mizuno et al.   BMC Medical Genomics

Pretreatment neutrophil count as an independent prognostic factor in advanced non-small-cell lung cancer: An analysis of Japan Multinational Trial Organisation LC00-03

(2009) Satoshi Teramukai et al.   EUROPEAN JOURNAL OF CANCER

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases

(2008) L. Xu et al.   MOLECULAR CANCER RESEARCH

Gene Expression Signature of Cigarette Smoking and Its Role in Lung Adenocarcinoma Development and Survival

(2008) Maria Teresa Landi et al.   PLoS One