Bioinformatics Methods to Select Prognostic Biomarker Genes from Large Scale Datasets: A Review

SnapShot: TCGA-Analyzed Tumors

(2018) Amy Blum et al.   CELL

Clinical use of biomarkers in breast cancer: Updated guidelines from the European Group on Tumor Markers (EGTM)

(2017) M.J. Duffy et al.   EUROPEAN JOURNAL OF CANCER

Topologically inferring pathway activity for precise survival outcome prediction: breast cancer as a case

(2017) Wei Liu et al.   Molecular BioSystems

Reference standards for next-generation sequencing

(2017) Simon A. Hardwick et al.   NATURE REVIEWS GENETICS

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies

(2017) Gift Nyamundanda et al.   Scientific Reports

Convex Modeling of Interactions With Strong Heredity

(2016) Asad Haris et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Exact Post-Selection Inference for Sequential Regression Procedures

(2016) Ryan J. Tibshirani et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Empirical extensions of the lasso penalty to reduce the false discovery rate in high-dimensional Cox regression models

(2016) Nils Ternès et al.   STATISTICS IN MEDICINE

Cancer Markers Selection Using Network-Based Cox Regression: A Methodological and Computational Practice

(2016) Antonella Iuliano et al.   Frontiers in Physiology

Pathway and network analysis of cancer genomes

(2015)   NATURE METHODS

Highly informative marker sets consisting of genes with low individual degree of differential expression

(2015) V. V. Galatenko et al.   Scientific Reports

Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent

(2015) Noah Simon et al.   Journal of Statistical Software

Fitting Accelerated Failure Time Models in Routine Survival Analysis withRPackageaftgee

(2015) Sy Han Chiou et al.   Journal of Statistical Software

Using High-Throughput Transcriptomic Data for Prognosis: A Critical Overview and Perspectives

(2014) Eytan Domany   CANCER RESEARCH

Deregulation of cell signaling in cancer

(2014) Filippo G. Giancotti   FEBS LETTERS

Integrated genomic characterization of adrenocortical carcinoma

(2014) Guillaume Assié et al.   NATURE GENETICS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthmaversuscontrols

(2013) Ching Yong Yick et al.   EUROPEAN RESPIRATORY JOURNAL

Pathway-based personalized analysis of cancer

(2013) Y. Drier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment

(2013) Wei Zhang et al.   PLoS Computational Biology

Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer

(2012) Fang-Han Hsu et al.   BMC GENOMICS

A tutorial on rank-based coefficient estimation for censored data in small- and large-scale problems

(2012) Matthias Chung et al.   STATISTICS AND COMPUTING

Screen and clean: a tool for identifying interactions in genome-wide association studies

(2010) Jing Wu et al.   GENETIC EPIDEMIOLOGY

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

An integrative pathway-based clinical–genomic model for cancer survival prediction

(2010) Xi Chen et al.   STATISTICS & PROBABILITY LETTERS

On the adaptive elastic-net with a diverging number of parameters

(2009) Hui Zou et al.   ANNALS OF STATISTICS

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

The sparsity and bias of the Lasso selection in high-dimensional linear regression

(2008) Cun-Hui Zhang et al.   ANNALS OF STATISTICS

Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies

(2008) Clive J. Hoggart et al.   PLoS Genetics