DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data

CALD1, CNN1, and TAGLN identified as potential prognostic molecular markers of bladder cancer by bioinformatics analysis

(2019) Yun Liu et al.   MEDICINE

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

(2018) Han Chen et al.   CELL

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Upregulation of kinesin family member 4A enhanced cell proliferation via activation of Akt signaling and predicted a poor prognosis in hepatocellular carcinoma

(2018) Yanlin Huang et al.   Cell Death & Disease

The crucial role of multiomic approach in cancer research and clinically relevant outcomes

(2018) Miaolong Lu et al.   EPMA Journal

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage

(2018) Olivier Poirion et al.   Nature Communications

LinkedOmics: analyzing multi-omics data within and across 32 cancer types

(2017) Suhas V Vasaikar et al.   NUCLEIC ACIDS RESEARCH

Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models

(2017) Safoora Yousefi et al.   Scientific Reports

Extracellular matrix gene expression profiling using microfluidics for colorectal carcinoma stratification

(2016) Christopher J. Hayes et al.   Biomicrofluidics

Methylation status of homeobox genes in common human cancers

(2016) Maria Fernanda Setúbal Destro Rodrigues et al.   GENOMICS

Aberrant differential expression of EZH1 and EZH2 in Polycomb repressive complex 2 among B- and T/NK-cell neoplasms

(2016) Lamia Abdalkader et al.   PATHOLOGY

High-dimensional genomic data bias correction and data integration using MANCIE

(2016) Chongzhi Zang et al.   Nature Communications

Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy

(2016) M Tong et al.   Oncogenesis

A pan-cancer analysis of prognostic genes

(2016) Jordan Anaya et al.   PeerJ

Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis

(2016) Travers Ching et al.   EBioMedicine

Identifying Cancer Subtypes from miRNA-TF-mRNA Regulatory Networks and Expression Data

(2016) Taosheng Xu et al.   PLoS One

High Expression of KIF20A Is Associated with Poor Overall Survival and Tumor Progression in Early-Stage Cervical Squamous Cell Carcinoma

(2016) Weijing Zhang et al.   PLoS One

Diagnostic biases in translational bioinformatics

(2015) Henry Han   BMC Medical Genomics

The methyltransferases enhancer of zeste homolog (EZH) 1 and EZH2 control hepatocyte homeostasis and regeneration

(2015) Woo Kyun Bae et al.   FASEB JOURNAL

Transcriptional Activation of HumanCDCA8Gene Regulated by Transcription Factor NF-Y in Embryonic Stem Cells and Cancer Cells

(2015) Can Dai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

Therapeutic potential of targeting cell division cycle associated 5 for oral squamous cell carcinoma

(2015) Norihiko Tokuzen et al.   Oncotarget

Identification of a multi-cancer gene expression biomarker for cancer clinical outcomes using a network-based algorithm

(2015) Emmanuel Martinez-Ledesma et al.   Scientific Reports

KAP1 Promotes Proliferation and Metastatic Progression of Breast Cancer Cells

(2014) J. B. Addison et al.   CANCER RESEARCH

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer

(2014) Sijia Huang et al.   PLoS Computational Biology

Global methylation silencing of clusteredproto-cadheringenes in cervical cancer: serving as diagnostic markers comparable to HPV

(2014) Kai-Hung Wang et al.   Cancer Medicine

Oncogenic role of kinesin proteins and targeting kinesin therapy

(2013) Xinran Liu et al.   CANCER SCIENCE

Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer

(2013) A. A. Margolin et al.   Science Translational Medicine

Collagen as a double-edged sword in tumor progression

(2013) Min Fang et al.   TUMOR BIOLOGY

Increased CDC20 expression is associated with pancreatic ductal adenocarcinoma differentiation and progression

(2012) David Z Chang et al.   Journal of Hematology & Oncology

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS