Group Lasso Regularized Deep Learning for Cancer Prognosis from Multi-Omics and Clinical Features

DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network

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Deep Visual-Semantic Alignments for Generating Image Descriptions

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Adjuvant Pertuzumab and Trastuzumab in Early HER2-Positive Breast Cancer

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

(2017) Safoora Yousefi et al.   Scientific Reports

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability

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Addition of docetaxel, zoledronic acid, or both to first-line long-term hormone therapy in prostate cancer (STAMPEDE): survival results from an adaptive, multiarm, multistage, platform randomised controlled trial

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Mastering the game of Go with deep neural networks and tree search

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Coming of age: ten years of next-generation sequencing technologies

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iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes

(2016) Chengliang Dong et al.   Genome Medicine

Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD)

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Deep learning

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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

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Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

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

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Cancer Systems Biology: a peek into the future of patient care?

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The human splicing code reveals new insights into the genetic determinants of disease

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The Cancer Genome Atlas Pan-Cancer analysis project

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Survival analysis

(2012) Robert Flynn   JOURNAL OF CLINICAL NURSING

A Sparse-Group Lasso

(2012) Noah Simon et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

The variant call format and VCFtools

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

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The group lasso for logistic regression

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Survival analysis with high-dimensional covariates

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