MOLI: multi-omics late integration with deep neural networks for drug response prediction

DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays

(2019) Amrit Singh et al.   BIOINFORMATICS

Network-based integration of multi-omics data for prioritizing cancer genes

(2018) Christos Dimitrakopoulos et al.   BIOINFORMATICS

Kernelized rank learning for personalized drug recommendation

(2018) Xiao He et al.   BIOINFORMATICS

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

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

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

Estimation of The Percentage of US Patients With Cancer Who Benefit From Genome-Driven Oncology

(2018) John Marquart et al.   JAMA Oncology

Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities

(2018) Marinka Zitnik et al.   Information Fusion

Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy

(2018) Jin-Ku Lee et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology

(2017) Raunak Shrestha et al.   GENOME RESEARCH

Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies

(2017) Paul Geeleher et al.   GENOME RESEARCH

Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics

(2017) Michael Q. Ding et al.   MOLECULAR CANCER RESEARCH

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

(2017) Ahmet Zehir et al.   NATURE MEDICINE

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer

(2017) Emanuel Gonçalves et al.   Cell Systems

A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events

(2017) Colm J. Ryan et al.   Cell Systems

Evaluating the molecule-based prediction of clinical drug responses in cancer

(2016) Zijian Ding et al.   BIOINFORMATICS

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Multitask learning improves prediction of cancer drug sensitivity

(2016) Han Yuan et al.   Scientific Reports

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach

(2015) Muxuan Liang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response

(2015) Hui Gao et al.   NATURE MEDICINE

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines

(2014) Paul Geeleher et al.   GENOME BIOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Pattern discovery and cancer gene identification in integrated cancer genomic data

(2013) Qianxing Mo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Cellular Heterogeneity and Molecular Evolution in Cancer

(2012) Vanessa Almendro et al.   Annual Review of Pathology-Mechanisms of Disease

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

(2012) Wanjuan Yang et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Algorithms for Nonnegative Matrix Factorization with the β-Divergence

(2011) Cédric Févotte et al.   NEURAL COMPUTATION

Cancer Biomarkers: Are We Ready for the Prime Time?

(2010) Alok Mishra et al.   Cancers

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING