Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era

SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug–target interactions and drug repositioning

(2016) Zengrui Wu et al.   BRIEFINGS IN BIOINFORMATICS

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes

(2016) Feixiong Cheng et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

How good can cryo-EM become?

(2016) Robert M Glaeser   NATURE METHODS

Data gaps limit the translational potential of preclinical research

(2016) Robin J. Kleiman et al.   Science Translational Medicine

In silico methods for drug repurposing and pharmacology

(2016) Rachel A. Hodos et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Suppression of KRas-mutant cancer through the combined inhibition of KRAS with PLK1 and ROCK

(2016) Jieqiong Wang et al.   Nature Communications

Psmir: a database of potential associations between small molecules and miRNAs

(2016) Fanlin Meng et al.   Scientific Reports

Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science

(2015) Chen Zhang et al.   Biomarkers in Medicine

Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals

(2015) Tao Zeng et al.   BRIEFINGS IN BIOINFORMATICS

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

(2015) Feixiong Cheng et al.   BRIEFINGS IN BIOINFORMATICS

In Silico Prescription of Anticancer Drugs to Cohorts of 28 Tumor Types Reveals Targeting Opportunities

(2015) Carlota Rubio-Perez et al.   CANCER CELL

Dual Targeting of the Autophagic Regulatory Circuitry in Gliomas with Repurposed Drugs Elicits Cell-Lethal Autophagy and Therapeutic Benefit

(2015) Ksenya Shchors et al.   CANCER CELL

Immunological Effects of Conventional Chemotherapy and Targeted Anticancer Agents

(2015) Lorenzo Galluzzi et al.   CANCER CELL

Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution

(2015) Nicholas McGranahan et al.   CANCER CELL

CRISPR/Cas9: molecular tool for gene therapy to target genome and epigenome in the treatment of lung cancer

(2015) M Sachdeva et al.   CANCER GENE THERAPY

Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation

(2015) M. Li et al.   CANCER RESEARCH

Elucidating Compound Mechanism of Action by Network Perturbation Analysis

(2015) Jung Hoon Woo et al.   CELL

Cyclooxygenase-Dependent Tumor Growth through Evasion of Immunity

(2015) Santiago Zelenay et al.   CELL

SoNar, a Highly Responsive NAD+/NADH Sensor, Allows High-Throughput Metabolic Screening of Anti-tumor Agents

(2015) Yuzheng Zhao et al.   Cell Metabolism

Clonotyping for precision oncology

(2015) Ha X. Dang et al.   DRUG DISCOVERY TODAY

Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial

(2015) Christophe Le Tourneau et al.   LANCET ONCOLOGY

Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach

(2015) Junfei Zhao et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Genetics: Big hopes for big data

(2015) Jill U. Adams   NATURE

Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation

(2015) Tea Pemovska et al.   NATURE

Personalized medicine: Time for one-person trials

(2015) Nicholas J. Schork   NATURE

Mapping the effects of drugs on the immune system

(2015) Brian A Kidd et al.   NATURE BIOTECHNOLOGY

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer

(2015) Alexandre Calon et al.   NATURE GENETICS

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

Drug repurposing in oncology—patient and health systems opportunities

(2015) Francesco Bertolini et al.   Nature Reviews Clinical Oncology

NCI-MATCH trial pushes cancer umbrella trial paradigm

(2015) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

The right dose for every patient: a key step for precision medicine

(2015) Richard W. Peck   NATURE REVIEWS DRUG DISCOVERY

CancerResource—updated database of cancer-relevant proteins, mutations and interacting drugs

(2015) Bjoern-Oliver Gohlke et al.   NUCLEIC ACIDS RESEARCH

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

DGIdb 2.0: mining clinically relevant drug–gene interactions

(2015) Alex H. Wagner et al.   NUCLEIC ACIDS RESEARCH

ccmGDB: a database for cancer cell metabolism genes

(2015) Pora Kim et al.   NUCLEIC ACIDS RESEARCH

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Metformin and prostate cancer stem cells: a novel therapeutic target

(2015) M J Mayer et al.   PROSTATE CANCER AND PROSTATIC DISEASES

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

The future of immune checkpoint therapy

(2015) P. Sharma et al.   SCIENCE

Immunological mechanisms of the antitumor effects of supplemental oxygenation

(2015) Stephen M. Hatfield et al.   Science Translational Medicine

Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data

(2015) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Cancer systems biology and modeling: Microscopic scale and multiscale approaches

(2015) Ali Masoudi-Nejad et al.   SEMINARS IN CANCER BIOLOGY

Cancer modeling and network biology: Accelerating toward personalized medicine

(2015) Ali Masoudi-Nejad et al.   SEMINARS IN CANCER BIOLOGY

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset

(2015) B. Seashore-Ludlow et al.   Cancer Discovery

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

(2015) Eduard Porta-Pardo et al.   PLoS Computational Biology

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

(2015) Feixiong Cheng et al.   PLoS Computational Biology

Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem

(2015) Lei Xie et al.   Frontiers in Pharmacology

Itraconazole therapy in a pancreatic adenocarcinoma patient: A case report

(2015) Nicholas R Lockhart et al.   JOURNAL OF ONCOLOGY PHARMACY PRACTICE

EGFR-mutated lung cancer: a paradigm of molecular oncology

(2015)   Oncotarget

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

(2015) Feixiong Cheng et al.   Oncotarget

Itraconazole suppresses the growth of glioblastoma through induction of autophagy

(2014) Rui Liu et al.   Autophagy

Metformin: From Mechanisms of Action to Therapies

(2014) Marc Foretz et al.   Cell Metabolism

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer

(2014) Quan Wang et al.   GENES CHROMOSOMES & CANCER

Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

(2014) Nanjie Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome

(2014) Feixiong Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Cell competition is a tumour suppressor mechanism in the thymus

(2014) Vera C. Martins et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

(2014) Jens G Lohr et al.   NATURE BIOTECHNOLOGY

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

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

(2014) Yitan Zhu et al.   NATURE METHODS

Learning from Big Health Care Data

(2014) Sebastian Schneeweiss   NEW ENGLAND JOURNAL OF MEDICINE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

(2014) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

(2014) Qiaonan Duan et al.   NUCLEIC ACIDS RESEARCH

Hot spots in protein–protein interfaces: Towards drug discovery

(2014) Engin Cukuroglu et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

RNAi Therapies: Drugging the Undruggable

(2014) S. Y. Wu et al.   Science Translational Medicine

DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information

(2014) I Amelio et al.   Cell Death & Disease

Diurnal suppression of EGFR signalling by glucocorticoids and implications for tumour progression and treatment

(2014) Mattia Lauriola et al.   Nature Communications

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach

(2014) Huy Vuong et al.   Genome Medicine

Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine

(2014) Lei Xie et al.   PLoS Computational Biology

An open investigation of the reproducibility of cancer biology research

(2014) Timothy M Errington et al.   eLife

Pharmaco-miR: linking microRNAs and drug effects

(2013) J. L. Rukov et al.   BRIEFINGS IN BIOINFORMATICS

Novel Modeling of Cancer Cell Signaling Pathways Enables Systematic Drug Repositioning for Distinct Breast Cancer Metastases

(2013) H. Zhao et al.   CANCER RESEARCH

The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

(2013) O. D. Abaan et al.   CANCER RESEARCH

Drug repositioning by structure-based virtual screening

(2013) Dik-Lung Ma et al.   CHEMICAL SOCIETY REVIEWS

Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development

(2013) Miquel Duran-Frigola et al.   CHEMISTRY & BIOLOGY

In Silico ADMET Prediction: Recent Advances, Current Challenges and Future Trends

(2013) Feixiong Cheng et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines

(2013) Guangxu Jin et al.   DRUG DISCOVERY TODAY

Adverse Drug Events: Database Construction and in Silico Prediction

(2013) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs)

(2013) Feixiong Cheng et al.   Molecular BioSystems

Network-based drug repositioning

(2013) Zikai Wu et al.   Molecular BioSystems

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Computational approaches to identify functional genetic variants in cancer genomes

(2013)   NATURE METHODS

TCPA: a resource for cancer functional proteomics data

(2013) Jun Li et al.   NATURE METHODS

canSAR: updated cancer research and drug discovery knowledgebase

(2013) Krishna C. Bulusu et al.   NUCLEIC ACIDS RESEARCH

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

Interaction-based discovery of functionally important genes in cancers

(2013) Dario Ghersi et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Repurposing Itraconazole as a Treatment for Advanced Prostate Cancer: A Noncomparative Randomized Phase II Trial in Men With Metastatic Castration-Resistant Prostate Cancer

(2013) E. S. Antonarakis et al.   ONCOLOGIST

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks

(2013) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance

(2013) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Repositioning metformin for cancer prevention and treatment

(2013) Brendan J. Quinn et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Individualized Systems Medicine Strategy to Tailor Treatments for Patients with Chemorefractory Acute Myeloid Leukemia

(2013) T. Pemovska et al.   Cancer Discovery

A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors

(2013) N. S. Jahchan et al.   Cancer Discovery

Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

(2013) M. J. Ellis et al.   Cancer Discovery

Biomarker-Guided Repurposing of Chemotherapeutic Drugs for Cancer Therapy: A Novel Strategy in Drug Development

(2013) Jan Stenvang et al.   Frontiers in Oncology

SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression

(2012) X. Liu et al.   BIOINFORMATICS

Metformin intake is associated with better survival in ovarian cancer

(2012) Sanjeev Kumar et al.   CANCER

Understanding genomic alterations in cancer genomes using an integrative network approach

(2012) Edwin Wang   CANCER LETTERS

Abstract 3499: CD56 targeted chimeric antigen receptors for immunotherapy of multiple myeloma

(2012) Reuben Benjamin et al.   CANCER RESEARCH

Identification of Drugs Including a Dopamine Receptor Antagonist that Selectively Target Cancer Stem Cells

(2012) Eleftherios Sachlos et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

In silico drug repositioning – what we need to know

(2012) Zhichao Liu et al.   DRUG DISCOVERY TODAY

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

(2012) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Prediction of chemical–protein interactions: multitarget-QSAR versus computational chemogenomic methods

(2012) Feixiong Cheng et al.   Molecular BioSystems

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

GlaxoSmithKline opens the door on clinical data sharing

(2012) Charlotte Harrison   NATURE REVIEWS DRUG DISCOVERY

Diagnosing the decline in pharmaceutical R&D efficiency

(2012) Jack W. Scannell et al.   NATURE REVIEWS DRUG DISCOVERY

Aspirin Use, TumorPIK3CAMutation, and Colorectal-Cancer Survival

(2012) Xiaoyun Liao et al.   NEW ENGLAND JOURNAL OF MEDICINE

ChemProt-2.0: visual navigation in a disease chemical biology database

(2012) Sonny Kim Kjærulff et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Wanjuan Yang et al.   NUCLEIC ACIDS RESEARCH

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Prediction of Chemical-Protein Interactions Network with Weighted Network-Based Inference Method

(2012) Feixiong Cheng et al.   PLoS One

Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

(2012) R. J. Leary et al.   Science Translational Medicine

Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses

(2012) Wei Jiang et al.   Scientific Reports

Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer

(2012) Daichi Shigemizu et al.   PLoS Computational Biology

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Targeting apoptosis pathways by Celecoxib in cancer

(2011) Verena Jendrossek   CANCER LETTERS

A Novel Method of Transcriptional Response Analysis to Facilitate Drug Repositioning for Cancer Therapy

(2011) G. Jin et al.   CANCER RESEARCH

Itraconazole Inhibits Angiogenesis and Tumor Growth in Non-Small Cell Lung Cancer

(2011) B. T. Aftab et al.   CANCER RESEARCH

PREDICT: a method for inferring novel drug indications with application to personalized medicine

(2011) A. Gottlieb et al.   Molecular Systems Biology

Cancer genomics: from discovery science to personalized medicine

(2011) Lynda Chin et al.   NATURE MEDICINE

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Optimization of Dosing for EGFR-Mutant Non-Small Cell Lung Cancer with Evolutionary Cancer Modeling

(2011) J. Chmielecki et al.   Science Translational Medicine

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

(2011) J. T. Dudley et al.   Science Translational Medicine

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

NSAID Sulindac and Its Analog Bind RXRα and Inhibit RXRα-Dependent AKT Signaling

(2010) Hu Zhou et al.   CANCER CELL

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

PROMISCUOUS: a database for network-based drug-repositioning

(2010) J. von Eichborn et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metformin Selectively Targets Cancer Stem Cells, and Acts Together with Chemotherapy to Block Tumor Growth and Prolong Remission

(2009) H. A. Hirsch et al.   CANCER RESEARCH

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH