Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics

Machine and deep learning approaches for cancer drug repurposing

(2020) Naiem T. Issa et al.   SEMINARS IN CANCER BIOLOGY

Turning liabilities into opportunities: Off-target based drug repurposing in cancer

(2020) Vinayak Palve et al.   SEMINARS IN CANCER BIOLOGY

MYC and Twist1 cooperate to drive metastasis by eliciting crosstalk between cancer and innate immunity

(2020) Renumathy Dhanasekaran et al.   eLife

Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin

(2020) Amir Ata Saei et al.   Redox Biology

Repurposing Drugs for Acute Myeloid Leukemia: A Worthy Cause or a Futile Pursuit?

(2020) Anna V. Wojcicki et al.   Cancers

Bioinformatics Analysis of Global Proteomic and Phosphoproteomic Data Sets Revealed Activation of NEK2 and AURKA in Cancers

(2020) Barnali Deb et al.   Biomolecules

Breaking through the glioblastoma micro-environment via extracellular vesicles

(2020) Thomas Simon et al.   ONCOGENE

DNA Methylation as a Therapeutic Target for Bladder Cancer

(2020) Sandra P. Nunes et al.   Cells

Machine learning approaches to drug response prediction: challenges and recent progress

(2020) George Adam et al.   npj Precision Oncology

Repurposing old drugs to fight multidrug resistant cancers

(2020) Jelena Dinić et al.   DRUG RESISTANCE UPDATES

Drug Targets Identified More Discerningly

(2020) Richard A. Stein   Genetic Engineering & Biotechnology News

Drug repurposing for cancer treatments: a well-intentioned, but misguided strategy

(2020) Audrey A Tran et al.   LANCET ONCOLOGY

Advances in drug delivery technology for the treatment of glioblastoma multiforme

(2020) Gi Doo Cha et al.   JOURNAL OF CONTROLLED RELEASE

Network-Based Assessment of Adverse Drug Reaction Risk in Polypharmacy Using High-Throughput Screening Data

(2019) Guillermo de Anda-Jáuregui et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Navigating metabolic pathways to enhance antitumour immunity and immunotherapy

(2019) Xiaoyun Li et al.   Nature Reviews Clinical Oncology

Combination Therapies and Drug Delivery Platforms in Combating Pancreatic Cancer

(2019) Fan Lei et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Molecular Alterations and Poziotinib Efficacy, a pan‐HER inhibitor, in Human Epidermal Growth Factor Receptor 2 (HER2)‐positive breast cancers: Combined Exploratory Biomarker Analysis from a Phase II Clinical Trial of Poziotinib for Refractory HER2‐positive Breast Cancer Patients

(2019) Ji‐Yeon Kim et al.   INTERNATIONAL JOURNAL OF CANCER

Drug repurposing in oncology: Compounds, pathways, phenotypes and computational approaches for colorectal cancer

(2019) Patrycja Nowak-Sliwinska et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Antibody–Drug Conjugates: Future Directions in Clinical and Translational Strategies to Improve the Therapeutic Index

(2019) Steven Coats et al.   CLINICAL CANCER RESEARCH

Targeted therapy with anlotinib for patient with recurrent glioblastoma

(2019) Yajuan Lv et al.   MEDICINE

Crosstalk between autophagy and epithelial-mesenchymal transition and its application in cancer therapy

(2019) Hong-Tao Chen et al.   Molecular Cancer

Exploiting machine learning for end-to-end drug discovery and development

(2019) Sean Ekins et al.   NATURE MATERIALS

Role of c-MET Inhibitors in Overcoming Drug Resistance in Spheroid Models of Primary Human Pancreatic Cancer and Stellate Cells

(2019) Omidreza Firuzi et al.   Cancers

Statins as Potential Therapeutics for Lung Cancer

(2019) Ali Fatehi Hassanabad et al.   AMERICAN JOURNAL OF CLINICAL ONCOLOGY-CANCER CLINICAL TRIALS

vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer

(2019) Javier Perales-Patón et al.   BIOINFORMATICS

Adefovir dipivoxil sensitizes colon cancer cells to vemurafenib by disrupting the KCTD12-CDK1 interaction

(2019) Jie Yang et al.   CANCER LETTERS

Drug repurposing to overcome resistance to various therapies for colorectal cancer

(2019) Winnie Fong et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Exosomes and their role in tumorigenesis and anticancer drug resistance

(2019) Neta Milman et al.   DRUG RESISTANCE UPDATES

Mesenchymal transition and increased therapy resistance of glioblastoma cells is related to astrocyte reactivity

(2019) Mia Niklasson et al.   JOURNAL OF PATHOLOGY

In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data

(2019) Remzi Celebi et al.   Scientific Reports

Predicting Synergism of Cancer Drug Combinations Using NCI-ALMANAC Data

(2019) Pavel Sidorov et al.   Frontiers in Chemistry

Antibody–drug conjugates for cancer

(2019) Cindy H Chau et al.   LANCET

Trastuzumab duocarmazine in locally advanced and metastatic solid tumours and HER2-expressing breast cancer: a phase 1 dose-escalation and dose-expansion study

(2019) Udai Banerji et al.   LANCET ONCOLOGY

The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies

(2019) Lindsay Angus et al.   NATURE GENETICS

Artificial intelligence in digital pathology — new tools for diagnosis and precision oncology

(2019) Kaustav Bera et al.   Nature Reviews Clinical Oncology

Computer-aided drug repurposing for cancer therapy: Approaches and opportunities to challenge anticancer targets

(2019) Carla Mottini et al.   SEMINARS IN CANCER BIOLOGY

Antibody Drug Conjugates for Cancer Treatment

(2019) Christine M. Walko et al.   JAMA Oncology

Unique Aberrations in Intimal Sarcoma Identified by Next-Generation Sequencing as Potential Therapy Targets

(2019) Jason Roszik et al.   Cancers

Mebendazole as a Candidate for Drug Repurposing in Oncology: An Extensive Review of Current Literature

(2019) Guerini et al.   Cancers

Integrated Transcriptome Analysis Reveals KLK5 and L1CAM Predict Response to Anlotinib in NSCLC at 3rd Line

(2019) Jun Lu et al.   Frontiers in Oncology

Pan-Cancer Landscape and Analysis of ERBB2 Mutations Identifies Poziotinib as a Clinically Active Inhibitor and Enhancer of T-DM1 Activity

(2019) Jacqulyne P. Robichaux et al.   CANCER CELL

HER2-Overexpressing/Amplified Breast Cancer as a Testing Ground for Antibody–Drug Conjugate Drug Development in Solid Tumors

(2019) Mark D. Pegram et al.   CLINICAL CANCER RESEARCH

Tumor vasculature remolding by thalidomide increases delivery and efficacy of cisplatin

(2019) Yanwei Shen et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Vinca alkaloids, thalidomide and eribulin‐induced peripheral neurotoxicity: From pathogenesis to treatment

(2019) Badrul Islam et al.   JOURNAL OF THE PERIPHERAL NERVOUS SYSTEM

A systems approach to clinical oncology uses deep phenotyping to deliver personalized care

(2019) James T. Yurkovich et al.   Nature Reviews Clinical Oncology

Dissecting the m6A methylation affection on afatinib resistance in non-small cell lung cancer

(2019) Qianqian Meng et al.   PHARMACOGENOMICS JOURNAL

A machine learning algorithm predicts molecular subtypes in pancreatic ductal adenocarcinoma with differential response to gemcitabine-based versus FOLFIRINOX chemotherapy

(2019) Georgios Kaissis et al.   PLoS One

The crosstalk between STAT3 and p53/RAS signaling controls cancer cell metastasis and cisplatin resistance via the Slug/MAPK/PI3K/AKT-mediated regulation of EMT and autophagy

(2019) Fan Liang et al.   Oncogenesis

Drug repurposing for cancer therapy, easier said than done

(2019) Aurora Gonzalez-Fierro et al.   SEMINARS IN CANCER BIOLOGY

A novel computational approach for drug repurposing using systems biology

(2018) Azam Peyvandipour et al.   BIOINFORMATICS

The rise of deep learning in drug discovery

(2018) Hongming Chen et al.   DRUG DISCOVERY TODAY

A phase II trial of the pan-HER inhibitor poziotinib, in patients with HER2-positive metastatic breast cancer who had received at least two prior HER2-directed regimens: results of the NOV120101-203 trial

(2018) Yeon Hee Park et al.   INTERNATIONAL JOURNAL OF CANCER

Rational development of synergistic combinations of chemotherapy and molecular targeted agents for colorectal cancer treatment

(2018) Diego Tosi et al.   BMC CANCER

Abstract 3303: A comprehensive TCGA Pan-Cancer molecular study of gynecologic and breast cancers

(2018) Ashton Berger et al.   CANCER RESEARCH

Network Propagation Predicts Drug Synergy in Cancers

(2018) Hongyang Li et al.   CANCER RESEARCH

COSMIC-3D provides structural perspectives on cancer genetics for drug discovery

(2018) Harry C. Jubb et al.   NATURE GENETICS

A small molecule targeting myoferlin exerts promising anti-tumor effects on breast cancer

(2018) Tao Zhang et al.   Nature Communications

Impact of Deep Learning Assistance on the Histopathologic Review of Lymph Nodes for Metastatic Breast Cancer

(2018) David F. Steiner et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

Artificial Intelligence–Based Breast Cancer Nodal Metastasis Detection

(2018) Yun Liu et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Crosstalk in cancer resistance and metastasis

(2018) Saeed Norouzi et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Drug repurposing: progress, challenges and recommendations

(2018) Sudeep Pushpakom et al.   NATURE REVIEWS DRUG DISCOVERY

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Staurosporine, an inhibitor of hormonally up-regulated neu-associated kinase

(2018) Joelle N. Zambrano et al.   Oncotarget

Identification of Casiopeina II-gly secondary targets through a systems pharmacology approach

(2018) Guillermo de Anda-Jáuregui et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Novel Strategies on Personalized Medicine for Breast Cancer Treatment: An Update

(2017) Carmen Chan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deep Learning Algorithms for Detection of Lymph Node Metastases From Breast Cancer

(2017) Jeffrey Alan Golden   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Identification of human flap endonuclease 1 (FEN1) inhibitors using a machine learning based consensus virtual screening

(2017) Amit Laxmikant Deshmukh et al.   Molecular BioSystems

Drug therapy: Exploiting synthetic lethality to improve cancer therapy

(2017) Diede Brunen et al.   Nature Reviews Clinical Oncology

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

(2017) Amar Koleti et al.   NUCLEIC ACIDS RESEARCH

Using a novel computational drug-repositioning approach (DrugPredict) to rapidly identify potent drug candidates for cancer treatment

(2017) A B Nagaraj et al.   ONCOGENE

Drug repurposing in cancer

(2017) Linda Sleire et al.   PHARMACOLOGICAL RESEARCH

Quantifying the Benefits of Genome-Driven Oncology

(2017) Alison M. Schram et al.   Cancer Discovery

High-Throughput Genomics and Clinical Outcome in Hard-to-Treat Advanced Cancers: Results of the MOSCATO 01 Trial

(2017) Christophe Massard et al.   Cancer Discovery

Gene network inherent in genomic big data improves the accuracy of prognostic prediction for cancer patients

(2017) Yun Hak Kim et al.   Oncotarget

Anti-cancer effect of novel PAK1 inhibitor via induction of PUMA-mediated cell death and p21-mediated cell cycle arrest

(2017) Tae-Gyun Woo et al.   Oncotarget

RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer

(2017) Jesús Espinal-Enríquez et al.   Scientific Reports

Replication Study: Discovery and preclinical validation of drug indications using compendia of public gene expression data

(2017) Irawati Kandela et al.   eLife

ksRepo: a generalized platform for computational drug repositioning

(2016) Adam S. Brown et al.   BMC BIOINFORMATICS

Tumor Evolution Inferred by Patterns of microRNA Expression through the Course of Disease, Therapy, and Recurrence in Breast Cancer

(2016) M. Dadiani et al.   CLINICAL CANCER RESEARCH

Scaffold Repurposing of Old Drugs Towards New Cancer Drug Discovery

(2016) Haijun Chen et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Secondary pharmacology: screening and interpretation of off-target activities – focus on translation

(2016) Steven Whitebread et al.   DRUG DISCOVERY TODAY

Tumor suppressor crosstalk: Hippo and p53

(2016) N. Furth et al.   EUROPEAN JOURNAL OF CANCER

Safety, pharmacokinetics, and antitumor properties of anlotinib, an oral multi-target tyrosine kinase inhibitor, in patients with advanced refractory solid tumors

(2016) Yongkun Sun et al.   Journal of Hematology & Oncology

Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

Modeling of signaling crosstalk-mediated drug resistance and its implications on drug combination

(2016) Xiaoqiang Sun et al.   Oncotarget

The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology

(2016) Artur Kadurin et al.   Oncotarget

NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning

(2016) Xing Chen et al.   PLoS Computational Biology

Drug–target interaction prediction: databases, web servers and computational models

(2015) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

Crosstalk events in the estrogen signaling pathway may affect tamoxifen efficacy in breast cancer molecular subtypes

(2015) Guillermo de Anda-Jáuregui et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Pembrolizumab for the treatment of PD-L1 positive advanced or metastatic non-small cell lung cancer

(2015) Thu Oanh Dang et al.   Expert Review of Anticancer Therapy

High-dimensional QSAR prediction of anticancer potency of imidazo[4,5-b]pyridine derivatives using adjusted adaptive LASSO

(2015) Zakariya Yahya Algamal et al.   JOURNAL OF CHEMOMETRICS

Pathway-based personalized analysis of breast cancer expression data

(2015) Anna Livshits et al.   Molecular Oncology

Computational oncology — mathematical modelling of drug regimens for precision medicine

(2015) Dominique Barbolosi et al.   Nature Reviews Clinical Oncology

Drug repurposing in oncology—patient and health systems opportunities

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

Improved Overall Survival in Melanoma with Combined Dabrafenib and Trametinib

(2015) Caroline Robert et al.   NEW ENGLAND JOURNAL OF MEDICINE

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

Systems oncology: Towards patient-specific treatment regimes informed by multiscale mathematical modelling

(2015) Gibin G. Powathil et al.   SEMINARS IN CANCER BIOLOGY

Crosstalk with cancer-associated fibroblasts induces resistance of non-small cell lung cancer cells to epidermal growth factor receptor tyrosine kinase inhibition

(2015) Chung Choe et al.   OncoTargets and Therapy

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

(2015) C. Swanton et al.   Cancer Discovery

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling

(2015) Isidro Cortes-Ciriano et al.   Journal of Cheminformatics

Pathway Analysis: State of the Art

(2015) Miguel A. García-Campos et al.   Frontiers in Physiology

Cationic Polyamidoamine Dendrimers as Modulators of EGFR Signaling In Vitro and In Vivo

(2015) Saghir Akhtar et al.   PLoS One

The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set

(2015) Heloisa Helena Milioli et al.   PLoS One

100 Small molecules selectively targeting breast cancer cells

(2014) J. Sakoff et al.   EUROPEAN JOURNAL OF CANCER

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality

(2014) H. Xu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Acquired resistance to TKIs in solid tumours: learning from lung cancer

(2014) D. Ross Camidge et al.   Nature Reviews Clinical Oncology

Fine-tuning antibody–drug conjugates

(2014) Alexandra Flemming   NATURE REVIEWS DRUG DISCOVERY

Synergistic and Antagonistic Drug Combinations Depend on Network Topology

(2014) Ning Yin et al.   PLoS One

Epigenetic mechanisms of importance for drug treatment

(2014) Maxim Ivanov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Personalizing oncology treatments by predicting drug efficacy, side-effects, and improved therapy: mathematics, statistics, and their integration

(2014) Zvia Agur et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

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

(2014) Mattia Lauriola et al.   Nature Communications

The Dynamics of Signaling as a Pharmacological Target

(2013) Marcelo Behar et al.   CELL

APOBEC3B is an enzymatic source of mutation in breast cancer

(2013) Michael B. Burns et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Pathway-based personalized analysis of cancer

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

Computational Modeling of ERBB2-Amplified Breast Cancer Identifies Combined ErbB2/3 Blockade as Superior to the Combination of MEK and AKT Inhibitors

(2013) D. C. Kirouac et al.   Science Signaling

Role of epidermal growth factor receptor in breast cancer

(2012) Hiroko Masuda et al.   BREAST CANCER RESEARCH AND TREATMENT

Complexity in the signaling network: insights from the use of targeted inhibitors in cancer therapy

(2012) J. S. Logue et al.   GENES & DEVELOPMENT

Cereblon is a direct protein target for immunomodulatory and antiproliferative activities of lenalidomide and pomalidomide

(2012) A Lopez-Girona et al.   LEUKEMIA

Dacomitinib (PF-00299804), an Irreversible Pan-HER Inhibitor, Inhibits Proliferation of HER2-Amplified Breast Cancer Cell Lines Resistant to Trastuzumab and Lapatinib

(2012) O. Kalous et al.   MOLECULAR CANCER THERAPEUTICS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Intratumor Heterogeneity: Seeing the Wood for the Trees

(2012) T. A. Yap et al.   Science Translational Medicine

Monoclonal antibodies for the treatment of cancer

(2012) Casey W. Shuptrine et al.   SEMINARS IN CANCER BIOLOGY

Literature mining, ontologies and information visualization for drug repurposing

(2011) C. Andronis et al.   BRIEFINGS IN BIOINFORMATICS

Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing

(2011) Tudor I. Oprea et al.   Molecular Informatics

Accelerated clinical discovery using self-reported patient data collected online and a patient-matching algorithm

(2011) Paul Wicks et al.   NATURE BIOTECHNOLOGY

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

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

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

Pathway Commons, a web resource for biological pathway data

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

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Monoclonal antibodies for cancer immunotherapy

(2009) Louis M Weiner et al.   LANCET

Pharmacogenetics in Breast Cancer Therapy

(2008) S.-H. Tan et al.   CLINICAL CANCER RESEARCH

Targeted therapy for cancer using PARP inhibitors

(2008) Christopher J Lord et al.   CURRENT OPINION IN PHARMACOLOGY