4.7 Review

Network pharmacology: curing causal mechanisms instead of treating symptoms

Related references

Note: Only part of the references are listed.
Review Biochemical Research Methods

On the limits of active module identification

Olga Lazareva et al.

Summary: In network and systems medicine, active module identification methods (AMIMs) are widely used for discovering candidate molecular disease mechanisms, but most tested AMIMs do not produce biologically more meaningful candidate disease modules on widely used PPI networks than on random networks. Most AMIMs mainly learn from node degrees and fail to exploit the biological knowledge encoded in the edges of PPI networks, indicating a need for novel algorithms to overcome these limitations.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

Soluble Guanylate Cyclase Agonists Induce Bronchodilation in Human Small Airways

Cynthia J. Koziol-White et al.

AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY (2020)

Editorial Material Biochemistry & Molecular Biology

A New Pathway to Airway Relaxation: Targeting the Other Cyclase in Asthma

Maggie Lam et al.

AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

A Therapy for Most with Cystic Fibrosis

Christine E. Bear

Review Medicine, Research & Experimental

Update on targeted cancer therapies, single or in combination, and their fine tuning for precision medicine

Sara S. Bashraheel et al.

BIOMEDICINE & PHARMACOTHERAPY (2020)

Article Oncology

Toward a More Precise Future for Oncology

Yonina R. Murciano-Goroff et al.

CANCER CELL (2020)

Article Biochemistry & Molecular Biology

Optical Mapping of cAMP Signaling at the Nanometer Scale

Andreas Bock et al.

Article Multidisciplinary Sciences

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

Sepideh Sadegh et al.

NATURE COMMUNICATIONS (2020)

Review Pharmacology & Pharmacy

On the Clinical Pharmacology of Reactive Oxygen Species

Ana Casas et al.

PHARMACOLOGICAL REVIEWS (2020)

Review Pharmacology & Pharmacy

AKAP Signaling Islands: Venues for Precision Pharmacology

Mitchell H. Omar et al.

TRENDS IN PHARMACOLOGICAL SCIENCES (2020)

Article Geriatrics & Gerontology

Repository of proposed pathways and protein-protein interaction networks in age-related macular degeneration

Fran M. Pool et al.

NPJ AGING AND MECHANISMS OF DISEASE (2020)

Article Medicine, Research & Experimental

Calcium-dependent blood-brain barrier breakdown by NOX5 limits postreperfusion benefit in stroke

Ana I. Casas et al.

JOURNAL OF CLINICAL INVESTIGATION (2019)

Article Biochemistry & Molecular Biology

GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets

Joaquim Aguirre-Plans et al.

JOURNAL OF MOLECULAR BIOLOGY (2019)

Article Multidisciplinary Sciences

From single drug targets to synergistic network pharmacology in ischemic stroke

Ana I. Casas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Network-based prediction of drug combinations

Feixiong Cheng et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

Molecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study

Jason K. Sicklick et al.

NATURE MEDICINE (2019)

Review Biochemistry & Molecular Biology

Advances in gene therapy for cystic fibrosis lung disease

Ziying Yan et al.

HUMAN MOLECULAR GENETICS (2019)

Article Biochemical Research Methods

Assessment of network module identification across complex diseases

Sarvenaz Choobdar et al.

NATURE METHODS (2019)

Article Pharmacology & Pharmacy

Elexacaftor/Ivacaftor/Tezacaftor: First Approval

Sheridan M. Hoy

DRUGS (2019)

Article Multidisciplinary Sciences

Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration

Andrew P. Voigt et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Pharmacology & Pharmacy

Larotrectinib: First Global Approval

Lesley J. Scott

DRUGS (2019)

Article Multidisciplinary Sciences

Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling

Qingnan Liang et al.

NATURE COMMUNICATIONS (2019)

Article Medicine, Research & Experimental

L-Citrulline increases nitric oxide and improves control in obese asthmatics

Fernando Holguin et al.

JCI INSIGHT (2019)

Article Biochemistry & Molecular Biology

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Denise N. Slenter et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Francisco Sanchez-Vega et al.

Article Multidisciplinary Sciences

HER kinase inhibition in patients with HER2-and HER3-mutant cancers

David M. Hyman et al.

NATURE (2018)

Article Chemistry, Medicinal

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

Joaquim Aguirre-Plans et al.

PHARMACEUTICALS (2018)

Article Mathematical & Computational Biology

A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection

Friederike Langhauser et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2018)

Article Multidisciplinary Sciences

NOX4-dependent neuronal autotoxicity and BBB breakdown explain the superior sensitivity of the brain to ischemic damage

Ana I. Casas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Pharmacology & Pharmacy

Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects

Matthieu Chartier et al.

BMC PHARMACOLOGY & TOXICOLOGY (2017)

Article Multidisciplinary Sciences

Simple and complex retinal dystrophies are associated with profoundly different disease networks

Christina Kiel et al.

SCIENTIFIC REPORTS (2017)

Review Pharmacology & Pharmacy

Critical Review of Umbrella, Basket, and Platform Designs for Oncology Clinical Trials

Richard Simon

CLINICAL PHARMACOLOGY & THERAPEUTICS (2017)

Article Oncology

The Microenvironmental Landscape of Brain Tumors

Daniela F. Quail et al.

CANCER CELL (2017)

Article Mathematical & Computational Biology

On the performance of de novo pathway enrichment

Richa Batra et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2017)

Article Hematology

Reactive Oxygen Species Can Provide Atheroprotection via NOX4-Dependent Inhibition of Inflammation and Vascular Remodeling

Stephen P. Gray et al.

ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY (2016)

Article Pharmacology & Pharmacy

Clinical Relevance of Cyclic GMP Modulators: A Translational Success Story of Network Pharmacology

J. M. Oettrich et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2016)

Article Endocrinology & Metabolism

NOS knockout or inhibition but not disrupting PSD-95-NOS interaction protect against ischemic brain damage

Christoph Kleinschnitz et al.

JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM (2016)

Review Pharmacology & Pharmacy

Precision Oncology Medicine: The Clinical Relevance of Patient-Specific Biomarkers Used to Optimize Cancer Treatment

Keith T. Schmidt et al.

JOURNAL OF CLINICAL PHARMACOLOGY (2016)

Correction Multidisciplinary Sciences

Universal resilience patterns in complex networks (vol 530, pg 307, 2016)

Jianxi Gao et al.

NATURE (2016)

News Item Multidisciplinary Sciences

New tricks for old drugs

Nicola Nosengo

NATURE (2016)

Article Multidisciplinary Sciences

Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets

Arunachalam Vinayagam et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Biochemistry & Molecular Biology

Pharmacology and Clinical Drug Candidates in Redox Medicine

V. Thao-Vi Dao et al.

ANTIOXIDANTS & REDOX SIGNALING (2015)

Review Biochemistry & Molecular Biology

Clinical Relevance of Biomarkers of Oxidative Stress

Jeroen Frijhoff et al.

ANTIOXIDANTS & REDOX SIGNALING (2015)

Editorial Material Multidisciplinary Sciences

Time for one-person trials

Nicholas J. Schork

NATURE (2015)

Article Multidisciplinary Sciences

Uncovering disease-disease relationships through the incomplete interactome

Joerg Menche et al.

SCIENCE (2015)

Article Multidisciplinary Sciences

Tissue-based map of the human proteome

Mathias Uhlen et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

NADPH Oxidase, NOX1, Mediates Vascular Injury in Ischemic Retinopathy

Jennifer L. Wilkinson-Berka et al.

ANTIOXIDANTS & REDOX SIGNALING (2014)

Article Cell Biology

Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

Deborah M. Cholon et al.

SCIENCE TRANSLATIONAL MEDICINE (2014)

Article Cardiac & Cardiovascular Systems

NADPH Oxidase 1 Plays a Key Role in Diabetes Mellitus-Accelerated Atherosclerosis

Stephen P. Gray et al.

CIRCULATION (2013)

Article Peripheral Vascular Disease

Animal Models in Obesity and Hypertension

Gabriella Segal-Lieberman et al.

CURRENT HYPERTENSION REPORTS (2013)

Review Oncology

Diagnostic, prognostic, and predictive biomarkers in pancreatic cancer

Jordan M. Winter et al.

JOURNAL OF SURGICAL ONCOLOGY (2013)

Article Multidisciplinary Sciences

Dysfunctional nitric oxide signalling increases risk of myocardial infarction

Jeanette Erdmann et al.

NATURE (2013)

Article Multidisciplinary Sciences

Mutational landscape and significance across 12 major cancer types

Cyriac Kandoth et al.

NATURE (2013)

Article Multidisciplinary Sciences

Genomic responses in mouse models poorly mimic human inflammatory diseases

Junhee Seok et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Multidisciplinary Sciences

Cancer Genome Landscapes

Bert Vogelstein et al.

SCIENCE (2013)

Article Biotechnology & Applied Microbiology

Exploring the human diseasome: the human disease network

Kwang-Il Goh et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2012)

Article Cardiac & Cardiovascular Systems

Personalized Cardiovascular Medicine and Drug Development Time for a New Paradigm

Joseph Loscalzo

CIRCULATION (2012)

Review Genetics & Heredity

NADPH oxidases as a source of oxidative stress and molecular target in ischemia/reperfusion injury

Pamela W. M. Kleikers et al.

JOURNAL OF MOLECULAR MEDICINE-JMM (2012)

Editorial Material Biotechnology & Applied Microbiology

Ivacaftor

Pamela B. Davis et al.

NATURE REVIEWS DRUG DISCOVERY (2012)

Article Biotechnology & Applied Microbiology

Diagnosing the decline in pharmaceutical R&D efficiency

Jack W. Scannell et al.

NATURE REVIEWS DRUG DISCOVERY (2012)

Review Biology

Animal models for the study of arterial hypertension

Waleska C. Dornas et al.

JOURNAL OF BIOSCIENCES (2011)

Letter Biotechnology & Applied Microbiology

Believe it or not: how much can we rely on published data on potential drug targets?

Florian Prinz et al.

NATURE REVIEWS DRUG DISCOVERY (2011)

Review Pharmacology & Pharmacy

Rationalizing the chemical space of protein-protein interaction inhibitors

Olivier Sperandio et al.

DRUG DISCOVERY TODAY (2010)

Editorial Material Biotechnology & Applied Microbiology

Patrick Vallance

Patrick Vallance

NATURE REVIEWS DRUG DISCOVERY (2010)

Article Biochemistry & Molecular Biology

Post-Stroke Inhibition of Induced NADPH Oxidase Type 4 Prevents Oxidative Stress and Neurodegeneration

Christoph Kleinschnitz et al.

PLOS BIOLOGY (2010)

Article Ethics

Are animal models predictive for humans?

Niall Shanks et al.

Philosophy Ethics and Humanities in Medicine (2009)

Review Oncology

Prognostic versus predictive value of biomarkers in oncology

C. N. A. M. Oldenhuis et al.

EUROPEAN JOURNAL OF CANCER (2008)

Review Biochemistry & Molecular Biology

Network pharmacology: the next paradigm in drug discovery

Andrew L. Hopkins

NATURE CHEMICAL BIOLOGY (2008)

Article Multidisciplinary Sciences

The human disease network

Kwang-Il Goh et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Clinical Neurology

1,026 experimental treatments in acute stroke

VE O'Collins et al.

ANNALS OF NEUROLOGY (2006)

Article Chemistry, Medicinal

sc-PDB: an annotated database of druggable binding sites from the protein data bank

E Kellenberger et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)

Article Biochemistry & Molecular Biology

DrugBank: a comprehensive resource for in silico drug discovery and exploration

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Chronic inhibition of cyclic GMP phosphodiesterase 5A prevents and reverses cardiac hypertrophy

E Takimoto et al.

NATURE MEDICINE (2005)

Article Biochemical Research Methods

PISCES: a protein sequence culling server

GL Wang et al.

BIOINFORMATICS (2003)

Review Medicine, General & Internal

Cystic fibrosis

F Ratjen et al.

LANCET (2003)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)