4.7 Article

SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets

Related references

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

synergy: a Python library for calculating, analyzing and visualizing drug combination synergy

David J. Wooten et al.

Summary: Combining multiple pharmacological agents can provide significant benefits over single agent treatment, with synergistic combinations exceeding the sum of their parts. The Synergy Python library offers a wide range of synergy models, tools for evaluating confidence intervals and conducting power analysis, as well as standardized tools for analyzing and visualizing drug combinations and their synergies and antagonisms.

BIOINFORMATICS (2021)

Article Computer Science, Information Systems

Anticancer drug synergy prediction in understudied tissues using transfer learning

Yejin Kim et al.

Summary: The study aimed to develop a drug synergy prediction model to address the imbalance in research among different cancer tissues. The results showed improved prediction accuracy in both data-rich and understudied tissues.

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2021)

Article Multidisciplinary Sciences

The tumor therapy landscape of synthetic lethality

Biyu Zhang et al.

Summary: Synthetic lethality is becoming an important cancer therapeutic paradigm, but comprehensive selective treatment opportunities for various tumors have not been fully explored. The Synthetic Lethality Knowledge Graph (SLKG) integrates data on different tumors, drugs, and drug targets to provide therapy options for synthetic lethality and synthetic dosage lethality, prioritizing the identification of repurposable drug candidates and combinations with supporting evidence for novel tumor therapy discovery.

NATURE COMMUNICATIONS (2021)

Article Oncology

The Aurora kinase/β-catenin axis contributes to dexamethasone resistance in leukemia

Kinjal Shah et al.

Summary: Glucocorticoids are commonly used in cancer treatment, and this study found that sensitivity to dexamethasone is correlated with gene expression patterns in patients with acute lymphoblastic leukemia. Resistance to dexamethasone may involve key signaling proteins such as Aurora kinase, S6K, and others.

NPJ PRECISION ONCOLOGY (2021)

Article Pharmacology & Pharmacy

An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine

Michelle Whirl-Carrillo et al.

Summary: Clinical annotations in PharmGKB summarize the association between variant-drug pairs and are assigned a level of evidence. To ensure consistency and transparency, a scoring system has been developed to automate LOE assignment. This system improves the quality and reliability of clinical annotations.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Article Biochemistry & Molecular Biology

DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal

Shuyu Zheng et al.

Summary: DrugComb is an online portal for the deposition and analysis of drug combination screening datasets, continuously updated to improve functionality and coverage, providing convenience for research on multiple diseases.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

PubChem in 2021: new data content and improved web interfaces

Sunghwan Kim et al.

Summary: PubChem, a popular chemical information resource, has made substantial improvements in the past two years by adding data from over 100 new sources, updating its homepage and record pages, introducing new services like the Periodic Table and Pathway pages, and creating a special data collection related to COVID-19 and SARS-CoV-2 in response to the pandemic.

NUCLEIC ACIDS RESEARCH (2021)

Review Pharmacology & Pharmacy

Charting the Fragmented Landscape of Drug Synergy

Christian T. Meyer et al.

TRENDS IN PHARMACOLOGICAL SCIENCES (2020)

Editorial Material Microbiology

Resisting antimicrobial resistance

Carl Nathan

NATURE REVIEWS MICROBIOLOGY (2020)

Article Biochemistry & Molecular Biology

SynergyFinder 2.0: visual analytics of multi-drug combination synergies

Aleksandr Ianevski et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Biochemistry & Molecular Biology

Perspective Rational Cancer Treatment Combinations: An Urgent Clinical Need

Julia Boshuizen et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

Guided screen for synergistic three-drug combinations

Melike Cokol-Cakmak et al.

PLOS ONE (2020)

Article Multidisciplinary Sciences

Multiple low dose therapy as an effective strategy to treat EGFR inhibitor-resistant NSCLC tumours

Joao M. Fernandes Neto et al.

NATURE COMMUNICATIONS (2020)

Article Chemistry, Medicinal

Modulation of Triple Artemisinin-Based Combination Therapy Pharmacodynamics by Plasmodium falciparum Genotype

Megan R. Ansbro et al.

ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE (2020)

Article Biochemistry & Molecular Biology

DrugComb: an integrative cancer drug combination data portal

Bulat Zagidullin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer

Alina Malyutina et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Multidisciplinary Sciences

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Michael P. Menden et al.

NATURE COMMUNICATIONS (2019)

Review Pharmacology & Pharmacy

Applying synergy metrics to combination screening data: agreements, disagreements and pitfalls

Anna H. C. Vlot et al.

DRUG DISCOVERY TODAY (2019)

Review Multidisciplinary Sciences

A view on drug resistance in cancer

Neil Vasan et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

ChEMBL: towards direct deposition of bioassay data

David Mendez et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Oncology

Epigenetic therapy in immune-oncology

Peter A. Jones et al.

NATURE REVIEWS CANCER (2019)

Article Biochemistry & Molecular Biology

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

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Oncology

Network Propagation Predicts Drug Synergy in Cancers

Hongyang Li et al.

CANCER RESEARCH (2018)

Article Biochemical Research Methods

DeepSynergy: predicting anti-cancer drug synergy with Deep Learning

Kristina Preuer et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

SynergyFinder: a web application for analyzing drug combination dose-response matrix data

Aleksandr Ianevski et al.

BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

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

Michael K. Gilson et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Combenefit: an interactive platform for the analysis and visualization of drug combinations

Giovanni Y. Di Veroli et al.

BIOINFORMATICS (2016)

Article Oncology

An Unbiased Oncology Compound Screen to Identify Novel Combination Strategies

Jennifer O'Neil et al.

MOLECULAR CANCER THERAPEUTICS (2016)

Article Multidisciplinary Sciences

BRAID: A Unifying Paradigm for the Analysis of Combined Drug Action

Nathaniel R. Twarog et al.

SCIENTIFIC REPORTS (2016)

Article Chemistry, Medicinal

ZINC 15-Ligand Discovery for Everyone

Teague Sterling et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)

Review Pharmacology & Pharmacy

What is synergy? The Saariselka agreement revisited

Jing Tang et al.

FRONTIERS IN PHARMACOLOGY (2015)

Article Biochemistry & Molecular Biology

Searching for Drug Synergy in Complex Dose-Response Landscapes Using an Interaction Potency Model

Bhagwan Yadav et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2015)

Article Multidisciplinary Sciences

Mechanism-independent method for predicting response to multidrug combinations in bacteria

Kevin Wood et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Medicine, General & Internal

How to obtain the P value from a confidence interval

Douglas G. Altman et al.

BMJ-BRITISH MEDICAL JOURNAL (2011)