4.7 Review

A pleiotropic-epistatic entangelement model of drug response

Related references

Note: Only part of the references are listed.
Review Biology

Epistasis and evolution: recent advances and an outlook for prediction

Milo S. Johnson et al.

Summary: As organisms evolve, the effects of mutations change due to interactions with other accumulated mutations. This leads to adaptability or robustness shifts that shape subsequent evolution. Recent advances in measuring, modeling, and predicting epistasis along evolutionary trajectories are reviewed, focusing on simple patterns of global epistasis that emerge in data. These patterns can be predicted by a small number of variables, offering promise for modeling epistasis and predicting evolution.

BMC BIOLOGY (2023)

Article Biochemical Research Methods

Predicting anti-cancer drug combination responses with a temporal cell state network model

Deepraj Sarmah et al.

Summary: Cancer chemotherapy combines multiple drugs, but predicting the effects of drug combinations on cancer cell proliferation remains challenging. The study explored the possibility of building a computational model that predicts drug combination response based on feasible single drug response experiments. The researchers tested this idea using simple cell culture systems and found good agreement between computational model predictions and experimental measurements. This work demonstrates how currently available or attainable information could be sufficient for prediction of drug combination responses.

PLOS COMPUTATIONAL BIOLOGY (2023)

Review Pharmacology & Pharmacy

A personalized pharmaco-epistatic network model of precision medicine

Li Feng et al.

Summary: Precision medicine relies on understanding the genetic causes of an individual's drug response. The functional graph (FunGraph) theory presented here combines functional mapping and evolutionary game theory to chart comprehensive pharmacogenetic architecture for each patient. FunGraph visualizes and investigates the movement of epistasis in cells and how it relates to patient-specific genetic architecture in response to organismic physiology. The future implementation of FunGraph for precision medicine is discussed.

DRUG DISCOVERY TODAY (2023)

Article Psychology, Clinical

Genetic correlation, pleiotropy, and causal associations between substance use and psychiatric disorder

Seon-Kyeong Jang et al.

Summary: This study uses genetically informative methods to investigate the genetic etiology of substance use and psychiatric disorders. The findings suggest that there is a high degree of pleiotropy and shared neurodevelopmental pathways, neurotransmission, and intracellular trafficking involved in these conditions.

PSYCHOLOGICAL MEDICINE (2022)

Article Cell Biology

A Single-Cell Omics Network Model of Cell Crosstalk during the Formation of Primordial Follicles

Qian Wang et al.

Summary: In this study, a computational model was developed to investigate the molecular mechanisms underlying the interaction between fetal germ cells and surrounding granulosa cells. By analyzing single-cell RNA-seq data of human embryos, previously unknown mechanisms of follicle development were identified.

CELLS (2022)

Article Anesthesiology

Mechanism-based pharmacodynamic model for propofol haemodynamic effects in healthy volunteers

Hong Su et al.

Summary: We developed a mechanism-based pharmacodynamic model to quantitatively characterize the magnitude of propofol-induced hemodynamic effects during general anesthesia. This model has the potential to predict hemodynamic alterations and may have clinical implications.

BRITISH JOURNAL OF ANAESTHESIA (2022)

Article Gastroenterology & Hepatology

Modeling spatial interaction networks of the gut microbiota

Xiaocang Cao et al.

Summary: This study integrates different theories to infer quasi-dynamic microbial networks from static abundance data, revealing various characteristics of microbial interactions and demonstrating their dynamic adaptability across space.

GUT MICROBES (2022)

Review Physics, Multidisciplinary

Recovering dynamic networks in big static datasets

Rongling Wu et al.

Summary: The promise of big data lies in its potential to uncover important interdependencies among thousands of variables, with networks emerging as a powerful tool for detecting these connections. However, utilizing networks to extract useful information from big data presents conceptual, technical, and computational challenges.

PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS (2021)

Article Biochemical Research Methods

EpiGraphDB: a database and data mining platform for health data science

Yi Liu et al.

Summary: The study developed EpiGraphDB, a graph database and analytical platform for human population health data science. Three case studies demonstrated the practical value of the platform, including addressing mis-inference, identifying new drug targets, and integrating evidence from different sources.

BIOINFORMATICS (2021)

Review Pharmacology & Pharmacy

100 years of modelling ligand-receptor binding and response: A focus on GPCRs

David B. Finlay et al.

BRITISH JOURNAL OF PHARMACOLOGY (2020)

Article Biochemistry & Molecular Biology

Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping

Kerry A. Geiler-Samerotte et al.

PLOS BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Quantifying Drug Combination Synergy along Potency and Efficacy Axes

Christian T. Meyer et al.

CELL SYSTEMS (2019)

Article Genetics & Heredity

The Causes and Consequences of Genetic Interactions (Epistasis)

Júlia Domingo et al.

Annual Review of Genomics and Human Genetics (2019)

Article Mathematical & Computational Biology

An omnidirectional visualization model of personalized gene regulatory networks

Chixiang Chen et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2019)

Article Pharmacology & Pharmacy

Understanding and reducing complex systems pharmacology models based on a novel input-response index

Jane Knoechel et al.

JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS (2018)

Review Biochemistry & Molecular Biology

An Expanded View of Complex Traits: From Polygenic to Omnigenic

Evan A. Boyle et al.

Article Biotechnology & Applied Microbiology

Computational identification of genes modulating stem height-diameter allometry

Libo Jiang et al.

PLANT BIOTECHNOLOGY JOURNAL (2016)

Review Biology

Mapping complex traits as a dynamic system

Lidan Sun et al.

PHYSICS OF LIFE REVIEWS (2015)

Article Pharmacology & Pharmacy

Pharmacodynamic Models: Parameterizing the Hill Equation, Michaelis-Menten, the Logistic Curve, and Relationships Among These Models

Russell Reeve et al.

JOURNAL OF BIOPHARMACEUTICAL STATISTICS (2013)

Article History & Philosophy Of Science

The Hill equation and the origin of quantitative pharmacology

Rudolf Gesztelyi et al.

ARCHIVE FOR HISTORY OF EXACT SCIENCES (2012)

Article Genetics & Heredity

Sequencing drug response with HapMap

M Lin et al.

PHARMACOGENOMICS JOURNAL (2005)