Multi-omic network inference from time-series data
Abstract Biological phenotypes emerge from complex interactions across molecular layers. Yet, data-driven approaches to infer these regulatory networks have primarily focused on single-omic studies, overlooking inter-layer regulatory relationships. To address these limitations, we developed MINIE, a...
| Published in: | npj Systems Biology and Applications |
|---|---|
| Main Authors: | María Moscardó García, Atte Aalto, Arthur N. Montanari, Alexander Skupin, Jorge Gonçalves |
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-10-01
|
| Online Access: | https://doi.org/10.1038/s41540-025-00591-1 |
Similar Items
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease
by: Katarina Mihajlović, et al.
Published: (2024-05-01)
by: Katarina Mihajlović, et al.
Published: (2024-05-01)
Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data
by: Daniel Ruiz-Perez, et al.
Published: (2021-04-01)
by: Daniel Ruiz-Perez, et al.
Published: (2021-04-01)
Integrative multi-omics module network inference with Lemon-Tree.
by: Eric Bonnet, et al.
Published: (2015-02-01)
by: Eric Bonnet, et al.
Published: (2015-02-01)
MultiGNN: A Graph Neural Network Framework for Inferring Gene Regulatory Networks from Single-Cell Multi-Omics Data
by: Dongbo Liu, et al.
Published: (2025-05-01)
by: Dongbo Liu, et al.
Published: (2025-05-01)
A generalized higher-order correlation analysis framework for multi-omics network inference.
by: Weixuan Liu, et al.
Published: (2025-04-01)
by: Weixuan Liu, et al.
Published: (2025-04-01)
Time Series Forecasting with Missing Data Using Generative Adversarial Networks and Bayesian Inference
by: Xiaoou Li
Published: (2024-04-01)
by: Xiaoou Li
Published: (2024-04-01)
Leveraging multi-omics data to infer regulators of mRNA 3’ end processing in glioblastoma
by: Aleksei Mironov, et al.
Published: (2024-08-01)
by: Aleksei Mironov, et al.
Published: (2024-08-01)
Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization
by: Weixuan Liu, et al.
Published: (2024-08-01)
by: Weixuan Liu, et al.
Published: (2024-08-01)
Overview of observational data-based time series causal inference
by: Zefan ZENG, et al.
Published: (2023-07-01)
by: Zefan ZENG, et al.
Published: (2023-07-01)
Integrated Multi-Omics Analysis for Inferring Molecular Players in Inclusion Body Myositis
by: Judith Cantó-Santos, et al.
Published: (2023-08-01)
by: Judith Cantó-Santos, et al.
Published: (2023-08-01)
Synthesizing Time-Series Gene Expression Data to Enhance Network Inference Performance Using Autoencoder
by: Cao-Tuan Anh, et al.
Published: (2025-05-01)
by: Cao-Tuan Anh, et al.
Published: (2025-05-01)
Approximate inference of gene regulatory network models from RNA-Seq time series data
by: Thomas Thorne
Published: (2018-04-01)
by: Thomas Thorne
Published: (2018-04-01)
Systematic analysis and optimization of early warning signals for critical transitions using distribution data
by: Daniele Proverbio, et al.
Published: (2023-07-01)
by: Daniele Proverbio, et al.
Published: (2023-07-01)
Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA
by: Daniel Ruiz-Perez, et al.
Published: (2024-10-01)
by: Daniel Ruiz-Perez, et al.
Published: (2024-10-01)
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data
by: Stefano Magni, et al.
Published: (2024-05-01)
by: Stefano Magni, et al.
Published: (2024-05-01)
scapGNN: A graph neural network-based framework for active pathway and gene module inference from single-cell multi-omics data.
by: Xudong Han, et al.
Published: (2023-11-01)
by: Xudong Han, et al.
Published: (2023-11-01)
Causal network inference from gene transcriptional time-series response to glucocorticoids.
by: Jonathan Lu, et al.
Published: (2021-01-01)
by: Jonathan Lu, et al.
Published: (2021-01-01)
The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data
by: Suzanne Paley, et al.
Published: (2024-01-01)
by: Suzanne Paley, et al.
Published: (2024-01-01)
A novel mutual information-based Boolean network inference method from time-series gene expression data.
by: Shohag Barman, et al.
Published: (2017-01-01)
by: Shohag Barman, et al.
Published: (2017-01-01)
RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
by: Masato Ishikawa, et al.
Published: (2023-12-01)
by: Masato Ishikawa, et al.
Published: (2023-12-01)
Stochastic models allow improved inference of microbiome interactions from time series data.
by: Román Zapién-Campos, et al.
Published: (2024-11-01)
by: Román Zapién-Campos, et al.
Published: (2024-11-01)
From time-series transcriptomics to gene regulatory networks: A review on inference methods.
by: Malvina Marku, et al.
Published: (2023-08-01)
by: Malvina Marku, et al.
Published: (2023-08-01)
The chronODE framework for modelling multi-omic time series with ordinary differential equations and machine learning
by: Beatrice Borsari, et al.
Published: (2025-08-01)
by: Beatrice Borsari, et al.
Published: (2025-08-01)
MOTA: Network-Based Multi-Omic Data Integration for Biomarker Discovery
by: Ziling Fan, et al.
Published: (2020-04-01)
by: Ziling Fan, et al.
Published: (2020-04-01)
MOSBY enables multi-omic inference and spatial biomarker discovery from whole slide images
by: Yasin Şenbabaoğlu, et al.
Published: (2024-08-01)
by: Yasin Şenbabaoğlu, et al.
Published: (2024-08-01)
GraphOmics: an interactive platform to explore and integrate multi-omics data
by: Joe Wandy, et al.
Published: (2021-12-01)
by: Joe Wandy, et al.
Published: (2021-12-01)
Visual analysis of multi-omics data
by: Austin Swart, et al.
Published: (2024-09-01)
by: Austin Swart, et al.
Published: (2024-09-01)
OmicsON - Integration of omics data with molecular networks and statistical procedures.
by: Cezary Turek, et al.
Published: (2020-01-01)
by: Cezary Turek, et al.
Published: (2020-01-01)
Multi‐sample inference network
by: Daojun Liang, et al.
Published: (2019-09-01)
by: Daojun Liang, et al.
Published: (2019-09-01)
Multi-omic network signatures of disease
by: David L Gibbs, et al.
Published: (2014-01-01)
by: David L Gibbs, et al.
Published: (2014-01-01)
Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets
by: Ricard Argelaguet, et al.
Published: (2018-06-01)
by: Ricard Argelaguet, et al.
Published: (2018-06-01)
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data
by: Henriette Miko, et al.
Published: (2021-01-01)
by: Henriette Miko, et al.
Published: (2021-01-01)
Peeling back the layers of coral holobiont multi-omics data
by: Amanda Williams, et al.
Published: (2023-09-01)
by: Amanda Williams, et al.
Published: (2023-09-01)
JOB: Japan Omics Browser provides integrative visualization of multi-omics data
by: Yugo Takahashi, et al.
Published: (2025-05-01)
by: Yugo Takahashi, et al.
Published: (2025-05-01)
MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer
by: Xiaoying Wang, et al.
Published: (2024-01-01)
by: Xiaoying Wang, et al.
Published: (2024-01-01)
MULTI-LABEL PREDICTION IN TIME SERIES DATA USING DEEP NEURAL NETWORKS
by: Wenyu Zhang, et al.
Published: (2019-12-01)
by: Wenyu Zhang, et al.
Published: (2019-12-01)
Multi-fusion strategy network-guided cancer subtypes discovering based on multi-omics data
by: Jian Liu, et al.
Published: (2024-11-01)
by: Jian Liu, et al.
Published: (2024-11-01)
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data
by: Arno van Hilten, et al.
Published: (2024-08-01)
by: Arno van Hilten, et al.
Published: (2024-08-01)
Patient-Specific Network for Personalized Breast Cancer Therapy with Multi-Omics Data
by: Claudia Cava, et al.
Published: (2021-02-01)
by: Claudia Cava, et al.
Published: (2021-02-01)
PaCMAP-embedded convolutional neural network for multi-omics data integration
by: Hazem Qattous, et al.
Published: (2024-01-01)
by: Hazem Qattous, et al.
Published: (2024-01-01)
Similar Items
-
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease
by: Katarina Mihajlović, et al.
Published: (2024-05-01) -
Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data
by: Daniel Ruiz-Perez, et al.
Published: (2021-04-01) -
Integrative multi-omics module network inference with Lemon-Tree.
by: Eric Bonnet, et al.
Published: (2015-02-01) -
MultiGNN: A Graph Neural Network Framework for Inferring Gene Regulatory Networks from Single-Cell Multi-Omics Data
by: Dongbo Liu, et al.
Published: (2025-05-01) -
A generalized higher-order correlation analysis framework for multi-omics network inference.
by: Weixuan Liu, et al.
Published: (2025-04-01)
