ArticleNucleic acids research2021
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-omics time-series analysis in microbiome research: a systematic review.Briefings in bioinformatics · 2025Pooled it
- Pathway potency in methylation altered network reveals lung cancer branching evolution and hallmarks.iScience · 2026Article
- Network-informed deconvolution of bulk immune gene co-expression reveals single-cell programs and spatial organization.Frontiers in immunology · 2026Article
- Temporal network analysis in systems biology: concepts, inference, and validation.Frontiers in bioinformatics · 2026Review
- Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives.Journal of advanced research · 2025Review
- MicroRNAs in long COVID: roles, diagnostic biomarker potential and detection.Human genomics · 2025Review
- A multi-step completion process model of cell plasticity.Briefings in bioinformatics · 2025Article
- iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments.Analytical chemistry · 2025Article
- BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells.Briefings in bioinformatics · 2024Article
- ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities.Bioinformatics (Oxford, England) · 2024Article
- Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks.Bioinformatics (Oxford, England) · 2024Article
- Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics.Stem cell research & therapy · 2023Article
- Computational approaches to understand transcription regulation in development.Biochemical Society transactions · 2023Review
- The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in bioinformatics · 2023Article
- From multi-omics approaches to personalized medicine in myocardial infarction.Frontiers in cardiovascular medicine · 2023Review
- MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks.Computational and structural biotechnology journal · 2022Article
- Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Uncovering how transcription factors regulate their targets at DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) and assign mechanisms in normal and diseased states. RNA-seq is a standard method measuring gene regulation using an established set of analysis stages. However, none of the currently available pipeline methods for interpreting ordered genomic data (in time or space) use time-series models to assign cause and effect relationships within GRNs, are adaptive to diverse experimental designs, or enable user interpretation through a web-based platform. Furthermore, methods integrating ordered RNA-seq data with protein-DNA binding data to distinguish direct from indirect interactions are urgently needed. We present TIMEOR (Trajectory Inference and Mechanism Exploration with Omics data in R), the first web-based and adaptive time-series multi-omics pipeline method which infers the relationship between gene regulatory events across time. TIMEOR addresses the critical need for methods to determine causal regulatory mechanism networks by leveraging time-series RNA-seq, motif analysis, protein-DNA binding data, and protein-protein interaction networks. TIMEOR's user-catered approach helps non-coders generate new hypotheses and validate known mechanisms. We used TIMEOR to identify a novel link between insulin stimulation and the circadian rhythm cycle. TIMEOR is available at https://github.com/ashleymaeconard/TIMEOR.git and http://timeor.brown.edu.
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Registered trials
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