ArticleNucleus (Austin, Tex.)2021
4DNvestigator: time series genomic data analysis toolbox.
Article in Nucleus (Austin, Tex.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Genomic insights into chromosomal fusion and its evolutionary implications for zokors.Molecular biology and evolution · 2026Article
- Remodeling of three-dimensional genome architecture in cardiac development and aging.BMC genomics · 2026Article
- A Survey on Hyperlink Prediction.IEEE transactions on neural networks and learning systems · 2024Article
- Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens.Nature communications · 2024Article
- Reprogramming of 3D genome structure underlying HSPC development in zebrafish.Stem cell research & therapy · 2024Article
- Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet.Journal of animal science and biotechnology · 2024Article
- InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration.Database : the journal of biological databases and curation · 2023Article
- Deciphering multi-way interactions in the human genome.Nature communications · 2022Article
- Rearrangement of T Cell genome architecture regulates GVHD.iScience · 2022Article
- Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver.Cell discovery · 2022Article
- Generation and characterization of stable pig pregastrulation epiblast stem cell lines.Cell research · 2022Article
- Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis.Nature communications · 2022Article
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Authors and funding
7 authors.
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Abstract
Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the '4DNvestigator', a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.