ArticleGenome research2020
Analysis of Hi-C data using SIP effectively identifies loops in organisms from
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed, 122 citations in OpenAlex.
- TFIIIC regulates SMC complex binding and 3D DNA contacts between tRNA genes.bioRxiv : the preprint server for biology · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.Genome biology · 2026Article
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- TM-Loop: Transformer multi-omics hierarchical detection of chromatin loop.Scientific reports · 2026Article
- Condensin IDC has a functional ATPase that is required for X-Chromosome dosage compensation in C. elegans.Genetics · 2026Article
- Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse.Communications biology · 2026Article
- Establishment and Maintenance of Repressed Chromatin States on Dosage-Compensated Sex Chromosomes.Biomolecules · 2026Review
- Unique territorial and compartmental organization of chromosomes in the holocentric silkworm.The EMBO journal · 2026Article
- Robin: an advanced tool for comparative loop caller result analysis leveraging large language models.NAR genomics and bioinformatics · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- CNNKSCEC: a deep learning-based framework for chromatin loop prediction with multi-source feature integration.Frontiers in genetics · 2026Article
- Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping.bioRxiv : the preprint server for biology · 2025Article
- Pathogenicity of Mediator Complex Subunit 27 (MED27) in a Neurodevelopmental Disorder with Cerebellar Atrophy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.bioRxiv : the preprint server for biology · 2025Article
- Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and function.Epigenetics & chromatin · 2025Article
- Article
- Unveiling Multi-Scale Architectural Features in Single-Cell Hi-C Data Using scCAFE.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Divergent 3D genome organization in livers of cave and surface morphs ofbioRxiv : the preprint server for biology · 2025Article
- Cohesin organizes 3D DNA contacts surrounding active enhancers inGenome research · 2025Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Chromatin loops are a major component of 3D nuclear organization, visually apparent as intense point-to-point interactions in Hi-C maps. Identification of these loops is a critical part of most Hi-C analyses. However, current methods often miss visually evident CTCF loops in Hi-C data sets from mammals, and they completely fail to identify high intensity loops in other organisms. We present SIP, Significant Interaction Peak caller, and SIPMeta, which are platform independent programs to identify and characterize these loops in a time- and memory-efficient manner. We show that SIP is resistant to noise and sequencing depth, and can be used to detect loops that were previously missed in human cells as well as loops in other organisms. SIPMeta corrects for a common visualization artifact by accounting for Manhattan distance to create average plots of Hi-C and HiChIP data. We then demonstrate that the use of SIP and SIPMeta can lead to biological insights by characterizing the contribution of several transcription factors to CTCF loop stability in human cells. We also annotate loops associated with the SMC component of the dosage compensation complex (DCC) in
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Registered trials
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.