Research graph
References from Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase. Local targets link to admitted publications; unresolved targets remain external evidence.
Cooler: scalable storage for Hi-C data and other genomically labeled arrays
10.1093/bioinformatics/btz540 · 2020 · External reference
Cooltools: enabling high-resolution Hi-C analysis in Python
10.1371/journal.pcbi.1012067 · 2024 · External reference
Pairtools: From sequencing data to chromosome contacts
10.1371/journal.pcbi.1012164 · 2024 · External reference
Visualization of cell cycle in mouse embryos with Fucci2 reporter directed by Rosa26 promoter
10.1242/dev.084111 · 2013 · External reference
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase
10.1038/s41556-019-0406-2 · 2019 · External reference
Organization and function of the 3D genome
10.1038/nrg.2016.112 · 2016 · External reference
The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification
10.1038/ncb2965 · 2014 · External reference
Concise review: control of cell fate through cell cycle and pluripotency networks
10.1002/stem.2345 · 2016 · External reference
Rethinking synchronization of mammalian cells for cell cycle analysis
10.1007/s00018-003-2253-2 · 2003 · External reference
Condensin-driven remodelling of X chromosome topology during dosage compensation
10.1038/nature14450 · 2015 · External reference
Chromosome territories, nuclear architecture and gene regulation in mammalian cells
10.1038/35066075 · 2001 · External reference
Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
10.1101/gr.183699.114 · 2015 · External reference
The spatial position and replication timing of chromosomal domains are both established in early G1 phase
10.1016/s1097-2765(00)80227-0 · 1999 · External reference
Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments
10.1016/j.cels.2016.07.002 · 2016 · External reference
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
10.1038/nature21711 · 2017 · External reference
Major nuclear locales define nuclear genome organization and function beyond A and B compartments
10.7554/elife.99116 · 2025 · External reference
A pathway for mitotic chromosome formation
10.1126/science.aao6135 · 2018 · External reference
Dynamics of microcompartment formation at the mitosis-to-G1 transition
10.1038/s41594-025-01687-2 · 2025 · External reference
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
10.7554/elife.25776 · 2017 · External reference
Array programming with NumPy
10.1038/s41586-020-2649-2 · 2020 · External reference
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization
10.1038/s41467-023-38429-1 · 2023 · External reference
The UCSC genome browser database: update 2006
10.1093/nar/gkj144 · 2006 · External reference
Global reorganization of replication domains during embryonic stem cell differentiation
10.1371/journal.pbio.0060245 · 2008 · External reference
Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
10.1093/gigascience/giz158 · 2020 · External reference
Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation
10.1101/gad.335794.119 · 2020 · External reference
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
10.1186/s13059-020-02215-9 · 2020 · External reference
FAN-c: framework for the analysis of c-like data
2024 · External reference
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
10.1126/science.1181369 · 2009 · External reference
Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes
10.1038/s41467-021-22666-3 · 2021 · External reference
Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq
10.1126/science.adg3797 · 2023 · External reference
Fork coupling directs DNA replication elongation and termination
10.1126/science.adj7606 · 2024 · External reference
Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
10.1093/nar/gkaf549 · 2025 · External reference
CALDER2
2026 · External reference
pyGenomeTracks: reproducible plots for multivariate genomic datasets
10.1093/bioinformatics/btaa692 · 2021 · External reference
Genomic repeats categorize genes with distinct functions for orchestrated regulation
10.1016/j.celrep.2020.02.048 · 2020 · External reference
Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome
10.1038/s41422-020-00466-6 · 2021 · External reference
Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments
10.1186/s12859-022-04654-6 · 2022 · External reference
Pentad
2026 · External reference
Direct imaging of DNA in living cells reveals the dynamics of chromosome formation
10.1083/jcb.144.5.813 · 1999 · External reference
Cutadapt removes adapter sequences from high-throughput sequencing reads
10.14806/ej.17.1.200 · 2011 · External reference
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization
10.1038/s41588-019-0474-z · 2019 · External reference
Choice of random rather than imprinted X inactivation in female embryonic stem cell-derived extra-embryonic cells
10.1242/dev.056606 · 2011 · External reference
Cell-cycle dynamics of chromosomal organization at single-cell resolution
10.1038/nature23001 · 2017 · External reference
Organization of the mitotic chromosome
10.1126/science.1236083 · 2013 · External reference
Nuclear compartmentalization at the G1/S transition plays a key role in DNA replication control
10.1038/s41467-026-75264-6 · 2026 · External reference
Replisome loading reduces chromatin motion independent of DNA synthesis
10.7554/elife.87572 · 2023 · External reference
A new class of disordered elements controls DNA replication through initiator self-assembly
10.7554/elife.48562 · 2019 · External reference
H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization
10.1016/j.molcel.2021.02.032 · 2021 · External reference
Replication dynamics identifies the folding principles of the inactive X chromosome
10.1038/s41594-023-01052-1 · 2023 · External reference
Topologically associating domains are stable units of replication-timing regulation
10.1038/nature13986 · 2014 · External reference
BEDTools: a flexible suite of utilities for comparing genomic features
10.1093/bioinformatics/btq033 · 2010 · External reference
deepTools2: a next generation web server for deep-sequencing data analysis
10.1093/nar/gkw257 · 2016 · External reference
Cohesin loss eliminates all loop domains
10.1016/j.cell.2017.09.026 · 2017 · External reference
Visualizing spatiotemporal dynamics of multicellular cell-cycle progression
10.1016/j.cell.2007.12.033 · 2008 · External reference
Rules of engagement for condensins and cohesins guide mitotic chromosome formation
10.1126/science.adq1709 · 2025 · External reference
Fiji: an open-source platform for biological-image analysis
10.1038/nmeth.2019 · 2012 · External reference
Using and understanding RepeatMasker
10.1007/978-1-61779-603-6_2 · 2012 · External reference
TrackMate: an open and extensible platform for single-particle tracking
10.1016/j.ymeth.2016.09.016 · 2017 · External reference
GenomeFlow
2019 · External reference
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure
10.1093/bioinformatics/bty802 · 2019 · External reference
Cell cycle dynamics of lamina-associated DNA
10.15252/embr.202050636 · 2020 · External reference
Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression
10.1016/j.cell.2017.04.022 · 2017 · External reference
Spontaneous reactivation of the inactive X chromosome in mouse embryonal carcinoma cells
10.1159/000071573 · 2002 · External reference
Chromatin structure dynamics during the mitosis-to-G1 phase transition
10.1038/s41586-019-1778-y · 2019 · External reference
CTCF and transcription influence chromatin structure re-configuration after mitosis
10.1038/s41467-021-25418-5 · 2021 · External reference
Cell cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase
2026 · External reference
Cell cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase
2026 · External reference
Hi-C data analyses_custom code
10.5281/zenodo.20552820 · 2026 · External reference
Fucci_mESC_timelapse_imaging
10.5281/zenodo.17509930 · 2026 · External reference
L1/B1-EdU DNA FISH
10.5281/zenodo.20473330 · 2026 · External reference
DNA_FISH_A_compartment_consolidation
10.5281/zenodo.20552838 · 2026 · External reference
Cell cycle dynamics of chromosomal organisation at single-cell resolution
2017 · External reference
Linking genome structures to functions during lineage specification by simultaneous single-cell Hi-C and RNA-seq simultaneous single-cell Hi-C and RNA-seq
2023 · External reference
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
2017 · External reference
