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Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...://creativecommons.org/licenses/by-nc/4.0/.References ↵Abdennur N, Mirny LA. 2020. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36: 311–316. doi:10.1093/bioinformatics/btz540 ↵Ay F, Bailey TL, Noble WS. 2014. Statistical confidence estimation for Hi-C data reveals regulatory chromatin...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...performer, better preserving the signal’s shape. Our codebase and benchmarks provide practical tools for high-resolution chromatin modeling.Predicting chromatin accessibility from DNA sequence is one of the central challenges in regulatory genomics, with applications including the interpretation...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...and regulatory pattern of enhancers were poorly investigated in insects, and the dynamic changes of enhancer contacts and functions under different conditions remain elusive. Here, combining Hi-C, ATAC-seq, and H3K27ac ChIP-seq data, we generate the -wide enhancer–gene map of silkworm and identify super...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...hypothesized that epigenetic perturbation of R3 would alter chromatin conformation surrounding MYH6. We examined chromatin conformation by probe-enriched Hi-C of accessible regions (HiCARs) on treated iPSC-CMs and HL-1 cells (Supplemental Fig. S10; Wei et al. 2022). We found that R3 and C3 interact...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...). Taking IMR-90 as an example (from the hg19 assembly), the long-range cis-regulatory interactions (greater than megabases) may be weak or even undetected in raw Hi-C data at 40-kb resolution; these interactions are more significant treated by CTG (Supplemental Figs. S4, S5). The Hi-C contact matrix...
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Method: Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals
- M. Jordan Rowley,
- Axel Poulet,
- Michael H. Nichols,
- Brianna J. Bixler,
- Adrian L. Sanborn,
- Elizabeth A. Brouhard,
- Karen Hermetz,
- Hannah Linsenbaum,
- Gyorgyi Csankovszki,
- Erez Lieberman Aiden,
- and Victor G. Corces
Genome Res. March 2020 30: 447-458; Published in Advance March 3, 2020, doi:10.1101/gr.257832.119
...to extrude DNA (Lau and Csankovszki 2014). However, although published Hi-C contact maps reveal the presence of large self-interacting domains in the dosage-compensated X Chromosome and evidence of loop formation, current algorithms have not been successful at systematically annotating punctate signals...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...per condition, for a total of 355 nuclei. Statistical testing was done with two-tailed t-tests using GraphPad Prism (version 9.3.0).CTCF HiChIPHiChIP was performed in duplicate in both LGK (Wnt-OFF) and CHIR99021 (Wnt-ON)-treated cell lines using the Arima-HiC+ kit (Arima, Cat. #A101020) and according...
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Method: HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
- Tao Yang,
- Feipeng Zhang,
- Galip Gürkan Yardımcı,
- Fan Song,
- Ross C. Hardison,
- William Stafford Noble,
- Feng Yue,
- and Qunhua Li
Genome Res. November 2017 27: 1939-1949; Published in Advance August 30, 2017, doi:10.1101/gr.220640.117
..., Noble WS. 2014. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res 24: 999–1011. Bickmore WA. 2013. The spatial organization of the human . Annu Rev Genomics Hum Genet 14: 67–84. Casella G, Berger GL. 2002. Statistical inference, 2nd ed. Duxbury Press...
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Method: Chromatin interaction–aware gene regulatory modeling with graph attention networks
- Alireza Karbalayghareh,
- Merve Sahin,
- and Christina S. Leslie
Genome Res. May 2022 32: 930-944; Published in Advance April 8, 2022, doi:10.1101/gr.275870.121
...sequence data (Seq-GraphReg) with 3D chromatin interaction data from HiChIP, Hi-C, Micro-C, or HiCAR via a graph neural network to predict gene expression. The 1D input data can include any standard epigenomic assays such as histone modification ChIP-seq, transcription factor ChIP-seq, or chromatin...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...from those in common to those in more patient-unique ESR1 peaks. Black dots represent outliers. (C) Aggregate region analyses (ARAs) showing the average Hi-C contacts (observed over expected scores) at ESR1 binding sites shared by an increasing number of patients from left to right. The matrices...

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