Long-range enhancer–promoter contacts in gene expression control

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898

Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716

Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895

Coactivator condensation at super-enhancers links phase separation and gene control

Sabari, B. R., Dall’Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., Shrinivas, K., Abraham, B. J., Hannett, N. M., Zamudio, A. V., Manteiga, J. C., et al. (2018) · Science · doi:10.1126/science.aar3958 · Cited by 2,595

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233

Genome organization by SATB1 binding to base-unpairing regions (BURs) provides a scaffold for SATB1-regulated gene expressionPreprint

Kohwi, Y., Wong, X., Grange, M., Sexton, T., Richards, H. W., Kitagawa, Y., Sakaguchi, S., Liang, Y., Chuong, C., Botchkarev, V. A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.19.473323 · Cited by 3

Theoretical Principles of Enhancer-Promoter Communication in Transcriptional BurstingPreprint

Wang, Z., Zhang, Z., Luo, S., Zhou, T., & Zhang, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.24.477520 · Cited by 2

MYCN driven oncogenesis involves cooperation with WDR5 to activate canonical MYC targets and G9a to repress differentiation genesPreprint

Liu, Z., Zhang, X., Xu, M., Hong, J. J., Ciardiello, A. K., Lei, H., Shern, J. F., & Thiele, C. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.11.548643 · Cited by 3

Competition between transcription and loop extrusion modulates promoter and enhancer dynamicsPreprint

Sexton, T., Platania, A., Erb, C., Barbieri, M., Molcrette, B., Grandgirard, E., de Kort, M. A. C., Meaburn, K. J., Taylor, T., Shchuka, V. M., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3164817/v1 · Cited by 3

Large-scale analysis of the integration of enhancer-enhancer signals by promotersPreprint

Martinez-Ara, M., Comoglio, F., & van Steensel, B. (2023) · eLife · doi:10.7554/elife.91994.1 · Cited by 3

Altered postnatal chromatin development in the nucleus accumbens primes lifelong stress sensitivityPreprint

Rashford, R. L., Fang, L. Z., DeBerardine, M., Kim, H. J. J., Hirschfield, L. W., Cervi, E., Barrett, M. R., Thompson, J. M., Creed, M. C., & Peña, C. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.12.589272 · Cited by 3

Single-allele chromatin folding is organized by recurrent motifs that are reweighted across cell types and statesPreprint

Messina, O., Fiche, J.-B., Ganesh, G., Youhanna, C. E., Kemkem, Y., Mesnager, A., Ferrer, J. P., Villalba, A., Scharfmann, R., Akerman, İ., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.18.613689 · Cited by 4

Mammalian enhancers and GWASs act proximally and seldom skip active genesPreprint

Narita, T., & Choudhary, C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.29.625864 · Cited by 3

Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion

Lee, U., Laguillo-Diego, A., Wong, W., Ni, Z., Cheng, L., Li, J., Pelham-Webb, B., Pertsinidis, A., Leslie, C., & Apostolou, E. (2025) · doi:10.1101/2025.02.13.638153 · Cited by 3

Gene regulatory networks linked to GABA signalling emerge as relevant for glioblastoma pathogenesisPreprint

Nissen, I., Dakhel, S., Chakraborty, C., Nygaard, A. H., Kirkeby, A., Hörnblad, A., Erdem, C., & Remeseiro, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.30.651564 · Cited by 3

Promoter strength and position govern promoter competition via transcript-dependent insulationPreprint

Koska, M., Nagano, M., Swigut, T., Boettiger, A. N., Hansen, A. S., & Wysocka, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.06.652547 · Cited by 3

Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activityPreprint

Arnould, C., Keukeleire, P., Inoue, F., Cui, X., An, K., Murray, E., Zhang, X., Drmanac, R., Peters, B. A., Shendure, J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.11.658967 · Cited by 3

Identification and characterization of putative enhancer regions that direct Il6 transcription in murine macrophages

Kano, N., Miki, T., Uehara, Y., Ori, D., & Kawai, T. (2024) · International Immunology · doi:10.1093/intimm/dxae024 · Cited by 2

EPI-DynFusion: enhancer-promoter interaction prediction model based on sequence features and dynamic fusion mechanisms

Zhang, A., Jia, J., Sun, M., & Wei, X. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1614222 · Cited by 4

Predictive prioritization of enhancers associated with pancreatic disease risk

Wang, L., Baek, S., Prasad, G., Wildenthal, J., Guo, K., Sturgill, D. M., TruongVo, T., Char, E., Pegoraro, G., McKinnon, K. M., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101040 · Cited by 5

Linking chromatin interaction network topology to three-dimensional genome conformation: An analytical framework for chromatin structure

Zhang, Z., Wang, Z., & Zhang, J. (2025) · Physical review. E · doi:10.1103/r8rd-fykm · Cited by 2

CpG Methylation‐Driven Pleiotropic Spliced Isoforms of PRSS3 Facilitate Gastric Intratumor Heterogeneity and Metastasis

Pang, M., Xu, H., Li, D., et al. (2025) · Cancer Science · doi:10.1111/cas.70227 · Cited by 2

Integrating Hi-C data and RNA-seq data to reveal the 3D genome in sheep

Xu, Q., Zhang, X., Li, F., Tian, H., Zhang, D., Huang, K., Zhang, Y., Zhao, Y., Li, X., Zhao, L., et al. (2025) · BMC Genomics · doi:10.1186/s12864-025-12318-x · Cited by 2

AP-1 promotes oncogenic transcription in lung cancer cells by bridging promoter-enhancer interactions

Tan, X., Kroneberg, M., Sun, F., Diaz, K. A., Flora, A., & Carey, M. (2025) · Cancer Gene Therapy · doi:10.1038/s41417-025-00974-w · Cited by 3

Pan-cancer epigenetic landscape of human tumor-associated macrophages reveals crucial enhancers governing their heterogenous formation by Pol II pausing modulation

Xiong, C., Ning, H., Wang, X., Xie, Y., Liu, Z., Hu, D., & Gao, X. (2026) · Journal of Advanced Research · doi:10.1016/j.jare.2026.01.048 · Cited by 2

In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2

MacKenzie, T. M. G., Ramirez, L., Jian, R., Jiang, L., & Snyder, M. P. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101570 · Cited by 2

The tyrosine kinase inhibitor LPM4870108 impairs learning and memory and induces transcriptomic and gene‑specific DNA methylation changes in rats

Duan, S., Li, C., Gao, Y., Meng, P., Ji, S., Xu, Y., Mao, Y., Wang, H., & Tian, J. (2022) · Archives of Toxicology · doi:10.1007/s00204-022-03226-0 · Cited by 2

Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation

Gao, Z., Smith, A., Scott, J. N. F., Bevington, S. L., & Boyes, J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad741 · Cited by 2

PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks

Wang, J., Zhang, H., Chen, N., Zeng, T., Ai, X., & Wu, K. (2023) · Animals · doi:10.3390/ani13182935 · Cited by 2

How Transcription Factor Clusters Shape the Transcriptional Landscape

Munshi, R. (2024) · Biomolecules · doi:10.3390/biom14070875 · Cited by 3

Enhancer‐dependent gene regulation in space, time, and malignancies

Blum, B., Dachtler, V., & Feldmann, A. (2025) · International Journal of Cancer · doi:10.1002/ijc.35350 · Cited by 2

Transcriptional Regulation of Mouse Mast Cell Differentiation and the Role of Human Lung Mast Cells in Airway Inflammation

Gao, J., Zhao, D., Nouri, H. R., Chu, H. W., & Huang, H. (2025) · Immunological Reviews · doi:10.1111/imr.70026 · Cited by 3

Regulatory roles of three-dimensional structures of chromatin domains

Li, K. Y., Cao, Q., Chow, S. H.-C., Nicoletti, C., Puri, P., Wang, H., Leung, D., & Yip, K. Y.-L. (2025) · Genome biology · doi:10.1186/s13059-025-03659-7 · Cited by 3

DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data

Lv, H., Cao, P., Long, W., Yin, X., Xu, S., & Fu, L. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf301 · Cited by 2

Functional Annotation of De Novo Variants Found Near GWAS Loci Associated With Cleft Lip With or Without Cleft Palate

Curtis, S. W., Cook, L., Paraiso, K. D., Visel, A., Cotney, J. L., Murray, J. C., Beaty, T. H., Marazita, M. L., Carlson, J. C., & Leslie, E. J. (2025) · Birth Defects Research · doi:10.1002/bdr2.2499 · Cited by 2

Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties

Yuan, S., Ni, P., & Su, Z. (2025) · BMC Biology · doi:10.1186/s12915-025-02313-9 · Cited by 1

Regulation and dysregulation of spatial chromatin structure in the central nervous system

Fujita, Y. (2021) · Anatomical Science International · doi:10.1007/s12565-020-00567-7 · Cited by 2

Contact maps and brain disease risk

Koch, L. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0206-3 · Cited by 2

Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies

Kanapeckaitė, A., Burokienė, N., Mažeikienė, A., Cottrell, G. S., & Widera, D. (2021) · Biophysical Reports · doi:10.1016/j.bpr.2021.100028 · Cited by 2

Integration of Count Difference and Curve Similarity in Negative Regulatory Element Detection

He, N., Wang, W., Fang, C., Tan, Y., Li, L., & Hou, C. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.818344 · Cited by 2

Shared cis-regulatory modules control expression of the tandem paralogs midline and H15 in the follicular epithelium

Stevens, C. A., Stott, H. L., Desai, S. V., & Yakoby, N. (2022) · Development · doi:10.1242/dev.201016 · Cited by 3

Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants

Chen, Y., Paramo, M. I., Zhang, Y., Li, Y., Shah, S. R., Jin, Y., Zhang, J., Pan, X., & Yu, H. (2023) · Annual Review of Genetics · doi:10.1146/annurev-genet-030723-120717 · Cited by 3

Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

Li, Y., Fan, H., Qin, W., Wang, Y., Chen, S., Bao, W., & Sun, M.-A. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.029 · Cited by 3

Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome

Shaw, D. E., Naftaly, A. F. S., & White, M. A. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae020 · Cited by 4

Dan forms condensates in neuroblasts and regulates nuclear architecture and progenitor competence in vivo

Benchorin, G., Cho, R. J., Li, M. J., Molotkova, N., & Kohwi, M. (2024) · Nature Communications · doi:10.1038/s41467-024-49326-6 · Cited by 3

Leverage Large-Scale Biological Networks to Decipher the Genetic Basis of Human Diseases Using Machine Learning

Wang, H., Yang, J., & Wang, J. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0826-5_11 · Cited by 2

Roles and regulation of endogenous retroviruses in pluripotency and early development

Schlesinger, S., Branco, M. R., & Mermoud, J. E. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-814085-7.00007-6 · Cited by 2

Promoter-Interacting Expression Quantitative Trait Loci (pieQTLs) in Human Immune Cell TypesPreprint

Chandra, V., Bhattacharyya, S., Schmiedel, B. J., Madrigal, A., Feupe, S. F., Seumois, G., Kronenberg, M., Peters, B., Ay, F., & Vijayanand, P. (2019) · SSRN Electronic Journal · doi:10.2139/ssrn.3402070 · Cited by 2

HiCRes: a computational method to estimate and predict the resolution of HiC librariesPreprint

Marchal, C., Singh, N., Corso‐Díaz, X., & Swaroop, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.22.307967 · Cited by 2

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survivalPreprint

Abassah‐Oppong, S., Mannion, B. J., Zoia, M., Rouco, R., Tissières, V., Spurrell, C. H., Roland, V., Darbellay, F., Ljubojevic, A., Gamart, J., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.22.393173 · Cited by 2

Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer CellsPreprint

Chen, P.-S. B., Fiaux, P. C., Li, B., Zhang, K., Kubo, N., Jiang, S., Hu, R., Wu, S.-H., Wang, M.-C., Wang, W., et al. (2021) · bioRxiv · doi:10.1101/2021.02.04.429675 · Cited by 3

Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for inductionPreprint

Dimitrova, E., Feldmann, A., van der Weide, R. H., Flach, K. D., Lastuvkova, A., de Wit, E., & Klose, R. J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.04.467119 · Cited by 2

Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markersPreprint

Xie, Y., Ruan, F., Li, Y., Luo, M., Zhang, C., Chen, Z., Xie, Z., Weng, Z., Chen, W., Chen, W., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.21.489011 · Cited by 2

SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C dataPreprint

Lee, L., Yu, M., Li, X., Zhu, C., Zhang, Y.-X., Yu, H.-Y., Chen, Z.-Y., Mishra, S., Ren, B., Li, Y., et al. (2022) · bioRxiv · doi:10.1101/2022.08.05.502991 · Cited by 9

Probabilistic association of differentially expressed genes withcis-regulatory elementsPreprint

Roberts, B. S., Anderson, A. G., Partridge, E. C., Cooper, G. M., & Myers, R. (2024) · Genome Research · doi:10.1101/gr.278598.123 · Cited by 2

A New Approach for Discovering Functional Links Connecting Non-Coding Regulatory Variants to Gene TargetsPreprint

Farooq, H., Du, L., Delafrouz, P., Wei, J., Chronis, C., & Liang, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.13.598913 · Cited by 3

3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibilityPreprint

Trang, B. K., Sharma, P. K., Cook, L. E., Mount, Z., Thomas, R. M., Kulkarni, N. N., Cabrera, E. C., Rachimi, S., Pahl, M. C., Pippin, J. A., et al. (2024) · medRxiv · doi:10.1101/2024.08.12.24311676 · Cited by 2

Predictive Prioritization of Enhancers Associated with Pancreas Disease RiskPreprint

Wang, L., Baek, S., Prasad, G., Wildenthal, J., Guo, K., Sturgill, D. M., TruongVo, T., Char, E., Pegoraro, G., McKinnon, K. M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.07.611794 · Cited by 2

G-quadruplex profiling in complex tissues using single-cell CUT&TagPreprint

Lyu, J., Hetey, S., Castelo‐Branco, G., Bartošovič, M., & Elsässer, S. J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.03.647101 · Cited by 2

Programmed DNA breaks drive chromatin reconfiguration and facilitate transcriptional potentiation at neuronal early response genesPreprint

Heady, L., Rueda, R., Segev, A., Morton, K. G., & Madabhushi, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.06.652469 · Cited by 2

Revisiting models of enhancer–promoter communication in gene regulationPreprint

Barshad, G., & Danko, C. G. (2025) · Genome Research · doi:10.1101/gr.278389.123 · Cited by 4

Genome reorganization and its functional impact during breast cancer progressionPreprint

Reed, K. S. M., Fritz, A. J., Greenyer, H. W., Heselmeyer‐Haddad, K., Frietze, S. E., Stein, J. L., Stein, G. S., & Misteli, T. (2025) · eLife · doi:10.7554/elife.108135 · Cited by 1

High-throughput in silico screen uncovers key regulators of 3D genome architecturePreprint

Bai, J., Lyu, Q., Tan, J., Issner, R., Tischer, B., Liu, H., Goel, V. Y., Ling, X., Bernstein, B., Tsirigos, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.09.693120 · Cited by 2

Yeast ATM and ATR use different mechanisms to spread histone H2A phosphorylation around a DNA double-strand breakPreprint

Li, K., Bronk, G., Kondev, J., & Haber, J. E. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2019.12.17.877266 · Cited by 2

NIPBL-mediated 3D genome folding translates enhancer priming into gene activation and safeguards lineage fidelity during embryonic transitionsPreprint

Ni, Z., Ma, X., Do, S., Cheng, L., Glenn, R. A., Vierbuchen, T., & Pertsinidis, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.30.686824 · Cited by 2

Heterogeneity of enhancers embodies shared and representative functional groups underlying developmental and cell type-specific gene regulation

Song, W., & Ovcharenko, I. (2022) · Gene · doi:10.1016/j.gene.2022.146640 · Cited by 1

Distal and proximal control of rhythmic gene transcription

Román-Figueroa, A., Tenorio-Hernández, L., & Furlan-Magaril, M. (2022) · Frontiers in Systems Biology · doi:10.3389/fsysb.2022.1026424 · Cited by 1

Regulatory non-coding RNAs-biogenesis, mechanisms of action and role in gene expression regulation

Samoilă, I., Șelaru, A., (Ignat), S. N., Costache, M., & Dinescu, S. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-90406-3.00004-x · Cited by 1

A body map of super-enhancers and their function in pig

Yang, Y., Li, X., Zhu, M., Liu, Y., Qian, K., Chu, M., & Pan, Z. (2023) · Frontiers in Veterinary Science · doi:10.3389/fvets.2023.1239965 · Cited by 2

3D organization of enhancers in MuSCs

He, L., Sun, H., & Wang, H. (2024) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2024.01.011 · Cited by 1

Nutrigenomics and nutrigenetics: Special emphasis on optimization of human health and animal performance

Alrawi, R. A., Shareef, O. M., Abdulrahman, J. M., & Al-Rawi, R. (2024) · International Journal of Science and Technology Research Archive · doi:10.53771/ijstra.2024.6.1.0113 · Cited by 1

Prediction of Enhancer–Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE

Hecker, D., & Schulz, M. H. (2012) · Methods in molecular biology · doi:10.1007/978-1-0716-4136-1_20 · Cited by 1

Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus

Ma, F., Ollikainen, N., Du, H., Braikia, F.-Z., Cui, N., Bianchi, A. H., Dunn, C., Nguyen, C., Fan, J., De, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57373-w · Cited by 2

Genomic locus of lncRNA-Gm26793 forms an inter-chromosomal interaction with Cubn to ensure proper stem cell differentiation in vitro and in vivo

Liu, Z., Wan, X., Chen, J., Ma, Y., Fu, Y., Chen, Y., Wen, M., Yang, Y., Qian, Y., Zhang, Y., et al. (2025) · Cell Discovery · doi:10.1038/s41421-025-00805-0 · Cited by 1

Deciphering Haplotype-level Chromosome Conformation Alteration in Down Syndrome by Haplotype-resolved Multi-omics Analysis

Wu, C., Tianshu, Z., Ke, W., Xiong, W., Zhang, Z., Zhang, S., Wang, J., Deng, L., Yan, K., Wang, M., et al. (2025) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzaf054 · Cited by 1

A comprehensive review of computational methods for predicting DNA N4-methylcytosine sites

Wang, Z., Geng, A., Xu, J., Meng, Y., Zhang, Z., Wei, L., Zou, Q., & Cui, F. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.148221 · Cited by 1

Single-molecule chromatin profiling reveals cell type-specific A/B compartment alteration and multi-enhancer transcriptional coordination

Liu, L.-R., Zhong, J., Bai, X., Ye, C.-L., Hou, C., Ding, J., Chi, W., Xiao, C., & Niu, L. (2025) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2025.09.011 · Cited by 1

Using Network Models to Understand Biological Signaling Architecture

White, R., Reeves, E. B., Fudge, G. L., Zigáčková, D., Deweese, J. E., & Keener, J. P. (2025) · IEEE Transactions on Molecular Biological and Multi-Scale Communications · doi:10.1109/tmbmc.2025.3625536 · Cited by 1

Engineering the Link: From Genome Interaction Maps to Functional Insight

Petersen, F., Westermann, S., Smialkovska, V., Mathony, J., Feldmann, A., & Niopek, D. (2025) · Advanced Biology · doi:10.1002/adbi.202500525 · Cited by 2

High-throughput capture of actively transcribed region-interacting sequences reveals an intricate promoter-centered regulatory network

Li, X., Xu, J., Yan, X., Zhong, J., Hou, C., Xiao, C., Niu, L., & Chi, W. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.10.018 · Cited by 4

Transomic analysis reveals DNA methylation and transcription factor roles in obese liver protein expression

Maehara, H., Hatano, A., Shirai, M., Kokaji, T., Suzuki, Y., Matsumoto, M., Egami, R., Kubota, H., Araki, H., Miura, F., et al. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00606-x · Cited by 1

3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility

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An EGR1-dependent cascade modulates genome architecture at the CSF1R locus

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