# Topics and Trends in Most Cited Genomics and Chromatin Dynamics Papers, Class of 2026

*Canonical URL: https://pri.pepkio.com/top-papers/genomics-and-chromatin-dynamics/2026*

## What topics and trends defined most-cited Genomics and Chromatin Dynamics research in the Class of 2026?

The Class of 2026 in Genomics and Chromatin Dynamics shifts focus from traditional mapping of enhancer-promoter interactions toward the biophysics of gene regulation. A remarkable surge in research on biomolecular condensates and phase separation underscores a new mechanistic frontier, while broader studies on chromatin accessibility and static transcription factors saw relative declines.

## At a glance

| Fact | Value |
| --- | --- |
| Field | Genomics and Chromatin Dynamics |
| Cohort label | Class of 2026 (2024 publications) |
| Papers analyzed | 3,567 |
| Papers ranked | 20 |
| Top topics in ranked papers | Enhancer-promoter interactions, Chromatin accessibility, Phase separation |
| Publication window | Jan 1, 2024 – Dec 31, 2024 |
| Eligibility | Research articles; reviews excluded |
| Citation window | 18 months post-publication |
| 18m citation range | 55–137 |
| Data source | OpenAlex · Retrieved September 2026 |
| License | CC BY 4.0 |

## Rankings

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | Cooltools: Enabling high-resolution Hi-C analysis in Python | Open2C, Nezar Abdennur, Sameer Abraham, Geoffrey Fudenberg, Ilya M Flyamer, Aleksandra A Galitsyna, Anton Goloborodko, Maxim Imakaev, Betul A Oksuz, Sergey V Venev, Yao Xiao | Open2C, Nezar Abdennur, Sameer Abraham, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A. Galitsyna, Anton Goloborodko, Maxim Imakaev, Betül Akgöl Oksuz, Sergey V. Venev | University of Massachusetts Chan Medical School, United States | PLoS Computational Biology | 137 | 10.1371/journal.pcbi.1012067 |
| 2 | Transcription regulation by biomolecular condensates | Gaofeng Pei, Heankel Lyons, Pilong Li, Benjamin R Sabari | Pilong Li, Benjamin R. Sabari | Tsinghua University, China | Nature Reviews Molecular Cell Biology | 116 | 10.1038/s41580-024-00789-x |
| 3 | Machine-guided design of cell-type-targeting cis-regulatory elements | Sager J Gosai, Rodrigo I Castro, Natalia Fuentes, John C Butts, Kousuke Mouri, Michael Alasoadura, Susan Kales, Thanh Thanh L Nguyen, Ramil R Noche, Arya S Rao, Mary T Joy, Pardis C Sabeti, Steven K Reilly, Ryan Tewhey | Sager J. Gosai, Rodrigo Castro, Steven K. Reilly, Ryan Tewhey | Broad Institute of MIT and Harvard, United States | Nature | 112 | 10.1038/s41586-024-08070-z |
| 4 | TRAP1 drives smooth muscle cell senescence and promotes atherosclerosis via HDAC3-primed histone H4 lysine 12 lactylation | Xuesong Li, Minghong Chen, Xiang Chen, Xian He, Xinyu Li, Huiyuan Wei, Yongkang Tan, Jiao Min, Tayyiba Azam, Mengdie Xue, Yunjia Zhang, Mengdie Dong, Quanwen Yin, Longbin Zheng, Hong Jiang, Da Huo, Xin Wang, Shaoliang Chen, Yong Ji, Hongshan Chen | Shaoliang Chen, Yong Ji, Hongshan Chen | Nanjing Medical University, China | European Heart Journal | 105 | 10.1093/eurheartj/ehae379 |
| 5 | HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription | Ziping Niu, Chen Chen, Siyu Wang, Congcong Lu, Zhiyue Wu, Aiyuan Wang, Jing Mo, Jianji Zhang, Yanpu Han, Ye Yuan, Yingao Zhang, Yong Zang, Chaoran He, Xue Bai, Shanshan Tian, Guijin Zhai, Xudong Wu, Kai Zhang | Chen Chen, Kai Zhang | Tianjin Medical University, China | Nature Communications | 102 | 10.1038/s41467-024-47900-6 |
| 6 | Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation | Jin H Yang, Anders S Hansen | Anders S. Hansen | Massachusetts Institute of Technology, United States | Nature Reviews Molecular Cell Biology | 99 | 10.1038/s41580-024-00710-6 |
| 7 | Genome organization around nuclear speckles drives mRNA splicing efficiency | Prashant Bhat, Amy Chow, Benjamin Emert, Olivia Ettlin, Sofia A Quinodoz, Mackenzie Strehle, Yodai Takei, Alex Burr, Isabel N Goronzy, Allen W Chen, Wesley Huang, Jose Lorenzo M Ferrer, Elizabeth Soehalim, Say-Tar Goh, Tara Chari, Delaney K Sullivan, Mario R Blanco, Mitchell Guttman | Mitchell Guttman | California Institute of Technology, United States | Nature | 98 | 10.1038/s41586-024-07429-6 |
| 8 | Direct observation of a condensate effect on super-enhancer controlled gene bursting | Manyu Du, Simon Hendrik Stitzinger, Jan-Hendrik Spille, Won-Ki Cho, Choongman Lee, Mohammed Hijaz, Andrea Quintana, Ibrahim I Cissé | Ibrahim I. Cissé | Max Planck Institute for Immunobiology and Epigenetics, Germany | Cell | 96 | 10.1016/j.cell.2023.12.005 |
| 9 | ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data | Zhaonan Zou, Tazro Ohta, Shinya Oki | Shinya Oki | Kumamoto University, Japan | Nucleic Acids Research | 94 | 10.1093/nar/gkae358 |
| 10 | DPF2 reads histone lactylation to drive transcription and tumorigenesis | Guijin Zhai, Ziping Niu, Zixin Jiang, Fei Zhao, Siyu Wang, Chen Chen, Wei Zheng, Aiyuan Wang, Yong Zang, Yanpu Han, Kai Zhang | Guijin Zhai, Ziping Niu, Zixin Jiang, Kai Zhang | Tianjin Medical University, China | Proceedings of the National Academy of Sciences | 81 | 10.1073/pnas.2421496121 |
| 11 | Histone lactylation couples cellular metabolism with developmental gene regulatory networks | Fjodor Merkuri, Megan Rothstein, Marcos Simoes-Costa | Marcos Simões-Costa | Cornell University, United States | Nature Communications | 77 | 10.1038/s41467-023-44121-1 |
| 12 | Chromosomal instability as a driver of cancer progression | Xuelan Chen, Albert S Agustinus, Jun Li, Melody DiBona, Samuel F Bakhoum | Samuel F. Bakhoum | Memorial Sloan Kettering Cancer Center, United States | Nature Reviews Genetics | 75 | 10.1038/s41576-024-00761-7 |
| 13 | Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications | Cristina Policarpi, Marzia Munafò, Stylianos Tsagkris, Valentina Carlini, Jamie A Hackett | Jamie A. Hackett | European Molecular Biology Laboratory (EMBL), Italy | Nature Genetics | 74 | 10.1038/s41588-024-01706-w |
| 14 | Single-cell nascent RNA sequencing unveils coordinated global transcription | Dig B Mahat, Nathaniel D Tippens, Jorge D Martin-Rufino, Sean K Waterton, Jiayu Fu, Sarah E Blatt, Phillip A Sharp | Phillip A. Sharp | Massachusetts Institute of Technology, United States | Nature | 64 | 10.1038/s41586-024-07517-7 |
| 15 | On the genetic basis of tail-loss evolution in humans and apes | Bo Xia, Weimin Zhang, Guisheng Zhao, Xinru Zhang, Jiangshan Bai, Ran Brosh, Aleksandra Wudzinska, Emily Huang, Hannah Ashe, Gwen Ellis, Maayan Pour, Yu Zhao, Camila Coelho, Yinan Zhu, Alexander Miller, Jeremy S Dasen, Matthew T Maurano, Sang Y Kim, Jef D Boeke, Itai Yanai | Bo Xia, Jef D. Boeke, Itai Yanai | NYU Langone Health, United States | Nature | 61 | 10.1038/s41586-024-07095-8 |
| 16 | Affinity-optimizing enhancer variants disrupt development | Fabian Lim, Joe J Solvason, Genevieve E Ryan, Sophia H Le, Granton A Jindal, Paige Steffen, Simran K Jandu, Emma K Farley | Fabian Lim, Joe J Solvason, Genevieve E Ryan | University of California San Diego, United States | Nature | 61 | 10.1038/s41586-023-06922-8 |
| 17 | Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data | Qiuyue Yuan, Zhana Duren | Zhana Duren | Clemson University, United States | Nature Biotechnology | 60 | 10.1038/s41587-024-02182-7 |
| 18 | Increased enhancer–promoter interactions during developmental enhancer activation in mammals | Zhuoxin Chen, Valentina Snetkova, Grace Bower, Sandra Jacinto, Benjamin Clock, Atrin Dizehchi, Iros Barozzi, Brandon J Mannion, Ana Alcaina-Caro, Javier Lopez-Rios, Diane E Dickel, Axel Visel, Len A Pennacchio, Evgeny Z Kvon | Evgeny Z. Kvon | University of California, Irvine, United States | Nature Genetics | 56 | 10.1038/s41588-024-01681-2 |
| 19 | Position-dependent function of human sequence-specific transcription factors | Sascha H Duttke, Carlos Guzman, Max Chang, Nathaniel P Delos Santos, Bayley R McDonald, Jialei Xie, Aaron F Carlin, Sven Heinz, Christopher Benner | Sascha H. Duttke, Sven Heinz, Christopher Benner | Washington State University, United States | Nature | 56 | 10.1038/s41586-024-07662-z |
| 20 | Sequence basis of transcription initiation in the human genome | Kseniia Dudnyk, Donghong Cai, Chenlai Shi, Jian Xu, Jian Zhou | Donghong Cai, Chenlai Shi, Jian Zhou | University of Texas Southwestern Medical Center, United States | Science | 55 | 10.1126/science.adj0116 |

## Topic trends

### What Topics Define the Class of 2026?

The Class of 2026 for Genomics and Chromatin Dynamics is strongly characterized by topics examining the physical and spatial organization of the genome. While foundational elements like enhancer-promoter interactions and chromatin accessibility remain the most frequently cited concepts, there is a pronounced focus on three-dimensional architectural components such as chromatin loops and cis-regulatory elements. Notably, the emergence of biophysical mechanisms is evident, with phase separation and biomolecular condensates capturing significant attention. This suggests a paradigm shift where researchers are increasingly integrating soft-matter physics to explain how dynamic nuclear compartments govern gene regulation. Technologies enabling high-resolution and high-throughput investigation, such as massively parallel reporter assays, are also prominent, underscoring a broader push toward understanding the functional consequences of spatial genomic organization at single-cell and molecular scales.

*Leading research themes*

### How Did Topics Shift from the Class of 2025 to the Class of 2026?

Comparing the Class of 2025 to the Class of 2026 reveals a distinct transition in research priorities within chromatin dynamics. The most striking risers are concepts tied to transient cellular states and physical organization—specifically biomolecular condensates, metabolic reprogramming, and histone recycling, all of which grew from minimal presence in the previous cohort to notable prominence. This surge highlights an accelerating interest in how metabolic inputs and biophysical phase transitions dynamically modulate the epigenome. Conversely, more traditional regulatory topics saw relative declines. Chromatin accessibility and enhancer-promoter interactions, while still highly cited overall, decreased in relative frequency, alongside methodological topics like deep learning models and broad categories such as transcription factors. This shift implies that the field is moving beyond simply cataloging accessible regions and static regulatory networks, toward a mechanistic focus on the real-time physical and metabolic constraints that shape chromatin topology.

*How topics shifted year over year*

## Cite this ranking

```
Pepkio Research Index (PRI). Topics and Trends in Most Cited Genomics and Chromatin Dynamics Papers, Class of 2026. https://pri.pepkio.com/top-papers/genomics-and-chromatin-dynamics/2026. Accessed 2026-10-28.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459
```