Topics and Trends in Most Cited Genomics and Chromatin Dynamics Papers

Ranked by citations 18 months after publication

Class of 2026 (Papers Published in 2024)

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.

See details ↓

Updated September 13, 2026

At a glance

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

20 papers ranked by 18-month citation count

#1 of 3,567
13718m citations

Cooltools: Enabling high-resolution Hi-C analysis in Python

Open2C et al.PLoS Computational Biology202410.1371/journal.pcbi.1012067

Open2C, Nezar Abdennur, Sameer Abraham, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A. Galitsyna, Anton Goloborodko, Maxim Imakaev, Betül Akgöl Oksuz, Sergey V. VenevUniversity of Massachusetts Chan Medical School, United States

cooltoolsHi-C analysisChromosome conformation capture3C technologiesContact frequency3D genome organizationcooler formathigh-resolution datasetscomputational analysis pipelinePython APIcommand line interfacescalable analysisgenome folding datasetsopen2chigh-performance computing clustersinteractive analysis environments
Badge
#2 of 3,567
11618m citations

Transcription regulation by biomolecular condensates

Gaofeng Pei, Heankel Lyons et al.Nature Reviews Molecular Cell Biology202410.1038/s41580-024-00789-x

Pilong Li, Benjamin R. SabariTsinghua University, China

biomolecular condensatesTranscriptional regulationPhase separationtranscriptional condensatesintrinsically disordered regionstranscriptional machineryEnhancer-promoter interactionsMediator complexRNA polymerase IITranscription factorsChromatin structureGene expression regulationcondensate dynamicsmultivalent interactions
Badge
#3 of 3,567
11218m citations

Machine-guided design of cell-type-targeting cis-regulatory elements

Sager J Gosai, Rodrigo I Castro et al.Nature202410.1038/s41586-024-08070-z

Sager J. Gosai, Rodrigo Castro, Steven K. Reilly, Ryan TewheyBroad Institute of MIT and Harvard, United States

Cis-regulatory elementsCell type specificityDeep learning modelsin silico optimizationmassively parallel reporter assaysRegulatory sequence designtissue-specific gene expressionmotif vocabularyoff-target activity reductionregulatory code engineeringin vivo CRE validationtherapeutic CRE applicationscell-type-targeting sequencestranscriptional specificity
Badge
#4 of 3,567
10518m citations

TRAP1 drives smooth muscle cell senescence and promotes atherosclerosis via HDAC3-primed histone H4 lysine 12 lactylation

Xuesong Li et al.European Heart Journal202410.1093/eurheartj/ehae379

Shaoliang Chen, Yong Ji, Hongshan ChenNanjing Medical University, China

TRAP1vascular smooth muscle cell senescenceatherosclerosisHistone H4 lysine 12 lactylationHDAC3metabolic reprogrammingaerobic glycolysislactate productionSenescence-associated secretory phenotypemitonuclear communicationVSMC-specific knockoutApoeKO miceoncogenic RasPROTAC-mediated degradationhistone lysine delactylaseChromatin immunoprecipitationsenescence-associated β-galactosidasepharmacological inhibition
Badge
#5 of 3,567
10218m citations

HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription

Ziping Niu, Chen Chen, Siyu Wang, Congcong Lu et al.Nature Communications202410.1038/s41467-024-47900-6

Chen Chen, Kai ZhangTianjin Medical University, China

lysine lactylationHBO1lysine lactyltransferasehistone H3K9laE508 catalytic siteQuantitative proteomicsJADE1BRPF2scaffold proteinsCUT&Tagtranscription start sitesTranscriptional regulationtumorigenesisHBO1 knockoutHistone modificationsmetabolic regulation of gene expression
Badge
#6 of 3,567
9918m citations

Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation

Jin H Yang et al.Nature Reviews Molecular Cell Biology202410.1038/s41580-024-00710-6

Anders S. HansenMassachusetts Institute of Technology, United States

Enhancer-promoter selectivityEnhancer-promoter interactionspromoter activationspatiotemporal regulationtranscriptional specificityChromatin loopsCis-regulatory elementsTranscription factor bindingcis-regulatory mechanisms
Badge
#7 of 3,567
9818m citations

Genome organization around nuclear speckles drives mRNA splicing efficiency

Prashant Bhat et al.Nature202410.1038/s41586-024-07429-6

Mitchell GuttmanCalifornia Institute of Technology, United States

nuclear specklesmRNA splicing efficiency3D genome organizationsplicing factor compartmentalizationchromatin-speckle interactionsnuclear bodiesco-transcriptional splicingsubnuclear localizationgene positioningsplicing kineticstranscription-splicing couplingChromosome organizationchromatin domains
Badge
#8 of 3,567
9618m citations

Direct observation of a condensate effect on super-enhancer controlled gene bursting

Manyu Du et al.Cell202410.1016/j.cell.2023.12.005

Ibrahim I. CisséMax Planck Institute for Immunobiology and Epigenetics, Germany

condensate effectSuper-enhancersTranscriptional burstingdirect observationTranscriptional regulationPhase separationEnhancer-promoter interactionstranscriptional condensatesburst frequencyburst amplitudeLive-cell imagingsingle-cell transcription dynamics
Badge
#9 of 3,567
9418m citations

ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data

Zhaonan Zou et al.Nucleic Acids Research202410.1093/nar/gkae358

Shinya OkiKumamoto University, Japan

ChIP-AtlasChromatin immunoprecipitationATAC-seqDNase-seqBisulfite-seqepigenomic landscapesChromatin structureHi-CeQTLChromHMMFANTOM5 enhancersGWAS SNPsClinVar variantsDiff Analysisdifferentially bound regionsdifferentially accessible regionsdifferentially methylated regionsCis-regulatory elementsChromosome organizationdata-mining tools
Badge
#10 of 3,567
8118m citations

DPF2 reads histone lactylation to drive transcription and tumorigenesis

Guijin Zhai, Ziping Niu, Zixin Jiang et al.Proceedings of the National Academy of Sciences202410.1073/pnas.2421496121

Guijin Zhai, Ziping Niu, Zixin Jiang, Kai ZhangTianjin Medical University, China

lysine lactylationKlahistone lactylationH3K14laDPF2cervical cancerlactate accumulationmetabolic reprogrammingmultivalent photoaffinity probeQuantitative proteomicsCUT&Taghistone reader proteinoncogenic gene expressionDPF2-H3K14la interactionstructure-guided mutationTranscriptional regulationcell survivalhistone mark effector
Badge
#11 of 3,567
7718m citations

Histone lactylation couples cellular metabolism with developmental gene regulatory networks

Fjodor Merkuri et al.Nature Communications202410.1038/s41467-023-44121-1

Marcos Simões-CostaCornell University, United States

histone lactylationglycolysisgene regulatory networksneural crestpre-somitic mesodermChromatin accessibilityactive enhancersLDHA/Blactyl-CoASOX9YAP/TEADmetabolic reprogrammingEmbryonic developmentcell migrationepigenetic mechanismNC GRN deployment
Badge
#12 of 3,567
7518m citations

Chromosomal instability as a driver of cancer progression

Xuelan Chen et al.Nature Reviews Genetics202410.1038/s41576-024-00761-7

Samuel F. BakhoumMemorial Sloan Kettering Cancer Center, United States

chromosomal instabilitycancer progressionaneuploidystructural chromosomal aberrationsMitotic errorscentrosome amplificationkinetochore-microtubule attachmentsspindle assembly checkpointDNA damage responsereplication stresschromothripsisMicronucleicopy number alterationstumor heterogeneityMetastasistherapeutic resistanceChromosomal missegregationGenomic instability
Badge
#13 of 3,567
7418m citations

Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications

Cristina Policarpi et al.Nature Genetics202410.1038/s41588-024-01706-w

Jamie A. HackettEuropean Molecular Biology Laboratory (EMBL), Italy

epigenome editingchromatin modificationsH3K4me3H3K27me3H2AK119ubsingle-cell transcriptional readoutspromoter targetingchromatin landscape remodelingDNA sequence motifscis-regulatory contextcombinatorial modificationstranscriptional silencing penetrancemodular epigenome editing platformcausal transcriptional instructioncontext-dependent gene regulationhistone lysine methylationhistone ubiquitinationswitch-like transcriptional effectssingle-cell heterogeneityprecision perturbation
Badge
#14 of 3,567
6418m citations

Single-cell nascent RNA sequencing unveils coordinated global transcription

Dig B Mahat et al.Nature202410.1038/s41586-024-07517-7

Phillip A. SharpMassachusetts Institute of Technology, United States

scGRO-seqsingle-cell nascent RNA sequencingclick chemistryTranscriptional burstingburst sizeburst frequencydivergent transcription initiationenhancer-gene coordinationSuper-enhancersunstable RNAsco-transcriptionRNA polymerase quantificationreplication-dependent histone genesnon-polyadenylated histone gene transcriptionCell cycle dynamicsEnhancer networkstemporal transcription regulationepisodic transcription
Badge
#15 of 3,567
6118m citations

On the genetic basis of tail-loss evolution in humans and apes

Weimin Zhang, Guisheng Zhao, Xinru Zhang et al.Nature202410.1038/s41586-024-07095-8

Bo Xia, Jef D. Boeke, Itai YanaiNYU Langone Health, United States

tail-loss evolutionhominoidsAlu element insertionTBXT genealternative splicingExon skippinganthropomorphous apeshuman bipedalismmouse modelsembryonic tail budneural tube defectsintron insertioninverted Alu pairingtail-loss phenotypeadaptive costhominoid ancestor
Badge
#16 of 3,567
6118m citations

Affinity-optimizing enhancer variants disrupt development

Fabian Lim, Joe J Solvason, Genevieve E Ryan et al.Nature202410.1038/s41586-023-06922-8

Fabian Lim, Joe J Solvason, Genevieve E RyanUniversity of California San Diego, United States

ZRS enhancerShh expressionlimb developmentpolydactylyETS binding sitesETS-A sitelow-affinity binding sitesaffinity-optimizing variantssingle-nucleotide variants (SNVs)gain-of-function gene expressionIRF sitesHOX sitesAP-1 sitesenhanceropathiespenetrancesuboptimal binding affinitytissue-specific enhancer activityTranscription factor binding affinitypathogenic variants in enhancers
Badge
#17 of 3,567
6018m citations

Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data

Qiuyue Yuan et al.Nature Biotechnology202410.1038/s41587-024-02182-7

Zhana DurenClemson University, United States

LINGERgene regulatory network inferenceSingle-cell multiomicsChromatin accessibilityRNA sequencinglifelong neural networkatlas-scale external dataTranscription factor binding motifsmanifold regularizationtranscription factor activity estimationgenome-wide association studiesdisease-associated variantsbulk gene expression datasingle-cell gene expressiondriver regulatorscase-control studies
Badge
#18 of 3,567
5618m citations

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Zhuoxin Chen et al.Nature Genetics202410.1038/s41588-024-01681-2

Evgeny Z. KvonUniversity of California, Irvine, United States

Enhancer-promoter interactionsdevelopmental enhancer activationChromatin loopsGene expression regulationTranscriptional regulationChromosome conformation captureHi-C4C-seqdevelopmental gene expressionCis-regulatory elementsChromatin structureenhancer dynamicspromoter contactsTranscription factorsmammalian developmentLong-range interactionschromatin contact frequency
Badge
#19 of 3,567
5618m citations

Position-dependent function of human sequence-specific transcription factors

Sascha H Duttke et al.Nature202410.1038/s41586-024-07662-z

Sascha H. Duttke, Sven Heinz, Christopher BennerWashington State University, United States

transcription start sitessequence-specific transcription factorsposition-dependent transcription factor functionpromotersenhancersTF binding site positioningNRF1NFYSp1Genetic variationmassively parallel reporter assaysTranscription initiationTF spacingactivator-to-repressor switchingregulatory element architecturenon-coding DNA polymorphismsmotif positioning patternssynthetic regulatory elementsTSS-relative binding site analysis
Badge
#20 of 3,567
5518m citations

Sequence basis of transcription initiation in the human genome

Donghong Cai, Chenlai Shi et al.Science202410.1126/science.adj0116

Donghong Cai, Chenlai Shi, Jian ZhouUniversity of Texas Southwestern Medical Center, United States

Transcription initiationbase-pair resolution predictionDeep learning modelsPuffinexplainable modelhuman promoterssequence patternsposition-specific effectsbidirectional transcriptiontranscription start sitesgene expression variationCell type specificitysequence determinantsmammalian species conservationpromoter activitysequence rules
Badge

Dominant research themes and year-over-year shifts in Genomics and Chromatin Dynamics

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
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
How topics shifted year over year
Methodology

PRI identifies high-impact research using a transparent, topic-agnostic framework applied consistently across scientific domains. Bibliographic records are drawn from OpenAlex, including publication dates, citation relationships, and document types.

This ranking covers the Class of 2026 cohort: journal articles published in 2024. Reviews and other non-article document types are excluded to ensure comparability.

Research impact is quantified with an 18-month post-publication citation window—the number of citing works published within 18 months of each paper's publication date. This metric captures early impact while controlling for publication age.

An LLM-based relevance classifier then reviews each candidate's title and abstract to confirm substantive alignment with the target domain. Only papers classified as relevant appear in the final ranking.

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

Full methodologyGitHubbioRxiv preprint

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 2026-10-24.

Methodology
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