Single-cell nascent RNA sequencing unveils coordinated global transcription

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · cited 1× · see citing works

Spatial reconstruction of single-cell gene expression data

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055 · see citing works

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013 · see citing works

New cell lines from mouse epiblast share defining features with human embryonic stem cells

Tesar, P. J., Chenoweth, J. G., Brook, F. A., Davies, T. J., Evans, E. P., Mack, D. L., Gardner, R. L., & McKay, R. D. G. (2007) · Nature · doi:10.1038/nature05972 · Cited by 2,153 · see citing works

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracyPreprint

Smith, T. S., Heger, A., & Sudbery, I. M. (2017) · Genome Research · doi:10.1101/gr.209601.116 · Cited by 2,072 · see citing works

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986 · see citing works

Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature · doi:10.1038/nature03441 · Cited by 1,872 · see citing works

Stochastic mRNA Synthesis in Mammalian Cells

Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y., & Tyagi, S. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040309 · Cited by 1,737 · see citing works

Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors

Whitfield, M. L., Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., et al. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.02-02-0030 · Cited by 1,527 · see citing works

Visualization of Single RNA Transcripts in Situ

Femino, A. M., Fay, F. S., Fogarty, K., & Singer, R. H. (1998) · Science · doi:10.1126/science.280.5363.585 · Cited by 1,504 · see citing works

Transcriptional enhancers: from properties to genome-wide predictions

Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356 · see citing works

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

Deng, Q., Ramsköld, D., Reinius, B., & Sandberg, R. (2014) · Science · doi:10.1126/science.1245316 · Cited by 1,345 · see citing works

Gene co-expression analysis for functional classification and gene–disease predictions

van Dam, S., Võsa, U., van der Graaf, A., Franke, L., & de Magalhães, J. P. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbw139 · Cited by 1,086 · see citing works

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

Long, H. K., Prescott, S. L., & Wysocka, J. (2016) · Cell · doi:10.1016/j.cell.2016.09.018 · Cited by 945 · see citing works

Mammalian genes are transcribed with widely different bursting kinetics

Suter, D. M., Molina, N., Gatfield, D., Schneider, K., Schibler, U., & Naef, F. (2011) · Science · doi:10.1126/science.1198817 · Cited by 927 · see citing works

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. (2013) · Science · doi:10.1126/science.1229386 · Cited by 849 · see citing works

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

Marzluff, W. F., Wagner, E. J., & Duronio, R. J. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2438 · Cited by 768 · see citing works

RNA polymerase is poised for activation across the genome

Muse, G. W., Gilchrist, D. A., Nechaev, S., Shah, R., Parker, J. S., Grissom, S. F., Zeitlinger, J., & Adelman, K. (2007) · Nature Genetics · doi:10.1038/ng.2007.21 · Cited by 762 · see citing works

FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

Dodt, M., Roehr, J. T., Ahmed-Begrich, R., & Dieterich, C. (2012) · Biology · doi:10.3390/biology1030895 · Cited by 721 · see citing works

Enhancer Control of Transcriptional Bursting

Fukaya, T., Lim, B., & Levine, M. (2016) · Cell · doi:10.1016/j.cell.2016.05.025 · Cited by 721 · see citing works

Transcriptional Pulsing of a Developmental Gene

Chubb, J. R., Trcek, T., Shenoy, S. M., & Singer, R. H. (2006) · Current Biology · doi:10.1016/j.cub.2006.03.092 · Cited by 714 · see citing works

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., & Lis, J. T. (2014) · Nature Genetics · doi:10.1038/ng.3142 · Cited by 693 · see citing works

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

Habib, N., Li, Y., Heidenreich, M., Swiech, L., Avraham-Davidi, I., Trombetta, J. J., Hession, C., Zhang, F., & Regev, A. (2016) · Science · doi:10.1126/science.aad7038 · Cited by 601 · see citing works

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

Rabani, M., Levin, J. Z., Fan, L., Adiconis, X., Raychowdhury, R., Garber, M., Gnirke, A., Nusbaum, C., Hacohen, N., Friedman, N., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1861 · Cited by 583 · see citing works

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

Jonkers, I., Kwak, H., & Lis, J. T. (2014) · eLife · doi:10.7554/elife.02407 · Cited by 581 · see citing works

Genomic encoding of transcriptional burst kinetics

Larsson, A. J. M., Johnsson, P., Hagemann-Jensen, M., Hartmanis, L., Faridani, O. R., Reinius, B., Segerstolpe, Å., Rivera, C. M., Ren, B., & Sandberg, R. (2019) · Nature · doi:10.1038/s41586-018-0836-1 · Cited by 534 · see citing works

Single-Cell Gene Expression Profiling

Levsky, J. M., Shenoy, S. M., Pezo, R. C., & Singer, R. H. (2002) · Science · doi:10.1126/science.1072241 · Cited by 526 · see citing works

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., Waters, C. T., Munson, K. M., Core, L. J., & Lis, J. T. (2016) · Nature Protocols · doi:10.1038/nprot.2016.086 · Cited by 492 · see citing works

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

Hah, N., Danko, C. G., Core, L. J., Waterfall, J. J., Siepel, A. C., Lis, J. T., & Kraus, W. L. (2011) · Cell · doi:10.1016/j.cell.2011.03.042 · Cited by 488 · see citing works

Rates of in situ transcription and splicing in large human genes

Singh, J., & Padgett, R. A. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1666 · Cited by 487 · see citing works

THE CYTOPLASMIC SYNTHESIS OF HISTONES IN HELA CELLS AND ITS TEMPORAL RELATIONSHIP TO DNA REPLICATION

Robbins, E., & Borun, T. W. (1967) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.57.2.409 · Cited by 421 · see citing works

Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications

Gu, W., Crawford, E. D., O’Donovan, B. D., Wilson, M. R., Chow, E. D., Retallack, H., & DeRisi, J. L. (2016) · Genome biology · doi:10.1186/s13059-016-0904-5 · Cited by 346 · see citing works

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

Shah, S., Takei, Y., Zhou, W., Lubeck, E., Yun, J., Eng, C.-H. L., Koulena, N., Cronin, C. J., Karp, C., Liaw, E. J., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.035 · Cited by 316 · see citing works

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Dreos, R., Ambrosini, G., Groux, R., Périer, R. C., & Bücher, P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1069 · Cited by 275 · see citing works

Defining the Status of RNA Polymerase at Promoters

Core, L. J., Waterfall, J. J., Gilchrist, D. A., Fargo, D. C., Kwak, H., Adelman, K., & Lis, J. T. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.034 · Cited by 252 · see citing works

scSLAM-seq reveals core features of transcription dynamics in single cells

Erhard, F., Baptista, M. A. P., Krammer, T., Hennig, T., Lange, M., Arampatzi, P., Jürges, C. S., Theis, F. J., Saliba, A.-E., & Dölken, L. (2019) · Nature · doi:10.1038/s41586-019-1369-y · Cited by 233 · see citing works

High-throughput total RNA sequencing in single cells using VASA-seq

Salmén, F., Jonghe, J. D., Kamiński, T. S., Alemany, A., Parada, G. E., Verity-Legg, J., Yanagida, A., Kohler, T. N., Battich, N., van den Brekel, F., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01361-8 · Cited by 233 · see citing works

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon, A., Ferguson, M., de Turris, V., Palangat, M., Chow, C. C., & Larson, D. R. (2014) · eLife · doi:10.7554/elife.03939 · Cited by 228 · see citing works

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

Rabani, M., Raychowdhury, R., Jovanovic, M., Rooney, M., Stumpo, D. J., Pauli, A., Hacohen, N., Schier, A. F., Blackshear, P. J., Friedman, N., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.015 · Cited by 226 · see citing works

Identification of active transcriptional regulatory elements from GRO-seq data

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., Cheung, V. G., Kraus, W. L., Lis, J. T., & Siepel, A. C. (2015) · Nature Methods · doi:10.1038/nmeth.3329 · Cited by 216 · see citing works

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

Li, Y., Rivera, C. M., Ishii, H., Jin, F., Selvaraj, S., Lee, A. Y., Dixon, J. R., & Ren, B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114485 · Cited by 212 · see citing works

Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye.

Zhou, L., Myers, A. N., van der Steen, J., Wang, L., & Wittwer, C. (2004) · Clinical Chemistry · doi:10.1373/clinchem.2004.034322 · Cited by 211 · see citing works

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genesPreprint

Moorthy, S. D., Davidson, S., Shchuka, V. M., Singh, G., Malek-Gilani, N., Langroudi, L., Martchenko, A., So, V., Macpherson, N. N., & Mitchell, J. A. (2016) · Genome Research · doi:10.1101/gr.210930.116 · Cited by 190 · see citing works

Transcriptional coupling of distant regulatory genes in living embryos

Levo, M., Raimundo, J., Bing, X. Y., Sisco, Z., Batut, P. J., Ryabichko, S., Gregor, T., & Levine, M. S. (2022) · Nature · doi:10.1038/s41586-022-04680-7 · Cited by 188 · see citing works

In Vivo Kinetics of mRNA Splicing and Transport in Mammalian Cells

Audibert, A., Weil, D., & Dautry, F. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.19.6706-6718.2002 · Cited by 149 · see citing works

Nucleotide-Resolution Genome-Wide Mapping of Oxidative DNA Damage by Click-Code-Seq

Wu, J., McKeague, M., & Sturla, S. J. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b03715 · Cited by 123 · see citing works

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers

Tome, J. M., Tippens, N. D., & Lis, J. T. (2018) · Nature Genetics · doi:10.1038/s41588-018-0234-5 · Cited by 112 · see citing works

Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning

Riba, A., Oravecz, A., Durik, M., Jiménez, S., Alunni, V., Cerciat, M., Jung, M., Keime, C., Keyes, W. M., & Molina, N. (2022) · Nature Communications · doi:10.1038/s41467-022-30545-8 · Cited by 106 · see citing works

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells

Ochiai, H., Hayashi, T., Umeda, M., Yoshimura, M., Harada, A., Shimizu, Y., Nakano, K., Saitoh, N., Kimura, H., Liu, Z., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz6699 · Cited by 105 · see citing works

Spatial mapping of the total transcriptome by in situ polyadenylation

McKellar, D. W., Mantri, M., Hinchman, M. M., Parker, J. S. L., Sethupathy, P., Cosgrove, B. D., & Vlaminck, I. D. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01517-6 · Cited by 103 · see citing works

Transcription imparts architecture, function and logic to enhancer units

Tippens, N. D., Liang, J. H., Leung, A. K.-Y., Wierbowski, S. D., Ozer, A., Booth, J. G., Lis, J. T., & Yu, H. (2020) · Nature Genetics · doi:10.1038/s41588-020-0686-2 · Cited by 101 · see citing works

Major histocompatibility complex (Mhc) class Ib gene duplications, organization and expression patterns in mouse strain C57BL/6

Ohtsuka, M., Inoko, H., Kulski, J. K., & Yoshimura, S. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-178 · Cited by 96 · see citing works

The stability and fate of a spliced intron from vertebrate cells

Clement, J. Q., Qian, L., Kaplinsky, N. J., & Wilkinson, M. (1999) · RNA · doi:10.1017/s1355838299981190 · Cited by 89 · see citing works

Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics

Pimmett, V. L., Dejean, M., Fernandez, C., Trullo, A., Bertrand, E., Radulescu, O., & Lagha, M. (2021) · Nature Communications · doi:10.1038/s41467-021-24461-6 · Cited by 88 · see citing works

MYC amplifies gene expression through global changes in transcription factor dynamics

Patange, S., Ball, D. A., Wan, Y., Karpova, T., Girvan, M., Levens, D., & Larson, D. R. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110292 · Cited by 86 · see citing works

Nascent RNA and the Coordination of Splicing with TranscriptionPreprint

Neugebauer, K. M. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a032227 · Cited by 77 · see citing works

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

Chae, M., Danko, C. G., & Kraus, W. L. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0656-3 · Cited by 73 · see citing works

A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotencyPreprint

Xie, L., Torigoe, S. E., Xiao, J., Mai, D. H., Li, L., Davis, F. P., Dong, P., Marie-Nelly, H., Grimm, J. B., Lavis, L. D., et al. (2017) · Genes & Development · doi:10.1101/gad.303321.117 · Cited by 63 · see citing works

Versatile 5‘-Functionalization of Oligonucleotides on Solid Support: Amines, Azides, Thiols, and Thioethers via Phosphorus Chemistry

Miller, G. P., & Kool, E. T. (2004) · The Journal of Organic Chemistry · doi:10.1021/jo035765e · Cited by 56 · see citing works

Regulation of cell cycle progression by forkhead transcription factor FOXO3 through its binding partner DNA replication factor Cdt1

Zhang, Y., Xing, Y., Zhang, L., Mei, Y., Yamamoto, K., Mak, T. W., & You, H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203210109 · Cited by 49 · see citing works

Cell cycle dynamics of mouse embryonic stem cells in the ground state and during transition to formative pluripotency

Waisman, A., Sevlever, F., Costa, M. E., Cosentino, M. S., Miriuka, S., Ventura, A. C., & Guberman, A. (2019) · Scientific Reports · doi:10.1038/s41598-019-44537-0 · Cited by 49 · see citing works

TATA and paused promoters active in differentiated tissues have distinct expression characteristics

Ramalingam, V., Natarajan, M., Johnston, J., & Zeitlinger, J. (2021) · Molecular Systems Biology · doi:10.15252/msb.20209866 · Cited by 26 · see citing works

Transcription factor antagonism regulates heterogeneity in embryonic stem cell states

Hu, S., Metcalf, E., Mahat, D. B., Chan, L., Sohal, N., Chakraborty, M., Hamilton, M., Singh, A., Singh, A., Lees, J. A., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.10.022 · Cited by 24 · see citing works

Genome editing demonstrates that the −5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment

Agrawal, P., Blinka, S., Pulakanti, K., Reimer, M. H., Stelloh, C. T., Meyer, A. E., & Rao, S. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.015152 · Cited by 17 · see citing works

Identification of G1-Regulated Genes in Normally Cycling Human Cells

Beyrouthy, M. J., Alexander, K. E., Baldwin, A. E., Whitfield, M. L., Bass, H. W., McGee, D., & Hurt, M. M. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003943 · Cited by 16 · see citing works

Myc Amplifies Gene Expression Through Global Changes in Transcription Factor DynamicsPreprint

Patange, S., Ball, D. A., Karpova, T., et al. (2020) · SSRN Electronic Journal · doi:10.2139/ssrn.3698898 · Cited by 5 · see citing works

Identification of G1‐Regulated Genes in Normally Cycling Human Cells

Beyrouthy, M. J., Alexander, K. E., Baldwin, A. E., Whitfield, M. L., Bass, H. W., McGee, D., & Hurt, M. M. (2008) · The FASEB Journal · doi:10.1096/fasebj.22.1_supplement.636.4 · Cited by 1 · see citing works

Untitled work

Kolb (2001) · doi:10.1002/1521-3773(20010601)40:11

Advances and applications in single-cell and spatial genomics

Wang, J., Ye, F., Chai, H., Jiang, Y., Wang, T., Ran, X., Xia, Q., Xu, Z., Fu, Y., Zhang, G., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2770-x · Cited by 69 · see citing works

An RNA-centric view of transcription and genome organization

Henninger, J. E., & Young, R. A. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.08.021 · Cited by 56 · see citing works

RNA polymerase II at histone genes predicts outcome in human cancer

Henikoff, S., Zheng, Y., Paranal, R. M., Xu, Y., Greene, J. E., Henikoff, J. G., Russell, Z. R., Szulzewsky, F., Thirimanne, H. N., Kugel, S., et al. (2025) · Science · doi:10.1126/science.ads2169 · Cited by 50 · see citing works

Mutant p53 exploits enhancers to elevate immunosuppressive chemokine expression and impair immune checkpoint inhibitors in pancreatic cancer

Mahat, D. B., Kumra, H., Castro, S. A., Metcalf, E., Nguyen, K. B., Morisue, R., Ho, W. W., Chen, I. X., Sullivan, B., Yim, L., et al. (2025) · Immunity · doi:10.1016/j.immuni.2025.06.005 · Cited by 43 · see citing works

Multi-omics decodes host-specific and environmental microbiome interactions in sepsis

Lu, J., Zhang, W., He, Y., Jiang, M., Liu, Z., Zhang, J., Zheng, L., Zhou, B., Luo, J., He, C., et al. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1618177 · Cited by 31 · see citing works

Transcriptional bursting dynamics in gene expression

Zhang, Q., Cao, W., Wang, J., Yin, Y., Sun, R., Tian, Z., Hu, Y., Tan, Y., & Zhang, B. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1451461 · Cited by 18 · see citing works

Astragalus polysaccharides inhibits tumor proliferation and enhances cisplatin sensitivity in bladder cancer by regulating the PI3K/AKT/FoxO1 axis

Chen, R., Li, Y., Zuo, L., Xiong, H., Sun, R., Song, X., & Liu, H. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.143739 · Cited by 19 · see citing works

Regulation of RNA polymerase II transcription through re-initiation and bursting

Nagel, M., & Taatjes, D. J. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.04.011 · Cited by 17 · see citing works

Efficient profiling of total RNA in single cells with STORM-seqPreprint

Johnson, B. K., Majewski, M. F., Jang, H. J., Siwicki, R. A., Wegener, M., Semwal, A., Morrison, J., Gallik, K., Hagemann-Jensen, M., Foy, K. K., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.14.484332 · Cited by 16 · see citing works

Centromeres drive and take a break

Talbert, P. B., & Henikoff, S. (2025) · Chromosome Research · doi:10.1007/s10577-025-09777-z · Cited by 15 · see citing works

Timing is everything: transcription bursting in developmentPreprint

Kim, J. M., & Larson, D. R. (2025) · Genes & Development · doi:10.1101/gad.352465.124 · Cited by 13 · see citing works

Spatiotemporal Dynamics of Central Nervous System Diseases: Advancing Translational Neuropathology via Single‐Cell and Spatial Multiomics

Xia, M., Liu, Q., Zhang, W., Ge, J., & Mei, Z. (2025) · MedComm · doi:10.1002/mco2.70328 · Cited by 14 · see citing works

Single-cell nascent transcription reveals sparse genome usage and plasticity

Ma, S., Hong, Y., Chen, J., Xu, J., & Shen, X. (2025) · Cell · doi:10.1016/j.cell.2025.09.003 · Cited by 12 · see citing works

Gene regulatory landscape dissected by single-cell four-omics sequencing

Chen, Y., Liu, Z., Xu, H., Liu, J., Wang, M., Chi, Y., LIANG, B., Liu, M., Peng, Y., Ge, H., et al. (2026) · Nature · doi:10.1038/s41586-026-10322-z · Cited by 12 · see citing works

A perspective on integrating digital pathology, proteomics, clinical data and AI analytics in cancer research

Guedes, J., Woldmar, N., Szasz, A. M., Wieslander, E., Pawłowski, K., Horvatovich, P., Malm, J., Szadai, L., Németh, I. B., Marko-Varga, G., et al. (2025) · Journal of Proteomics · doi:10.1016/j.jprot.2025.105493 · Cited by 11 · see citing works

Epigenetics behind CD8+ T cell activation and exhaustion

Zu, H., & Chen, X. (2024) · Genes and Immunity · doi:10.1038/s41435-024-00307-1 · Cited by 12 · see citing works

Chromatin-centric insights into DNA replication

Liu, Y., Zhangding, Z., Liu, X., & Hu, J. (2025) · Trends in Genetics · doi:10.1016/j.tig.2024.12.003 · Cited by 10 · see citing works

Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods

Alfonso-Gonzalez, C., & Hilgers, V. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00895-4 · Cited by 13 · see citing works

Molecular models of bidirectional promoter regulation

Nemsick, S., & Hansen, A. S. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102865 · Cited by 10 · see citing works

ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation

Zhang, M., Zhang, W., & Ma, X. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae437 · Cited by 11 · see citing works

A systems view of cellular heterogeneity: Unlocking the “wheel of fate”

Movasat, H., Giacopino, E., Shahdoost, A., Nokoorani, Y. D., Abrbekouh, A. H., Tahamtani, Y., & Shakiba, N. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101300 · Cited by 14 · see citing works

Cohesin mutations in acute myeloid leukemia

Boucher, A. C., Murray, J. D., & Rao, S. (2024) · Leukemia · doi:10.1038/s41375-024-02406-4 · Cited by 9 · see citing works

SVA Regulation of Transposable Element Clustered Transcription within the Major Histocompatibility Complex Genomic Class II Region of the Parkinson’s Progression Markers Initiative

Kulski, J. K., Pfaff, A. L., & Kõks, S. (2024) · Genes · doi:10.3390/genes15091185 · Cited by 9 · see citing works

Better together: how cooperativity influences transcriptional bursting.

Fountas, C., & Lenstra, T. (2024) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2024.102274 · Cited by 4 · see citing works

Real-time visualization of reconstituted transcription reveals RNAPII activation mechanisms at single promoters

Palacio, M., & Taatjes, D. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116251 · Cited by 10 · see citing works

Time-resolved single-cell transcriptomic sequencing

Xu, X., Wen, Q. J., Lan, T., Zeng, L., Zeng, Y., Lin, S., Qiu, M., Na, X., & Yang, C. J. (2024) · Chemical Science · doi:10.1039/d4sc05700g · Cited by 10 · see citing works

Schlafen5, regulated by the AP-1 family transcription factor c-Fos, affects diabetic wound healing through modulating PI3K/Akt/NRF2 axis

Fan, Y., Lou, J., Wei, Z.-Q., Zhou, C., Shen, H., Wei, Z.-Y., Mao, X., Hong, L., Qian, J., Jin, M., et al. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.137805 · Cited by 8 · see citing works

Benchmarking metabolic RNA labeling techniques for high-throughput single-cell RNA sequencing

Zhang, X., Peng, M., Zhu, J., Zhai, X., Wei, C., Jiao, H., Wu, Z., Huang, S., Liu, M., Li, W., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61375-z · Cited by 8 · see citing works

Ligand tricks for faster clicks: bioconjugation via the CuAAC reaction

Amiri, A., Abedanzadeh, S., Khodabandehloo, M. H., Shaabani, A., & Moosavi‐Movahedi, A. A. (2025) · Chemical Communications · doi:10.1039/d5cc04435a · Cited by 8 · see citing works

Nascent RNA at the crossroad of transcription and replication

Zhu, M., Zhang, Y., Guo, T., & Ren, J. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.05.010 · Cited by 7 · see citing works

Two distinct chromatin modules regulate proinflammatory gene expression

Seufert, I., Gerosa, I., Varamogianni-Mamatsi, V., Vladimirova, A., Sen, E., Mantz, S., Rademacher, A., Schumacher, S., Liakopoulos, P., Kolovos, P., et al. (2024) · bioRxiv · doi:10.1038/s41556-025-01819-2 · Cited by 6 · see citing works

Mechanistic inference of stochastic gene expression from structured single-cell data

Miles, C. E. (2025) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2025.100555 · Cited by 6 · see citing works

Multimodal insights into adult neurogenesis: An integrative review of multi-omics approaches

Li, J., Huang, L., Xiao, W., Kong, J., Hu, M., Pan, A., Yan, X., Huang, F., & Wan, L. (2025) · Heliyon · doi:10.1016/j.heliyon.2025.e42668 · Cited by 6 · see citing works

Targeting super-enhancers in liver cancer: from pathogenic mechanisms to clinical applications

Li, C., Yao, Z., Sun, A., Cao, J., & Wang, Z. (2025) · Frontiers in Pharmacology · doi:10.3389/fphar.2025.1589455 · Cited by 5 · see citing works

Gene expression noise in development: genome-wide dynamics

Bax, D. J. C., Strik, J., Schepens, L. A. P., Lenstra, T. L., Hansen, M. M. K., & Marks, H. (2026) · Trends in Genetics · doi:10.1016/j.tig.2025.12.001 · Cited by 5 · see citing works

Single-cell RNA-sequencing and genome-wide Mendelian randomisation along with abundant machine learning methods identify a novel B cells signature in gastric cancer

Ma, Q., Gao, J., Hui, Y., Zhang, Z.-M., Qiao, Y.-J., Yang, B.-F., Gong, T., Zhao, D.-M., & Huang, B.-R. (2025) · Discover Oncology · doi:10.1007/s12672-025-01759-1 · Cited by 5 · see citing works

Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single-cell RNA-seq

Schofield, J. A., & Hahn, S. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114593 · Cited by 5 · see citing works

Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promotersPreprint

Palacio, M., & Taatjes, D. (2025) · bioRxiv · doi:10.1101/2025.01.06.631569 · Cited by 4 · see citing works

Viral RNA pUGylation promotes antiviral immunity in C. elegans

Lowe, D. D., Shukla, A., & Kennedy, S. G. (2025) · Journal of Virology · doi:10.1128/jvi.01169-25 · Cited by 2 · see citing works

Acetylation-Mediated Epigenetic Consequences for Biological Control and Cancer

Fritz, A. J., McKay, K. T., Greenyer, H. W., Pacht, E., Toor, R. H., Ullah, R., Porto, J. R. D., Person, A. G., Korzec, S. J., Bright, K. M., et al. (2025) · Results and problems in cell differentiation · doi:10.1007/978-3-031-91459-1_2 · Cited by 4 · see citing works

Integrating bulk and single-cell RNA data with machine learning to explore mitophagy in periodontitis

Hu, Q., Zhang, Y., Ming, H., Yuan, Z.-Y., Chen, F., Hao, W., Tan, X., & Zhang, X. (2025) · Medicine · doi:10.1097/md.0000000000044002 · Cited by 3 · see citing works

Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo

Chovatiya, G. L., Huang, S. Y., Wang, A. B., Versluis, P. P., Bai, C. K., DeBerardine, M., Liao, Y.-C., Ray, J., Ozer, A., Lis, J. T., et al. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.09.017 · Cited by 3 · see citing works

Adaptive drug resistance mechanisms driven by non-coding RNA–protein interaction networks in hepatocellular carcinoma

Tian, Y., Ouyang, K., Wu, H., Liao, H., He, L., Luo, T., Ma, K., Mao, X., Wang, F., & Xiong, H. (2025) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2025.105060 · Cited by 3 · see citing works

Exploring exosomal lncRNAs: unlocking the molecular code of tumor metastasis and drug resistance

Zhang, R., Li, M., Lu, S., Wang, A., & Zhang, S. (2025) · Cancer Cell International · doi:10.1186/s12935-025-04025-0 · Cited by 3 · see citing works

Sequential RNA polymerase II activation drives human hematopoiesis

Janssens, D. H., Codomo, C. A., Otto, D. J., Silberstein, L., Ahmad, K., & Henikoff, S. (2026) · Cell Reports · doi:10.1016/j.celrep.2025.116802 · Cited by 3 · see citing works

Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq)

Meyer, M., Olanrewaju, O., Montilla‐Perez, P., McDonald, A. L., Rickard, E. M., Telese, F., Benner, C. W., Savenkova, M. I., & Duttke, S. H. C. (2026) · Nature Protocols · doi:10.1038/s41596-025-01285-y · Cited by 3 · see citing works

Emerging roles of circular RNAs and enhancer RNAs: new insights into the development and management of neurodegenerative disorders

Ziaei, A., Kargar, M., Shirvani-Farsani, Z., & MehrabMohseni, M. (2026) · Biomarker Research · doi:10.1186/s40364-025-00886-9 · Cited by 3 · see citing works

Targeting lncRNA-mediated networks to overcome doxorubicin resistance in cancer

Qiu, M., Wang, Z., Teng, Y., Li, M., Wu, F., & Tian, Y. (2026) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2026.105214 · Cited by 3 · see citing works

Shining a light on cell biology of the nucleus with single-cell sequencing

van den Berg, J., & Zeller, P. J. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102468 · Cited by 3 · see citing works

RNA Dynamics Regulate Transcriptional Condensate Vivacity to Drive Gene CoordinationPreprint

Ogami, K., Zheng, M., Yoshino, S., Sugimoto, Y., Seida, M., Mori, T., Yoshizawa, R., Onimaru, K., Kadota, M., Kuraku, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.06.658161 · Cited by 3 · see citing works

Biomolecular Condensates in the Regulation of Transcription and Chromatin Architecture

Selivanovskiy, A. V., Razin, S. V., & Ulianov, S. V. (2025) · Biochemistry (Moscow) · doi:10.1134/s0006297925602746 · Cited by 2 · see citing works

A moments-based approach for inferring mechanisms of transcriptional regulation using nascent RNA data

Wen, K., Liao, Y., Wang, J., Choubey, S., & Jiao, F. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.01.030 · Cited by 2 · see citing works

Deciphering molecular spatiotemporal information of brain cells by chemical labeling

He, Y., Wang, L., Li, X., Chen, F., & Zhao, Y. (2026) · Science China Chemistry · doi:10.1007/s11426-025-3095-x · Cited by 2 · see citing works

Functional epigenetic dynamics and transcriptional heterogeneity: Recent advances

van Loosen, Q. C., van Saparoea, A. C. H. V. D. B., Cossins, B. C., & Verschure, P. J. (2026) · Current Opinion in Biomedical Engineering · doi:10.1016/j.cobme.2026.100664 · Cited by 2 · see citing works

Bridging Simplicity and Depth in Single-Cell Proteomics: A Cost-Effective Workflow and an Expanded Framework for Data Evaluation

Chi, S., Rogalski, J. C., Zhong, H., Martínez, E. G., Ebrahimi, A., Wong, R., Bailey, M. L., Marra, M. A., Maier, C. S., Snutch, T. P., et al. (2026) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6c00046 · Cited by 2 · see citing works

How Polyphenol Metabolites Spatiotemporally Reprogram Transcription Factors and Human Proteostasis: A Metabolite-Centric Framework

de la Lastra, J. M. P., Andrés, C. M. C., Munguira, E. B., Juan, C. A., & Lebeña, E. P. (2026) · Current Issues in Molecular Biology · doi:10.3390/cimb48050529 · Cited by 2 · see citing works

Molecular co-accessibility identifies coordinated regulation between distant cis-regulatory elements

Boulanger, M., Chatsirisupachai, K., Badayeva, Y., Snajder, R., Bonder, M. J., Lapouge, K., Remans, K., & Krebs, A. R. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.07.020 · Cited by 3 · see citing works

Deciphering transcriptional bursts and enhancer dynamics: Advancing cancer therapeutics through single‐cell global run‐on sequencing

Pan, X., Na, F., & Chen, X. (2024) · MedComm – Oncology · doi:10.1002/mog2.88 · Cited by 2 · see citing works

Nuclear biophysics: Spatial coordination of transcriptional dynamics?

Yoo, T. Y., Gouveia, B., & Needleman, D. J. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102561 · Cited by 2 · see citing works

Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo DevelopmentPreprint

Nieto, C., Vahdat, Z., Lim, B., & Singh, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.02.651973 · Cited by 2 · see citing works

The spatial choreography of mRNA biosynthesis

Ventura-Gomes, A., & Carmo‐Fonseca, M. (2025) · Journal of Cell Science · doi:10.1242/jcs.263504 · Cited by 1 · see citing works

PIS as a regulator of cellular heterogeneity, prognostic significance, and immune landscape in thyroid cancer

Wu, X., Dai, L., Zhang, W., Le, Q., Xie, Y., & Wang, Y. (2025) · Translational Oncology · doi:10.1016/j.tranon.2025.102296 · Cited by 1 · see citing works

High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples

Li, Y., Shah, S. R., Ozer, A., Zhu, Y., Pan, X., Xia, T., Zhang, J., Leung, A. K.-Y., Wei, M., Lis, J. T., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03218-w · Cited by 1 · see citing works

Using the simple telegraph model to decipher transcriptional burst regulation across genome-wide data

Chen, L., Wu, Y., Yang, C., Fang, S., Liao, Y., Wu, Y., Zhang, H., Jiang, G., Yu, J., & Jiao, F. (2026) · iScience · doi:10.1016/j.isci.2026.117127 · Cited by 1 · see citing works

CCDC86 modulates immune cell infiltration and disease progression in head and neck squamous cell carcinoma

He, F., Liu, Y., Zhang, X., Zhang, R., Qiu, J., & Sijia, N. (2025) · Discover Oncology · doi:10.1007/s12672-025-03918-w · Cited by 1 · see citing works

RNA Glycosylation in Plant Science: Progress, Challenges, and Applications for Crop Resilience and Food Quality

Naz, M., Bin, Y., & Chen, Z. (2026) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c12776 · Cited by 1 · see citing works

Identification of COL8A2, MICAL2, and TNFSF10 as potential biomarkers associated with both exercise response and osteoarthritis: a multi-omics integration study

Wang, H., Lu, H., Zhou, X., Tian, Y., Dan, J., Li, Y., Li, X., Wang, J., & Li, L. (2026) · 3 Biotech · doi:10.1007/s13205-025-04685-9 · Cited by 1 · see citing works

DNER as a novel protein contributes to HSCR pathogenesis: multi-omics combined Mendelian randomization analysis

Liu, W., Xu, W., Huang, J., Xu, J., Fu, Z., Yan, H., Jia, W., Yu, H., Zheng, B., Pan, W., et al. (2026) · Pediatric Research · doi:10.1038/s41390-026-04789-9 · Cited by 1 · see citing works

Now You See Me: Visualizing nuclear complexity by selective staining

Casali, C., Cavallo, M., Diaf, A., Milanesi, G., & Biggiogera, M. (2026) · Methods · doi:10.1016/j.ymeth.2026.03.005 · Cited by 1 · see citing works

Isoliquiritigenin alleviates ethanol-induced gastric ulcers by modulating the TNF signaling pathway and targeting IL-6

Li, Y., Jin, Y., Shu, W., Li, H., zhang, C., Wang, X., Zhang, G., He, X., Li, Z., Luo, M., et al. (2026) · Journal of Functional Foods · doi:10.1016/j.jff.2026.107255 · Cited by 1 · see citing works

sc-rDSeq: a robust and cost-effective full-length total RNA sequencing method for single cells reveals multilayered heterogeneity in drug-resistant lung cancer cells

Sun, X., Dadon, S.-L., Ennis, D., Fan, W., Awawdy, M., Reuveni, E., Alajem, A., & Ram, O. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag312 · Cited by 2 · see citing works

Deciphering the dual effects of transcription on DNA replication elongation by replication-associated Micro-C

Zhangding, Z., Liu, X., Liang, H., 范雅絮, Peng, Y., Rao, W., Chen, W., & Hu, J. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.034 · Cited by 2 · see citing works

Multi-omics insights into SERPINE2-driven post-metastatic microenvironmental reprogramming in advanced cancers: implications for molecular targeting and immunotherapy

Yi, Y., Lai, J., Zhāng, P., & Zhang, R. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1815463 · Cited by 1 · see citing works

A NOTCH2 pathogenic variant alters the osteoblast and vascular cell transcriptome of mouse femurs

CANALIS, E. M., Schilling, L., & Denker, E. (2026) · Bone · doi:10.1016/j.bone.2026.117909 · Cited by 1 · see citing works

SCSEQ: A web tool for analyzing single-cell RNA-seq data

Du, S., Sun, P., Shen, L., & He, J. (2026) · GigaScience · doi:10.1093/gigascience/giag029 · Cited by 1 · see citing works

The interplay of Drp1 post-translational modifications as a regulatory network driving mitochondrial fission in diabetic kidney disease

Wu, R., & Mao, Y. (2026) · Current Proteomics · doi:10.1016/j.curpro.2026.100105 · Cited by 1 · see citing works

Simultaneous measurements of translation rate and transcriptome uncovers linked regulation within an active bacterial cell population

Baumann, C. T., Hydorn, M. A., Cooke, S. F., Dworkin, J. E., & Rosenthal, A. Z. (2026) · Science Advances · doi:10.1126/sciadv.adz1707 · Cited by 1 · see citing works

Single-cell and spatial transcriptomics analysis of osteoarthritis: pathway regulation, cell interaction networks, and therapeutic translation

Yang, D., Lü, J., Liu, Q., Gong, G. N., Chen, J., Song, Z., Ye, Z., Wang, S., Xiao, Y., & Wang, G. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-08603-2 · Cited by 1 · see citing works

The molecular basis of transcription initiation by RNA polymerase II

Chen, X., & Xu, Y. (2026) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-026-01019-2 · Cited by 1 · see citing works

RNA-mediated SOX2 temporal dynamics govern dual chromatin-engagement modes at NanogPreprint

Li, B., Wong, Y. Y., Kobayashi, Y., Rodriguez, N. F., Davidson, T., Graus, M. S., Smialkovska, V., Pachauri, S., Pradhan, S., Gao, X., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.10.612363 · Cited by 1 · see citing works

KAS-CUT&Tag for direct mapping of transcription bubblesPreprint

Wu, W., Greene, J. E., Ahmad, K., & Henikoff, S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.15.725569 · Cited by 1 · see citing works

Improve spatial domain identification for spatial transcriptomics using high-order neighbor feature hybrid graph convolutional networks

Liang, X., Yuan, S., Li, S., & Wang, J. (2024) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm62325.2024.10822729

Advances in single-cell RNA-seq for nascent transcriptome and epitranscriptome

Gao, M., & Liu, J. (2025) · Scientia Sinica Vitae · doi:10.1360/ssv-2024-0265

Anti-Phase Clustering of Regulatory Factors Shapes Gene Transcription BurstPreprint

Li, B., Wong, Y. Y., Rodriguez, N. F., Davidson, T., Graus, M. S., Smialkovska, V., Ohishi, H., Feldmann, A., Ochiai, H., & François, M. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5157778

Simultaneous measurements of translation rate and transcriptome in single bacterial cells by scTR-seq uncovers linked regulation within a specialized active cell populationPreprint

Baumann, C. T., Hydorn, M. A., Cooke, S. F., Dworkin, J. E., & Rosenthal, A. Z. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.22.649982

Functional enhancers: concept, screening, and validation

Lin, H., Chen, F., & Huang, J. (2025) · Scientia Sinica Vitae · doi:10.1360/ssv-2025-0113

Advances and breakthroughs in single-cell nucleic acid omics

Sun, Z., Li, Z., Tang, Y., & Dong, F. (2025) · Scientia Sinica Vitae · doi:10.1360/ssv-2025-0107

Mitigating Cell Cycle Effects in Multi‐Omics Data: Solutions and Analytical Frameworks

Nie, R., Zheng, C., Ren, L., Teng, Y., Sun, Y., Wang, L., Li, J., & Cai, J. (2025) · Advanced Science · doi:10.1002/advs.202505823

eNRSA: a faster and more powerful approach for nascent transcriptome analysis

Wang, J., Chen, H., Hiebert, S. W., Sheng, Q., Tansey, W. P., Shyr, Y., & Liu, Q. (2025) · GigaScience · doi:10.1093/gigascience/giaf071

Molecular co-accessibility identifies coordinated regulation between distant cis-regulatory elementsPreprint

Boulanger, M., Chatsirisupachai, K., Badayeva, Y., Snajder, R., Bonder, M., Lapouge, K., Remans, K., & Krebs, A. R. (2025) · bioRxiv · doi:10.1101/2025.08.05.668660 · Cited by 2 · see citing works

Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo DevelopmentPreprint

Nieto, C., Vahdat, Z., Lim, B., & Singh, A. (2025) · eLife · doi:10.7554/elife.107610

Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo DevelopmentPreprint

Nieto, C., Vahdat, Z., Lim, B., & Singh, A. (2025) · eLife · doi:10.7554/elife.107610.1 · Cited by 1 · see citing works

Single-cell transcriptome analysis highlights a critical role of ATG5 for endothelial cells in diabetic nephropathy

Zhang, Y., Che, L., Gao, H., Zeng, Q., Zhang, J., Zheng, Y., Li, Y., & Chen, X. (2025) · Human Cell · doi:10.1007/s13577-025-01302-y

A Conserved Stress-Inducible Hub Enhancer Governs Natriuretic Peptide Expression and Undergoes Dynamic and Reversible Activation in Human Heart FailurePreprint

Matsuoka, K., Inoue, H., Hyejin, J., Okamoto, C., Hasuike, H., Fu, H. Y., Kioka, H., Kuramoto, Y., Segawa, T., Nishimura, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.13.682224

Interspecific divergence of gene expression biophysics driven by both evolutionary systems drift and strong selective constraints on bursting ratePreprint

Felce, C., Schraiber, J. G., Krishnaswamy, M., Cope, A. L., Pachter, L. S., & Pennell, M. W. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.24.690267

Current progress and role of lncRNAs in HBV infection and progression of hepatocellular carcinoma

Mahmood, F., Awan, M. U. N., Luo, M.-T., Li, X., Peng, X.-B., Xu, J., Wei, J., & 周太成 (2025) · Genes & Diseases · doi:10.1016/j.gendis.2025.101878

Taking the pulse of RNA polymerase II in intact tissue with PReCIS-seq

Platt, S., & Myung, P. S. (2026) · Developmental Cell · doi:10.1016/j.devcel.2026.01.008

Integrating Bidirectional Mendelian Randomization with Multi-Omics Reveals Causal Serum Metabolites and Novel Metabolic Drivers of Multiple Myeloma

Liu, Y., Qin, D., Ye, H., Tang, L., & Li, X. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27041904

Leveraging Twin Information for Inference of Gene Regulatory NetworksPreprint

Arun, K. M., Scher, Y., Zhang, Y. D., Büschel, I., Kuznets-Speck, B., Marr, C., & Goyal, Y. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.22.707230

AI-enabled single-cell dissection of the palmitoylation landscape identifies a multicellular prognostic program in gastric cancer

Xu, J., Hu, Y., Qiao, Q., Lu, Y., Cen, F., Hou, S., Yang, H. B., Lv, J., Qin, Y., & Xia, S. (2026) · npj Precision Oncology · doi:10.1038/s41698-026-01359-4

Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcriptionPreprint

Mahat, D. B., Tippens, N. D., Martin-Rufino, J. D., Waterton, S. K., Fu, J., Blatt, S. E., & Sharp, P. A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.15.558015 · Cited by 4 · see citing works

Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

Choubey, S., Kondev, J., & Sánchez, Á. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004345 · Cited by 59 · see citing works

RESEARCH ARTICLE Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

Choubey, E., Kondev, J., & Sánchez, Á. (2016)

Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs

Cardiello, J. F., Sanchez, G. J., Allen, M. A., & Dowell, R. D. (2019) · Transcription · doi:10.1080/21541264.2019.1704128 · Cited by 24 · see citing works

Global Run-on Sequencing (GRO-Seq)

Tzerpos, P., Dániel, B., & Nagy, L. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1597-3_2 · Cited by 7 · see citing works