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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...sequencing (scRNA-seq) and single-cell DNA methylation (scDNAm) data face limitations, including unidirectionality, inadequate modeling of context-specific DNA methylation–expression associations, neglect of biological relevance in evaluation, and poor performance in limited paired training data. To fill...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...change in human and animal models have focused on DNA methylation. Multiple studies have characterized the DNA methylome response to both acute and chronic modes of resistance, high intensity, and endurance exercise in humans (Barrès et al. 2012; Nitert et al. 2012; Rowlands et al. 2014; Seaborne et al...
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Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
- Gianluca Mattei,
- Marta Baragli,
- Barbara Gega,
- Alessandra Mingrino,
- Martina Chieca,
- Tommaso Ducci,
- Gianmaria Frigè,
- Luca Mazzarella,
- Romina D'Aurizio,
- Francesco De Logu,
- Romina Nassini,
- Pier Giuseppe Pelicci,
- and Alberto Magi
Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
...with Salmon v. 0.14.1 and the reference transcriptome GRCh37 from Ensembl. Normalization and statistical analysis were performed with DESeq2 (v. 1.30.1). DEGs with adjusted P-value < 0.05, as scored by the Benjamin–Hopkins formula, and absolute log2FC > 0.5 were selected. DNA and RNA nanopore sequencing data...
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Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- Qiao Rui Xing,
- Chadi A El Farran,
- Ying Ying Zeng,
- Yao Yi,
- Tushar Warrier,
- Pradeep Gautam,
- James J. Collins,
- Jian Xu,
- Peter Dröge,
- Cheng-Gee Koh,
- Hu Li,
- Li-Feng Zhang,
- and Yuin-Han Loh
Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
...importance to gain comprehensive understanding of cell states. To tackle this, multimodal single-cell methods have been developed for concurrent measurement of and transcriptome (Dey et al. 2015; Macaulay et al. 2015) and of transcriptome and DNA methylome within a single-cell (Angermueller et al. 2016...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...(11-beta-hydroxylase enzyme; predicted CTFC_binding site), DGCR8 (mediates biogenesis of miRNAs; predicted active H3K27ac and repressive H3K27me3 binding site), and the DNA methyltransferases DNMT3A and DNMT3L (at predicted enhancer region). In the polar lineage, we observed significant...
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Research: Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism
- Margaret R. Starostik,
- Olukayode A. Sosina,
- and Rajiv C. McCoy
Genome Res. June 2020 30: 814-825; Published in Advance July 8, 2020, doi:10.1101/gr.262774.120
...patterns of mosaic aneuploidy that we previously described using published data from additional disaggregated embryos that were analyzed by single-cell post-bisulfite adaptor tagging (PBAT) DNA methylome sequencing (Zhu et al. 2018). The fact that these data were based on single-cell DNA-sequencing (scDNA...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...them to define transcriptome complexity is not trivial. Several methods have been developed to call transcript isoforms with a reference using long reads, including ToFU (Gordon et al. 2015) and SQANTI (Tardaguila et al. 2018), which were designed for PacBio cDNA reads. These methods depend heavily...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...in a murine MPN model. This study was replicated in MPN patients by profiling -wide gene expression and DNA methylation using patient blood samples collected longitudinally, before and following HC exposure. The effects of HC on the transcriptome were not only associated with cell cycle interruption but also...
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Research: Tracing human stem cell lineage during development using DNA methylation
- Lucas A. Salas,
- John K. Wiencke,
- Devin C. Koestler,
- Ze Zhang,
- Brock C. Christensen,
- and Karl T. Kelsey
Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
...is shown in Supplemental Figure S1. We initially compared -scale DNA methylation profiles of each of the six major blood cell lineages separately between umbilical cord blood (UCB) and adult whole peripheral blood (AWB) DNA samples. Across the separate models fit to each blood cell type, we identified 1255...
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Research: Bacterial infection remodels the DNA methylation landscape of human dendritic cells
- Alain Pacis,
- Ludovic Tailleux,
- Alexander M. Morin,
- John Lambourne,
- Julia L. MacIsaac,
- Vania Yotova,
- Anne Dumaine,
- Anne Danckaert,
- Francesca Luca,
- Jean-Christophe Grenier,
- Kasper D. Hansen,
- Brigitte Gicquel,
- Miao Yu,
- Athma Pai,
- Chuan He,
- Jenny Tung,
- Tomi Pastinen,
- Michael S. Kobor,
- Roger Pique-Regi,
- Yoav Gilad,
- and Luis B. Barreiro
Genome Res. December 2015 25: 1801-1811; Published in Advance September 21, 2015, doi:10.1101/gr.192005.115
...an integrated analysis of data on genome-wide DNA methylation, histone mark patterns, chromatin accessibility, and gene expression, before and after infection. We found that infection-induced demethylation rarely occurs at promoter regions and instead localizes to distal enhancer elements, including those...

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