Searching journal content for articles similar to O'Connell et al. 33 (2): 208.

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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
...Interdisciplinary Studies, Nankai University, Tianjin 300071, China Single-cell multiomic sequencing technologies have offered unprecedented insights into cellular heterogeneity by jointly profiling gene expression and epigenetic landscapes at single-cell resolution. However, the application of these technologies...
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Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
..., Illinois 60607, USA; 3Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA Corresponding author: zivbj@cs.cmu.eduAbstractRecent efforts to generate atlas-scale single-cell data provide opportunities for joint analysis across tissues...
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Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
- An Wang,
- Stephanie Hicks,
- Donald Geman,
- and Laurent Younes
Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
...for Imaging Science, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: awang87@jhu.eduAbstractThe selection of marker gene panels is critical for capturing the cellular and spatial heterogeneity in the expanding atlases of single-cell RNA sequencing (scRNA-seq) and spatial...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang Z-M, Barisic D, et al. 2024. ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. Nat Commun 15: 9432. doi:10.1038/s41467-024-53628-0 ↵Giresi PG, Kim J, McDaniell RM, Iyer VR...
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Method: Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing
- Wai Lim Ku,
- Lixia Pan,
- Yaqiang Cao,
- Weiwu Gao,
- and Keji Zhao
Genome Res. October 2021 31: 1831-1842; Published in Advance April 14, 2021, doi:10.1101/gr.260893.120
...: zhaok@nhlbi.nih.govAbstractRecently, multiple single-cell assays were developed for detecting histone marks at the single-cell level. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these problems, we introduce indexing single-cell...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
.... 2022), enabling the investigation of GRN from epigenomic landscapes (Loers and Vermeirssen 2024). Single-cell ATAC sequencing (scATAC-seq) technologies can identify chromatin accessibility profiles at the unprecedented resolution of the single-cell level (Fang et al. 2021; Chen et al. 2022...
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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
...-adipogenic progenitor cells, involving a total of 328 transcription factors acting at chromatin sites regulating 2025 genes. This web-accessible single-cell data set and regulatory circuitry map serve as a resource for understanding the molecular underpinnings of the metabolic and physiological effects of exercise...
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Method: Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach
- Fabien Wehbe,
- Levi Adams,
- Jordan Babadoudou,
- Samantha Yuen,
- Yoon-Seong Kim,
- and Yoshiaki Tanaka
Genome Res. January 2025 35: 135-146; Published in Advance December 2, 2024, doi:10.1101/gr.278812.123
...Johnson Medical School, Piscataway, New Jersey 08854, USA; 3Department of Biology, Bates College, Lewiston, Maine 04240, USA Corresponding author: yoshiaki.tanaka@umontreal.caAbstractApplication of single-cell/nucleus genomic sequencing to patient-derived tissues offers potential solutions to delineate...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...of Michigan, Ann Arbor, Michigan 48109, USA; 9Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: mohlke@med.unc.eduAbstractChromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...of cell fates from single-cell snapshots. However, the study suggested that scRNA-seq fails to capture the heritable properties that guide fate determination, where additional studies such as chromatin accessibility or proteomics information may help to identify the hidden information (VanHorn and Morris...
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