Searching journal content for articles similar to Ha et al. 22 (10): 1995.

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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...quantitative nucleotide resolution of methylation. It converts unmethylated cytosine to uracil by chemical deamination, while methylated DNA remains unconverted (Fig. 1B). After polymerase chain reaction (PCR), the methylated and unmethylated bases are distinguished as cytosine (C) to thymine (T) single...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...length as a function of the location of the midpoint of each fragment and colored the points based on their local density. The result is a near-nucleotide-resolution -wide view of chromatin occupancy for each deletion strain (Fig. 1D–F).View larger version: In this window In a new window Figure 1. Genome-wide...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...using ggRiboBesides visualizing Ribo-seq/RNA-seq profiles, ggRibo can integrate other omics data sets that offer single-nucleotide resolution (see Fig. 2D). To illustrate its utility in multiomic data comparison, we provide three examples below to showcase ggRibo’s capacity to reveal novel biological...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...a mammalian . Cell Syst 4: 344–356.e7. doi:10.1016/j.cels.2017.01.013 ↵Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D. 2017. Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol Cell 67: 411–422.e4. doi:10.1016/j.molcel.2017.06.027 ↵Kwak...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...cancer cells or tissues (Zhou et al. 2019; Kim et al. 2022; Wang et al. 2022; Dozmorov et al. 2023). Nonetheless, one study reports that triple-negative breast cancer cells display the most severe disruption of the 3D , including weakening of TAD borders, loss of 3D chromatin interactions leading...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...cytosine bases derived from UV-induced CPD lesions.Genome-wide map of CPD deamination in repair-deficient yeast cellsAlthough our aim was to analyze CPD deamination over a 48 h time course in nucleotide excision repair (NER)–deficient (i.e., rad14Δ) yeast cells, these cells are very sensitive to UV...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...and rarely contain an ESR1 motif. Unlike inactive ERBS, constitutive ERBS are prebound by coregulators and associated with enhancers, promoters, and transcriptional activity. Clinical data integration reveal that ERBS subclasses were associated with distinct breast cancer subtypes and clinical outcomes...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...window Figure 2. Genome-wide diversity and differentiation for common voles, M. arvalis, from the Orkney archipelago (brown) versus continental individuals (green). Density distributions (top) and Manhattan plots (bottom) for π, Tajima's D, and FST in 50 kb windows along the . Different chromosomes...
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Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
- Juniper J. Elacqua,
- Navpreet Ranu,
- Sarah E. DiIorio,
- and Paul C. Blainey
Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
...DENT-seq for -wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution Juniper J. Elacqua1,2,4, Navpreet Ranu1,2,4,5, Sarah E. DiIorio1,2,6 and Paul C. Blainey1,2,3 1MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA; 2Broad...
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Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...classifier for -wide detection. The limitation of the supervised classification framework primarily manifests in its detection speed and relatively small reception fields. Genome-wide detection with a binary classifier can be computationally inefficient as the small window causes scanning to be resource...
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