Searching journal content for articles similar to Sakallah et al. 4 (5): 265.

Displaying results 1-10 of 5980

For checked items

view abstracts
download to citation manager

Select this article
Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...-Loeffler-Institut, 17493 Greifswald, Germany; 3School of Health Sciences-Biomedical Sciences Program, Missouri State University, Springfield, Missouri 65897, USA A tightly regulated DNA damage response is critical to the overall integrity of the . Here, we combine transcriptomics and proteomics to study DNA damage...
Select this article
Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
..., playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads. And these errors...
Select this article
Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...rare in eukaryotes(Beaulaurier et al. 2019). Similar to 6mA and 5mC, 4mC plays critical roles in many biological processes, including DNA repair and replication. It operates as a core component in the antiphage immune system of bacteria, mainly reflected in the participation of 4mC in the bacterial...
OPEN ACCESS ARTICLE
Select this article
Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...of the phyla Firmicutes, Actinobacteria, and Bacteroidetes, which are among the most abundant bacteria found in Pristionchus nematodes and their beetle hosts (Meyer et al. 2017). Eighty-four bacterial strains were selected for whole- sequencing based on criteria such as fast growth, ease of DNA extractions...
Select this article
Method: Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
- Mara Lohde,
- Gabriel E. Wagner,
- Johanna Dabernig-Heinz,
- Adrian Viehweger,
- Sascha D. Braun,
- Stefan Monecke,
- Celia Diezel,
- Claudia Stein,
- Mike Marquet,
- Ralf Ehricht,
- Mathias W. Pletz,
- and Christian Brandt
Genome Res. November 2024 34: 2039-2047; Published in Advance October 23, 2024, doi:10.1101/gr.278848.123
..., Bettman B, et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323: 133–138. doi:10.1126/science.1162986 ↵Gao Q, Lu S, Wang Y, He L, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, et al. 2023. Bacterial DNA methyltransferase: a key to the epigenetic world with lessons learned...
OPEN ACCESS ARTICLE
Select this article
Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...promising results in bacterial s (Wick 2024a,b). To this end, each subsampled read set was corrected with HERRO through its integrated version within Dorado.De novo assemblyShort-read sequence data were assembled with fq2dna v21.06 (https://gitlab.pasteur.fr/GIPhy/fq2dna). Subsampled long-read data sets...
Select this article
Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...-ornstein@primemedicine.comAbstractGene editing makes precise changes in DNA to restore normal function or expression of genes; however, the advancement of gene editing to the clinic is limited by the potential genotoxicity of off-target editing. To comprehensively identify potential sites in the that may be recognized by gene editing agents...
OPEN ACCESS ARTICLE
Select this article
Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...(TAATNNGNNATTA) (Fig. 2C), which is expected to limit cooperativity between half-sites (Fig. 1D; Supplemental Fig. S1B; Wilson et al. 1993; Tucker and Wisdom 1999). We obtained the DNA-binding cooperativity index ω of WT and mutant HDs at the P5 library using bacterially expressed and affinity-purified HD...
OPEN ACCESS ARTICLE
Select this article
Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear s Yu-Chi Chen1,2, David L.J. Vendrami3,4,5,6, Maximilian L. Huber2, Luisa E.Y. Handel2, Christopher R. Cooney7, Joseph I. Hoffman3,4,5,6,8 and Toni I. Gossmann1,2,3,5 1Computational Systems Biology, Faculty...
Select this article
Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...called “fountains,” which have also been reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20–40 kb in C. elegans. Hi-C analysis upon cohesin and WAPL-1 depletion supports the idea that cohesin is preferentially loaded...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Sakallah et al. 4 (5): 265.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: