Searching journal content for articles similar to Rocha et al. 11 (6): 946.

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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
...restriction–modification system (RM system). This system safeguards bacteria against phage and other invasive foreign DNA (O'Brown et al. 2019; Yu et al. 2021; Xiong et al. 2022). Consequently, 4mC is recognized as a key regulator of gene expression, DNA repair, and antiphage immunity in prokaryotes...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...Andrew D. Bates1,2,3,6, Dawid Grzela2,4,6, Maciej Studzian2,5,6, Louise Brennan1,6, Moli Williams1,6, Conor Fawcett1,6, Beth Hammond1, Manreen Grewal1, Marcin Ratajewski2, Lukasz Pulaski2,5 and Urszula L. McClurg1,2 1Institute of Systems, Molecular and Integrative Biology, University of Liverpool...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...adaptive immunity, and MHC genes serve as key models in evolutionary genomics, offering insight into birth-and-death evolution, gene duplication, and the maintenance of genetic diversity. However, the organization and evolution of the MHC in species with giant s, such as salamanders, remain poorly...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...310022, China; 9State Key Laboratory for Macromolecule Drugs and Large-scale Manufacturing, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325030, China ↵10 These authors contributed equally to this work. Corresponding authors: wuyf@immunol.org, reny@genomics.cn, jingang...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...insights into the origins of human diseases. However, epigenomic data, such as chromatin accessibility and histone modifications, enhance the dynamic characteristics of CREs to gene regulation, making it more challenging to decipher the relationships between CREs and gene expression...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...information on a target site of interest.The advent of innovative methodologies, such as those integrating CRISPR/Cas systems with RNA-processing approaches, has expedited research in this domain, furnishing novel tools for dissecting the roles of post-transcriptional modifications in gene expression dynamics...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
..., Baltimore, Maryland 21218, USA; 2Howard Hughes Medical Institute, Baltimore, Maryland 21218, USA; 3Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, Maryland 21218, USA; 4Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...is restricted to the digestive tract. Fly on the right is 40 days old, and the blue dye can be seen throughout the entire body. (B) Top four GO terms on genes that gain H3K27me3 signal in aged enterocytes from differential analysis. (C,D) UCSC Genome Browser tracks of chitin synthesis (C) and chitinase (D...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...Yuwei Cao1,2, Lauren Patel1,3, Lauren Alcoser4, Eric Mendenhall5, Christopher Benner6, Sven Heinz6 and Alon Goren1 1Department of Medicine, Division of Genomics & Precision Medicine, University of California San Diego, La Jolla, California 92093, USA; 2Bioinformatics and Systems Biology Graduate...

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