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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
...Corynebacterium isolate sequenced in this study (Supplemental Fig. S8). This is very likely because of species-specific DNA modifications, such as methylation motifs that are uncommon or unique to C. rouxii, not being well represented in the training data sets of the basecalling model, especially because C...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
....Transcriptional regulation in eukaryotes is profoundly influenced by chromatin status, integrating diverse cellular signals to control gene expression (Berger 2007). Chromatin dynamics are modulated by multiple mechanisms, including histone modifications, DNA methylation, and chromatin remodeling complexes (Shilatifard 2006...
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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
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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Method: Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing
- Brigid M. O'Flaherty,
- Yan Li,
- Ying Tao,
- Clinton R. Paden,
- Krista Queen,
- Jing Zhang,
- Darrell L. Dinwiddie,
- Stephen M. Gross,
- Gary P. Schroth,
- and Suxiang Tong
Genome Res. June 2018 28: 869-877; Published in Advance April 27, 2018, doi:10.1101/gr.226316.117
...-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the s, allowing for identification of known viruses and full sequencing, while the second set targets regions conserved among viral families...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...Systems Biology of Signal Transduction, German Cancer 15 Research Center (DKFZ), 69120 Heidelberg, Germany 16 8 These authors contributed equally. Either author can be listed first. 17 * Correspondence: falk.butter@fli.de (FB) 18 19 Abstract 20 A tightly regulated DNA damage response is critical...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...-primes are hotspots for pathogenic variants and for variants that significantly alter gene expression or result in alternative splicing or variable DNA methylation. This can lead to further research regarding evolutionary adaptations in humans and can enable an improved understanding of human diseases...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...from whole blood and extracted DNA for whole nanopore sequencing (Methods). Approximately 45× coverage of nanopore sequencing reads was de novo assembled and phased, resulting in a highly contiguous personalized whole assembly (statistics in Supplemental Table S1). The IGH, IGL, and IGK loci were...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
...://www.ebi.ac.uk/ena) under accession number PRJEB20635, and three additional individuals were resequenced as described in Kardos et al. (2018). Briefly, DNA was prepared from blood or muscle tissue and paired-end libraries constructed for 150-bp sequencing on an Illumina HiSeq X instrument.The material included the female...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
....sohn@igb.fraunhofer.deAbstractHere, we present a method for enrichment of double-stranded cfDNA with an average length of ∼40 bp from cfDNA for high-throughput DNA sequencing. This class of cfDNA is enriched at gene promoters and binding sites of transcription factors or structural DNA-binding proteins, so that a -wide DNA footprint...
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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
...Science and Technology of China, Quzhou 324000, Zhejiang, China; 3College of Biomedical Engineering, Sichuan University, Chengdu 610041, Sichuan, China Corresponding author: luoximei@uestc.edu.cnAbstractDNA N4-methylcytosine (4mC), a key epigenetic modification regulating DNA repair and replication...
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