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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...by detecting exon–intron junctions or intron sequences from paired reads of backsplicing junctions (BSJs), and then retained introns and EIciRNAs were validated. (B) Correlation of Ct value examined by RT-qPCR and BSJ reads predicted by FEICP for 20 randomly selected EIciRNAs in HEK293 cells (left). Divergent...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
.... sgRNA binding sites: g1 and g2. PCR primers F2 and R2, and F1 and R1 shown as gray arrows used for amplification of the wild-type allele and the allele with deletion, respectively. (B) PCR-based identification of clones having the deletion of the Xist upstream region (D1) on the paternal allele (top...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
..., long-read cDNA sequencing coverage was &gt;100× at the critical gene for each of the samples. All seven variants with scores ≥0.10 yielded transcripts including pseudoexons ( Table 1 ), with all results confirmed by RT-PCR and Sanger sequencing ( Supplemental Fig. S1 ). No pseudoexons were detected...
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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
...-denatured, and ligated with the PEG-seq capture adapter as previously described.Target-specific primers for HEK4 and VEGFA (Supplemental Table S4) were designed upstream (5′) of each identified on- and off-target site and oriented within the same strand as the expected nick site. Seminested PCR was performed using 200...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...pause release (Wang et al. 2023). Additionally, we also found that DNase I hypersensitive sites (DHSs), markers of regulatory DNA and the basis for the discovery of various types of cis-regulatory elements (Thurman et al. 2012), were significantly enriched near TAD boundaries, revealing the role of TADs...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...and the translocation of one of its members, Cni-neib-1, to the center of Chr IV (Xie et al. 2024), we initially anticipated that the genomic region encompassing Cni-neib-1 would also exhibit rapid evolution. Unexpectedly, the ∼40 kb region surrounding Cni-neib-1 is invariant (>99% sequence identity) across both the cDNA...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
....Here, we present -wide Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), a high-accuracy, PCR-free, -wide cfDNA sequencing method based on a combination of RCA, and consensus calling of long-read nanopore sequences. The concatemeric RCA products ensure the physical...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...repeats, and amplified gene arrays (e.g., rDNAs).The short arms of the human acrocentric chromosomes, whose base-level structure was first revealed by the T2T-CHM13 reference (Nurk et al. 2022), are most challenging to assemble owing to their long, tandemly repeated rDNA arrays and enrichment...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...Taurine pan uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle Sotiria Milia1,4, Alexander S. Leonard1,4, Xena Marie Mapel1, Sandra Milena Bernal Ulloa2, Cord Drögemüller3 and Hubert Pausch1 1Animal Genomics, ETH Zurich, Zurich 8092, Switzerland...
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Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
- Yasine Malki,
- Guannan Kang,
- W.K. Jacky Lam,
- Qing Zhou,
- Suk Hang Cheng,
- Peter P.H. Cheung,
- Jinyue Bai,
- Ming Lok Chan,
- Chui Ting Lee,
- Wenlei Peng,
- Yiqiong Zhang,
- Wanxia Gai,
- Winsome W.S. Wong,
- Mary-Jane L. Ma,
- Wenshuo Li,
- Xinzhou Xu,
- Zhuoran Gao,
- Irene O.L. Tse,
- Huimin Shang,
- L.Y. Lois Choy,
- Peiyong Jiang,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
...to the manufacturer's instructions. Adaptor-ligated DNA was amplified using eight cycles of PCR. Quality control of the prepared libraries was done by Qubit and Agilent 4200 TapeStation (Agilent).Sequencing and alignmentTarget-captured DNA libraries were sequenced on the NextSeq 500 System (Illumina) with 75 bp × 2...
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