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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...a sample, reverse-transcribing it into stable cDNA, and finally sequencing using (mostly) Illumina technology (Bentley et al. 2008). RNA-seq has multiple technical variations, either to identify specific types of transcripts or to characterize other RNA products. For instance, small RNA sequencing (s...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...-molecule sequencing technologies (Oxford Nanopore Technologies [ONT] and Pacific Biosciences [PacBio]) have enabled readouts of long, native DNA molecules, including cytosine methylation. ONT recently upgraded their Nanopore sequencing chemistry and kits from the R9 to the R10 version, which yielded increased...
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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
...Following the ligation reaction, samples are enzymatically fragmented to the appropriate size for Illumina sequencing (∼200–800 bp) by adding 2 µL of NEBNext dsDNA fragmentase in 1× fragmentation buffer (NEB) to final volume of 50 µL. The fragmentation reaction is incubated for 1 h at 37°C, terminated by adding 10 µ...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...) attributed this bias to the use of cesium chloride DNA purification by Kim et al. (2014), which separates DNA based on density. Because the light AT-rich sequences form a band separated from the main DNA band (satellite bands) (see Kit 1961; Rae 1970; Gall and Atherton 1974; Altemose 2022) and because some...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...of centromeric regions that limits 319 DNA accessibility and favors conserved repair mechanisms, reducing the occurrence 320 of large-scale SVs (Kashi and King 2006). Sequence annotation revealed that over 60% 321 of INS inserted in satellite/center, satellite, and simple repeat regions harbored 322 inserted...
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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...Mbp) and simpler in structure, consisting of a single circular chromosome in most cases, than those of eukaryotes. The rapid development of DNA sequencing technologies and the increase in computational power have driven a significant expansion in the number of both sequenced prokaryotic s from...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...on a single chromosome (RD_P276, RD_P278, RD_P273, RD_P166, RD_P550, RD_P275), and three were complex rearrangements involving either more than three BPJs (RD_P272, RD_P586) or more than one chromosome (RD_P328) (Table 2). In traditional cytogenetics, a simple sSMC is defined as a continuous DNA fragment...
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Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
- Inswasti Cahyani,
- John Tyson,
- Nadine Holmes,
- Josh Quick,
- Chris Moore,
- Nick Loman,
- and Matthew Loose
Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
...with actively threading (sequencing) DNA molecules will continue sequencing; pores without DNA are inactivated. This process terminates at a fixed time, which is 10 min by default. After this period, all pores are inactivated. Molecules still traversing a pore at that point will be ejected, but UHMW DNA...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...://github.com/nanoporetech/dorado), extracting both DNA sequence and 5mC methylation signals during basecalling. We then perform, in the cloud (a high-performance computing platform), mapping to the reference sequence using Sentieon-accelerated minimap2 (https://www.sentieon.com/), followed by variant calling with Clair3 for SNVs and indels...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...is widespread, gene and cell-type specific, and responsive to stimuli, we know little 279 about factors enhancing or preventing its usage (Lee et al. 2018; Singh et al. 2018). Epigenetic 280 modifications like DNA methylation modulate gene expression without altering DNA sequence, 281 which is analogous...
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