Searching journal content for articles similar to Berno 6 (2): 80.

Displaying results 1-10 of 354

For checked items

view abstracts
download to citation manager

Select this article
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...
Select this article
Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...sequence difference, with 0.1%–0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference and ignored the contribution of larger-scale structural variants (SVs). We constructed a pan graph that integrates six new and two existing long...
OPEN ACCESS ARTICLE
Select this article
Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...and colored by its GMM cluster label. Each k-mer is associated with a theoretical modeling count and an empirical sequencing count; these counts are aggregated based on cluster labels. The correlation between these aggregates evaluates how high-dimensional structural features determine sequencing biases...
Select this article
Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...ASM calls. Hence, we verified the genomic DNA sequences near the m6A modification sites using Sanger sequencing (Supplemental Table 5; Methods). In six selected ASM sites, we confirmed annotated SNPs (Nudt1, D site), and the absence of unannotated genetic variants. These results indicate...
Select this article
Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...individuals) for the generation of graph-s that describe genetic variation among individuals (4 bp insertion seen only in one individual; T/C SNV that is more common in the group). (F) Sequencing of native DNA strands in LRS enables concomitant assessment of base modifications, such as differentiating between...
OPEN ACCESS ARTICLE
Select this article
Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
- Jesper Eisfeldt,
- Adam Ameur,
- Felix Lenner,
- Esmee Ten Berk de Boer,
- Marlene Ek,
- Josephine Wincent,
- Raquel Vaz,
- Jesper Ottosson,
- Tord Jonson,
- Sofie Ivarsson,
- Sofia Thunström,
- Alexandra Topa,
- Simon Stenberg,
- Anna Rohlin,
- Anna Sandestig,
- Margareta Nordling,
- Pia Palmebäck,
- Magnus Burstedt,
- Frida Nordin,
- Eva-Lena Stattin,
- Maria Sobol,
- Panagiotis Baliakas,
- Marie-Louise Bondeson,
- Ida Höijer,
- Kristine Bilgrav Saether,
- Lovisa Lovmar,
- Hans Ehrencrona,
- Malin Melin,
- Lars Feuk,
- and Anna Lindstrand
Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
...captured by other genomics technologies, such as highly repetitive or homologous regions. Furthermore, sequencing of the native DNA also provides methylation information. With decreasing cost, it is increasingly attractive to use lrGS in unsolved rare disease cases. Yet, lrGS differs markedly from short...
OPEN ACCESS ARTICLE
Select this article
Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
...that involve changes in the DNA sequence of at least 50 bp, including deletions, duplications, insertions, inversions, and translocations. SVs are common (∼20,000/individual) and constitute the largest proportion of genetic variation between individuals (Feuk et al. 2006). Established risk-conferring SVs...
OPEN ACCESS ARTICLE
Select this article
Method: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
- Yunheng Han and
- Erin K. Molloy
Genome Res. July 2023 33: 1042-1052; Published in Advance May 17, 2023, doi:10.1101/gr.277629.122
...that offers accuracy and scalability under these challenging scenarios. TREE-QMC builds upon weighted Quartet Max Cut, which takes weighted quartets as input and then constructs a species tree in a divide-and-conquer fashion, at each step forming a graph and seeking its max cut. The wQMC method has been...
Select this article
Method: Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
- Romualdas Vaisvila,
- V.K. Chaithanya Ponnaluri,
- Zhiyi Sun,
- Bradley W. Langhorst,
- Lana Saleh,
- Shengxi Guan,
- Nan Dai,
- Matthew A. Campbell,
- Brittany S. Sexton,
- Katherine Marks,
- Mala Samaranayake,
- James C. Samuelson,
- Heidi E. Church,
- Esta Tamanaha,
- Ivan R. Corrêa, Jr.,
- Sriharsa Pradhan,
- Eileen T. Dimalanta,
- Thomas C. Evans, Jr.,
- Louise Williams,
- and Theodore B. Davis
Genome Res. July 2021 31: 1280-1289; Published in Advance June 17, 2021, doi:10.1101/gr.266551.120
.... However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. This method detects 5mC and 5hmC using two sets of enzymatic reactions. In the first reaction, TET2 and T4-BGT convert 5m...
OPEN ACCESS ARTICLE
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...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Berno 6 (2): 80.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: