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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
...fails at multiple levels: read initiation (very few reads start within satellite regions), read elongation (satellite-containing reads are shorter on average), and basecalling (quality scores drop as sequencing enters a satellite sequence). These findings challenge the assumption that long-read...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...regions compared with short reads. Still, a technical challenge is to deal with sequencing errors for certain technologies; for example, Oxford Nanopore Technologies (ONT) long reads can have 90%−99% sequencing accuracy depending on the chemistry and basecalling (Sereika et al. 2022). We focus on small...
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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
..., after read alignment (onto hg38) and read filtering, resulted in a mean HiFi read depth of 9.8 (Supplemental Table S6).DNA sequencingGenomic DNA was isolated from peripheral blood according to standard protocol and long-read HiFi sequenced using SMRT sequencing technology (Pacific Biosciences, Menlo...
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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
...Resolving complex duplication variants in autism spectrum disorder using long-read sequencing Jesper Eisfeldt1,2, Edward J. Higginbotham3,4, Felix Lenner5, Jennifer Howe3,4, Bridget A. Fernandez6,7, Anna Lindstrand1,2, Stephen W. Scherer3,4,8 and Lars Feuk5 1Department of Molecular Medicine...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
.... Analysis of these chimeric reads revealed that HBV integration mediated “fold-back” (head-to-end) connections, inducing duplications of the chromosome, and the chromosome regions showed single-end reads with the integrated HBV. Moreover, the chromosomes were fused with different chromosomes, including Chr...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...Long-read sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders Susan M. Hiatt1, James M.J. Lawlor1, Lori H. Handley1, Donald R. Latner1, Zachary T. Bonnstetter1, Candice R. Finnila1, Michelle L. Thompson1, Lori Beth Boston1, Melissa Williams1, Ivan Rodriguez...
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Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
- Nathan Hammond,
- Linda Liao,
- Pun Wai Tong,
- Zena Ng,
- Thuy-Mi P. Nguyen,
- Chandler Ho,
- Yao Yang,
- and Stuart A. Scott
Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
...; 2Department of Pathology, Stanford University, Stanford, California 94305, USA ↵3 Present address: Influx Bio, San Francisco, CA 94124, USA Corresponding author: sascott@stanford.eduAbstractLong-read sequencing has the capacity to interrogate difficult genomic regions and phase variants; however...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...conformation capture technique, identifies large-scale rearrangements by capturing the spatial proximity of genomic regions, and has been widely used for variant phasing and assembly (Liao et al. 2023). A recent study used a combination of long-read and Hi-C sequencing to reveal chromosome-scale structure...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...assessment of genomic and epigenomic changes within complex regions (Logsdon et al. 2020; Mahmoud et al. 2021; Vollger et al. 2025). Nevertheless, long-read sequencing requires specialized analysis techniques to unlock its full potential, often requiring in-depth knowledge of rapidly evolving bioinformatic...
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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
...of these limitations, long-read sequencing (LRS) technologies were developed, enabling the -wide sequencing of native DNA fragments at multiple orders of magnitude larger than those in SR-GS, over 10 kb and up to megabases in size. In this mini-review, we review the existing evidence for LRS to increase diagnostic...
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