Searching journal content for articles similar to Surget-Groba and Montoya-Burgos 20 (10): 1432.

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  1. Method: HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
    • Xian Fan,
    • Mark Chaisson,
    • Luay Nakhleh,
    • and Ken Chen
    Genome Res. May 2017 27: 793-800; Published in Advance January 19, 2017, doi:10.1101/gr.214767.116
    .... A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491–498. Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. 2009. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput...
  2. 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
    ...-read sequencing is rapidly emerging as a transformative technology for cancer research by providing a comprehensive view across the , transcriptome, and epi, including the ability to detect alterations that previous technologies have overlooked. In this Perspective, we explore the current applications of long...
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  3. 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
    ...et al. 2022).Transcriptome-wide patterns of m6A RNA modifications have typically been studied using short-read sequencing coupled with either antibody-dependent methods such as methylated RNA immunoprecipitation sequencing (MeRIP-seq) (Meyer et al. 2012) or enzymatic/chemical approaches (Garcia...
  4. Method: Simulation of nanopore sequencing signal data with tunable parameters
    • Hasindu Gamaarachchi,
    • James M. Ferguson,
    • Hiruna Samarakoon,
    • Kisaru Liyanage,
    • and Ira W. Deveson
    Genome Res. May 2024 34: 778-783; Published in Advance May 1, 2024, doi:10.1101/gr.278730.123
    ...for the simulation of genomic next-generation sequencing data. Nat Rev Genet 17: 459–469. doi:10.1038/nrg.2016.57 ↵Gamaarachchi H, Lam CW, Jayatilaka G, Samarakoon H, Simpson JT, Smith MA, Parameswaran S. 2020. GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC...
    OPEN ACCESS ARTICLE
  5. Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
    • Qian Qin,
    • Victoria Popic,
    • Kirsty Wienand,
    • Houlin Yu,
    • Emily White,
    • Akanksha Khorgade,
    • Asa Shin,
    • Christophe Georgescu,
    • Catarina D. Campbell,
    • Arthur Dondi,
    • Niko Beerenwinkel,
    • Francisca Vazquez,
    • Aziz M. Al'Khafaji,
    • and Brian J. Haas
    Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
    ...their cDNA, or in the case of ONT, the option of direct RNA sequencing. Early applications of these technologies have been constrained due to low throughput and high error rates. Recent advances in both long-read platforms have enabled high-throughput long-read transcriptome sequencing at high sequencing...
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  6. Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
    • Tianfu Zeng,
    • Haotian Liao,
    • Lin Xia,
    • Siyao You,
    • Yanqun Huang,
    • Jiaxun Zhang,
    • Yahui Liu,
    • Xuyan Liu,
    • and Dan Xie
    Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
    ...-throughput sequencing is challenging. Here, we applied long-read nanopore sequencing and multisite sampling in a cohort of 42 samples from five patients. We found that adjacent nontumor tissue is not entirely normal, as significant somatic SV alterations were detected in these nontumor s. The adjacent nontumor tissue...
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  7. Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
    • Haotian Teng,
    • Marcus Stoiber,
    • Ziv Bar-Joseph,
    • and Carl Kingsford
    Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
    ...-level and site-level prediction scores. Xron is a standalone, end-to-end m6A-distinguishing basecaller capable of detecting methylated bases directly from raw sequencing signals, enabling de novo methylome assembly.RNA modification plays essential roles in various biological processes, including stem cell...
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  8. Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    • Ezequiel Calvo-Roitberg,
    • Rachel F. Daniels,
    • and Athma A. Pai
    Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
    ...are the gold standard for high-throughput transcriptome profiling (Wang et al. 2009). RNA-sequencing (RNA-seq) has been used to investigate gene expression (The ENCODE Project Consortium 2012), canonical and alternative mRNA splicing (Wright et al. 2022a), noncoding RNAs, and post-transcriptional modifications...
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  9. Resource: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
    • Samia N. Naccache,
    • Scot Federman,
    • Narayanan Veeraraghavan,
    • Matei Zaharia,
    • Deanna Lee,
    • Erik Samayoa,
    • Jerome Bouquet,
    • Alexander L. Greninger,
    • Ka-Cheung Luk,
    • Barryett Enge,
    • Debra A. Wadford,
    • Sharon L. Messenger,
    • Gillian L. Genrich,
    • Kristen Pellegrino,
    • Gilda Grard,
    • Eric Leroy,
    • Bradley S. Schneider,
    • Joseph N. Fair,
    • Miguel A. Martínez,
    • Pavel Isa,
    • John A. Crump,
    • Joseph L. DeRisi,
    • Taylor Sittler,
    • John Hackett, Jr.,
    • Steve Miller,
    • and Charles Y. Chiu
    Genome Res. July 2014 24: 1180-1192; Published in Advance June 4, 2014, doi:10.1101/gr.171934.113
    ...A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples Samia N. Naccache 1 , 2 , Scot Federman 1 , 2 , Narayanan Veeraraghavan 1 , 2 , Matei Zaharia 3 , Deanna...
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  10. Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
    • Keyi Geng,
    • Lara G. Merino,
    • Linda Wedemann,
    • Aniek Martens,
    • Małgorzata Sobota,
    • Yerma P. Sanchez,
    • Jonas Nørskov Søndergaard,
    • Robert J. White,
    • and Claudia Kutter
    Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
    ...developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on...
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