Searching journal content for articles similar to Ferrández-Peral et al. 32 (8): 1448.

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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
...with CRISPR for targeted sequencing and expanding direct RNA-seq technologies will offer deeper insights into genomic and transcriptomic complexities. The integration of long-read sequencing into clinical diagnostics represents a crucial frontier, with several sequencing centers beginning to validate...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge CB10 1SA, United Kingdom Corresponding author: ana.conesa@csic.esAbstractLong-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...-cell methodsThe first long-read sequencing platform to be commercialized was the single-molecule real-time (SMRT) sequencing method from Pacific Biosciences (PacBio), where a zero-mode waveguide confines the fluorescent signal generated as DNA polymerase synthesizes a new strand while using the original strand...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...level of splicing junction events due to the limitation of the short-read sequencing technology.The recent development of long-read single-molecule sequencing technologies has enabled the capture of the full-length isoform diversity (Byrne et al. 2019), further facilitating the comparative analysis...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...uniform and less biased GC coverage, and even the ability to differentiate between 5mC and 5-hydroxymethylcytosine (5hmC) in some cases.Single moleculeDirect DNA sequencing using long-read sequencing (LRS) platforms like Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) offers new...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...sequence in Drosophila (Zile et al. 2020; Li et al. 2021). Recent studies using deep transcriptomics and ribosome-profiling identified thousands of species-specific sequences with evidence of transcription and translation that form the raw material for incipient de novo gene formation (Ruiz-Orera et al...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
....TcGTs are major contributors to neurodevelopmental transcript expressionTo unequivocally determine the relative contributions of TcGT isoforms versus canonical isoforms to neurodevelopmental gene expression, we used a recent single-molecule real-time long-read Pacific Biosciences (PacBio) sequencing data set...
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
...distinguish between nearly identical genes/paralogs. We used biotinylated probes to enrich for full-length cDNA from duplicated regions, which were then amplified, size-fractionated, and sequenced using single-molecule, long-read sequencing technology, permitting us to distinguish between highly identical...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
..., Koutseva N, Zaghlul S, Graves T, Rock S, et al. 2014. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508: 494–499. doi:10.1038/nature13206 ↵Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. 2015. Assembling large s with single-molecule sequencing...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
...in sequencing technology (Zook and Salit 2015), especially long-read sequencing (Chaisson et al. 2015a) and single-molecule mapping (Koren et al. 2012) technologies. Interpretation of the consequences of genetic variation has typically relied on reference sequences, relative to which genes and variants...
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