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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...disease and complex traits but can be difficult to resolve with short-read sequencing. We present STRkit, a software package for genotyping STRs using long-read sequencing (LRS) that uses proximate single-nucleotide variants to improve genotyping accuracy without a priori haplotype information. We show...
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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. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...AGACGGGGTTTCACCGTGTTAGCCAGGACGGTCTTGATCTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAAAGTG Figure 2. A complex sSMC involving Chromosomes X, 7, and 5. (A) Schematic of the chromosomes involved and the resulting structure of the derivative Chromosome 7 identified in RD_P328. (B) Integrative Genomics Viewer images of short-read sequencing (srGS) and long-read sequencing (lrGS) data...
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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
.... These collaborative efforts have yielded invaluable insights into the molecular mechanisms underlying cancer initiation, progression, and metastasis, uncovering recurring patterns of genomic alterations, novel cancer genes, and pathways. Consequently, short-read sequencing for both tumor and germline is routinely...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...bacterial de novo from short-read data is rarely possible owing to complex, repetitive genomic regions such as insertion sequences (ISs) and other repetitive elements (Ring et al. 2018). Short reads also struggle to reconstruct extrachromosomal elements, such as plasmids (Arredondo-Alonso et al. 2017...
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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
.... 2020; Glinos et al. 2022; Veiga et al. 2022; Zhang et al. 2022), and represents a data source of great value for the de novo annotation of the Earth BioGenome Project (Lawniczak et al. 2022). Despite its strengths, LRS presents several shortcomings. The quality of long-read RNA sequencing (lr...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...- and short-read transcriptome data from multiple developmental stages and tissues across seven species. Using comparative genomics, expression profiles, phylogenetic analysis, and structural modeling, we trace MHC gene duplications and signatures of adaptive evolution, and identify putative classical...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...in inherited and de novo acquired disorders (Mirkin 2007; Hannan 2018; Trost et al. 2020; Mitra et al. 2021). Indels and other mutations occurring within microsatellite regions are, however, frequently overlooked. In cases in which indel rates have been estimated in mice by short-read sequencing, they have...
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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
...disease diagnostics in Sweden.Although short-read (sr) genomic analysis approaches such as exome and sequencing (GS) have been highly successful in identifying disease-causing genetic variants for diagnostic purposes, the primary focus of analysis remains on single-nucleotide variations (SNVs) and small...
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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
..., using a standard protocol that generally included PCR amplification (86/96). Genomes were sequenced at an approximate mean depth of 30×, with at least 80% of base positions reaching 20× coverage. Exomes were sequenced to a mean depth of 71×. For short-read reanalysis, srES and srGS reads were aligned...
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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
...using microarray or short-read sequencing (GS), these methods frequently fail to characterize breakpoints at nucleotide resolution, requiring additional molecular methods for validation and fine-mapping. Here, we use Oxford Nanopore Technologies PromethION long-read GS to characterize complex genomic...
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