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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...1, Raony Cardenas1, Thyago Cardoso1, Luis F. Paulin2, Philippe Sanio2, Joseph Mafofo1, Haiguo Wu1, Val Zvereff1, Albarah El-Khani1, Fahed Al Marzooqi1, Tiago R. Magalhães1, Fritz J. Sedlazeck2,3,4 and Javier Quilez1 1M42, Abu Dhabi, United Arab Emirates; 2Human Genome Sequencing Center, Baylor...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...Single-cell strand sequencing of a macaque reveals multiple nested inversions and breakpoint reuse during primate evolution Flavia Angela Maria Maggiolini1, Ashley D. Sanders2, Colin James Shew3, Arvis Sulovari4, Yafei Mao4, Marta Puig5, Claudia Rita Catacchio1, Maria Dellino1, Donato Palmisano1...
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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
...; however, its oncogenic mechanisms remain incompletely understood because of limitations in detection methods and sample availability. In this study, we employ Oxford Nanopore Technologies (ONT) whole- sequencing and full-length transcriptome sequencing to characterize HBV integration events at the genomic...
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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
...to population-wide sequencing efforts, the Genome in a Bottle Consortium (GIAB), the Platinum Genomes Project (Eberle et al. 2017), and related efforts, have developed benchmarks for germline variant calling using a small number of extensively characterized normal cell lines. The first GIAB benchmark from 2014...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon , providing the first comprehensive map of 238...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...x Genomics libraries derived from human lymphocytes. TCR and BCR genes undergo rearrangements to increase diversity to address various antigens. Due to the extraordinary diversity of these genes, substantial depth is needed to characterize the different isoforms, thus an unenriched single-cell...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254...
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Method: Direct chromosome-length haplotyping by single-cell sequencing
- David Porubský,
- Ashley D. Sanders,
- Niek van Wietmarschen,
- Ester Falconer,
- Mark Hills,
- Diana C.J. Spierings,
- Marianna R. Bevova,
- Victor Guryev,
- and Peter M. Lansdorp
Genome Res. November 2016 26: 1565-1574; Published in Advance September 19, 2016, doi:10.1101/gr.209841.116
...to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid genomes along the entire length of all chromosomes. We demonstrate this by building a complete haplotype...
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Method: Assessment of megabase-scale somatic copy number variation using single-cell sequencing
- Kristin A. Knouse,
- Jie Wu,
- and Angelika Amon
Genome Res. March 2016 26: 376-384; Published in Advance January 15, 2016, doi:10.1101/gr.198937.115
...CNVs of this magnitude are associated with disease and experience negative selection. However, it is unknown whether organismal function requires that every cell maintain a balanced genome. It is possible that large somatic CNVs are tolerated or even positively selected. Single-cell sequencing...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...-end mapping (PEM) data from large fragments (∼40-kb fosmid clones) (Kidd et al. 2008), are often not able to jump across the breakpoint IRs and determine the inversion orientation. New methods like single-cell sequencing of one DNA strand (Strand-seq) (Sanders et al. 2016; Chaisson et al. 2019) or Bionano...
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