Searching journal content for articles similar to Bishara et al. 25 (10): 1570.

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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...dependence on trios (Lorig-Roach et al. 2024), no assembler can yet assemble all chromosomes of a typical human . Genomic features that remain a challenge, even for UL-read sequencing, include many functionally relevant regions of the such as recent segmental duplications, tandemly duplicated satellite...
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Method: CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
- Kaiyuan Zhu,
- Matthew G. Jones,
- Jens Luebeck,
- Xinxin Bu,
- Hyerim Yi,
- King L. Hung,
- Ivy Tsz-Lo Wong,
- Shu Zhang,
- Paul S. Mischel,
- Howard Y. Chang,
- and Vineet Bafna
Genome Res. September 2024 34: 1344-1354; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
..., heterogeneity of ecDNA structures might result in multiple overlapping focal amplifications derived from the same genomic regions. To address these shortcomings of short-read technology, existing methods (e.g., AmpliconArchitect [AA]) (Deshpande et al. 2019; Hung et al. 2022) must use heuristics: for example...
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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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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
....In conclusion, long-read sequencing has already made significant contributions to the field of genomics, particularly in the areas of SV characterization, de novo assembly, and pan construction. As the technology continues to evolve, its potential to uncover novel genetic and epigenetic variation in population...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...balanced rearrangements and novel variations with high precision. In contrast, genomic technologies (whole-exome/ sequencing) are very precise but do not easily provide chromosome-level characterizations. Long-read technologies are currently too expensive for clinical use. OGM thus represents a happy...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...the Damona pedigree are not optimal for the detection of dnSV. More modern, long-read technologies may have uncovered additional events. We observed a modest (yet nominally significant) effect of the sequence depth of the sire on the number of detected dnSV in the offspring: 0.01 extra dnSV per additional...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...to a single reference (Quadrana et al. 2016; Carpentier et al. 2019; Domínguez et al. 2020; Wyler et al. 2020; Qiu et al. 2021). With continued advancements in long-read sequencing technologies and improved assembly algorithms, there is a growing movement in genomics toward pangenomic-based approaches (Bayer...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...processing (Rhie et al. 2021). In contrast, assemblies generated from long-read sequencing are largely free from these sources of error. This higher accuracy combined with greater contiguity makes long-read sequencing more suitable for genomic analyses such as linking phenotype to genotype, detection...
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Method: Resolving the full spectrum of human genome variation using Linked-Reads
- Patrick Marks,
- Sarah Garcia,
- Alvaro Martinez Barrio,
- Kamila Belhocine,
- Jorge Bernate,
- Rajiv Bharadwaj,
- Keith Bjornson,
- Claudia Catalanotti,
- Josh Delaney,
- Adrian Fehr,
- Ian T. Fiddes,
- Brendan Galvin,
- Haynes Heaton,
- Jill Herschleb,
- Christopher Hindson,
- Esty Holt,
- Cassandra B. Jabara,
- Susanna Jett,
- Nikka Keivanfar,
- Sofia Kyriazopoulou-Panagiotopoulou,
- Monkol Lek,
- Bill Lin,
- Adam Lowe,
- Shazia Mahamdallie,
- Shamoni Maheshwari,
- Tony Makarewicz,
- Jamie Marshall,
- Francesca Meschi,
- Christopher J. O'Keefe,
- Heather Ordonez,
- Pranav Patel,
- Andrew Price,
- Ariel Royall,
- Elise Ruark,
- Sheila Seal,
- Michael Schnall-Levin,
- Preyas Shah,
- David Stafford,
- Stephen Williams,
- Indira Wu,
- Andrew Wei Xu,
- Nazneen Rahman,
- Daniel MacArthur,
- and Deanna M. Church
Genome Res. April 2019 29: 635-645; Published in Advance March 20, 2019, doi:10.1101/gr.234443.118
...in cancer and genetic disorders. https://bionanogenomics.com/wp-content/uploads/2017/02/Bionano_Human-Structural-Variations-White-Paper.pdf. ↵Bishara A, Liu Y, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S. 2015. Read clouds uncover variation in complex regions of the human . Genome...
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Research: Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
- Morteza Roodgar,
- Benjamin H. Good,
- Nandita R. Garud,
- Stephen Martis,
- Mohan Avula,
- Wenyu Zhou,
- Samuel M. Lancaster,
- Hayan Lee,
- Afshin Babveyh,
- Sophia Nesamoney,
- Katherine S. Pollard,
- and Michael P. Snyder
Genome Res. August 2021 31: 1433-1446; Published in Advance July 22, 2021, doi:10.1101/gr.265058.120
...) (Nayfach et al. 2016; Garud et al. 2019). We then developed a statistical model for linking genomic regions with higher-than-expected read cloud sharing given the observed levels of read cloud impurity (Methods). Using this hybrid approach, we documented the ecological and evolutionary responses of the gut...
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