Searching journal content for articles similar to Schadt et al. 23 (1): 129.

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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
...haplotype, meaning they often cannot conclusively determine if there has been a complete loss of function in genes from compound heterozygous mutations (Sedlazeck et al. 2018). In addition to these limitations for detecting DNA variations and mutations, short-reads also face related challenges resolving...
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Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
- Arun B. Dutta,
- Daniel S. Lank,
- Roza K. Przanowska,
- Piotr Przanowski,
- Lixin Wang,
- Bao Nguyen,
- Ninad M. Walavalkar,
- Fabiana M. Duarte,
- and Michael J. Guertin
Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
...of peaks in the class indicated in the lower right; the x-axis represents time, and the y-axis indicates normalized accessibility. (C) De novo motif analysis identified the top six DNA motifs enriched within dynamic peaks. The individual TFs listed in the wedge below the DNA sequence logo recognize...
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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
...of ONT include direct RNA sequencing (which preserves base modification information lost during traditional cDNA synthesis), in which the RNA molecules are either ligated directly to the RNA molecule or subjected to “splinting” using single-strand reverse transcription to generate a hybrid DNA...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation and the identification of exogenously placed DNA N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as coprocessing single...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...to determine the tissue of origin of individual long cfDNA molecules for the detection of HCC (AUC = 0.91). In addition, various deep learning algorithms have also been applied in nanopore sequencing for basecalling and detection of base modifications in a variety of biological contexts (Boža et al. 2017; Rang...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...or duplication of segments of DNA. Amplification of segments of DNA sequence, a type of copy number variation (CNV), is an important source of rapid adaptive evolution. In the short term, gene amplification can result in increased gene expression, which provides a selective advantage facilitating adaptation...
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Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
- Wilfried M. Guiblet,
- Marzia A. Cremona,
- Monika Cechova,
- Robert S. Harris,
- Iva Kejnovská,
- Eduard Kejnovsky,
- Kristin Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
...in accommodating the alternative DNA structure within the polymerase active site.The alterations in polymerization kinetics at non-B DNA motifs are not readily explained by either base modifications or by nucleotide composition. First, IPD patterns for most non-B DNA motifs were still clearly detectable...
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Method: Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms
- Kerstin C. Maier,
- Saskia Gressel,
- Patrick Cramer,
- and Björn Schwalb
Genome Res. September 2020 30: 1332-1344; Published in Advance September 4, 2020, doi:10.1101/gr.257857.119
...from an entire gene locus can be considered, as is the case with cDNA short-read sequencing approaches such as RNA-seq, 4sU-seq, or TT-seq.Nano-ID has many advantages over other sequencing-based transcriptomic strategies because the original native RNA molecule is sequenced. In particular...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...transcription and massively parallel sequencing (Helm and Motorin 2017; Yang et al. 2018). However, it provides poor resolution in terms of modification site. Third generation sequencing technology, for example, the Pacific Biosciences (PacBio) RSII platform, is able to produce long reads and detect DNA...
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Resource: Variation Ontology for annotation of variation effects and mechanisms
- Mauno Vihinen
Genome Res. February 2014 24: 356-364; Published in Advance October 25, 2013, doi:10.1101/gr.157495.113
..., consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence...
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