Searching journal content for articles similar to Chen et al. 19 (1): 136.

Displaying results 1-10 of 415

For checked items

view abstracts
download to citation manager

Select this article
Method: Simulation of nanopore sequencing signal data with tunable parameters
- Hasindu Gamaarachchi,
- James M. Ferguson,
- Hiruna Samarakoon,
- Kisaru Liyanage,
- and Ira W. Deveson
Genome Res. May 2024 34: 778-783; Published in Advance May 1, 2024, doi:10.1101/gr.278730.123
...the properties of their simulated data set, users can flexibly adjust the noise parameters; technical variables like DNA translocation speed (Fig. 1B), data acquisition rate (Fig. 1C), and digitization (Fig. 1D); and pseudoexperimental variables like coverage depth and read-length distribution. They may opt...
OPEN ACCESS ARTICLE
Select this article
Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
..., Universitat Pompeu Fabra, 08003 Barcelona, Spain; 8Institució Catalana de Recerca i Estudis Avançats, ICREA, 08003 Barcelona, Spain Corresponding author: lu.cheng.ac@gmail.comAbstractIdentifying and illustrating patterns in DNA sequences are crucial tasks in various biological data analyses. In this task...
OPEN ACCESS ARTICLE
Select this article
Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
..., University of Vermont, Burlington, Vermont 05405, USA Corresponding author: jwyrick@wsu.eduAbstractUV light induces cyclobutane pyrimidine dimers (CPDs) and other mutagenic lesions in cellular DNA. Cytosine-containing CPDs can subsequently undergo rapid deamination to uracil, a process that has been linked...
OPEN ACCESS ARTICLE
Select this article
Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
- Bin Zhao,
- John A. Lees,
- Hongjin Wu,
- Chao Yang,
- and Daniel Falush
Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
...for further 406 iterative-PopPUNK analysis using integrated simulator, msformatter and ms2dna (available 407 from http://guanine.evolbio.mpg.de/bioBox), and the corresponding genealogical trees 408 were extracted for comparison with iterative-PopPUNK clusters. 409 410 To analyze of simulated s, we set...
ACCEPTED MANUSCRIPT
Select this article
Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...retrotransposons jump between species. Proc Natl Acad Sci 96: 12211–12212. doi:10.1073/pnas.96.22.12211 ↵Fletcher W, Yang Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol 26: 1879–1888. doi:10.1093/molbev/msp098 ↵Gabaldón T...
Select this article
Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...85721, USA Corresponding authors: rod.wing@kaust.edu.sa, jzhang@mail.hzau.edu.cn, zhoufei@mail.hzau.edu.cn, yongjunlin@mail.hzau.edu.cnAbstractTransfer of chloroplast or mitochondrial DNA into the nuclear is a common phenomenon in many species. However, little is known about the evolutionary fate...
Select this article
Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...sequencing with NanoRCSWe designed NanoRCS to improve the accuracy of nanopore cfDNA sequencing. First, 5 ng of cfDNA molecules are circularized with a specifically designed flexible DNA backbone (Fig. 1A). The circularized DNA molecules serve as a template to create long concatemers by RCA, which...
OPEN ACCESS ARTICLE
Select this article
Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
..., et al. 2022. The complete sequence of a human . Science 376: 44–53. doi:10.1126/science.abj6987 ↵Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841–842. doi:10.1093/bioinformatics/btq033 ↵Razin A, Cedar H. 1991. DNA methylation...
Select this article
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
...@cuhk.edu.hkAbstractThe discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttransplantation monitoring. The advent of high-throughput sequencing...
OPEN ACCESS ARTICLE
Select this article
Method: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil
- Mădălina Giurgiu,
- Nadine Wittstruck,
- Elias Rodriguez-Fos,
- Rocío Chamorro González,
- Lotte Brückner,
- Annabell Krienelke-Szymansky,
- Konstantin Helmsauer,
- Anne Hartebrodt,
- Philipp Euskirchen,
- Richard P. Koche,
- Kerstin Haase,
- Knut Reinert,
- and Anton G. Henssen
Genome Res. September 2024 34: 1355-1364; Published in Advance August 7, 2024, doi:10.1101/gr.279123.124
...with LASSO regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de novo assembly and alignment-based methods in simulated long-read sequencing data for both simple and complex ecDNAs...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Chen et al. 19 (1): 136.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: