Searching journal content for articles similar to Coppieters et al. 30 (8): 1201.

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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...default settings with the ssal_repeats_v5.1 library. RepeatMasker takes a library of TE consensus sequences and detects whole and fragmented parts of these consensuses across the using a BLAST-like algorithm. The output file contains the genomic coordinates of the annotation, as well as various quality...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...Evidence for selfing in a vertebrate from whole- sequencing Astrid Böhne1, Zeynep Oğuzhan1, Ioannis Chrysostomakis1, Simon Vitt2, Denis Meuthen2,3, Sebastian Martin1, Sandra Kukowka1 and Timo Thünken2 1Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn...
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Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
- Hongyu Zheng,
- Hirak Sarkar,
- and Benjamin J. Raphael
Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
...is for a mixture of multiple cells. In contrast, in situ sequencing- (Ke et al. 2013; Wang et al. 2018) and in situ hybridization-based SRT such as 10x Genomics Xenium (Janesick et al. 2023; Oliveira et al. 2025), merFISH (Chen et al. 2015), CosMx (NanoString), and MERSCOPE (Vizgen) measure the expression...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
..., USA; 2NVIDIA Corporation, Santa Clara, California 95051, USA Corresponding author: wwang7@mdanderson.orgAbstractAccurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were overcome by consensus mutation calling...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...clusters to model the haplotype encodings, which has also been observed in a different application of the Gaussian mixture VAE (GMVAE) model (Bozkurt Varolgüneş et al. 2020). At a lower C, for example, 20, we observed slightly worse performances for all superpopulations in the 1000 Genomes Project...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...) associated with disease. Limitations remain with respect to cost, scalability, and platform-dependent read accuracy and the tradeoffs between sequence coverage and sensitivity of variant discovery are important experimental considerations for the application of LRS. We compare the genetic variant...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...to disease risk. Collecting sequencing data from families allows us to identify genomic events such as meiotic crossovers and shared genetic material between family members that is impossible to detect in unrelated individuals.Crossover detection using family data is one of the major approaches used to study...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...-cell/nucleus RNA-seq data is critical for understanding heterogeneity in complex biological samples, yet the technological discrepancy across sequencing platforms limits deconvolution accuracy. To address this, we utilize an experimental design to match inter-platform biological signals, hence revealing...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...of microRNA expression analyses is reflected by the existence of thousands of sRNA-seq studies in which matched total RNA-seq data are often unavailable. The lack of paired sequencing experiments limits the analysis of microRNA–gene regulatory networks. Here, we explore whether protein-coding gene...
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Method: Whole-genome bisulfite sequencing with improved accuracy and cost
- Masako Suzuki,
- Will Liao,
- Frank Wos,
- Andrew D. Johnston,
- Justin DeGrazia,
- Jennifer Ishii,
- Toby Bloom,
- Michael C. Zody,
- Soren Germer,
- and John M. Greally
Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
...in the population, allowing detection of changes of transcriptional regulation patterns involving minor proportions of cells, whereas chromatin immunoprecipitation followed by sequencing (ChIP-seq) is substantially less quantitative, although capable of identifying allele-specific chromatin states (Ding et al. 2014...

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