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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...compared with the unfiltered SNPs. Two application scenarios, including low- and high-density feature SNPs (about 1000 and about 30,000 SNPs), were designed to conduct these comparisons. Because the performance of the classifier can influence the evaluation of breed diversity, we, respectively, selected...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., or attention mechanisms, drive performance in these high-resolution predictions. To address these knowledge gaps, we systematically evaluate classic architectural choices and introduce ConvNeXt V2 blocks, originally developed for computer vision, as high-resolution feature extractors in deep learning models...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...to interact with or specific chromatin states.View larger version: In this window In a new window Figure 2. The diverse binding profiles of mC readers across the Arabidopsis . (A) Distribution of ChIP-seq peaks in genomic features. The total numbers of peaks for each sample are indicated at the bottom...
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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
...member by merging the phased reads across all single cells into two high-density read files per individual (one representing H1; the other, H2) (Supplemental Fig. S5). During this step, duplicate reads were filtered, and sequencing reads from all single-cell haplotypes were merged together for each...
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Method: Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics
- Zhen Li,
- Xiaoyang Chen,
- Xuegong Zhang,
- Rui Jiang,
- and Shengquan Chen
Genome Res. October 2023 33: 1757-1773; Published in Advance October 30, 2023, doi:10.1101/gr.277891.123
...data, self-attention mechanism (Liu et al. 2021) to capture spatial patterns, and a ripple walk sampler (Bai et al. 2021) to enable scalable subgraph-based training and prediction. Featured as the first ST method which integrates reference data from various sources, PAST aims to extract latent...
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Corrigendum: Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. June 2025 35: 1472-1; doi:10.1101/gr.280860.125
...and apologize for any confusion this may have caused.doi: 10.1101/gr.280860.125 Published by Cold Spring Harbor Laboratory Press Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana Jonathan Cahn , James P.B. Lloyd , Ino D. Karemaker , Pascal W.T.C. Jansen , Jahnvi Pflueger...
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Method: Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
- Ou Wang,
- Robert Chin,
- Xiaofang Cheng,
- Michelle Ka Yan Wu,
- Qing Mao,
- Jingbo Tang,
- Yuhui Sun,
- Ellis Anderson,
- Han K. Lam,
- Dan Chen,
- Yujun Zhou,
- Linying Wang,
- Fei Fan,
- Yan Zou,
- Yinlong Xie,
- Rebecca Yu Zhang,
- Snezana Drmanac,
- Darlene Nguyen,
- Chongjun Xu,
- Christian Villarosa,
- Scott Gablenz,
- Nina Barua,
- Staci Nguyen,
- Wenlan Tian,
- Jia Sophie Liu,
- Jingwan Wang,
- Xiao Liu,
- Xiaojuan Qi,
- Ao Chen,
- He Wang,
- Yuliang Dong,
- Wenwei Zhang,
- Andrei Alexeev,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- Xun Xu,
- Radoje Drmanac,
- and Brock A. Peters
Genome Res. May 2019 29: 798-808; Published in Advance April 2, 2019, doi:10.1101/gr.245126.118
...sequence and the capture adapter (Fig. 1A). At this point the DNA/transposase complexes are disrupted, producing subfragments <1 kb in size. Owing to the large number of beads and high density of capture oligos per bead, the amount of excess adapter is four orders of magnitude greater than the amount...
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Methods: Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing
- Daniel Summerer,
- Haiguo Wu,
- Bettina Haase,
- Yang Cheng,
- Nadine Schracke,
- Cord F. Stähler,
- Mark S. Chee,
- Peer F. Stähler,
- and Markus Beier
Genome Res. September 2009 19: 1616-1621; Published in Advance July 28, 2009, doi:10.1101/gr.091942.109
...Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing Daniel Summerer 1 , 4 , Haiguo Wu 2 , Bettina Haase 1 , Yang Cheng 1 , Nadine Schracke 1 , Cord F. Stähler 1 , Mark S. Chee 3...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...errors and aneuploidy (Koehler et al. 1996; Lamb et al. 1996; Rockmill et al. 2006). Plants, animals, and fungi also typically possess repetitive pericentromeric heterochromatin, containing a high density of transposable elements (Allshire and Karpen 2008; Malik and Henikoff 2009; Nambiar and Smith 2016...
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