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Methods: High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis
- Marilyn A.L. West,
- Hans van Leeuwen,
- Alexander Kozik,
- Daniel J. Kliebenstein,
- R.W. Doerge,
- Dina A. St. Clair,
- and Richard W. Michelmore
Genome Res. June 2006 16: 787-795; Published in Advance May 15, 2006, doi:10.1101/gr.5011206
...: 796 – 815 . ↵ Borevitz J.O. , Liang D. , Plouffe D. , Chang H.-S. , Zhu T. , Weigel D. , Berry C.C. , Winzeler E. , Chory J. ( 2003 ) Large-scale identification of single-feature polymorphisms in complex s. Genome Res. 13 : 513 – 523 . ↵ Brem R.B. , Kruglyak L. ( 2005 ) The landscape of genetic...
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Methods: Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
- Michael R. Miller,
- Joseph P. Dunham,
- Angel Amores,
- William A. Cresko,
- and Eric A. Johnson
Genome Res. February 2007 17: 240-248; Published in Advance December 22, 2006, doi:10.1101/gr.5681207
...that use direct hybridization of labeled genomic DNA to short oligonucleotide arrays ( Winzeler et al. 1998 ; Borevitz et al. 2003 ). Like SNPs, single feature polymorphisms (SFPs) can be discovered and typed at a high density given the availability of a short oligonucleotide array. However, the barriers...
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RESOURCE: Sequencing of natural strains of Arabidopsis thaliana with short reads
- Stephan Ossowski,
- Korbinian Schneeberger,
- Richard M. Clark,
- Christa Lanz,
- Norman Warthmann,
- and Detlef Weigel
Genome Res. December 2008 18: 2024-2033; Published in Advance September 25, 2008, doi:10.1101/gr.080200.108
..., D. , Plouffe, D. , Chang, H. , Zhu, T. , Weigel, D. , Berry, C. , Winzeler, E. , Chory, J. ( 2003 ) Large-scale identification of single-feature polymorphisms in complex s . Genome Res. 13 : 513 – 523 . ↵ Borevitz, J.O. , Hazen, S.P. , Michael, T.P. , Morris, G.P. , Baxter, I.R. , Hu, T.T. , Chen, H...
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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
...that nanopore-based detection methods depend on machine learning (ML) models to interpret sequencing signals accurately (Liu et al. 2019; Wang et al. 2021; Chen et al. 2025; Galeone et al. 2025). Therefore, developing bioinformatics tools for the large-scale, accurate, and efficient 4mC site identification...
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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
...and east of China (red), and south-west of China (green).In total, this large-scale and complex data set could satisfy the comprehensive evaluation of HITSNP.The performance of HITSNP in feature SNP filtrationWe compared the utility of the “feature SNP screening” module of HITSNP with FST, In, SS, and PCA...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...-tissue regulation of reproduction.With the development of high-throughput sequencing and the large-scale application of -wide association studies (GWASs), a substantial number of genomic variants that are associated with complex traits have been identified in humans and farmed animals (Abdellaoui et al. 2023; Tan...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...9691 polymorphic STRs (pSTRs) had complete genotype data for more than 90% of the strains. Compared with the reference , the pSTRs showed more contraction than expansion. We found that STRs with different motif lengths were enriched in different genomic features, among which coding regions showed...
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Method: Predicting transfer RNA gene activity from sequence and genome context
- Bryan P. Thornlow,
- Joel Armstrong,
- Andrew D. Holmes,
- Jonathan M. Howard,
- Russell B. Corbett-Detig,
- and Todd M. Lowe
Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
...). This supports the idea that CpG-derived genomic data are particularly highly informative of tRNA gene activity.One might expect that the tRNAscan-SE general bit score should be the most informative single feature. However, we start with relatively high-quality tRNAs with likely pseudogenes already removed using...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...at the central position, where each sequence possibility is represented. When hybridized to labeled genomic DNA, the highest signal intensity is expected for the perfect match oligonucleotide, thereby predicting the base in the corresponding target DNA sample. Large-scale polymorphism discovery using...
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Research: Genetic architecture of regulatory variation in Arabidopsis thaliana
- Xu Zhang,
- Andrew J. Cal,
- and Justin O. Borevitz
Genome Res. May 2011 21: 725-733; Published in Advance April 5, 2011, doi:10.1101/gr.115337.110
.... 2003. Large-scale identification of single-feature polymorphisms in complex s. Genome Res 13: 513–523. Brem RB, Yvert G, Clinton R, Kruglyak L. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752–755. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT...
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