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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
...; Eusebi et al. 2020). Many studies compare and utilize different types of marker techniques, including mitochondrial DNA barcoding (mtDNA) (Guo et al. 2006), the Y-Chromosome technique (Bruford et al. 2003), minisatellite and microsatellite markers (Ćurković et al. 2016), and single...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...-seq experiments (Montefiori et al. 2017). Our method was efficient for the depletion of chloroplast DNA (by 67%), whereas the depletion of mitochondrial DNA was only marginal, possibly reflecting the different abundance of the two organelle s in the starting genomic sample. Still, in lentil, the fraction...
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Research: High-throughput allele-specific expression across 250 environmental conditions
- Gregory A. Moyerbrailean,
- Allison L. Richards,
- Daniel Kurtz,
- Cynthia A. Kalita,
- Gordon O. Davis,
- Chris T. Harvey,
- Adnan Alazizi,
- Donovan Watza,
- Yoram Sorokin,
- Nancy Hauff,
- Xiang Zhou,
- Xiaoquan Wen,
- Roger Pique-Regi,
- and Francesca Luca
Genome Res. December 2016 26: 1627-1638; Published in Advance October 19, 2016, doi:10.1101/gr.209759.116
...linked to autoimmune responsivity through its association to lupus Sigurdsson et al 2005 Graham et al 2006 2007 Interestingly phthalates may play a role in lupus etiology since they induce anti DNA antibodies Lim and Ghosh 2005 while vitamin B5 deficiency is found in lupus patients Leung 2004...
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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
...of ONG0400650 in O. sativa. Green color indicates ptDNA sequence. (D) Synteny of the ONG0400650 region in O. barthii, O. glaberrima, and O. sativa. The NORG is not present in O. barthii and O. glaberrima. Green color indicates NUPTs.DiscussionIn this study, a high-throughput identification pipeline...
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Methods: Overlapping pools for high-throughput targeted resequencing
- Snehit Prabhu and
- Itsik Pe'er
Genome Res. July 2009 19: 1254-1261; Published in Advance May 15, 2009, doi:10.1101/gr.088559.108
...Overlapping pools for high-throughput targeted resequencing Snehit Prabhu , 1 and Itsik Pe'er , 1 Department of Computer Science, Columbia University, New York, New York 10025, USA Abstract Resequencing genomic DNA from pools of individuals...
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Methods: High-throughput genotyping by whole-genome resequencing
- Xuehui Huang,
- Qi Feng,
- Qian Qian,
- Qiang Zhao,
- Lu Wang,
- Ahong Wang,
- Jianping Guan,
- Danlin Fan,
- Qijun Weng,
- Tao Huang,
- Guojun Dong,
- Tao Sang,
- and Bin Han
Genome Res. June 2009 19: 1068-1076; Published in Advance May 6, 2009, doi:10.1101/gr.089516.108
...-based mapping approach with -based high-throughput strategies. The availability of sequences opened the door to high-throughput genotyping. This was initially accomplished by adopting microarray technology, which detects single nucleotide polymorphisms (SNPs) through hybridizing genomic DNA to oligonucleotides...
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Method: Efficient storage of high throughput DNA sequencing data using reference-based compression
- Markus Hsi-Yang Fritz,
- Rasko Leinonen,
- Guy Cochrane,
- and Ewan Birney
Genome Res. May 2011 21: 734-740; Published in Advance January 18, 2011, doi:10.1101/gr.114819.110
...Ewan Birney Markus HsiYang Fritz genome;gr.114819.110 1088-9051 10.1101/gr.114819.110 Efficient storage of high throughput DNA sequencing data using reference-based compression Method Efficient storage of high throughput DNA sequencing data using reference-based compression Markus Hsi-Yang Fritz, Rasko...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...show the density distributions of (A) DNA, (B) LTR, (C) SINE, (D) LINE, for 3124 randomly sampled 1656-bp genomic windows (number of, and average length of identified hotspots). The red lines indicate the observed mean TE densities in the defined hotspot regions.We also identified 1283 recombination...
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Method: Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
- Nadin Rohland and
- David Reich
Genome Res. May 2012 22: 939-946; Published in Advance January 20, 2012, doi:10.1101/gr.128124.111
.... 2009. Direct multiplex sequencing (DMPS)—a novel method for targeted high-throughput sequencingof ancient andhighlydegradedDNA.GenomeRes19:1843–1848. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ, Margulies EH, Green ED, et al. 2010. Systematic comparison...
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Methods: A probabilistic approach for SNP discovery in high-throughput human resequencing data
- Rose Hoberman,
- Joana Dias,
- Bing Ge,
- Eef Harmsen,
- Michael Mayhew,
- Dominique J. Verlaan,
- Tony Kwan,
- Ken Dewar,
- Mathieu Blanchette,
- and Tomi Pastinen
Genome Res. September 2009 19: 1542-1552; Published in Advance July 15, 2009, doi:10.1101/gr.092072.109
...resequencing of human genomic regions requires careful attention to systematic biases in sample preparation as well as sequence contexts, and that their impact can be alleviated by machine learning-based sequence analyses allowing more accurate extraction of true DNA variants. Footnotes ↵ 6...

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