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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...the fundamental limitations of short-read sequencing for allele-specific analysis by detecting an increased number of single-nucleotide polymorphisms (SNPs) on a read, enabling its precise allelic assignment (Cho et al. 2014). This feature has been leveraged to characterize the genetic effects of rare and common...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...quality. Rare residual errors were reflected by the low density of SNPs detected as homozygous (1.1/Mbp, 161 total) and heterozygous (6.8/Mbp, 1038 total).Analysis of the mapping read depth supported full haplotype phasing with a single peak corresponding to the expected haploid 1× depth (Supplemental Fig...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
..., Germany; 12Department of Statistical Bioinformatics, University of Regensburg, 93053 Regensburg, Germany ↵13 These authors contributed equally to this work. Corresponding author: robin.kosch@protonmail.comAbstractHigh-throughput bottom-up proteomic data cover thousands of proteins and related co- and post...
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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
...structure analyses, genetic diversity evaluation, and ancestry estimation (Kennedy et al. 2003; Zimmerman et al. 2020). Simultaneously, the latest advances in SNP high-throughput arrays and WGS facilitate the SNPs applied in the usual genetic analyses. However, compared with WGS, SNP arrays were primarily...
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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
...that the same homologous regions are examined in each individual (Peterson et al. 2012).High-throughput low-cost genotyping has largely been achieved by the analysis of single-nucleotide polymorphisms on microarray-based platforms (SNP arrays). These allow up to several thousand SNPs to be tested simultaneously...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...each range of ASE genes: 0 (purple) to more than 10 (yellow). Pie charts match their adjacent ASE gene and QTL set intersections. (F) The AIL F16 QTL Ddiab6d showed context-dependent additive effects. Box plots of serum insulin levels across SNP rs6393943 genotypes in F16 mice (LL, LG/J homozygous; LS...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
...(SNPs) (Xiao et al. 2019; Liu et al. 2020b; Zhang et al. 2020a). Many human genetic variants may affect m6A levels, leading to changes in gene expression (Zhang et al. 2020b; Xiong et al. 2021). However, accurately measuring the m6A changes in response to genetic variants and determining the interplay...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...(Danecek et al. 2021) was used for sorting and filtering by quality. Picard was used for filtering duplicates.Once reads were mapped and filtered, we used WASP (van de Geijn et al. 2015) to identify reads that showed a bias in mapping for either allele in the graph . The WASP “snp2h5” command was used...
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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
...indicates the average ASE SNPs across all individual samples and conditions High throughput allele specific expression Genome Research 1629 www org indicated cases when the ASE was only observed in genes induced by the treatment Studies that only consider baseline eQTL or ASE may fail to characterize...
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Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
- Sanyuan Ma,
- Tong Zhang,
- Ruolin Wang,
- Pan Wang,
- Yue Liu,
- Jiasong Chang,
- Aoming Wang,
- Xinhui Lan,
- Le Sun,
- Hao Sun,
- Run Shi,
- Wei Lu,
- Dan Liu,
- Na Zhang,
- Wenbo Hu,
- Xiaogang Wang,
- Weiqing Xing,
- Ling Jia,
- and Qingyou Xia
Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
...High-throughput and -scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori Sanyuan Ma1, Tong Zhang1, Ruolin Wang1, Pan Wang1, Yue Liu1,2, Jiasong Chang1,3, Aoming Wang1, Xinhui Lan1, Le Sun1, Hao Sun1, Run Shi1, Wei Lu1, Dan Liu1, Na Zhang1, Wenbo Hu1, Xiaogang...

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