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Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
- Jianjie He,
- Kai Zhang,
- Shuxiang Yan,
- Mi Tang,
- Weixian Zhou,
- Yongtai Yin,
- Kang Chen,
- Chunyu Zhang,
- and Maoteng Li
Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
...@mail.hzau.edu.cn, limaoteng426@hust.edu.cnAbstractThe recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the complexity, it is a big challenge to accomplish large-scale targeted mutagenesis...
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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 versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...information on a target site of interest.The advent of innovative methodologies, such as those integrating CRISPR/Cas systems with RNA-processing approaches, has expedited research in this domain, furnishing novel tools for dissecting the roles of post-transcriptional modifications in gene expression dynamics...
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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: Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
- Jiasong Chang,
- Ruolin Wang,
- Kai Yu,
- Tong Zhang,
- Xiaoxu Chen,
- Yue Liu,
- Run Shi,
- Xiaogang Wang,
- Qingyou Xia,
- and Sanyuan Ma
Genome Res. May 2020 30: 757-767; Published in Advance May 18, 2020, doi:10.1101/gr.249045.119
...palindromic repeat technology (CRISPR)-Cas9 in Bombyx mori cells. We first constructed a single guide RNA (sgRNA) library containing 94,000 sgRNAs, which targeted 16,571 protein-coding genes. We then generated knockout collections in BmE cells using the piggyBac transposon. We identified 1006 genes...
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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
...CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant s Marzia Rossato1,2,6, Luca Marcolungo1,6, Luca De Antoni1, Giulia Lopatriello1, Elisa Bellucci3, Gaia Cortinovis3, Giulia Frascarelli3, Laura Nanni3, Elena Bitocchi3, Valerio Di Vittori3, Leonardo Vincenzi1, Filippo...
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Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...Technology, #07922) (see Supplemental Methods; Supplemental Table S11).Preparation of vectors for transfectionTwo vectors were purchased: (1) CMV-rtTA-HygR vector (Addgene, #102423) and (2) CRISPR-Cas9 vectors containing gRNA sequence for TP53 (Addgene, #121917). To generate the pPB-CMVmin-APOBEC (A3A or A3B...
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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...et al. 2003; Vemireddy et al. 2007). However, the throughput of capillary electrophoresis is limited to small numbers of loci and samples (Hill et al. 2009; Guichoux et al. 2011).High-throughput sequencing can profile many more microsatellites than capillary electrophoresis; however, the sequencing...
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Method: Ultrafast functional profiling of RNA-seq data for nonmodel organisms
- Peng Liu,
- Jessica Ewald,
- Jose Hector Galvez,
- Jessica Head,
- Doug Crump,
- Guillaume Bourque,
- Niladri Basu,
- and Jianguo Xia
Genome Res. April 2021 31: 713-720; Published in Advance March 17, 2021, doi:10.1101/gr.269894.120
...accuracy and high throughput. Nucleic Acids Res 32: 1792–1797. doi:10.1093/nar/gkh340 ↵Eldem V, Zararsiz G, Taşçi T, Duru IP, Bakir Y, Erkan M. 2017. Transcriptome analysis for Non-model organism: current status and best-practices. In Applications of RNA-Seq and omics strategies: from microorganisms...
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Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
- Matthew A. Lalli,
- Denis Avey,
- Joseph D. Dougherty,
- Jeffrey Milbrandt,
- and Robi D. Mitra
Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
...gap in the functional genomics toolbox and enable direct comparison across genes to assess their mechanistic convergence. Recent technological advancements coupling CRISPR-Cas9 transcriptional repression to single-cell RNA sequencing (scRNA-seq) enable high-throughput perturbation of multiple genes...

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