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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
...of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollutant cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene...
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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...al. 2019), or GAM (Beagrie et al. 2017). Among these, Hi-C and its derivatives have been the most widely used for chromatin structure reconstruction, offering invaluable insights into chromatin conformations across genomic scales (Lieberman-Aiden et al. 2009; Rao et al. 2014; Harris et al. 2023...
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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
...revealed that 52.1% of the colonies (185) harbored individual sgRNAs, representing 171 correct unique ones and an accuracy efficiency of 95.7%, and most of the mutations were 1-nt changes (Supplemental Fig. S2D). We hypothesized that the high percentage (47.9%) of the colonies harboring multiple sg...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...Inferring and comparing metabolism across heterogeneous sets of annotated s using AuCoMe Arnaud Belcour1,4, Jeanne Got1,4, Méziane Aite1, Ludovic Delage2, Jonas Collén2, Clémence Frioux3, Catherine Leblanc2, Simon M. Dittami2, Samuel Blanquart1, Gabriel V. Markov2,5 and Anne Siegel1,5 1Univ Rennes...
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Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
- Alexander Morin,
- Eric Ching-Pan Chu,
- Aman Sharma,
- Alex Adrian-Hamazaki,
- and Paul Pavlidis
Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
...IP-seq of TRs and experiments that perturb a TR and measure the differential abundance of gene transcripts are a primary means by which direct relationships are tested on a genomic scale. It has been reported that there is a poor overlap in the evidence across gene regulation strategies, emphasizing the need...
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Method: Genome-scale identification of cellular pathways required for cell surface recognition
- Sumana Sharma,
- S. Josefin Bartholdson,
- Amalie C.M. Couch,
- Kosuke Yusa,
- and Gavin J. Wright
Genome Res. September 2018 28: 1372-1382; Published in Advance June 18, 2018, doi:10.1101/gr.231183.117
...and C) or technical (D and E) replicate experiments is shown.Genome-scale, cell-based CRISPR-KO screens identify directly interacting receptorsMany extracellular proteins are known to bind HS, and the finding that HS binding in our assay could be additive rather than codependent on other receptors...
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Research: Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors
- Mi Ni Huang,
- Willie Yu,
- Wei Wei Teoh,
- Maude Ardin,
- Apinya Jusakul,
- Alvin Wei Tian Ng,
- Arnoud Boot,
- Behnoush Abedi-Ardekani,
- Stephanie Villar,
- Swe Swe Myint,
- Rashidah Othman,
- Song Ling Poon,
- Adriana Heguy,
- Magali Olivier,
- Monica Hollstein,
- Patrick Tan,
- Bin Tean Teh,
- Kanaga Sabapathy,
- Jiri Zavadil,
- and Steven G. Rozen
Genome Res. September 2017 27: 1475-1486; Published in Advance July 24, 2017, doi:10.1101/gr.220038.116
...in Supplemental Figure S1. (B) Extreme transcription-strand bias for genes with high expression levels; see Supplemental Figure S2 for transcription-strand bias for all cell line replicates. Transcribed strand (Tr); nontranscribed strand (NT). Genome-scale aflatoxin mutational signatures Genome Research 1477 www...
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Research: Genome-scale analysis of aberrant DNA methylation in colorectal cancer
- Toshinori Hinoue,
- Daniel J. Weisenberger,
- Christopher P.E. Lange,
- Hui Shen,
- Hyang-Min Byun,
- David Van Den Berg,
- Simeen Malik,
- Fei Pan,
- Houtan Noushmehr,
- Cornelis M. van Dijk,
- Rob A.E.M. Tollenaar,
- and Peter W. Laird
Genome Res. February 2012 22: 271-282; Published in Advance June 9, 2011, doi:10.1101/gr.117523.110
...hypermethylation. Together, we identified four distinct DNA methylation subgroups of CRC and provided novel insight regarding the role of CIMP-specific DNA hypermethylation in gene silencing.Colorectal cancer (CRC) arises through the accumulation of multiple genetic and epigenetic changes. Somatic mutations in APC...
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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
...Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity Natalia J. Martinez 1 , 2 , 3 , Maria C. Ow 2 , 3 , John S. Reece-Hoyes 1 , 2 , M. Inmaculada Barrasa 1 , 2 , Victor R. Ambros 2 , 4 , and Albertha J.M. Walhout 1 , 2 , 4 1 Program in Gene Function...
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Method: Network-based hierarchical population structure analysis for large genomic data sets
- Gili Greenbaum,
- Amir Rubin,
- Alan R. Templeton,
- and Noah A. Rosenberg
Genome Res. December 2019 29: 2020-2033; Published in Advance November 6, 2019, doi:10.1101/gr.250092.119
...for extracting and interpreting population structure at a genomic scale, as well as significant computational difficulties.Methods such as F-statistics (Excoffier et al. 1992; Holsinger and Weir 2009), principal components analysis (PCA) and other representations of data sets using techniques of multivariate...

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