Searching journal content for articles similar to Kalafus et al. 14 (4): 672.

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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...of the differences in the underlying chemistry, Quagga required hand annotation to find true-positive stripes (Supplemental Fig. 6).Quagga is also algorithmically efficient. For stripe calling from GM12878 Hi-C data, Quagga required 99 min compared with 65 min for Zebra and 505 min for Stripenn. In all tools...
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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
...and efficiency, a small fraction of p200-lib was coinjected with a piggyBac transposase expression vector (A3-Helper) into 500 G0 embryos. Approximately 300 embryos hatched and were reared to adulthood. Twenty broods positive for 3Xp3-EGFP expression were obtained from 132 G1 broods. The transformation rate...
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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
...; Supplemental Dataset S3). These results showed that 84.2% of the transgenics (929) harbored at least one single sgRNA, indicating a high transformation efficiency (Supplemental Fig. S4B). Moreover, among the 929 positive transgenic lines, 88.3% of them (820) contained single sgRNAs; 11.3% of them (103...
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Method: Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2
- Daniel N. Baker and
- Ben Langmead
Genome Res. July 2023 33: 1218-1227; Published in Advance July 6, 2023, doi:10.1101/gr.277655.123
...that account for multiplicities, as well as methods—like Dashing 2's feature hashing method—for efficiently compiling multiplicity information before sketching.We have concentrated on comparing SetSketch to the more commonly used methods of MinHash (as implemented in Mash and Sourmash), HLL (as implemented...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...phenotype (Nevins and Potti 2007). One key application of signature scoring is cell annotation, as it offers a highly efficient and reliable method for classifying cells into types and states (Neftel et al. 2019). Notably, the quality of gene signatures plays a critical role in this process, as the accuracy...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...is increasing rapidly. Accurate inference of cell lineage tree from large single-cell data is computationally challenging. In this paper, we present ScisTree2, a fast and accurate cell lineage tree inference and genotype calling approach based on the infinite-sites model. ScisTree2 relies on an efficient local...
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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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Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
- Han Shu,
- Jing Chen,
- Chang Xu,
- Jialu Hu,
- Yongtian Wang,
- Jiajie Peng,
- Qinghua Jiang,
- Xuequn Shang,
- and Tao Wang
Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
...observed in the 10x Visium data set. This trend continued in the Stereo-seq data set, confirming successful integration across donors. Additionally, we evaluated computational efficiency. stMSA processed up to 20 slices with <12 GB of GPU memory, whereas Stitch3D, SPACEL, and SEDR struggled to handle...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...are extracted from each read using a 64-bit rolling hash and minimizer parameters of k-mer length k = 425 and window size w = 19. The sequences of the minimizers are ignored, and only the hash value and start and end positions within the read are stored. A maximum copy count (default, 1000) is used to filter...
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Method: Efficient taxa identification using a pangenome index
- Omar Ahmed,
- Massimiliano Rossi,
- Christina Boucher,
- and Ben Langmead
Genome Res. July 2023 33: 1069-1077; Published in Advance May 31, 2023, doi:10.1101/gr.277642.123
...Efficient taxa identification using a pan index Omar Ahmed1, Massimiliano Rossi2, Christina Boucher2 and Ben Langmead1 1Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA; 2Department of Computer and Information Science and Engineering, Herbert Wertheim College...
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