Searching journal content for articles similar to Lindqvist et al. 6 (12): 1170.

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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
- Degui Zhi,
- Xiaoqian Jiang,
- and Arif Harmanci
Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
...requirements, rely on high-level expertise in security, and require each algorithm to be implemented from scratch. In this study, we focus on outsourcing of genotype imputation, a fundamental task that utilizes population-level reference panels, and develop protocols that rely on using “proxy panels...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...in single-marker linear models, yet they contribute substantially to phenotype through nonlinear or interaction effects in ML models. This explains the discrepancies in SNP effect prioritization between the two approaches (Supplemental Fig. S5). Evaluating SHAP interaction results across two or more sites...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
...as a multislice joint analysis framework featuring a precorrection mechanism that enables the precise identification of complex spatial domains, advancing disease pathology insights. STMSC assumes that precise three-dimensional (3D) reconstruction is essential for an in-depth investigation of tissue components...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...for alleles; and neither LongTR nor STRdust outputs read-level data, limiting their use for motif composition analysis or detecting within-allele somatic instability.Here, we aim to develop and evaluate a new STR genotyping software, STRkit, which uses STR-proximate SNV information contained in long reads...
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Research: Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing
- Samantha L. Sholes,
- Kayarash Karimian,
- Ariel Gershman,
- Thomas J. Kelly,
- Winston Timp,
- and Carol W. Greider
Genome Res. April 2022 32: 616-628; Published in Advance October 26, 2021, doi:10.1101/gr.275868.121
...of nanopore and Southern density distributions were similar, and there was no significant difference in the means by Welch's t-test (Supplemental Fig. S3A).Because the Y′ probe measures 17 telomere length distributions simultaneously, it is challenging to detect potential small effects and chromosome-specific...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
..., with significantly improved raw read accuracy (Q20+), offers a potential solution to this problem. The aim of this study is to evaluate the performance of ONT's latest chemistry for bacterial genomic typing against the gold-standard Illumina technology, focusing on three respiratory pathogens of public health...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...of 0.125 M. The cell pellets were washed with PBS and stored in −80°C.Chromatin shearingCells were lysed with either the LB3 lysis buffer (10 mM Tris-HCl at pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.1% deoxycholate, 0.5% N-lauroylsarcosine, 1× protease inhibitor cocktail) or the EBB lysis buffer (0.5% Empigen...
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Research: Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
- Akihiro Fujimoto,
- Masashi Fujita,
- Takanori Hasegawa,
- Jing Hao Wong,
- Kazuhiro Maejima,
- Aya Oku-Sasaki,
- Kaoru Nakano,
- Yuichi Shiraishi,
- Satoru Miyano,
- Go Yamamoto,
- Kiwamu Akagi,
- Seiya Imoto,
- and Hidewaki Nakagawa
Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
....28 in the deletions of MSS, and 0.29 in the insertions of MSS (Supplemental Table S4).Microsatellites are highly polymorphic and have also been used as genetic markers for population genetics studies (Ellegren 2004). To evaluate the genetic polymorphism, we detected germline polymorphism with MIVcall method...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...computational toolkit for genotyping the variable genes of the IG lambda and kappa, and the TR loci with short-read whole sequence data, using an integer linear programming formulation, as an update to the ImmunoTyper-SR suite, which focused on IGHV region only. We evaluate its genotyping performance using...
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