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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...modality with high fidelity, thereby bridging domain discrepancies between scRNAseq and scDNAmprofiles. Finally, decoders are employed to reconstruct the original high-dimensional inputs from their corresponding latent embeddings, with loss functions specifically tailored to each data modality, ensuring...
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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
..., complex sequencing library across many types of microsatellite motifs and motif lengths.Additionally, emerging sequencing technologies may further reduce stutter. We compared stutter profiles of PCR-free WGS sequenced by the recently released Pacific Biosciences (PacBio) Onso platform, which uses...
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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
...002). Many of these so-called “challenge” BACs were deliberately selected from genomic regions that pose significant assembly challenges (i.e., regions with SDs), making them useful for assembly benchmarking (Chin and Khalak 2019; Miga et al. 2020; Shafin et al. 2020; Vollger et al. 2020). Table 3...
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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
...regulation, and cell differentiation. Nevertheless, StripeDiff does not provide a user-friendly package to directly call all stripes with common contact map files.Here we introduce Quagga, a statistically rigorous, algorithmically efficient, and interpretable tool to identify stripes. Quagga's biggest...
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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...efficiency below 35% (Supplemental Figs. S3, S4; Supplemental Table S1C; Ren et al. 2014). Similarly, from 22 sgRNAs designed for use in mammalian cells, 13 had a cleavage efficiency below 35% associated with disturbances of the sgRNA secondary structure (Supplemental Fig. S5; Supplemental Table S1D; Graf et...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...coding-like NUMTs within nuclear regions, particularly in areas of low recombination (Gossmann et al. 2014). This selective pressure could further suppress the rate of mutation accumulation in NUMTs.MethodsData collection and selectionGenome assemblies for all mammalian species (available before November...
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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
..., UCell, and JASMINE—across nine healthy and cancer scRNA-seq data sets demonstrates their insufficiency in fulfilling this requirement. To address this limitation, we present Adjusted Neighborhood Scoring (ANS), a deterministic algorithm with enhanced control gene selection that significantly improves...
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Method: Targeted, programmable, and precise tandem duplication in the mammalian genome
- Yaoge Jiao,
- Min Li,
- Xingyu He,
- Yanhong Wang,
- Junwei Song,
- Yun Hu,
- Li Li,
- Lifang Zhou,
- Lurong Jiang,
- Junyan Qu,
- Lifang Xie,
- Qiang Chen,
- and Shaohua Yao
Genome Res. May 2023 33: 779-786; Published in Advance June 9, 2023, doi:10.1101/gr.277261.122
...Targeted, programmable, and precise tandem duplication in the mammalian Yaoge Jiao1,4, Min Li1,4, Xingyu He1,4, Yanhong Wang1,4, Junwei Song1, Yun Hu1, Li Li1, Lifang Zhou1, Lurong Jiang1, Junyan Qu2, Lifang Xie3, Qiang Chen1 and Shaohua Yao1 1Department of Biotherapy, Cancer Center and State Key...
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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
...the most complex repeats, this project relied on the semimanual combination of long, accurate Pacific Biosciences (PacBio) HiFi and ultralong Oxford Nanopore Technologies sequencing reads. The Verkko assembler later automated this process, achieving complete assemblies for approximately half...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...constructed comprehensive multiple alignments for 95 eutherian and 94 avian species (Supplemental Fig. S1; Supplemental Tables S1, S2), which covered all orders of the two taxa. We then reconstructed mammalian and avian ancestral s by selecting 10 high-quality s from different orders of Mammalia and Aves...

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