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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...and de novo haploid assemblies demonstrates the enduring quality of the reference assembly. Genome Res 27: 849–864. doi:10.1101/gr.213611.116 ↵Sevim V, Bashir A, Chin C-S, Miga KH. 2016. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics 32...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...-SFARI.The substantial reduction in sequencing costs has made generating whole-exome or whole- sequences for large family collections feasible. This development allows for the direct observation and analysis of genetic variants across the entire frequency spectrum, spanning from common to rare and de novo mutations...
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Research: Optical genome mapping enables accurate testing of large repeat expansions
- Bart van der Sanden,
- Kornelia Neveling,
- Syukri Shukor,
- Michael D. Gallagher,
- Joyce Lee,
- Stephanie L. Burke,
- Maartje Pennings,
- Ronald van Beek,
- Michiel Oorsprong,
- Ellen Kater-Baats,
- Eveline Kamping,
- Alide A. Tieleman,
- Nicol C. Voermans,
- Ingrid E. Scheffer,
- Jozef Gecz,
- Mark A. Corbett,
- Lisenka E.L.M. Vissers,
- Andy Wing Chun Pang,
- Alex Hastie,
- Erik-Jan Kamsteeg,
- and Alexander Hoischen
Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
....7.2 using default parameters against the GRCh38/hg38 reference . The de novo assembly was then used to estimate the repeat length for both alleles by calculating the genomic distance between the reference start and end label flanking the repeat locus of interest (Fig. 4A; Supplemental Table S5...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
..., Feusier J, Gupta M, Nicholas TJ, Brown J, Baird L, et al. 2021a. De novo structural mutation rates and gamete-of-origin biases revealed through sequencing of 2,396 families. Am J Hum Genet 108: 597–607. doi:10.1016/j.ajhg.2021.02.012 ↵Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR...
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Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
...improvements in assembly algorithms.Advances in sequencing technology have been a driving force in molecular biology and genomics, in particular for de novo assembly (Alhakami et al. 2017; Sohn and Nam 2018; Sun et al. 2022b). Single-molecule sequencing (SMS) technologies currently on the market can generate...
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Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
- John S. Sproul,
- Scott Hotaling,
- Jacqueline Heckenhauer,
- Ashlyn Powell,
- Dez Marshall,
- Amanda M. Larracuente,
- Joanna L. Kelley,
- Steffen U. Pauls,
- and Paul B. Frandsen
Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
...of RE sequences and is integral to the standard RE identification and annotation programs RepeatModeler2 (Flynn et al. 2020) and RepeatMasker (Smit and Hubley 2019). Of the 20 insect orders in our data set, 14 are represented in Repbase; however, of those, six are represented by a single insect family...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...or that their status as ORFans resulted from loss in multiple lineages via repeated pseudogenization. To acknowledge this uncertainty, the authors refer to these as “de novo gene candidates,” but considering the massive size of their database (4.7 million protein families from 4644 species in the human gut microbiome...
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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
...-copy regions of the lentil with or without CRISPR-Cas9-mediated repeat depletion. Integrative Genome Browser Visualization (IGV) (Thorvaldsdóttir et al. 2013) of Illumina sequencing data mapped to two representative genomic sites of ∼180 kbp (A) and ∼50 kbp (B). Tracks in blue, green, and red represent...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...These authors contributed equally to this work. Corresponding authors: n.tesi@amsterdamumc.nl, a.n.salazar@amsterdamumc.nl, h.holstege@amsterdamumc.nlAbstractTandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...parts using the Qiagen blood and tissue kit following the standard protocol, including treatment with 4 µL RNase and 25 µL Proteinase K. The DNA extraction product was cleaned and concentrated with ZymoResearch genomic DNA Clean & Concentrator kit. For most samples, the RNase treatment was repeated...

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