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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
...per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling—“stutter” artifacts—with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...development of strategies to infer parent-of-origin effects in humans using large-scale biobanks may lead to the discovery of novel imprinted loci (Hofmeister et al. 2025). However, technically and conceptually, it is difficult to identify all the genes subject to imprinting. Beyond the canonical image...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...this gene could provide a viable therapeutic target in dogs (Urick and Bell 2020; Kawaguchi et al. 2021; Urick et al. 2021).Sequencing strategies for large-scale genomic analysesIn the past 10 years, there has been a steady decrease in the cost of short-read whole- sequencing (WGS) (Cullen and Friedenberg...
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Method: Fast and accurate out-of-core PCA framework for large scale biobank data
- Zilong Li,
- Jonas Meisner,
- and Anders Albrechtsen
Genome Res. September 2023 33: 1599-1608; Published in Advance August 24, 2023, doi:10.1101/gr.277525.122
...with 1,306,127 cells and 23,771 genes for estimating the top K = 40 PCsDiscussionWe presented PCAone, an out-of-core PCA framework tailored for large-scale data analyses. Through various data sets, we have shown the advantage of our implemented IRAM method, PCAoneArnoldi, which is 10× faster than...
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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
...; Koustas and Sjoblom 2016; Yu et al. 2019; Ooga et al. 2023) and humans (Song et al. 2015; Ghosh et al. 2017; Choux et al. 2018; Mani et al. 2019; Barberet et al. 2021; Håberg et al. 2022), with downstream consequences for the expression of key genes required for totipotency and early development (Hayashi...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
..., the band containing the rDNA gene cluster. Alignments of the X Chromosome between HiFi assemblies from iso-1, A4, and A3 to Release 6 (Fig. 2A) show that the newly assembled segments h27-h28 comprise arrays of segmental duplications with varying copy numbers in the three strains. The entire region (∼98...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...enhancer activity in the phNPCs, and we link these regions to over 2200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including neuronal system, nervous system development, and developmental delay. We functionally validate a subset...
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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...small, ranging from 0.6 Mb to 4.8 Mb (mean = 2.3 Mb) (Supplemental Table S5). Although it is possible that small CNAs (<10 Mb) occurred more because they affected fewer genes and thus affected cell survival less than larger CNAs do, it is hard to distinguish between true and false positive calls...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...PCR primers designed against nonregulatory regions of the gene when enrichment is not expected, and ensuring DNA shearing with fragments that are not too long in order to prevent nonspecific GOI identification. ChIP has had a revolutionary impact on our understanding of biology and has spearheaded clinical...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...of population-specific caQTLs was limited by sample size in our study; caQTL mapping in larger, more diverse cohorts may identify more caQTLs that differ across populations. Large-scale functional assays will help confirm links between variants, regulatory elements, and genes predicted by caQTL studies...

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