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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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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...(Fig. 1E; Supplemental Figs. S21–S23) display expected genomic features in which more gene-poor chromosomes are located more frequently toward the nuclear periphery (Supplemental Figs. S24–S26). Our 3D modeling of all three cell types reveals major differences between 10A cells versus T1 and C1 cells...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Barcelona 08034, Spain; 3Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, USA; 4Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; 5Institute for Computational and Mathematical Engineering...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...not be expected in relation to Eurasian wolves, thus suggesting postdivergence gene flow between Iberian wolves and dogs.To further dissect the evolutionary history of this genomic region, we compared the population phylogenetic trees for the entire Chromosome 2 and for the 500 kb region using TreeMix (Pickrell...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...the missegregation of a specific chromosome. (B) Copy numbers of CSMD1, MICU3, and CRISPLD1 (a gene located on the q arm of Chromosome 8), in trisomic proband clones that were transiently transfected with KaryoCreate plasmids. Mean ± SEM; data from representative trials are shown (n ≥ 3 total trials). Genomic DNA...
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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
...the −log10 P-value from the GWAS. The blue and orange points represent SNPs associated with AGG and TW, respectively. The dashed curve marks the boundaries of the significant QTL loci for both traits within this genomic interval, which encompasses multiple candidate genes, including the AMH gene. (B...
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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
...unit variance, yielding RT Z-scores. We then categorized the into 12 chromosomal domains with their mean RT Z-scores: two major autosomal arms and their pericentromeric regions, the 4th, X, and Y Chromosomes, and a gene consensus for the ribosomal DNA (rDNA) locus (Fig. 5B). This allowed us...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...for downstream TFBS analysis, allowing the 142 identification of key regulatory motifs involved in the antiviral response. 143 To further characterise the genomic distribution of ATAC-seq and H3K27ac peaks, we 144 annotated consensus peaks relative to gene features and transcription start sites (TSS). The 145...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...conservation of the X Chromosome gene content across broad swathes of the insect phylogeny, as well as temporal dynamics to the rate of X Chromosome evolution (Meisel et al. 2019; Chauhan et al. 2021).ResultsGenome featuresWe used PacBio HiFi sequencing to generate sequences for a female (XX) migratory locust...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...polymerization and smooth muscle contraction. Here, we show that the genomic distribution of ACTB is SETD3-dependent and that this regulation modulates the transcription of genes involved in cell adhesion and mRNA translation in colorectal cancer cells. Proteomic analyses reveal that ACTB and SETD3 interact...

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