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Erratum: Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 660; doi:10.1101/gr.281963.126
...Cristian Groza, Bing Ge, Warren A. Cheung, Tomi Pastinen and Guillaume Bourque Genome Research 35: 644–652 (2025)Owing to production errors, the panel label of Figure 1E was missing and the hyphen in SV-CpG was incorrectly rendered as a square; and several of the line graph curves were incomplete...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...scientific and practical importance, the western honey bee Apis mellifera (L.) was among the first metazoans with a completed project (Weinstock et al. 2006). It has since served as a model for genomic studies of adaptation (Wallberg et al. 2014), invasion (Calfee et al. 2020), and social traits...
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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. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...for the genotype 366 and phenotype were consistent with those used in the chicken studies mentioned above. After 367 quality control, 2,549 pigs with complete growth-trait records and 2,610 pigs with complete 368 feeding behavior records were retained. The final number of SNPs used for genomic 369 prediction...
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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
..., are powering -wide association studies (GWAS), where many genetic variants (e.g., SNPs) are analyzed across different subjects to find the relationships between genetic and phenotypic traits (Mardis 2011; Wojcik et al. 2019), are used to develop new treatments and drugs (Shah and Gaedigk 2018), and to address...
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...and detection of modified nucleotides. Also, the extent to which SVs act as methylation quantitative trait loci (SV-mQTLs) is largely unknown. Here, we generated a pan graph summarizing SVs in 782 de novo assemblies obtained from Genomic Answers for Kids, capturing 14.6 million CpG dinucleotides that are absent...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...A novel quantitative trait locus implicates Msh3 in the propensity for -wide short tandem repeat expansions in mice Mikhail O. Maksimov1,2,12, Cynthia Wu3,12, David G. Ashbrook4, Flavia Villani4, Vincenza Colonna4,5, Nima Mousavi6, Nichole Ma1, Lu Lu4, Jonathan K. Pritchard7,8, Alon Goren1...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...and Thompson 2025), which may capture additional fine-scale relatedness. Finally, SPCs could also be evaluated as covariates in IBD-based mapping of quantitative trait loci, as their ability to resolve fine-scale population structure differences suggests they may help improve mapping accuracy (Chen et al. 2023...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...studies may overlook. On the other hand, analyses of genomic variation frequently reveal a complex interplay among sequence changes, including single-nucleotide polymorphisms (SNPs) and structural variations (SVs), which are associated with altered gene expression and phenotypic traits (Collins et al...
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Resource: Honey bee protein atlas at organ-level resolution
- Queenie W.T. Chan,
- Man Yi Chan,
- Michelle Logan,
- Yuan Fang,
- Heather Higo,
- and Leonard J. Foster
Genome Res. November 2013 23: 1951-1960; Published in Advance July 22, 2013, doi:10.1101/gr.155994.113
...by the research community: ‘‘with the at hand, prospects are bright for elucidating the molecular and genetic bases of many complex traits. . .’’ (The Honey Bee Genome Sequencing Consortium 2006). While an organism’s chromosomes can now be sequenced from telomere to telomere, defining the complete transcriptome...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...there is a degree of behavioral differentiation (Settepani et al. 2013), they do not show eusociality like in ants and bees (Crespi and Yanega 1995), as there are no casts or strict division of labor (Lubin and Bilde 2007). Phylogenetic relationships indicate that sociality in spiders evolves from subsocial...

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