Searching journal content for articles similar to Campbell et al. 18 (4): 555.

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  1. Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    • Olga M. Sigalova,
    • Mattia Forneris,
    • Frosina Stojanovska,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Adam Rabinowitz,
    • Fayrouz Hammal,
    • Benoît Ballester,
    • Judith B. Zaugg,
    • and Eileen E.M. Furlong
    Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
    ...by 30%–50%. This fine-grained “mutagenesis” can reconstruct functionalized binding motifs for all factors. To prioritize causal variants, we trained a convolutional neural network (Basenji) to accurately predict binding from DNA sequence. The model can also predict measured allelic imbalance for strong...
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  2. Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
    • Kohei Hagiwara,
    • Andrew Thrasher,
    • Nadezhda V Terekhanova,
    • and Jinghui Zhang
    Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
    ...if the variant allele fraction (VAF) in RNA (VAFRNA) is significantly deviated from its 60 expected VAF in DNA (VAFDNA). In non-cancerous tissues, the analysis of allelic imbalance of 61 germline heterozygous single-nucleotide polymorphisms (SNPs) in RNA, which measures a 62 significant deviation from...
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  3. Research: Gene regulation and speciation in house mice
    • Katya L. Mack,
    • Polly Campbell,
    • and Michael W. Nachman
    Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
    ...and trans changes is to compare expression differences between species with expression differences between alleles in inter-specific hybrids (Fig. 1; Cowles et al. 2002;Wittkopp et al. 2004). This approach has now been used in a number of crosses in flies, yeast, mice, and plants (Table 1). These studies...
  4. Methods: Survey of allelic expression using EST mining
    • Bing Ge,
    • Scott Gurd,
    • Tiffany Gaudin,
    • Carole Dore,
    • Pierre Lepage,
    • Eef Harmsen,
    • Thomas J. Hudson,
    • and Tomi Pastinen
    Genome Res. November 2005 15: 1584-1591; doi:10.1101/gr.4023805
    ...Survey of allelic expression using EST mining Bing Ge , Scott Gurd , Tiffany Gaudin , Carole Dore , Pierre Lepage , Eef Harmsen , Thomas J. Hudson , and Tomi Pastinen 1 McGill University and Genome...
  5. 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
    ...gDMRs (Table 1; Fig. 2).More than 20 transient gDMRs have been characterized in mice, the majority being methylated on the maternal allele (Table 2; Proudhon et al. 2012; Duffié et al. 2014; Strogantsev et al. 2015; Yang et al. 2022). Some of these were identified in mouse preimplantation embryos...
  6. Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
    • Yu Lin,
    • Jing Li,
    • Yiren Gu,
    • Long Jin,
    • Jingyi Bai,
    • Jiaman Zhang,
    • Yujie Wang,
    • Pengliang Liu,
    • Keren Long,
    • Mengnan He,
    • Diyan Li,
    • Can Liu,
    • Ziyin Han,
    • Yu Zhang,
    • Xiaokai Li,
    • Bo Zeng,
    • Lu Lu,
    • Fanli Kong,
    • Ying Sun,
    • Yongliang Fan,
    • Xun Wang,
    • Tao Wang,
    • An'an Jiang,
    • Jideng Ma,
    • Linyuan Shen,
    • Li Zhu,
    • Yanzhi Jiang,
    • Guoqing Tang,
    • Xiaolan Fan,
    • Qingyou Liu,
    • Hua Li,
    • Jinyong Wang,
    • Li Chen,
    • Liangpeng Ge,
    • Xuewei Li,
    • Qianzi Tang,
    • and Mingzhou Li
    Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
    ...). Beyond characterizing the spatial proximity of enhancers and promoters, we also measured allelic imbalances in the activity of enhancers and promoters by generating H3K27ac and H3K4me3 ChIP-seq signal enrichment profiles (Supplemental Figs. S1, S2G, S14I–P; Villar et al. 2015; Pérez-Rico et al. 2017...
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  7. Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
    • Jenna Kalleberg,
    • Jacob Rissman,
    • and Robert D. Schnabel
    Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
    ...impacts when used with non-human species. Here, we use bovine s to assess the limits of using human –trained variant callers, including the allele frequency channel (DV-AF) and joint-caller DeepTrio (DT). Our novel approach, TrioTrain, automates extending DV for diploid species lacking Genome...
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  8. Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
    • W.H. Adrian Tsui,
    • Spencer C. Ding,
    • Peiyong Jiang,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
    ...analysis. RMD quantifies the allelic imbalance at a maternally heterozygous SNP (AB), in which the fetus being homozygous at that locus (AA/BB) would imbalance the allelic counts (Lun et al. 2008). In contrast to RMD, which analyzes a single genomic locus, RHDO uses parental genotypes to phase a series...
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  9. Research: The landscape of genomic imprinting across diverse adult human tissues
    • Yael Baran,
    • Meena Subramaniam,
    • Anne Biton,
    • Taru Tukiainen,
    • Emily K. Tsang,
    • Manuel A. Rivas,
    • Matti Pirinen,
    • Maria Gutierrez-Arcelus,
    • Kevin S. Smith,
    • Kim R. Kukurba,
    • Rui Zhang,
    • Celeste Eng,
    • Dara G. Torgerson,
    • Cydney Urbanek,
    • the GTEx Consortium,
    • Jin Billy Li,
    • Jose R. Rodriguez-Santana,
    • Esteban G. Burchard,
    • Max A. Seibold,
    • Daniel G. MacArthur,
    • Stephen B. Montgomery,
    • Noah A. Zaitlen,
    • and Tuuli Lappalainen
    Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
    ...models for the different scenarios of allelic balance, imbalance, and monoallelic expression (Methods). We modeled and filtered for confounding factors (Supplemental Table S2; Proudhon and Bourc’his 2010; DeVeale et al. 2012), including biological processes of strong cis-eQTLs (The GTEx Consortium 2015...
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  10. Research: Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor
    • Brennan Decker,
    • Brian W. Davis,
    • Maud Rimbault,
    • Adrienne H. Long,
    • Eric Karlins,
    • Vidhya Jagannathan,
    • Rebecca Reiman,
    • Heidi G. Parker,
    • Cord Drögemüller,
    • Jason J. Corneveaux,
    • Erica S. Chapman,
    • Jeffery M. Trent,
    • Tosso Leeb,
    • Matthew J. Huentelman,
    • Robert K. Wayne,
    • Danielle M. Karyadi,
    • and Elaine A. Ostrander
    Genome Res. November 2015 25: 1646-1655; Published in Advance July 31, 2015, doi:10.1101/gr.190314.115
    ...diseases. It represents the most exhaustive breadth of canine genomic sampling, combined with the deepest sequencing for individuals within closed-breeding populations of dogs. Despite our unrivaled survey of canine genomic variation, we note that our approach misclassifies founder-inherited alleles...
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