Searching journal content for articles similar to Burke et al. 22 (8): 1549.

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  1. Method: Iterative improvement of deep learning models using synthetic regulatory genomics
    • André M. Ribeiro-dos-Santos and
    • Matthew T. Maurano
    Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
    ...the reference, such as disease- and trait-associated variants or engineered sequences. Recent work has applied synthetic regulatory genomics to characterized dozens of deletions, inversions, and rearrangements of DNase I hypersensitive sites (DHSs). Here, we use the state-of-the-art model Enformer to predict...
  2. Resource: Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    • Elizabeth G. King,
    • Chris M. Merkes,
    • Casey L. McNeil,
    • Steven R. Hoofer,
    • Saunak Sen,
    • Karl W. Broman,
    • Anthony D. Long,
    • and Stuart J. Macdonald
    Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
    ...Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource Elizabeth G. King 1 , Chris M. Merkes 2 , Casey L. McNeil 2 , Steven R. Hoofer 2 , Saunak Sen 3 , Karl W. Broman 4 , Anthony D...
    OPEN ACCESS ARTICLE
  3. Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
    • Xiran Liu,
    • Lorin Crawford,
    • and Sohini Ramachandran
    Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
    ...frequency on the variance through heterozygosity, a factor w controlling the dependence of variance on LD score of the variants, the proportion of SNPs designated as causal, and the narrow-sense heritability of a synthetic trait (see Supplemental Methods S1.4). We then simulated synthetic trait values using...
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  4. Research: Heritability and genetic basis of protein level variation in an outbred population
    • Leopold Parts,
    • Yi-Chun Liu,
    • Manu M. Tekkedil,
    • Lars M. Steinmetz,
    • Amy A. Caudy,
    • Andrew G. Fraser,
    • Charles Boone,
    • Brenda J. Andrews,
    • and Adam P. Rosebrock
    Genome Res. August 2014 24: 1363-1370; Published in Advance May 13, 2014, doi:10.1101/gr.170506.113
    ...regions in which the RM allele frequency was at least 20% different between the GFP low and high populations and defined these as protein level quantitative trait loci (pQTLs; false discovery rate = 22%) (Supplemental Table 7; Supplemental Fig. 7; Methods). For a subset of traits, we identified...
  5. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M Riley,
    • Randa Elsayed,
    • Mark D Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C Nelson
    Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...are superficially diverse, they share key commonalities in terms of 23 overall morphology, and organ configuration and function. Maintenance of these traits during 24 evolution is partially explained by conservation of critical genes governing embryonic 25 development. However, for conserved genes to deliver...
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  6. Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
    • Rachel M. Petersen,
    • Christopher M. Vockley,
    • and Amanda J. Lea
    Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
    ...traits, which at the molecular level often involves complex interactions between genetic variants, the epi, and gene expression. DNA methylation (DNAm) refers to the addition of methyl groups to cytosine bases, usually within CpG dinucleotide contexts (the most commonly methylated motif in mammals). DNAm...
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  7. Research: Genetic analysis of complex traits in the emerging Collaborative Cross
    • David L. Aylor,
    • William Valdar,
    • Wendy Foulds-Mathes,
    • Ryan J. Buus,
    • Ricardo A. Verdugo,
    • Ralph S. Baric,
    • Martin T. Ferris,
    • Jeff A. Frelinger,
    • Mark Heise,
    • Matt B. Frieman,
    • Lisa E. Gralinski,
    • Timothy A. Bell,
    • John D. Didion,
    • Kunjie Hua,
    • Derrick L. Nehrenberg,
    • Christine L. Powell,
    • Jill Steigerwalt,
    • Yuying Xie,
    • Samir N.P. Kelada,
    • Francis S. Collins,
    • Ivana V. Yang,
    • David A. Schwartz,
    • Lisa A. Branstetter,
    • Elissa J. Chesler,
    • Darla R. Miller,
    • Jason Spence,
    • Eric Yi Liu,
    • Leonard McMillan,
    • Abhishek Sarkar,
    • Jeremy Wang,
    • Wei Wang,
    • Qi Zhang,
    • Karl W. Broman,
    • Ron Korstanje,
    • Caroline Durrant,
    • Richard Mott,
    • Fuad A. Iraqi,
    • Daniel Pomp,
    • David Threadgill,
    • Fernando Pardo-Manuel de Villena,
    • and Gary A. Churchill
    Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
    ...; baseline body weight, a trait known to be highly polygenic; and liver mRNA expression profile. Thus, we highlight results from three types of traits–Mendelian, complex, and molecular. An ancestry-based approach proved superior to marker-based methods for mapping QTL in the pre-CC population...
  8. Research: Genic and nongenic contributions to natural variation of quantitative traits in maize
    • Xianran Li,
    • Chengsong Zhu,
    • Cheng-Ting Yeh,
    • Wei Wu,
    • Elizabeth M. Takacs,
    • Katherine A. Petsch,
    • Feng Tian,
    • Guihua Bai,
    • Edward S. Buckler,
    • Gary J. Muehlbauer,
    • Marja C.P. Timmermans,
    • Michael J. Scanlon,
    • Patrick S. Schnable,
    • and Jianming Yu
    Genome Res. December 2012 22: 2436-2444; Published in Advance June 14, 2012, doi:10.1101/gr.140277.112
    ...and Yu 2007; Riedelsheimer et al. 2012), and NAMGWAS scan (Tian et al. 2011) represented some new contributions to complex trait dissection and selection in plants, many of which are facing similar challenges. The maize NAM population consists of 5000 RILs derived from crossing 26 diverse founders...
    OPEN ACCESS ARTICLE
  9. 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
    ..., and cell state–dependent protein dynamics. In this review, we dissect the strengths, limitations, and biological relevance of current approaches for studying direct protein–DNA interactions, distinguishing between protein-centric and DNA-centric methodologies. We introduce a conceptual matrix of biological...
    OPEN ACCESS ARTICLE
  10. Review: Population genetic inference from genomic sequence variation
    • John E. Pool,
    • Ines Hellmann,
    • Jeffrey D. Jensen,
    • and Rasmus Nielsen
    Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
    ...Population genetic inference from genomic sequence variation John E. Pool 1 , 2 , Ines Hellmann 3 , Jeffrey D. Jensen 1 , 5 and Rasmus Nielsen 1 , 4 , 6 1 Department of Integrative Biology, University of California, Berkeley...
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