Searching journal content for articles similar to Ng and Henikoff 12 (3): 436.

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  1. Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
    • Shuai Wang,
    • Merritt Khaipho-Burch,
    • Lynn C. Johnson,
    • Zachary R. Miller,
    • Peter J. Bradbury,
    • Doug Speed,
    • William J. Allen,
    • M. Cinta Romay,
    • Jiquan Xue,
    • Edward S. Buckler,
    • Guillaume P. Ramstein,
    • and Baoxing Song
    Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
    ...line B73 and the 25 other NAM founder lines. Whether AlphaFold2 can predict the effects of single amino-acid polymorphisms (SAPs) is controversial (Stein and Mchaourab 2024), so we first compared the protein sequence from the same core pangene group to characterize the sequence diversity of orthologous...
  2. Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
    • Peter A. Audano and
    • Christine R. Beck
    Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
    ...confirm that SNP and indel polymorphisms are enriched at shifted breakpoints and are also absent from variant callsets. Breakpoint homology increases the likelihood of imprecise SV calls and the distance they are shifted, and tandem duplications are the most heavily affected SVs. Because graph methods...
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  3. Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
    • Alexandra J. Scott,
    • Colby Chiang,
    • and Ira M. Hall
    Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
    ...to predict from current annotations. Both common and rare SVs often affect the expression of multiple genes: SV-eQTLs affect an average of 1.82 nearby genes, whereas SNV- and indel-eQTLs affect an average of 1.09 genes, and 21.34% of rare expression-altering SVs show effects on two to nine different genes...
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  4. Research: Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
    • Naveen Kumar Kadri,
    • Chad Harland,
    • Pierre Faux,
    • Nadine Cambisano,
    • Latifa Karim,
    • Wouter Coppieters,
    • Sébastien Fritz,
    • Erik Mullaart,
    • Denis Baurain,
    • Didier Boichard,
    • Richard Spelman,
    • Carole Charlier,
    • Michel Georges,
    • and Tom Druet
    Genome Res. October 2016 26: 1323-1332; Published in Advance August 11, 2016, doi:10.1101/gr.204214.116
    ...(Table 1). Knowing that the six recombination-related genes account for 8.4% of the ORF space of the 104 candidates, the probability for this to occur by chance alone is 3.9 × 10−4. Moreover, the nonsynonymous variants in HFM1, MLH3, and MSH5 (but not RNF212) affect extremely conserved residues (phast...
  5. 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
    ...by refining biological feature engineering and 31 optimizing the hyperparameters. We demonstrate how gene-related biometrics influence target 32 traits and how accounting for interaction effects enhances prediction accuracy. In addition, we 33 apply Shapley Additive Explanations (SHAP) to quantify the SNP...
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  6. Research: Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster
    • Daniel R. Schrider,
    • Kristian Stevens,
    • Charis M. Cardeño,
    • Charles H. Langley,
    • and Matthew W. Hahn
    Genome Res. December 2011 21: 2087-2095; doi:10.1101/gr.116434.110
    ...that this type of polymorphism is quite common, with any two gametes in the North American population differing in the presence or absence of six retrogenes, accounting for ∼13% of gene copy-number heterozygosity. These retrogenes were identified by a straightforward method that can be applied using any type...
  7. Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
    • Pengju Zhao,
    • Jiayi He,
    • Chen Peng,
    • Yuelang Zhang,
    • Chong Wang,
    • Dongyou Yu,
    • Lingzhao Fang,
    • and Zhengguang Wang
    Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
    ...motifs from both JASPAR and predicted 257 models (Fig. 5A). Specifically, we employed 25 unvalidated TFBS of KZFP from JASPAR 258 2024 (Jaime et al. 2021) and generated 75 DNA binding motifs of KZFPs by analyzing their 259 tandem zinc finger domain sequences with the B1H-RC model (Najafabadi et al. 2015...
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  8. Research: RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression
    • Emilie Lalonde,
    • Kevin C.H. Ha,
    • Zibo Wang,
    • Amandine Bemmo,
    • Claudia L. Kleinman,
    • Tony Kwan,
    • Tomi Pastinen,
    • and Jacek Majewski
    Genome Res. April 2011 21: 545-554; Published in Advance December 20, 2010, doi:10.1101/gr.111211.110
    ...%–25% of the observed change in expression. This co- or post-transcriptional regulationmay take place at the level ofmRNA stability or splicing. Alternative splicing is involved in regulation of eQTL targets We have previously described a large number of genes that are affected by common splicing polymorphisms...
  9. Resource: The SynMall resource for characterizing the functional impact of synonymous variation
    • Chen Ye,
    • Xiaoyan Li,
    • Na Cheng,
    • Yansen Su,
    • and Junfeng Xia
    Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
    ...the amino acid sequence encoded by the affected codon, have historically been regarded as functionally neutral (Chamary et al. 2006). However, with the advent of high-throughput sequencing technologies, accumulating evidence has revealed that sSNVs may account for 6%–8% of all driver mutations in cancer...
  10. 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
    ...and stress responses in nematodes. A detailed examination of a recently evolved F-box gene family (fbxn family), which includes a speciation gene Cni-neib-1, demonstrates extensive polymorphism among populations, which may contribute to hybrid incompatibility. Collectively, our findings underscore...
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