Searching journal content for articles similar to Łastowski and Makałowski 10 (3): 273.

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  1. Method: A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    • Daniel A. Skelly,
    • Marnie Johansson,
    • Jennifer Madeoy,
    • Jon Wakefield,
    • and Joshua M. Akey
    Genome Res. October 2011 21: 1728-1737; Published in Advance August 26, 2011, doi:10.1101/gr.119784.110
    ...A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data Daniel A. Skelly 1 , 3 , Marnie Johansson 1 , Jennifer Madeoy 1 , Jon Wakefield 2 and Joshua M. Akey 1 , 3...
  2. 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
    ...from DNA variants to phenotypes, spans the entire central dogma of molecular biology; incorporates various nongenetic factors, such as environmental influences (Yao et al. 2025); and is one of the most challenging tasks in biological prediction. Genomic selection (GS) is the most advanced methodology...
  3. Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
    • Krzysztof H. Banecki,
    • Haoxi Chai,
    • Yijun Ruan,
    • and Dariusz Plewczynski
    Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
    ...by Banecki et al. (2024), and new ones are constantly being developed (Wang and Cheng 2025). Despite their methodological diversity, these approaches share key similarities. Notably, most models reconstruct chromatin structure using a single scHi-C map at a time, potentially overlooking contextual...
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  4. 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
    ...02912, USA Corresponding author: xiran_liu1@brown.eduAbstractA fundamental goal of genetics is to identify which and how genetic variants are associated with a trait, often using the regression results from -wide association (GWA) studies. Important methodological challenges account for inflation in GWA...
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  5. Method: Tree-based differential testing using inferential uncertainty for RNA-seq
    • Noor Pratap Singh,
    • Euphy Y. Wu,
    • Jason Fan,
    • Michael I. Love,
    • and Rob Patro
    Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
    .... This idea was first proposed in mmcollapse (Turro et al. 2014), also described by Robert and Watson (2015), and further expanded in Terminus (Sarkar et al. 2020), where these groups that contain multiple transcripts, rather than single transcripts, form the feature set for differential analysis...
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  6. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...(Ashford et al. 2019). In addition, using protein structure provides insights into how mutations affect protein function through effects at key functional sites. We hypothesized that protein domains may contain “tunable sites,” near to functional sites, which may be similarly altered in multiple tumor...
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  7. Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
    • Guanjue Xiang,
    • Xi He,
    • Belinda M. Giardine,
    • Kathryn J. Isaac,
    • Dylan J. Taylor,
    • Rajiv C. McCoy,
    • Camden Jansen,
    • Cheryl A. Keller,
    • Alexander Q. Wixom,
    • April Cockburn,
    • Amber Miller,
    • Qian Qi,
    • Yanghua He,
    • Yichao Li,
    • Jens Lichtenberg,
    • Elisabeth F. Heuston,
    • Stacie M. Anderson,
    • Jing Luan,
    • Marit W. Vermunt,
    • Feng Yue,
    • Michael E.G. Sauria,
    • Michael C. Schatz,
    • James Taylor,
    • Berthold Göttgens,
    • Jim R. Hughes,
    • Douglas R. Higgs,
    • Mitchell J. Weiss,
    • Yong Cheng,
    • Gerd A. Blobel,
    • David M. Bodine,
    • Yu Zhang,
    • Qunhua Li,
    • Shaun Mahony,
    • and Ross C. Hardison
    Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
    ...of the IDEAS methodology to combine peaks of accessibility across different cell types, running it in the signal intensity state (IS) mode only on chromatin accessibility signals (Xiang et al. 2021), which helps counteract excessive expansion of peak calls when combining them (Supplemental Fig. S6).Employing...
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  8. Review: De novo gene birth and the conundrum of ORFan genes in bacteria
    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
    ...postulated to originate from either horizontal transfer, rapid divergence from pre-existing genes, or de novo emergence from noncoding sequences. We assess the body of research that explores each of these hypotheses and demonstrate that the mystery of the origin of bacterial ORFans still remains unresolved...
  9. 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
    ...) regulatory divergence between paralogous 96 genes contributes to their differential expression during the antiviral response; and (iii) 97 expanded or salmonid-specific gene families exhibit distinct regulatory signatures that reflect 98 their functional roles in immunity. 99 To test these hypotheses, we...
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  10. Method: Geometric deep learning framework for de novo genome assembly
    • Lovro Vrček,
    • Xavier Bresson,
    • Thomas Laurent,
    • Martin Schmitz,
    • Kenji Kawaguchi,
    • and Mile Šikić
    Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
    ...the ones that are previously traversed and are thus discarded in the next iteration of the decoding algorithm.Since our methodology is optimized for haploid assembly, we evaluate GNNome on the homozygous human CHM13 (Nurk et al. 2022) derived from a hydatidiform mole, along with the inbred s of Mus...
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