Searching journal content for articles similar to Liu et al. 11 (10): 1716.

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  1. Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
    • Enzo Battistella,
    • Anant Maheshwari,
    • Barış Ekim,
    • Bonnie Berger,
    • and Victoria Popic
    Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
    ...-telangiectasia with double missense and in frame splice mutations. Am J Med Genet A 126A: 272–277. doi:10.1002/ajmg.a.20601 ↵Douglas JA, Boehnke M, Gillanders E, Trent JM, Gruber SB. 2001. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat Genet 28: 361–364. doi:10...
  2. Method: Calling amplified haplotypes in next generation tumor sequence data
    • Ninad Dewal,
    • Yang Hu,
    • Matthew L. Freedman,
    • Thomas LaFramboise,
    • and Itsik Pe'er
    Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
    ...heterozygous site in isolation; however, this ignores available valuable linkage information across sites. We, therefore, present a novel hidden Markov model-based method—Haplotype Amplification in Tumor Sequences (HATS)—that analyzes tumor and normal sequence data, along with training data for phasing...
  3. Review: Recent advances in methods to characterize archaic introgression in modern humans
    • David Peede,
    • Mayra M. Bañuelos,
    • Jazeps Medina Tretmanis,
    • Miriam Miyagi,
    • and Emilia Huerta-Sánchez
    Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
    ...with sufficiently large blocks to account for linkage disequilibrium (LD; Green et al. 2010; Durand et al. 2011; Patterson et al. 2012). Importantly, significant values are suggestive of introgression, as alternative demographic scenarios (e.g., ancestral population structure) can mimic these signals (Green et al...
    OPEN ACCESS ARTICLE
  4. LETTER: Haplotype and Linkage Disequilibrium Architecture for Human Cancer-Associated Genes
    • Penelope E. Bonnen,
    • Peggy J. Wang,
    • Marek Kimmel,
    • Ranajit Chakraborty,
    • and David L. Nelson
    Genome Res. December 1, 2002 12: 1846-1853; Published in Advance November 12, 2002, doi:10.1101/gr.483802
    ...Haplotype and Linkage Disequilibrium Architecture for Human Cancer-Associated Genes Penelope E. Bonnen 1 , Peggy J. Wang 1 , Marek Kimmel 2 , Ranajit Chakraborty 3 , and David L. Nelson 1 , 4 1Department of Molecular...
  5. LETTER: Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms
    • Xin Lu,
    • Tianhua Niu,
    • and Jun S. Liu
    Genome Res. September 2003 13: 2112-2117; doi:10.1101/gr.586803
    ...Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms Xin Lu 1 , Tianhua Niu 2 , and Jun S. Liu 1 , 3 1 Department of Statistics, Harvard University, Cambridge, Massachusetts 02138, USA 2...
  6. 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
    ...applications of ML in GEBV show promise, its comparative 66 performance with traditional methods remains contentious. Biologically, the prediction 67 accuracy of GS is linked to factors such as linkage disequilibrium (LD), heritability of traits 68 (Zhang et al. 2019), sample size (Daetwyler et al. 2010...
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  7. Method: Fast inference of genetic recombination rates in biobank scale data
    • Ardalan Naseri,
    • William Yue,
    • Shaojie Zhang,
    • and Degui Zhi
    Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
    ..., are correlated with the current genetic map because crossovers could have introduced them in the distant past. An early method based on population samples, LDhat, uses linkage disequilibrium (LD) patterns for fitting a Bayesian model via MCMC (McVean et al. 2004). Although the results of LDhat are noteworthy...
  8. 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
    ...variants into causal and noncausal, referring to variants neither truly associated with the phenotype nor in linkage disequilibrium (LD) with causal variants. We assumed that any systematic differences in calculated P-values or effect sizes of noncausal variants in between the two models are likely owing...
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  9. Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
    • Diana Lobo,
    • Hernán E. Morales,
    • Cock Van Oosterhout,
    • José Vicente López-Bao,
    • Pedro Silva,
    • Luis Llaneza,
    • Carolina Pacheco,
    • Diana Castro,
    • Germán Hernández-Alonso,
    • George Pacheco,
    • John Archer,
    • M. Thomas P. Gilbert,
    • Nuno Ferrand,
    • and Raquel Godinho
    Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
    ...the decay of linkage disequilibrium (LD) and the number of accumulated mutations in the introgressed 100 kb haplotype and flanking regions. Average TMRCA estimates ranged between about 1360 (861–1857min-max) and about 670 (375–1072min-max) generations ago, assuming local or the chromosome-wide average...
    OPEN ACCESS ARTICLE
  10. RECOMB Special/Methods: Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information
    • Eleazar Eskin
    Genome Res. April 2008 18: 653-660; Published in Advance March 18, 2008, doi:10.1101/gr.072785.107
    ...Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information Eleazar Eskin 1 Departments of Computer Science and Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA...
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