Searching journal content for articles similar to Shemirani et al. 36 (3): 534.

Displaying results 1-10 of 6334
For checked items
  1. Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
    • Wenhai Zhang,
    • Yuansheng Liu,
    • Guangyi Li,
    • Jialu Xu,
    • Enlian Chen,
    • Alexander Schönhuth,
    • and Xiao Luo
    Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
    ...in Paten et al. (2017). In the meantime, variation graphs have proven effective in addressing a wide range of computational genomics challenges. Examples are primary read mapping and variant calling (Garrison et al. 2018; Martiniano et al. 2020; Sirén et al. 2021), haplotype modeling (Rosen et al. 2017...
    OPEN ACCESS ARTICLE
  2. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ..., Stanford University School of Engineering, Stanford, California 94305, USA Corresponding author: geleta@berkeley.eduAbstractModern biobanks are providing numerous high-resolution genomic sequences of diverse populations. In order to account for diverse and admixed populations, new algorithmic tools...
    OPEN ACCESS ARTICLE
  3. Method: Haplotype-aware sequence alignment to pangenome graphs
    • Ghanshyam Chandra,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
    ...in the population (Singh et al. 2022). A variety of methods have been developed that use pan graphs for common applications, including genotyping, variant calling, haplotype reconstruction, metagenomic read classification, etc. (Eizenga et al. 2020). Efforts toward using pan graphs have been further catalyzed...
  4. Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
    • Junhai Qi,
    • Zhidong Yang,
    • Ting Yu,
    • and Guojun Li
    Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
    ..., this optimized efficiency unlocks the potential for population-level158 studies of alpha satellite regions, which involves processing thousands of s. Furthermore, our method facilitates159 the integration of these complex regions into pan graphs, a task that requires both accuracy and computational160 efficiency...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  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. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...of genetic architectures. Notable differences in the rate of LD decay were observed among the six populations (Supplemental Fig. S1). The heritability of the 20 traits ranged from 0.19 to 0.87 (Fig. 1B), and the additive and epistatic variance components exhibited significant differences (Supplemental Fig. S...
  6. Method: Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
    • Juri Kuronen,
    • Samuel T. Horsfield,
    • Anna K. Pöntinen,
    • Sudaraka Mallawaarachchi,
    • Sergio Arredondo-Alonso,
    • Harry Thorpe,
    • Rebecca A. Gladstone,
    • Rob J.L. Willems,
    • Stephen D. Bentley,
    • Nicholas J. Croucher,
    • Johan Pensar,
    • John A. Lees,
    • Gerry Tonkin-Hill,
    • and Jukka Corander
    Genome Res. July 2024 34: 1081-1088; Published in Advance August 12, 2024, doi:10.1101/gr.278485.123
    ....Use of de Bruijn graphs in assembly, reference representation, and variant calling has become commonplace in population genomics, in particular for bacteria (Bankevich et al. 2012; Holley and Melsted 2020; Colquhoun et al. 2021). A colored and compacted de Bruijn graph (cdBG) offers a powerful...
    OPEN ACCESS ARTICLE
  7. Method: Genetics-driven risk predictions leveraging the Mendelian randomization framework
    • Daniel Sens,
    • Liubov Shilova,
    • Ludwig Gräf,
    • Maria Grebenshchikova,
    • Bjoern M. Eskofier,
    • and Francesco Paolo Casale
    Genome Res. September 2024 34: 1276-1285; Published in Advance September 27, 2024, doi:10.1101/gr.279252.124
    ...and BRCA2 founder variants in a diverse population-based biobank. Genome Med 12: 2. doi:10.1186/s13073-019-0691-1 ↵Alfaro-Almagro F, Jenkinson M, Bangerter NK, Andersson JLR, Griffanti L, Douaud G, Sotiropoulos SN, Jbabdi S, Hernandez-Fernandez M, Vallee E, et al. 2018. Image processing and Quality Control...
    OPEN ACCESS ARTICLE
  8. 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
    ...be overlooked in traditional pairwise comparative analyses relying on a single reference per population or species.The nematode species pair Caenorhabditis briggsae and Caenorhabditis nigoni has emerged as a powerful model for dissecting the genetic and genomic bases of speciation. Although both species...
  9. Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
    • Nathan LaPierre,
    • Boyang Fu,
    • Steven Turnbull,
    • Eleazar Eskin,
    • and Sriram Sankararaman
    Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
    ..., as well as the confounding effects of population stratification and horizontal pleiotropy. Here, we show that family data can be leveraged to design MR tests that are provably robust to confounding from population stratification, assortative mating, and dynastic effects. We show in simulations that our...
  10. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...-frequency variants in heterogeneous populations. Here, we review currently used and recently developed targeted sequencing strategies that leverage existing long-read technologies to increase the resolution with which we can look at nucleic acids in a variety of biological contexts.There are several applications...
    OPEN ACCESS ARTICLE
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research