Searching journal content for articles similar to Lai 11 (6): 927.

Displaying results 1-10 of 25
For checked items
  1. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ...nucleotide polymorphisms (SNPs).View larger version: In this window In a new window Figure 1. Methods to detect -wide 5mC. DNAm can be detected through enrichment, bisulfite conversion, enzymatic modification, or single-molecule approaches. (A) Enrichment methods use restriction enzymes...
    OPEN ACCESS ARTICLE
  2. RESOURCE: PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
    • Ken Chen,
    • Michael D. McLellan,
    • Li Ding,
    • Michael C. Wendl,
    • Yumi Kasai,
    • Richard K. Wilson,
    • and Elaine R. Mardis
    Genome Res. May 2007 17: 659-666; Published in Advance April 6, 2007, doi:10.1101/gr.6151507
    ...continues to pose difficult challenges. In this paper, we present PolyScan, an algorithm and software implementation designed to provide de novo heterozygous indel detection and improved SNP identification in the context of high-throughput medical resequencing. Tests on a human diploid PCR-based sequence...
  3. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...associations. Tools such as ANNOVAR (Wang et al. 2010), SnpEff (Cingolani et al. 2012), and Ensembl Variant Effect Predictor (VEP; Hunt et al. 2022) are commonly used, enabling researchers to systematically annotate variants with known functional effects or potential impacts on genes and regulatory elements...
  4. 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
    ...sizes (CESs) compared with dbSNP polymorphisms (Supplemental Figs. 15, 16; Supplemental Note 5; Supplemental Code 1). In addition, FIE genes were depleted in germline missense mutations (P = 0.002, Welch's t-test) compared with genes without FIEs, indicating negative selection for germline missense...
    OPEN ACCESS ARTICLE
  5. Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
    • Jonas Meisner and
    • Anders Albrechtsen
    Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
    ...-hot encoded) and are the data of the ath haplotype of individual i in window w with L being the number of SNPs. Here describes the learned mean latent encoding of a given haplotype cluster, y, in the generative model, and is the learned mean reconstruction of the mean latent encoding.Ancestry proportions...
  6. Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
    • William J. Murphy and
    • Andrew J. Harris
    Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
    ...) endangered, (NT) near threatened, (*) unpublished. Images by C. Buell.Detailed phylogenomic analyses using whole- SNP and sequence data have clarified that rampant ancient gene flow is likely the primary cause underpinning the previous challenges in resolving the cat family tree (Fig. 1). Traces of past...
  7. Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
    • Reuben M. Buckley and
    • Elaine A. Ostrander
    Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
    ...sampling of these populations, along with adequate phenotyping, will likely lead to new genotype–phenotype discoveries (Surbakti et al. 2020).Interpretation of variant effectsIn trait mapping, the single nucleotide polymorphisms (SNPs) with the strongest phenotype association are often within the noncoding...
    OPEN ACCESS ARTICLE
  8. Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
    • Susan M. Hiatt,
    • James M.J. Lawlor,
    • Lori H. Handley,
    • Donald R. Latner,
    • Zachary T. Bonnstetter,
    • Candice R. Finnila,
    • Michelle L. Thompson,
    • Lori Beth Boston,
    • Melissa Williams,
    • Ivan Rodriguez Nunez,
    • Jerry Jenkins,
    • Whitley V. Kelley,
    • E. Martina Bebin,
    • Michael A. Lopez,
    • Anna C.E. Hurst,
    • Bruce R. Korf,
    • Jeremy Schmutz,
    • Jane Grimwood,
    • and Gregory M. Cooper
    Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
    ...Biosciences “HiFi” technology on 96 short-read-negative probands with rare diseases that were suspected to be genetic. We generated hg38-aligned variants and de novo phased assemblies, and subsequently annotated, filtered, and curated variants using clinical standards. New disease-relevant or potentially...
  9. Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
    • Bin Zhao,
    • John A. Lees,
    • Hongjin Wu,
    • Chao Yang,
    • and Daniel Falush
    Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
    ...a profile of k-mer similarities which is distinct from that due to SNPs, making it 79 possible to estimate distances for core and accessory separately by fitting the 80 pattern of distance profiles across multiple k-mer lengths. 81 82 Two machine learning algorithms, Bayesian Gaussian Mixture Model (BGMM...
    ACCEPTED MANUSCRIPT
  10. Perspective: Biological data sciences in genome research
    • Michael C. Schatz
    Genome Res. October 2015 25: 1417-1422; doi:10.1101/gr.191684.115
    ...). Indeed, although a typical person has more SNPs than any other class of mutations, the total number of bases that are mutated, and hence the largest aspect of genetic diversity in a person, is mostly due to copy number and other structural variations (Sebat et al. 2004; Zarrei et al. 2015). Finally...
    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