Searching journal content for articles similar to Wang et al. 17 (11): 1665.

Displaying results 1-10 of 6138
For checked items
  1. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...High-resolution, genotype-free mapping of genetic 1 variation with CRI-SPA-Map 2 3 Sheila Lutz*, Megan Lawler†, Samuel Amidon†, Frank W. Albert* 4 Department of Genetics, Cell Biology, & Development, 5 University of Minnesota, 6 6-160 Jackson Hall, 321 Church St SE 7 Minneapolis, MN 55455, USA 8...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  2. Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
    • Aayush Grover,
    • Till Muser,
    • Liine Kasak,
    • Lin Zhang,
    • Ekaterina Krymova,
    • and Valentina Boeva
    Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
    ...by the Genome Data Commons (GDC) Data Portal (Grossman et al. 2016). The choice of these patients was made due to the availability of the data on their somatic mutations and single-nucleotide polymorphisms (SNPs) in the International Cancer Genome Consortium (ICGC) and GDC data portals, respectively (Grossman...
    OPEN ACCESS ARTICLE
  3. Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
    • Shingo Kato,
    • Sachiko Masuda,
    • Arisa Shibata,
    • Takashi Itoh,
    • Mitsuo Sakamoto,
    • Ken Shirasu,
    • and Moriya Ohkuma
    Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
    ...- sequencing is now requested for describing novel prokaryotic species and designating their type strains, which serve as representative and well-characterized strains of the species. Indeed, the number of sequenced prokaryotic s has been rapidly increasing. However, a considerable number of isolated strains...
  4. 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
    ..., and contrast several metrics (including the LD structure and the SNP entropy) of the simulated sequences with that of real sequences as a genotype simulation quality assessment.MethodsVariational autoencodersRepresentation learning, also known as feature learning, attempts to recover a compact set of so...
    OPEN ACCESS ARTICLE
  5. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...genotypes proximate SNVs, whose locations are extracted from a user-provided VCF catalog file from, for example, dbSNP (Sherry et al. 2001). For diploid alleles, depending on what SNV data are present, STRkit either uses a Gaussian mixture model (GMM) allele-calling approach with copy numbers, segregates...
  6. Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
    • Xue Dong,
    • Mengzhu Hu,
    • Xiaonan Cui,
    • Wenjian Zhou,
    • Jingtao Cai,
    • Guangyao Mao,
    • and Weiyang Shi
    Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
    ...regulation layers and the complex mechanisms controlling cellular function.Whereas PCL-seq achieves high-resolution spatial profiling within individual ROIs, broader applications are currently constrained by technical limitations in throughput and ROI discrimination. The moderate ligation efficiency (∼60...
  7. Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
    • Kelley Paskov,
    • Brianna Chrisman,
    • Nathaniel Stockham,
    • Peter Yigitcan Washington,
    • Kaitlyn Dunlap,
    • Jae-Yoon Jung,
    • and Dennis P. Wall
    Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
    ...crossovers when applied to microarray data (Martin et al. 2015). WGS, with its much higher error rate, likely exacerbates this problem.Hidden Markov models (HMMs) have been used for decades to detect inheritance patterns and crossovers in family sequencing data (Lander and Green 1987; Kruglyak et al. 1996...
  8. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...14 putative pathogenic SNVs and indels, uncovered newly identified SINE-R/VNTR/Alu elements affecting the APC gene in two familial adenomatous polyposis patients, and demonstrated the utility of off-target reads from adaptive sampling for SNP genotyping, enabling polygenic risk score calculations...
    OPEN ACCESS ARTICLE
  9. Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
    • Øystein Monsen,
    • Lars Grønvold,
    • Alex Datsomor,
    • Thomas Harvey,
    • James Kijas,
    • Alexander Suh,
    • Torgeir R. Hvidsten,
    • and Simen Rød Sandve
    Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
    ...TE annotation from Lien et al. (2016). The total TE annotation covered 51.92% of the . Consistent with previous findings (Goodier and Davidson 1994; Lien et al. 2016), the dominating TE group was DNA transposons from the Tc1-Mariner superfamily with more than 655,000 copies, covering 327 million base...
  10. Research: Evidence for selfing in a vertebrate from whole-genome sequencing
    • Astrid Böhne,
    • Zeynep Oğuzhan,
    • Ioannis Chrysostomakis,
    • Simon Vitt,
    • Denis Meuthen,
    • Sebastian Martin,
    • Sandra Kukowka,
    • and Timo Thünken
    Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
    ...per chromosome) (Palaiokostas et al. 2013; Feulner et al. 2018). However, individual interspersed sites did not show the expected genotype given their neighboring single-nucleotide polymorphisms (SNPs) (i.e., isolated homozygous sites in a block of heterozygous sites and vice versa). This would...
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