Searching journal content for articles similar to Ulrich and Renard 34 (6): 914.

Displaying results 1-10 of 5247
For checked items
  1. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ...in expectation under a random model we propose here. We implemented these ideas in an open-source tool called Cliffy that performs efficient taxonomic classification of sequencing reads with respect to a compressed taxonomic index. When applied to simulated 16S rRNA reads, Cliffy's read-level accuracy is higher...
  2. Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
    • Rashid Al-Abri and
    • Gamze Gürsoy
    Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
    ...,146 TR loci from the TRGT catalog (see Methods) and used ScatTR to estimate the same loci from short-read data. To evaluate performance, we classified each locus as expanded or not based on whether its estimated length exceeded the fragment length. We then compared these classifications between Scat...
    OPEN ACCESS ARTICLE
  3. 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
    ..., which may impact STRkit's modeling of candidate repeat tract sequences or result in reads being filtered out to a greater degree versus other tools; future work could implement alternate allele clustering systems that do not assume an entirely tandem repeat sequence structure.Of the five callers, STRkit...
  4. 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
    ...'s Nanonet basecaller and sequence-based alignment using LAST (Kiełbasa et al. 2011). This approach was faster, scalable, flexible, and efficient in filtering out unwanted reads. RUBRIC worked well for background depletion, but did not achieve significant absolute target enrichment...
    OPEN ACCESS ARTICLE
  5. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ...paired-end).Raw FASTQ reads were mapped onto hg19/GRCh37 build using BWA aligner (v0.7.17) aligner (Li and Durbin 2009). Aligned fragments were filtered for mapping quality greater than 30 (MAPQ > 30) using SAMtools (v1.14) (Danecek et al. 2021). BAM files were converted into BEDPE files, and fragments...
  6. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, “Exon Nomenclature And Classification of Transcripts” (ENACT). This centralizes exonic loci such that protein sequence...
  7. Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
    • Fangyuan Yang,
    • Li-Jun Cao,
    • Petr Nguyen,
    • Zhong-Zheng Ma,
    • Jin-Cui Chen,
    • Wei Song,
    • and Shu-Jun Wei
    Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
    ...∼124 million years ago, accompanied by an SA fusion between the Merian elements M(20 + 17) and MZ. In contrast to partial autosomal fusions, the fused neo-Z Chromosome developed a hierarchical architecture, in which the three elements exhibit heterogeneous sequence features and evolutionary patterns...
  8. Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
    • Marcus W. Fedarko,
    • Mikhail Kolmogorov,
    • and Pavel A. Pevzner
    Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
    ...Flye output, edge sequences) assembled from these reads. strainFlye can also optionally take as input an assembly graph indicating contigs’ adjacencies for use in adjusting one of the alignment filtering steps (Supplemental Material, “Read alignment”).View larger version: In this window In a new window Figure...
  9. Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    ...) Overview of probabilistic MMR allocation by proximal uniquely mapped read (UMR) count. (C) Overview of the Allo algorithm combining UMR counts and image classification of read distribution.Allo's neural network takes the form of a CNN that is trained on images of UMR distributions at peaks (Supplemental...
  10. Method: Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
    • Netanya Keil,
    • Carolina Monzó,
    • Lauren McIntyre,
    • and Ana Conesa
    Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124
    ...is described in Figure 3A. The annotation category for all expressed genes (default: number of reads in gene [R] > 100) is provided in the gene_classification.csv file.View larger version: In this window In a new window Figure 3. Evaluation of WTC11 PacBio samples for under-annotated genes. (A) Decision tree...
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. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research