Searching journal content for articles similar to Torres et al. 18 (1): 172.

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  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
    ...from the resulting read-to-reference sequence alignments.Existing tools can be categorized into three types. The first are marker-based methods, such as MetaPhlAn4 (Blanco-Míguez et al. 2023) and mOTUs2 (Milanese et al. 2019). These methods utilize a subset of marker genes, typically gene families...
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  2. Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
    • Li Song,
    • Gali Bai,
    • X. Shirley Liu,
    • Bo Li,
    • and Heng Li
    Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
    ...immunoglobulin-like receptor (KIR) genes and human leukocyte antigen (HLA) genes play important roles in innate and adaptive immunity. They are highly polymorphic and cannot be genotyped with standard variant calling pipelines. Compared with HLA genes, many KIR genes are similar to each other in sequences...
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  3. Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    • Wei-Hao Lee,
    • Lechuan Li,
    • Ruth Dannenfelser,
    • and Vicky Yao
    Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
    ...technical and nontechnical factors while simultaneously offering direct interpretability of condition-associated genes. Through simulations across four different scenarios, we demonstrate that ALPINE outperforms existing methods in both isolating the effect of different phenotypic conditions...
  4. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...and is expected to improve the interpretation of transcriptomic data in future genomic studies.RNA sequencing (RNA-seq) has become an essential tool for characterizing transcriptomes (Stark et al. 2019), enabling comprehensive profiling of gene expression, including tissue-specific patterns, disease...
  5. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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  6. Method: Sequence-based correction of barcode bias in massively parallel reporter assays
    • Dongwon Lee,
    • Ashish Kapoor,
    • Changhee Lee,
    • Michael Mudgett,
    • Michael A. Beer,
    • and Aravinda Chakravarti
    Genome Res. September 2021 31: 1638-1645; Published in Advance July 20, 2021, doi:10.1101/gr.268599.120
    ...upstream or downstream from a reporter gene tagged by unique DNA sequences. However, tag sequences may themselves affect reporter gene expression and lead to major potential biases in the measured cis-regulatory activity. Here, we present a sequence-based method for correcting tag-sequence-specific effects...
  7. 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
    ...private, recurrent, and founder variants. For example, a breast cancer study using nanopore sequencing precisely profiled fourteen variants, ranging from single-exon alterations to whole-gene changes (Dixon et al. 2023). They confirmed a 6126 bp tandem duplication in three samples, and reported a shared 1...
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  8. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    .... Today, bacterial isolate differentiation and outbreak investigation are mainly carried out using single-nucleotide polymorphism (SNP) analysis and gene-by-gene methods, including core multilocus sequence typing (cgMLST) schemes. These schemes are available on curated databases like BIGSdb-Pasteur, Pub...
  9. Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
    • Jennifer Hammelman,
    • Konstantin Krismer,
    • Budhaditya Banerjee,
    • David K. Gifford,
    • and Richard I. Sherwood
    Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
    ...factors to bind and activate previously inactive genes. Massively parallel reporter assays (MPRAs) (Inoue and Ahituv 2015; White 2015) have been developed to measure the change to gene expression from the action of promoters (Mogno et al. 2013; Grossman et al. 2017) or enhancers (Melnikov et al. 2012...
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  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
    ...-cell library may not recapitulate the diversity present in the population. The authors enriched and sequenced these regions via a method called Repertoire and Gene Expression by Sequencing (RAGE-seq). This method splits a full-length cDNA pool into two, where one half undergoes short-read expression profiling...
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