Searching journal content for articles similar to Iovino et al. 34 (9): 1434.

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  1. Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
    • Zhezheng Song,
    • Tasfia Zahin,
    • Xiang Li,
    • and Mingfu Shao
    Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
    ...%) and in Supplemental Figure S53, A–C, through Supplemental Figure S55, A–C (for an error rate of 20%). EquiRep is able to make better or similar predictions in all cases, indicating that its algorithm is the least affected by the presence of embedding k-mers within repeat units.Evaluation using human satellite DNA...
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  2. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.A recent advancement in cancer...
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  3. Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
    • Qian Qin,
    • Victoria Popic,
    • Kirsty Wienand,
    • Houlin Yu,
    • Emily White,
    • Akanksha Khorgade,
    • Asa Shin,
    • Christophe Georgescu,
    • Catarina D. Campbell,
    • Arthur Dondi,
    • Niko Beerenwinkel,
    • Francisca Vazquez,
    • Aziz M. Al'Khafaji,
    • and Brian J. Haas
    Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
    ...transcript breakpoint at each gene for each method. Similar to the fusion gene ordering, only CTAT-LR-Fusion and JAFFAL demonstrated highly accurate fusion transcript breakpoint detection (ignoring gene ordering during breakpoint evaluation). While FusionSeeker, LongGF, and pbfusion demonstrated little...
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  4. Method: Leveraging protein language models for accurate multiple sequence alignments
    • Claire D. McWhite,
    • Isabel Armour-Garb,
    • and Mona Singh
    Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
    ...of the sequences and CPU memory. The time to produce an alignment depends on the number of sequences in the alignment and on the number of iterations required to place all amino acids (Supplemental Fig. 3A). After embedding, an alignment of 20 sequences when run on an NVIDIA A100 GPU (for similarity searches...
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  5. Method: Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation
    • Yang Zhou,
    • Qiongyu Sheng,
    • Jing Qi,
    • Jiao Hua,
    • Bo Yang,
    • Lei Wan,
    • and Shuilin Jin
    Genome Res. May 2023 33: 750-762; Published in Advance June 12, 2023, doi:10.1101/gr.277522.122
    ...single-cell integration (scInt), an integration method based on accurate, robust cell–cell similarity construction and unified contrastive biological variation learning from multiple scRNA-seq data sets. scInt provides a flexible and effective approach to transfer knowledge from the already integrated...
  6. Method: Accurate and efficient detection of gene fusions from RNA sequencing data
    • Sebastian Uhrig,
    • Julia Ellermann,
    • Tatjana Walther,
    • Pauline Burkhardt,
    • Martina Fröhlich,
    • Barbara Hutter,
    • Umut H. Toprak,
    • Olaf Neumann,
    • Albrecht Stenzinger,
    • Claudia Scholl,
    • Stefan Fröhling,
    • and Benedikt Brors
    Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
    ...-guided precision oncology is to search for evidence of gene fusions in RNA sequencing (RNA-seq) data.Although a variety of computational tools for the detection of gene fusions have been developed over the years, there is still no gold standard. The reliable prediction of gene fusions from short-read RNA-seq has...
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  7. 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
    ...for their ability to support accurate cell-type clustering and will revisit them with further evaluations in the batch effect removal section below. We note that scDisInFact provides functionality to reconstruct batch-removed counts whereas scParser does not, so we compare to both scDisInFact embeddings and counts...
  8. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...interpretationmodels can intelligently evaluate the combined search spaces to generate local and global interpretations. The Shapley additive explanations (SHAP) method (Lundberg et al. 2020; Novakovsky et al. 2023) has emerged as a prominent tool for explaining multiple biological features. However, it has not been...
  9. Method: Parente2: a fast and accurate method for detecting identity by descent
    • Jesse M. Rodriguez,
    • Sivan Bercovici,
    • Lin Huang,
    • Roy Frostig,
    • and Serafim Batzoglou
    Genome Res. February 2015 25: 280-289; Published in Advance October 1, 2014, doi:10.1101/gr.173641.114
    ...discovery rate can also scale quadratically. To enable accurate and efficient large-scale IBD detection, we present Parente2, a novel method for detecting IBD segments. Parente2 is based on an embedded log-likelihood ratio and uses a model that accounts for linkage disequilibrium by explicitly modeling...
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  10. Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
    • Han Shu,
    • Jing Chen,
    • Chang Xu,
    • Jialu Hu,
    • Yongtian Wang,
    • Jiajie Peng,
    • Qinghua Jiang,
    • Xuequn Shang,
    • and Tao Wang
    Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
    ...methods have been proposed to analyze individual slices. A critical step in these analyses is the identification of spatial domains, which involves clustering spots with similar molecular expression profiles and spatial locations in an unsupervised manner. Accurate integration of molecular expression...
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