Searching journal content for articles similar to Frazer et al. 13 (1): 1.

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  1. Method: Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
    • Xingyan Liu,
    • Qunlun Shen,
    • and Shihua Zhang
    Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
    ...insights into evolutionary and developmental biology (Marioni and Arendt 2017). Cross-species integration and comparison of scRNA-seq data sets allow us to explore, at single-cell resolution, the origins of cellular diversity and evolutionary mechanisms that shape cellular form and function (Marioni...
  2. Method: Cross-species analysis of enhancer logic using deep learning
    • Liesbeth Minnoye,
    • Ibrahim Ihsan Taskiran,
    • David Mauduit,
    • Maurizio Fazio,
    • Linde Van Aerschot,
    • Gert Hulselmans,
    • Valerie Christiaens,
    • Samira Makhzami,
    • Monika Seltenhammer,
    • Panagiotis Karras,
    • Aline Primot,
    • Edouard Cadieu,
    • Ellen van Rooijen,
    • Jean-Christophe Marine,
    • Giorgia Egidy,
    • Ghanem-Elias Ghanem,
    • Leonard Zon,
    • Jasper Wouters,
    • and Stein Aerts
    Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
    ...identity. A better understanding of how enhancers work will improve the interpretation of noncoding variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable...
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  3. Resource: Improved exome prioritization of disease genes through cross-species phenotype comparison
    • Peter N. Robinson,
    • Sebastian Köhler,
    • Anika Oellrich,
    • Sanger Mouse Genetics Project,
    • Kai Wang,
    • Christopher J. Mungall,
    • Suzanna E. Lewis,
    • Nicole Washington,
    • Sebastian Bauer,
    • Dominik Seelow,
    • Peter Krawitz,
    • Christian Gilissen,
    • Melissa Haendel,
    • and Damian Smedley
    Genome Res. February 2014 24: 340-348; Published in Advance October 25, 2013, doi:10.1101/gr.160325.113
    ...Damian Bauer, S Dominik, Seelow D Smedley genome;gr.160325.113 1088-9051 10.1101/gr.160325.113 Improved exome prioritization of disease genes through cross-species phenotype comparison Resource Improved exome prioritization of disease genes through cross-species phenotype comparison Peter N. Robinson,1...
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  4. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...species-specific modeling with ensemble deep learning architectures to systematically optimize feature encoding schemes. Evaluated across six species, EnDeep4mC demonstrates commendable prediction performance and significantly outperforms current state-of-the-art predictors. Cross-species validation...
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  5. Methods: Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
    • Yao-Ting Huang,
    • Feng-Chi Chen,
    • Chiuan-Jung Chen,
    • Hsin-Liang Chen,
    • and Trees-Juen Chuang
    Genome Res. July 2008 18: 1163-1170; Published in Advance March 27, 2008, doi:10.1101/gr.075556.107
    ...Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons Yao-Ting Huang 1 , 2 , Feng-Chi Chen 3 , 4 , 5 , Chiuan-Jung Chen 1 , Hsin-Liang Chen 1 , and Trees...
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  6. Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
    • Qunlun Shen,
    • Shuqin Zhang,
    • and Shihua Zhang
    Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
    .... To this end, we present a cross–data set cell type annotation methodology with a universal reference data and method selection strategy (CAMUS) to achieve highly accurate and efficient annotations. We demonstrate the advantages of CAMUS by conducting comprehensive analyses on 672 pairs of cross-species sc...
  7. Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
    • Qinhu Zhang,
    • Siguo Wang,
    • Zhipeng Li,
    • Wenzheng Bao,
    • Wenjian Liu,
    • and De-Shuang Huang
    Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
    ...trained on K562 data to predict GM12878 data. (C) The cross-species predictive performance of ScPGE, where K562→MEL indicates using a model trained on K562 data (Human) to predict MEL data (Mouse).Due to the generalization of the patterns across cells or species (Supplemental Fig. S7), we applied Sc...
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  8. Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
    • Marina Athanasouli,
    • Tobias Loschko,
    • and Christian Rödelsperger
    Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
    ...as worms can be grown on monoxenic cultures. Here, we present three different types of resources that may assist future research of cross-species interactions in the nematode Pristionchus pacificus and also in other organisms. First, by sequencing the s of 84 Pristionchus-associated bacteria, we establish...
  9. 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
    ...with ALPINE (all with the human-associated signatures). Among these are four mitochondrial genes (MT-CO2, MT-CO3, MT-ATP6, MT-ND3) that are the top-ranked genes by both methods. Although no cross-species comparison has been conducted on these genes, one study indicates that these mitochondrial genes play...
  10. Research: Widespread natural selection on metabolite levels in humans
    • Yanina Timasheva,
    • Kaido Lepik,
    • Orsolya Liska,
    • Balázs Papp,
    • and Zoltán Kutalik
    Genome Res. August 2024 34: 1121-1129; Published in Advance August 16, 2024, doi:10.1101/gr.278756.123
    ...concentrations for individual metabolites based on cross-species comparisons (Liska et al. 2023). In brief, this metabolite conservation score is based on the Brownian motion model of trait evolution. The rate parameter of the Brownian motion model provides a simple and robust measure of the effective rate...
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