Search Results

A comprehensive benchmarking study on computational tools for cross-omics label transfer from single-cell RNA to ATAC data.

• Authors : Wang Y; Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06511, United States.; Zhao H

Subjects: Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods ; Computational Biology*/Computational Biology*/Computational Biology*/methods ; Genomics*/Genomics*/Genomics*/methods

• Source: G3 (Bethesda, Md.) [G3 (Bethesda)] 2026 Apr 01; Vol. 16 (4).Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN:

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EasyGeSe - a resource for benchmarking genomic prediction methods.

• Authors : Quesada-Traver C; Ariza-Suarez D; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland.

Subjects: Genomics*/Genomics*/Genomics*/methods ; Benchmarking* ; Software*

• Source: BMC genomics [BMC Genomics] 2025 Oct 24; Vol. 26 (1), pp. 953. Date of Electronic Publication: 2025 Oct 24.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Benchmarking interpretability of deep learning for predictive genomics: Recall, precision, and variability of feature attribution.

• Authors : Reynolds J; School of Computer Science, Gallogly College of Engineering, University of Oklahoma, Norman, Oklahoma, United States of America.; Pan C

Subjects: Genomics*/Genomics*/Genomics*/methods ; Deep Learning*; Multifactorial Inheritance/Multifactorial Inheritance/Multifactorial Inheritance/genetics

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Dec 05; Vol. 21 (12), pp. e1013784. Date of Electronic Publication: 2025 Dec 05 (Print Publication: 2025).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Benchmarking Nanopore Sequencing for CLN2 (TPP1) Mutation Detection: Integrating Rapid Genomics and Orthogonal Validation for Precision Diagnostics.

• Authors : Teker B; Institute of Health Sciences, Istanbul University, 34452 Fatih, Türkiye.; Akan G

Subjects: Neuronal Ceroid-Lipofuscinoses*/Neuronal Ceroid-Lipofuscinoses*/Neuronal Ceroid-Lipofuscinoses*/genetics ; Neuronal Ceroid-Lipofuscinoses*/Neuronal Ceroid-Lipofuscinoses*/Neuronal Ceroid-Lipofuscinoses*/diagnosis ; Dipeptidyl-Peptidases and Tripeptidyl-Peptidases*/Dipeptidyl-Peptidases and Tripeptidyl-Peptidases*/Dipeptidyl-Peptidases and Tripeptidyl-Peptidases*/genetics Ceroid Lipofuscinosis, Neuronal, 2

• Source: International journal of molecular sciences [Int J Mol Sci] 2025 May 23; Vol. 26 (11). Date of Electronic Publication: 2025 May 23.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets.

• Authors : Song M; Research Center for Life Sciences Computing, Zhejiang Lab, Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121, China.; School of Life Science and Technology, ShanghaiTech University, Haike Road, Pudong New District, Shanghai 201210, China.

Subjects: Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods ; Neoplasms*/Neoplasms*/Neoplasms*/genetics ; Computational Biology*/Computational Biology*/Computational Biology*/methods

• Source: Briefings in bioinformatics [Brief Bioinform] 2025 Mar 04; Vol. 26 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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Benchmarking ensemble machine learning algorithms for multi-class, multi-omics data integration in clinical outcome prediction.

• Authors : Spooner A; School of Computer Science and Engineering, University of New South Wales, High St, Kensington, NSW 2052, Australia.; Moridani MK

Subjects: Genomics*/Genomics*/Genomics*/methods ; Machine Learning* ; Algorithms*

• Source: Briefings in bioinformatics [Brief Bioinform] 2025 Mar 04; Vol. 26 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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BVSim: A benchmarking variation simulator mimicking human variation spectrum.

• Authors : Luo Y; Department of Statistics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong 999077, China.; Zhang Z

Subjects: Genomics*/Genomics*/Genomics*/methods ; Computational Biology*/Computational Biology*/Computational Biology*/methods ; Software*

• Source: GigaScience [Gigascience] 2025 Jan 06; Vol. 14.Publisher: Oxford University Press Country of Publication: United States NLM ID: 101596872 Publication Model: Print Cited Medium: Internet ISSN:

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A harmonized benchmarking framework for implementation-aware evaluation of 46 polygenic risk score tools across binary and continuous phenotypes

• Authors : Muneeb, Muhammad; Ascher, David B.

Subjects: Genomics

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GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding

• Authors : Long, Weicai; Hou, Yusen; Feng, Junning

Subjects: Genomics; Computation and Language

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Benchmarking Heritability Estimation Strategies Across 86 Configurations and Their Downstream Effect on Polygenic Risk Score Performance

• Authors : Muneeb, Muhammad; Ascher, David B.

Subjects: Genomics; Methodology

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