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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 foundation cell models for post-perturbation RNA-seq prediction

• Authors : Gerold Csendes; Gema Sanz; Kristóf Z. Szalay

Subjects: Sequence Analysis, RNA; Research; Gene Expression Profiling

• Source: BMC GenomicsBMC Genomics, Vol 26, Iss 1, Pp 1-9 (2025)

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Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants

• Authors : Yoshinori Fukasawa

Subjects: Long-read sequencing; Variant calling; Polyploidy

• Source: BMC Genomics, Vol 27, Iss 1, Pp 1-15 (2026)

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Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.

• Authors : Maruzani R; Department of Health Data Science, Institute of Population Health, University of Liverpool, Waterhouse Building, Block F, Brownlow Street, Liverpool, L69 3GF, UK. .; Brierley L

Subjects: Circulating Tumor DNA*/Circulating Tumor DNA*/Circulating Tumor DNA*/genetics ; Circulating Tumor DNA*/Circulating Tumor DNA*/Circulating Tumor DNA*/blood ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods

• Source: BMC genomics [BMC Genomics] 2024 Sep 03; Vol. 25 (1), pp. 827. Date of Electronic Publication: 2024 Sep 03.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates.

• Authors : Luan T; Department of Computer Science, University of Maryland, College Park, MD, 20742, USA.; Commichaux S

Subjects: Benchmarking* ; Disease Outbreaks* ; Genome, Bacterial*

• Source: BMC genomics [BMC Genomics] 2024 Jul 08; Vol. 25 (1), pp. 679. Date of Electronic Publication: 2024 Jul 08.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Enhancing RNA-seq bias mitigation with the Gaussian self-benchmarking framework: towards unbiased sequencing data

• Authors : Qiang Su; Yi Long; Deming Gou

Subjects: RNA sequencing; Bias mitigation; Gaussian self-benchmarking (GSB)

• Source: BMC Genomics, Vol 25, Iss 1, Pp 1-19 (2024)

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From benchmarking alignment of genome assemblies to IMGT annotation: the paradigm of the bovine Bos taurus T cell receptor (TRG) locus.

• Authors : Zhou, Hao^1,2 (AUTHOR); Jiko, Chimari³ (AUTHOR); Gerle, Christoph⁴ (AUTHOR)

• Source: BMC Genomics. 9/25/2025, Vol. 26 Issue 1, p1-13. 13p.

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Benchmarking datasets for assembly-based variant calling using high-fidelity long reads.

• Authors : Lee H; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea.; Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea.

Subjects: High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods ; Benchmarking*; Sequence Analysis, DNA/Sequence Analysis, DNA/Sequence Analysis, DNA/methods

• Source: BMC genomics [BMC Genomics] 2023 Mar 27; Vol. 24 (1), pp. 148. Date of Electronic Publication: 2023 Mar 27.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Benchmarking full-length transcript single cell mRNA sequencing protocols.

• Authors : Probst V; Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.; Simonyan A

Subjects: Benchmarking* ; Transcriptome*; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

• Source: BMC genomics [BMC Genomics] 2022 Dec 29; Vol. 23 (1), pp. 860. Date of Electronic Publication: 2022 Dec 29.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Benchmarking subcellular localization and variant tolerance predictors on membrane proteins

• Authors : Orioli, Tommaso, Author; Vihinen, Mauno, Author; Lund University, Faculty of Medicine, Department of Experimental Medical Science, Protein Bioinformatics, Lunds universitet, Medicinska fakulteten, Institutionen för experimentell medicinsk vetenskap, Proteinbioinformatik, Originator ...

Subjects: Natural Sciences; Biological Sciences; Naturvetenskap

• Source: BMC Genomics. 20(8)

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