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442 Reviews — GigaScience — All Subjects

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Improved genome assembly of whale shark, the world's biggest fish: revealing "chromocline" in intragenomic heterogeneity
Kawaguchi, Y. W., Matsumoto, R., Kuraku, S.
10.1101/2025.09.06.674125 — Posted: 2025-09-10 — Discussion: 2026-02-24  GigaScience
Graph-Regularized Optimal Transport for Single-Cell Data Integration
Wang, Z., Zhan, Q., Shen, L.
10.1101/2024.10.30.621072 — Posted: 2024-11-02 — Discussion: 2026-02-24  GigaScience
Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs)
Gaio, D., Tackmann, J., Perez-Molphe-Montoya, E., Napflin, N., Patsch, D., Malfertheiner, L., von Mering, C.
10.1101/2025.04.24.650461 — Posted: 2025-04-27 — Discussion: 2026-02-24  GigaScience
Single-nucleus multiple-organ chromatin accessibility mapping in the rat
Li, R., Yuan, Y., Duan, S., Deng, Q., Ma, W., Liu, C., Gao, P., Lu, L., Liu, C.
10.1101/2024.11.11.622900 — Posted: 2024-11-11 — Discussion: 2026-02-24  GigaScience
Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine
Elmas, A., Layden, H., Ellis, J., Barlett, L., Zhao, X., Kawabata-Iwakawa, R., Obinata, H., Hiebert, S., Huang, K.-l.
10.1101/2024.10.17.618926 — Posted: 2024-10-21 — Discussion: 2026-01-30  GigaScience
SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets
Seal, S., Neelon, B.
10.1101/2025.03.29.646124 — Posted: 2025-04-03 — Discussion: 2026-01-29  GigaScience
nf-core/proteinfamilies: A scalable pipeline for the generation of protein families
Karatzas, E., Beracochea, M., Baltoumas, F. A., Aplakidou, E., Richardson, L., Fellows Yates, J. A., Lundin, D., nf-core community, , Buluc, A., Kyrpides, N., Georgakopoulos-Soares, I., Pavlopoulos, G. A., Finn, R. D.
10.1101/2025.08.12.670010 — Posted: 2025-08-16 — Discussion: 2026-01-29  GigaScience
Federated Knowledge Retrieval Elevates Large Language Model Performance on Biomedical Benchmarks
Joy, J., Su, A. I.
10.1101/2025.08.01.668022 — Posted: 2025-08-02 — Discussion: 2026-01-29  GigaScience
An Integrative Multi-Omics Random Forest Framework for Robust Biomarker Discovery
Zhang, W., Huang, H., Wang, L., Brian, L. D., Chen, S. X.
10.1101/2025.03.05.641533 — Posted: 2025-03-06 — Discussion: 2026-01-05  GigaScience
A sulfatide-centered ultra-high resolution magnetic resonance MALDI imaging benchmark dataset for MS1-based lipid annotation tools
Gruber, L., Schmidt, S., Enzlein, T., Hopf, C.
10.1101/2025.10.20.683394 — Posted: 2025-10-20 — Discussion: 2026-01-05  GigaScience

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