bioRxiv/medRxiv TRiP Review Activity

378 Reviews — GigaScience — All Subjects

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PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
Ji, Y., Shang, J., Guan, J., Zou, W., Liao, H., Tang, X., Sun, Y.
10.1101/2024.07.03.602011 — Posted: 2024-07-06 — Discussion: 2025-01-05  GigaScience
stMMR: accurate and robust spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation
Zhang, D., Yu, N., Li, W., Sun, X., Zou, Q., Li, X., Yuan, Z., Zhang, W., Gao, R.
10.1101/2024.02.22.581503 — Posted: 2024-02-24 — Discussion: 2024-12-05  GigaScience
demuxSNP: supervised demultiplexing scRNAseq using cell hashing and SNPs
Lynch, M. P., Wang, Y., Gatto, L., Culhane, A. C.
10.1101/2024.04.22.590526 — Posted: 2024-04-26 — Discussion: 2024-12-05  GigaScience
CAT Bridge: an efficient toolkit for compound-transcript association mining from multi-omics data
Yang, B., Meng, T., Wang, X., Li, J., Zhao, S., Wang, Y., Yi, S., Zhou, Y., Zhang, Y., Li, L., Guo, L.
10.1101/2024.01.21.576587 — Posted: 2024-01-24 — Discussion: 2024-12-05  GigaScience
De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus
Borges, C. H. d. S., Utsunomia, R., Varani, A. M., Uliano da Silva, M., Guerra, L. V., Butzge, A. J., Gomez Agudelo, J. F., Manso, S., Freitas, M. V., Ariede, R. B., Mastrochirico-Filho, V. A., Penaloza, C., Barria, A., Porto-Foresti, F., Foresti, F., Hattori, R. S., Guiguen, Y., Houston, R. D., Hashimoto, D. T.
10.1101/2024.03.07.583869 — Posted: 2024-03-12 — Discussion: 2024-12-05  GigaScience
An Unsupervised Contrastive Learning Model for Data Integration of Spatially Resolved Transcriptomics
Zhang, C., Liu, L., Zhang, Y., Li, M., Fang, S., Kang, Q., Chen, A., Xu, X., Zhang, Y., Li, Y.
10.1101/2023.08.08.552402 — Posted: 2023-08-12 — Discussion: 2024-11-23  GigaScience
Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)
Frazer, S. A., Baghbanzadeh, M., Rahnavard, A., Crandall, K. A., Oakley, T. H.
10.1101/2024.02.12.579993 — Posted: 2024-02-14 — Discussion: 2024-11-23  GigaScience
CoCoPyE: feature engineering for learning and prediction of genome quality indices
Birth, N., Leppich, N., Schirmacher, J., Andreae, N., Steinkamp, R., Blanke, M., Meinicke, P.
10.1101/2024.02.07.579156 — Posted: 2024-02-10 — Discussion: 2024-11-23  GigaScience
A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)
Simpson, A. M. R., Wood Charlson, E. M., Smith, M., Beilsmith, K., Koch, B., Walls, R. L., Wilhelm, R. C.
10.1101/2023.07.13.548835 — Posted: 2023-07-17 — Discussion: 2024-11-23  GigaScience
StereoSiTE: A framework to spatially and quantitatively profile the cellular neighborhood organized iTME
Liu, X., Qu, C., Liu, C., Zhu, N., Huang, H., Teng, F., Huang, C., Luo, B., Liu, X., Xu, Y., Xie, M., Xi, F., Li, M., Wu, L., Li, Y., Chen, A., Xu, X., Liao, S., Zhang, J.
10.1101/2022.12.31.522366 — Posted: 2022-12-31 — Discussion: 2024-11-23  GigaScience

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