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434 Reviews — GigaScience — All Subjects

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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
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
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
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
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
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation
Fuhrmann, L., Jablonski, K. P., Topolsky, I., Batavia, A. A., Borgsmueller, N., Icer Baykal, P., Carrara, M., Chen, C., Dondi, A., Dragan, M., Dreifuss, D., John, A., Langer, B., Okoniewski, M., du Plessis, L., Schmitt, U., Singer, F., Stadler, T., Beerenwinkel, N.
10.1101/2023.10.16.562462 — Posted: 2023-10-16 — Discussion: 2024-11-10  GigaScience
TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data
Klamann, C., Lau, C., Schwartz, G. W.
10.1101/2023.06.16.544954 — Posted: 2023-06-18 — Discussion: 2024-09-03  GigaScience
Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit
Lavikka, K., Oikkonen, J., Li, Y., Muranen, T., Micoli, G., Marchi, G., Lahtinen, A., Huhtinen, K., Lehtonen, R., Hietanen, S., Hynninen, J., Virtanen, A., Hautaniemi, S.
10.1101/2023.10.06.561159 — Posted: 2023-10-06 — Discussion: 2024-08-12  GigaScience
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Assmann, E., Agrawal, S., Orschler, L., Böttcher, S., Lackner, S., Hölzer, M.
10.1101/2023.06.02.543047 — Posted: 2023-06-02 — Discussion: 2024-08-12  GigaScience

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