bioRxiv/medRxiv TRiP Review Activity

477 Reviews — All Partners — Bioinformatics

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A network regularized linear model to infer spatial expression pattern for single cell
Gu, C., Chen, H., Liu, Z.
10.1101/2024.11.20.624541 — Posted: 2024-11-22 — Discussion: 2025-10-10  eLife
Translational buffering tunes gene expression in mouse and human
Rao, S., Le, A. Y., Persyn, L., Cenik, C.
10.1101/2025.05.16.654561 — Posted: 2025-05-21 — Discussion: 2025-10-10  Review Commons
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
Martin, N. X., Olsen, P., Quon, J., Campos, J., Valera Cuevas, N. J., Nagra, J., VanNess, M., Maltzer, Z., Gelfand, E., Oyama, A., Gary, A., Wang, Y., Alaya, A., Ruiz, A., Reynoldson, C., Bielstein, C., Pom, C. A., Huang, C., Slaughterback, C., Liang, E., Alexander, J., Ariza, J., Malone, J., Melchor, J., Colbert, K., Brouner, K., Shulga, L., Reding, M., Latimer, P., Sanchez, R., Barta, S., Egdorf, T., Madigan, Z., Pagan, C., Close, J., Long, B., Kunst, M., Lein, E., Zeng, H., McMillen, D. A., Waters, J.
10.1101/2024.12.04.626766 — Posted: 2024-12-07 — Discussion: 2025-10-09  eLife
Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework
Rieger, W. J., Boden, M., Arnold, F. H., Mora, A.
10.1101/2025.06.13.659624 — Posted: 2025-06-20 — Discussion: 2025-10-02  eLife
SPEX: A modular end-to-end analytics tool for spatially resolved omics of tissues
Pechuan Jorge, X., Li, X., Risom, T., Zubkov, A., Tabatsky, E., Prilipko, A., Ye, X., Shi, Z., Nowicka, m., Peale, F., Hibar, D., Ziai, J., Jesudason, R., Orlova, D.
10.1101/2022.08.22.504841 — Posted: 2022-08-23 — Discussion: 2025-09-30  GigaScience
Nanopore- and AI-empowered metagenomic viability inference
Urel, H., Benassou, S., Reska, T., Marti, H., Rayo, E., Martin, E. J., Schloter, M., Ferguson, J. M., Kesselheim, S., Borel, N., Urban, L.
10.1101/2024.06.10.598221 — Posted: 2024-06-11 — Discussion: 2025-09-30  GigaScience
WaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning
Nguyen, H.-H., Rudar, J., Lesperance, N., Vernygora, O., Taylor, G. W., Laing, C., Lapen, D., Leung, C. K., Lung, O.
10.1101/2025.02.25.639900 — Posted: 2025-02-28 — Discussion: 2025-09-30  GigaScience
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.
Chang, J. J.-Y., Yang, X., Teng, H., Reames, B., Corbin, V., Coin, L. J. M.
10.1101/2024.10.25.620206 — Posted: 2024-10-25 — Discussion: 2025-09-30  GigaScience
Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity
Greene, E., Muniz, R., Yamamura, H., Hoff, S. E., Bajaj, P., Lee, D. J., Thompson, E. M., Arada, A., Lee, G. M., Bonomi, M., Kollman, J. M., Fraser, J. S.
10.1101/2025.07.04.663231 — Posted: 2025-07-06 — Discussion: 2025-09-24  eLife
Macroscopic Analyses of RNA-Seq Data to Reveal Chromatin Modifications in Aging and Disease
Mahajan, A., Ratti, F., Wang, B., El-Samad, H., Kaufman, J. H., Gopalakrishnan, V.
10.1101/2025.05.14.654062 — Posted: 2025-05-18 — Discussion: 2025-09-23  eLife

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