bioRxiv/medRxiv TRiP Review Activity

122 Reviews — eLife — 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

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

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

Restoring data balance via generative models of T-cell receptors for antigen-binding prediction

Loffredo, E., Pastore, M., Cocco, S., Monasson, R.

10.1101/2024.07.10.602897 — Posted: 2024-07-15 — Discussion: 2025-09-15 eLife

Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learning

Roy, G., Syed, R., Lazaro, O., Robertson, S., McCabe, S. D., Rodriguez, D., Mawla, A. M., Johnson, T. S., Kalwat, M. A.

10.1101/2024.01.18.576260 — Posted: 2024-01-23 — Discussion: 2025-09-02 eLife

Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling

Hallinan, C., Ji, H. J., Salzberg, S. L., Fan, J.