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138 Reviews — eLife — Bioinformatics

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DUAL: deep unsupervised simultaneous simulation and denoising for cryo-electron tomography
Zeng, X., Ding, Y., Zhang, Y., Uddin, M., Dabouei, A., Xu, M.
10.1101/2024.03.02.583135 — Posted: 2024-03-06 — Discussion: 2026-07-01  eLife
Celldetective: an AI-enhanced image analysis toolfor unraveling dynamic cell interactions
Torro, R., Diaz Bello, B., El Arawi, D., Ammer, L., Chames, P., Sengupta, K., Limozin, L.
10.1101/2024.03.15.585250 — Posted: 2024-03-17 — Discussion: 2026-06-16  eLife
A comprehensive dimensional reduction framework to learn single-cell phenotypic topology uncovers T cell diversity
Sidarta-Oliveira, D., Velloso, L. A.
10.1101/2022.03.14.484134 — Posted: 2022-03-17 — Discussion: 2026-05-22  eLife
Gene specificity landscapes for comparative transcriptomic analysis across tissues, cell types, and species
Bot, E., Davila-Velderrain, J.
10.1101/2025.06.04.657813 — Posted: 2025-06-04 — Discussion: 2026-04-15  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.
10.1101/2025.03.31.646342 — Posted: 2025-04-03 — Discussion: 2026-04-01  eLife
Investigating the native functions of -carbon monoxide dehydrogenase through genomic context analysis
Land, H., Böhm, M.
10.1101/2025.09.14.676152 — Posted: 2025-09-19 — Discussion: 2026-03-02  eLife
A translational transcriptomic signature of vaccine reactogenicity for the evaluation of novel formulations
Becker, J., Roelens, M., Reynaud, K., Beloeil, L.
10.1101/2025.11.20.689650 — Posted: 2025-11-25 — Discussion: 2026-02-19  eLife
End-to-end proteogenomics for discovery of cryptic and non-canonical cancer proteoforms using long-read transcriptomics and multi-dimensional proteomics
Kulej, K., Preska Steinberg, A., Zhang, J., Casalena, G., Havasov, E., Shah, S. P., McPherson, A., Kentsis, A.
10.1101/2025.08.23.671943 — Posted: 2025-08-28 — Discussion: 2026-02-11  eLife
Leveraging Disease Association Degree for High-Accuracy MicroRNA Target Prediction
Chen, B.
10.1101/2025.11.06.686936 — Posted: 2025-11-11 — Discussion: 2026-02-09  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: 2025-12-30  eLife

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