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122 Reviews — eLife — Bioinformatics

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Protein language model embedded geometric graphs power inter-protein contact prediction
Si, Y., Yan, C.
10.1101/2023.01.07.523121 — Posted: 2023-01-08 — Discussion: 2024-03-11  eLife
A novel machine learning algorithm picks proteome signature to specifically identify cancer exosomes
Li, B., Kugeratski, F. G., Kalluri, R.
10.1101/2023.07.18.549557 — Posted: 2023-07-19 — Discussion: 2024-03-01  eLife
voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues
Schneider, A. L., Saraiva-Agostinho, N., Barbosa-Morais, N. L.
10.1101/2022.12.22.521681 — Posted: 2022-12-23 — Discussion: 2024-02-29  eLife
Sensitive remote homology search by local alignment of small positional embeddings from protein language models
Johnson, S. R., Peshwa, M., Sun, Z.
10.1101/2023.07.26.550718 — Posted: 2023-07-29 — Discussion: 2024-02-21  eLife
MetaPredict: A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes
Geller-McGrath, D., Konwar, K., Edgcomb, V. P., Pachiadaki, M., Roddy, J., Wheeler, T., McDermott, J. E.
10.1101/2022.12.21.521254 — Posted: 2022-12-22 — Discussion: 2024-02-09  eLife
ADeS: a deep learning based Apoptosis Detection System for live cell imaging.
Pulfer, A., Pizzagalli, D. U., Gagliardi, P. A., Hinderling, L., Lopez, P., Zayats, R., Barbera, P. C., Antonello, P., Segura, M. P., Giusti, A., Thelen, M., Gambardella, L. M., Murooka, T., Pertz, O., Krause, R., Gonzalez, S. F.
10.1101/2022.11.23.517318 — Posted: 2022-11-25 — Discussion: 2024-02-06  eLife
NetTCR 2.2 - Improved TCR specificity predictions by combining pan- and peptide-specific training strategies, loss-scaling and integration of sequence similarity
Jensen, M. F., Nielsen, M.
10.1101/2023.10.12.562001 — Posted: 2023-10-16 — Discussion: 2024-02-01  eLife
A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence
Pabis, K., Barardo, D., Selvarajoo, K., Gruber, J., Kennedy, B. K.
10.1101/2022.12.29.522277 — Posted: 2022-12-30 — Discussion: 2024-01-17  eLife
Deep Batch Active Learning for Drug Discovery
Bailey, M., Moayedpour, S., Li, R., Corrochano-Navarro, A., Kötter, A., Kogler-Anele, L., Riahi, S., Grebner, C., Hessler, G., Matter, H., Bianciotto, M., Mas, P., Bar-Joseph, Z., Jager, S.
10.1101/2023.07.26.550653 — Posted: 2023-07-29 — Discussion: 2024-01-17  eLife
Detection of new pioneer transcription factors as cell-type specific nucleosome binders
Peng, Y., Song, W., Teif, V., Ovcharenko, I., Landsman, D., Panchenko, A.
10.1101/2023.05.10.540098 — Posted: 2023-05-12 — Discussion: 2023-12-18  eLife

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