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138 Reviews — eLife — Bioinformatics

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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
A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture
Andradi-Brown, C., Wichers-Misterek, J. S., von Thien, H., Höppner, Y. D., Scholz, J. A. M., Smedegaard Hansson, H., Filtenborg Hocke, E., Gilberger, T. W., Duffy, M., Lavstsen, T., Baum, J., Otto, T. D., Cunnington, A. J., Bachmann, A.
10.1101/2023.03.21.533599 — Posted: 2023-03-24 — Discussion: 2023-12-18  eLife
The reprogrammed mouse heart phosphoproteome in response to the chronic stress of markedly high cardiac-specific adenylyl cyclase type 8 overexpression
Qu, J.-H., Chakir, K., Tarasov, K. V., Riordon, D. R., Perino, M. G., Silvester, A. J., Lakatta, E. G.
10.1101/2022.04.29.488779 — Posted: 2022-05-01 — Discussion: 2023-11-22  eLife
Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models
Vezina, B., Watts, S. C., Hawkey, J., Cooper, H. B., Judd, L. M., Jenney, A., Monk, J. M., Holt, K. E., Wyres, K. L.
10.1101/2023.02.26.530115 — Posted: 2023-02-27 — Discussion: 2023-09-19  eLife
ModCRE: a structure homology-modeling approach to predict TF binding in cis-regulatory elements
Fornes, O., Meseguer, A., Aguirre-Plans, J., GOHL, P., Mireia-Bota, P., MOLINA-FERNANDEZ, R., BONET, J., CHINCHILLA, A., PEGENAUTE, F., Gallego, O., Fernandez-Fuentes, N., Oliva, B.
10.1101/2022.04.17.488557 — Posted: 2022-04-17 — Discussion: 2023-08-21  eLife

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