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477 Reviews — All Partners — Bioinformatics

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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
When do longer reads matter? A benchmark of long read de novo assembly tools for eukaryotic genomes
Cosma, B. M., Shirali Hossein Zade, R., Jordan, E. N., van Lent, P., Peng, C., Pillay, S., Abeel, T.
10.1101/2023.01.30.526229 — Posted: 2023-02-02 — Discussion: 2024-01-02  GigaScience
Variance Analysis of LC-MS Experimental Factors and Their Impact on Machine Learning
Rehfeldt, T. G., Krawczyk, K., Echers, S. G., Marcatili, P., Palczynski, P., Roettger, R., Schwaemmle, V.
10.1101/2023.05.01.538996 — Posted: 2023-05-02 — Discussion: 2024-01-02  GigaScience
Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities
Wrenn, D. C., Drown, D. M.
10.1101/2023.06.27.546783 — Posted: 2023-06-30 — Discussion: 2023-12-25  Gigabyte
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
Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data
Kim, H., Lövkvist, C., Martin, P. C. N., Kim, J., Won, K. J.
10.1101/2022.02.16.480673 — Posted: 2022-02-19 — Discussion: 2023-12-12  EMBO Press

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