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138 Reviews — eLife — Bioinformatics

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Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
Gabriel, A. A., Racle, J., Falquet, M., Jandus, C., Gfeller, D.
10.1101/2023.10.11.561826 — Posted: 2023-10-14 — Discussion: 2024-09-09  eLife
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Hall, M. B., Wick, R. R., Judd, L. M., Nguyen, A. N. T., Steinig, E. J., Xie, O., Davies, M. R., Seemann, T., Stinear, T. P., Coin, L. J. M.
10.1101/2024.03.15.585313 — Posted: 2024-03-16 — Discussion: 2024-09-05  eLife
Identifying images in the biology literature that are problematic for people with a color-vision deficiency
Stevens, H. P., Winegar, C. V., Oakley, A. F., Piccolo, S. R.
10.1101/2023.11.29.569308 — Posted: 2023-11-30 — Discussion: 2024-08-29  eLife
ImmCellTyper: an integrated computational pipeline for systematic mining of Mass Cytometry data to assist deep immune profiling
Sun, J., Choy, D., Sompairac, N., Jamshidi, S., Mishto, M., Kordasti, S.
10.1101/2024.01.15.575790 — Posted: 2024-01-17 — Discussion: 2024-08-13  eLife
Alleviating cell-free DNA sequencing biases with optimal transport
Passemiers, A., Jatsenko, T., Vanderstichele, A., Busschaert, P., Coosemans, A., Timmerman, D., Lambrechts, D., Raimondi, D., Vermeesch, J. R., Moreau, Y.
10.1101/2024.04.04.588204 — Posted: 2024-04-07 — Discussion: 2024-08-02  eLife
Computational Engineering of a Therapeutic Antibody to Inhibit Multiple Mutants of HER2 Without Compromising Inhibition of the Canonical HER2
Peled, S., Guez-Haddad, J., Zur Biton, N., Nimrod, G., Fischman, S., Fastman, Y., Ofran, Y.
10.1101/2023.07.21.550003 — Posted: 2023-07-25 — Discussion: 2024-08-01  eLife
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold
Mischley, V., Maier, J., Chen, J., Karanicolas, J.
10.1101/2024.03.16.585347 — Posted: 2024-03-17 — Discussion: 2024-07-04  eLife
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann, J. K. S., Szczuka, M., Bouarroudj, L., Oussaren, M., Garcia, S., Howard, R. J., Delemotte, L., Lindahl, E., Baaden, M., Lindorff-Larsen, K., Chavent, M., Poulain, P.
10.1101/2023.05.02.538537 — Posted: 2023-05-02 — Discussion: 2024-06-28  eLife
Circulating Small Extracellular Vesicle RNA Profiling for the Detection of T1a stage Colorectal Cancer and Precancerous Advanced Adenoma
Min, L., Bu, F., Meng, J., Liu, X., Guo, Q., Zhao, L., Li, Z., Li, X., Zhu, S., Zhang, S.
10.1101/2023.06.04.543604 — Posted: 2023-06-06 — Discussion: 2024-06-27  eLife
H3-OPT: Accurate prediction of CDR-H3 loop structures of antibodies with deep learning
Tian, B., Chen, H., Fan, X., Zhu, S., Pei, Y., Zhang, X., Zhang, X., Liu, L., Qian, F.
10.1101/2023.08.19.553933 — Posted: 2023-08-21 — Discussion: 2024-05-30  eLife

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